From fd200e78546e9a34d0a6545c35290fd5bc121f24 Mon Sep 17 00:00:00 2001 From: Dylan Nielson Date: Fri, 2 Feb 2024 11:11:07 -0500 Subject: [PATCH] update notebooks --- notebooks/generate_and_evaluate_targets.ipynb | 31 +- notebooks/prep_normgrid_targeting.ipynb | 113 +- notebooks/run_liston_lab_pipeline.ipynb | 28802 +--------------- 3 files changed, 222 insertions(+), 28724 deletions(-) diff --git a/notebooks/generate_and_evaluate_targets.ipynb b/notebooks/generate_and_evaluate_targets.ipynb index 247a987..6217f8c 100644 --- a/notebooks/generate_and_evaluate_targets.ipynb +++ b/notebooks/generate_and_evaluate_targets.ipynb @@ -25,7 +25,7 @@ "from nibabel import cifti2 as ci\n", "from contarg.normgrid import load_liston_surfs, Surface\n", "# from contarg.stimgrid import run_opt_and_save_outputs\n", - "from contarg.utils import graph_from_triangles, get_stimroi_path, surf_data_from_cifti, load_timeseries, SurfROI, cross_spearman\n", + "from contarg.utils import graph_from_triangles, get_stimroi_path, surf_data_from_cifti, load_timeseries, SurfROI, cross_spearman, replace_cifti_data\n", "# from contarg.utils import get_stimroi_path, get_refroi_path, graph_from_triangles, , new_cifti_like, surf_data_from_cifti, cross_spearman, load_timeseries, find_bids_files, add_censor_columns, select_confounds, make_rel_symlink\n", "from scipy import stats\n", "from scipy.spatial.distance import pdist, cdist\n", @@ -383,6 +383,35 @@ "]" ] }, + { + "cell_type": "markdown", + "source": [ + "## This is the output you need for targeting" + ], + "metadata": { + "collapsed": false + } + }, + { + "cell_type": "code", + "execution_count": null, + "outputs": [], + "source": [ + "stim_stats_rev.sort_values('rep_rva_rank').loc[:, ses_comp_cols].head(10)" + ], + "metadata": { + "collapsed": false + } + }, + { + "cell_type": "markdown", + "source": [ + "## The rest of this coe is for comparing sessions" + ], + "metadata": { + "collapsed": false + } + }, { "cell_type": "code", "execution_count": 6, diff --git a/notebooks/prep_normgrid_targeting.ipynb b/notebooks/prep_normgrid_targeting.ipynb index 1187b1d..59eace5 100644 --- a/notebooks/prep_normgrid_targeting.ipynb +++ b/notebooks/prep_normgrid_targeting.ipynb @@ -20,7 +20,8 @@ " setup_uncert_sims,\n", " run_clusters,\n", " calc_stimgrid,\n", - " make_uncert_sims\n", + " make_uncert_sims,\n", + " make_uncert_surfaces\n", ")" ] }, @@ -740,9 +741,9 @@ " '--njobs',\n", " f'20',\n", " '--thresh-type=mt',\n", - " '--min-thresh=50',\n", - " '--max-thresh=80',\n", - " '--max-mt=80',\n", + " f'--min-thresh={mt_thresh}',\n", + " f'--max-thresh={maxMT}',\n", + " f'--max-mt={maxMT}',\n", " ]\n", " cmds.append(' '.join(cmd))" ] @@ -750,10 +751,6 @@ { "cell_type": "code", "execution_count": 24, - "id": "9179d2aa-aa4a-40cd-9703-1d148e943717", - "metadata": { - "tags": [] - }, "outputs": [ { "data": { @@ -768,47 +765,14 @@ ], "source": [ "cmds[0]" - ] - }, - { - "cell_type": "code", - "execution_count": 29, - "id": "4da24ca1-db3f-4da1-bab3-48d128aea1e9", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "!rm -rf /lscratch/$SLURM_JOB_ID/uncertsim-0" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "b3a7af00-6223-4f66-b9d9-07beddcdcbc9", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[Parallel(n_jobs=20)]: Using backend LokyBackend with 20 concurrent workers.\n" - ] - } ], - "source": [ - "! {cmds[0]}" - ] + "metadata": { + "collapsed": false + } }, { "cell_type": "code", "execution_count": 28, - "id": "7959e330-0f81-4248-a1e0-731837b851ab", - "metadata": { - "tags": [] - }, "outputs": [ { "data": { @@ -823,7 +787,10 @@ ], "source": [ "len(cmds)" - ] + ], + "metadata": { + "collapsed": false + } }, { "cell_type": "code", @@ -909,6 +876,62 @@ " print(jobid)" ] }, + { + "cell_type": "markdown", + "source": [ + " # Create surfaces from uncertainty sims" + ], + "metadata": { + "collapsed": false + } + }, + { + "cell_type": "code", + "execution_count": null, + "outputs": [], + "source": [ + "all_settings = []\n", + "for subject in subjects:\n", + " sim_dir = Path(anat_dir / f'sub-{subject}/Simulation/simulation-00')\n", + " if not sim_dir.exists():\n", + " sim_dir = Path(anat_dir / f'sub-{subject}/Simulation/simulation-01')\n", + " if not sim_dir.exists():\n", + " print(f\"{sim_dir} not found, skipping\")\n", + " uncert_dir = sim_dir / f'uncert{nsims}'\n", + " settings_path = uncert_dir / 'settings.pkl.gz'\n", + " all_settings.append(settings_path)" + ], + "metadata": { + "collapsed": false + } + }, + { + "cell_type": "code", + "execution_count": null, + "outputs": [], + "source": [ + "\n", + "jobs = []\n", + "for (subject, settings_path) in zip(subjects, all_settings):\n", + " src_surf_dir = liston_root / f'sub-{subject}/anat/T1w/fsaverage_LR32k/'\n", + " uncert_dir = settings_path.parent\n", + " jobs.append(delayed(make_uncert_surfaces)(subject, src_surf_dir, uncert_dir, overwrite=True))\n" + ], + "metadata": { + "collapsed": false + } + }, + { + "cell_type": "code", + "execution_count": null, + "outputs": [], + "source": [ + "Parallel(n_jobs=10, verbose=10)(jobs)" + ], + "metadata": { + "collapsed": false + } + }, { "cell_type": "markdown", "id": "f7a03ef7-64be-4f5d-86f0-bce215da0d7d", diff --git a/notebooks/run_liston_lab_pipeline.ipynb b/notebooks/run_liston_lab_pipeline.ipynb index aab4d21..2ba51be 100644 --- a/notebooks/run_liston_lab_pipeline.ipynb +++ b/notebooks/run_liston_lab_pipeline.ipynb @@ -21,63 +21,36 @@ "from joblib import Parallel, delayed" ] }, - { - "cell_type": "markdown", - "id": "53916ef0-e9af-4f64-a733-c079c13fd5c0", - "metadata": { - "tags": [] - }, - "source": [ - "# make a symlinked liston input directory structure" - ] - }, { "cell_type": "code", - "execution_count": 39, - "id": "e7c8c429-2d4d-4fc6-8f94-a0e25d6612f7", - "metadata": { - "tags": [] - }, + "execution_count": null, "outputs": [], "source": [ + "subjects = ['24546']\n", + "\n", + "liston_scripts_dir = Path('/data/MLDSST/nielsond/target_test/other_repos/Liston-Laboratory-MultiEchofMRI-Pipeline/MultiEchofMRI-Pipeline')\n", "bids_dir = Path('/data/EDB/TMSpilot/BIDS')\n", "liston_dir = Path('/data/EDB/TMSpilot/liston')\n", - "liston_dir.mkdir(exist_ok=True)" - ] - }, - { - "cell_type": "code", - "execution_count": 40, - "id": "e0f8147b-c6c8-4a3b-9ddf-16431e629fc4", + "liston_dir.mkdir(exist_ok=True)\n", + "\n", + "overwrite = False\n", + "\n", + "jobids = {}\n", + "\n", + "fd_thresh = 0.3" + ], "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "subjects = ['24546']\n" - ] + "collapsed": false + } }, { - "cell_type": "code", - "execution_count": 41, - "id": "f78ef4b1-2692-4b55-bfd5-3645d9766cdc", + "cell_type": "markdown", + "id": "53916ef0-e9af-4f64-a733-c079c13fd5c0", "metadata": { "tags": [] }, - "outputs": [ - { - "data": { - "text/plain": [ - "['24563', '24573', '24704', '24718', '24740']" - ] - }, - "execution_count": 41, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ - "subjects" + "# make a symlinked liston input directory structure" ] }, { @@ -107,29 +80,6 @@ "}" ] }, - { - "cell_type": "code", - "execution_count": 44, - "id": "4d90e994-edc1-4949-9fed-66ffb5c1361c", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/plain": [ - "['24546']" - ] - }, - "execution_count": 44, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "subjects" - ] - }, { "cell_type": "code", "execution_count": 43, @@ -460,7 +410,8 @@ "metadata": {}, "source": [ "# run hires HCP wrapper\n", - "example comand: \n", + "This runs Freesurfer along with some additional processing, it can take over 12 hours\n", + "example comand:\n", "`./anat_highres_HCP_wrapper_par.sh /data/EDB/TMSpilot/liston sub-24704 10`" ] }, @@ -473,7 +424,8 @@ }, "outputs": [], "source": [ - "anat_script_path = '/data/MLDSST/nielsond/target_test/other_repos/Liston-Laboratory-MultiEchofMRI-Pipeline/MultiEchofMRI-Pipeline/anat_highres_HCP_wrapper_par.sh'\n", + "anat_script_path = (liston_scripts_dir /'anat_highres_HCP_wrapper_par.sh').as_posix()\n", + "\n", "\n", "swarm_cmd_dir = liston_dir/'swarm/swarm_cmds'\n", "swarm_cmd_dir.mkdir(exist_ok=True, parents=True)\n", @@ -492,7 +444,7 @@ "source": [ "nthreads = 20\n", "cmds = []\n", - "for sub in ['24546']:\n", + "for sub in subjects:\n", " cmd = [\n", " 'bash',\n", " anat_script_path,\n", @@ -571,7 +523,7 @@ "outputs": [], "source": [ "anat_success = []\n", - "for sub in subjects + ['247183']:\n", + "for sub in subjects:\n", " row = dict(subject=sub)\n", " for fn in ['PreFreeSurfer', 'FreeSurfer', 'PostFreeSurfer']:\n", " ff = liston_dir / f'sub-{sub}/anat/qa/{fn}.txt'\n", @@ -684,87 +636,121 @@ }, { "cell_type": "markdown", - "id": "011e57b3-570c-4c99-90c8-04557c7e8667", - "metadata": {}, "source": [ - "# run func_preproc+denoise\n", - "./func_preproc+denoise_ME-fMRI_wrapper.sh /data/EDB/TMSpilot/liston sub-24704 15" - ] + "# Run simnibs headmodel\n", + "This takes about 4 hours and depends on the HIRES HCP Wrapper completimng" + ], + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "ename": "SyntaxError", + "evalue": "invalid syntax (2719176774.py, line 2)", + "output_type": "error", + "traceback": [ + "\u001B[0;36m Cell \u001B[0;32mIn[1], line 2\u001B[0;36m\u001B[0m\n\u001B[0;31m This takes about 4 hours and depends on the HIRES HCP Wrapper completing\u001B[0m\n\u001B[0m ^\u001B[0m\n\u001B[0;31mSyntaxError\u001B[0m\u001B[0;31m:\u001B[0m invalid syntax\n" + ] + } + ], + "execution_count": null }, { "cell_type": "code", - "execution_count": 53, - "id": "fcb600fa-8066-49b5-89ec-2a33cfc0f1f2", - "metadata": {}, + "execution_count": null, "outputs": [], "source": [ - "func_script_path = '/data/MLDSST/nielsond/target_test/other_repos/Liston-Laboratory-MultiEchofMRI-Pipeline/MultiEchofMRI-Pipeline/func_preproc+denoise_ME-fMRI_wrapper.sh'\n", + "outdir = Path('/data/EDB/TMSpilot/derivatives/contarg_liston_ohbm2024')\n", + "outdir.mkdir(exist_ok=True)\n", + "anat_dir = outdir / 'anat_preproc'\n", "\n", - "swarm_cmd_dir = liston_dir/'swarm/swarm_cmds'\n", - "swarm_cmd_dir.mkdir(exist_ok=True, parents=True)\n", - "swarm_log_dir = liston_dir/'swarm/swarm_log'\n", - "swarm_log_dir.mkdir(exist_ok=True, parents=True)" - ] + "# build headmodels\n", + "cmds = []\n", + "for hmsub in subjects:\n", + " ## WATCH OUT, session 1 is hardcoded!!\n", + " session = 1\n", + " ses_out_dir = anat_dir /f'sub-{hmsub}'\n", + " ses_out_dir.mkdir(exist_ok=True, parents=True)\n", + " proced_anat_dir = liston_dir / f'sub-{hmsub}/anat'\n", + " t1w_path = proced_anat_dir / 'T1w/T1w_acpc_dc_restore.nii.gz'\n", + " t2w_path = proced_anat_dir / 'T1w/T2w_acpc_dc_restore.nii.gz'\n", + " hm_outdir = ses_out_dir / f\"HeadModel/m2m_{hmsub}\"\n", + " if (not hm_outdir.exists()) or overwrite:\n", + " cmd = [\n", + " \"contarg\",\n", + " \"tans\",\n", + " \"headmodel\",\n", + " \"--t1\",\n", + " t1w_path.as_posix(),\n", + " \"--t2\",\n", + " t2w_path.as_posix(),\n", + " \"--out-dir\",\n", + " ses_out_dir.as_posix(),\n", + " \"--subject\",\n", + " hmsub\n", + " ]\n", + " cmds.append(' '.join(cmd))" + ], + "metadata": { + "collapsed": false + } }, { "cell_type": "code", - "execution_count": 102, - "id": "f13b2cbc-fd97-4d72-8802-0b7b3bccc8d4", + "execution_count": null, + "outputs": [], + "source": [ + "cmds" + ], "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/plain": [ - "['24563', '24573', '24704', '24718', '247183', '24740', '24742', '247183']" - ] - }, - "execution_count": 102, - "metadata": {}, - "output_type": "execute_result" + "collapsed": false, + "pycharm": { + "is_executing": true } - ], - "source": [ - "subjects + ['247183']" - ] + } }, { "cell_type": "code", - "execution_count": 139, - "id": "2a8381e7-f953-41f3-a497-0a66bece93b6", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/plain": [ - "['bash /data/MLDSST/nielsond/target_test/other_repos/Liston-Laboratory-MultiEchofMRI-Pipeline/MultiEchofMRI-Pipeline/func_smooth_subcort_concat.sh /data/MLDSST/nielsond/target_test/other_repos/Liston-Laboratory-MultiEchofMRI-Pipeline/MultiEchofMRI-Pipeline sub-24563 /data/EDB/TMSpilot/liston',\n", - " 'bash /data/MLDSST/nielsond/target_test/other_repos/Liston-Laboratory-MultiEchofMRI-Pipeline/MultiEchofMRI-Pipeline/func_smooth_subcort_concat.sh /data/MLDSST/nielsond/target_test/other_repos/Liston-Laboratory-MultiEchofMRI-Pipeline/MultiEchofMRI-Pipeline sub-24573 /data/EDB/TMSpilot/liston',\n", - " 'bash /data/MLDSST/nielsond/target_test/other_repos/Liston-Laboratory-MultiEchofMRI-Pipeline/MultiEchofMRI-Pipeline/func_smooth_subcort_concat.sh /data/MLDSST/nielsond/target_test/other_repos/Liston-Laboratory-MultiEchofMRI-Pipeline/MultiEchofMRI-Pipeline sub-24704 /data/EDB/TMSpilot/liston',\n", - " 'bash /data/MLDSST/nielsond/target_test/other_repos/Liston-Laboratory-MultiEchofMRI-Pipeline/MultiEchofMRI-Pipeline/func_smooth_subcort_concat.sh /data/MLDSST/nielsond/target_test/other_repos/Liston-Laboratory-MultiEchofMRI-Pipeline/MultiEchofMRI-Pipeline sub-24718 /data/EDB/TMSpilot/liston',\n", - " 'bash /data/MLDSST/nielsond/target_test/other_repos/Liston-Laboratory-MultiEchofMRI-Pipeline/MultiEchofMRI-Pipeline/func_smooth_subcort_concat.sh /data/MLDSST/nielsond/target_test/other_repos/Liston-Laboratory-MultiEchofMRI-Pipeline/MultiEchofMRI-Pipeline sub-24740 /data/EDB/TMSpilot/liston',\n", - " 'bash /data/MLDSST/nielsond/target_test/other_repos/Liston-Laboratory-MultiEchofMRI-Pipeline/MultiEchofMRI-Pipeline/func_smooth_subcort_concat.sh /data/MLDSST/nielsond/target_test/other_repos/Liston-Laboratory-MultiEchofMRI-Pipeline/MultiEchofMRI-Pipeline sub-24742 /data/EDB/TMSpilot/liston']" - ] - }, - "execution_count": 139, - "metadata": {}, - "output_type": "execute_result" - } + "execution_count": null, + "outputs": [], + "source": [ + "if len(cmds) > 0:\n", + " swarm_cmd_file = swarm_cmd_dir / 'headmodels'\n", + "\n", + " swarm_cmd_file.write_text('\\n'.join(cmds))\n", + " run_name = 'headmodels'\n", + " jobids[run_name] = ! swarm -f {swarm_cmd_file} -g 80 -t 22 --module matlab,freesurfer/6,fsl,simnibs/4.0,connectome-workbench,ANTs --time 12:00:00 --logdir {swarm_log_dir} --job-name {run_name} --partition norm\n", + " print(jobids[run_name])" ], + "metadata": { + "collapsed": false + } + }, + { + "cell_type": "markdown", + "id": "011e57b3-570c-4c99-90c8-04557c7e8667", + "metadata": {}, "source": [ - "cmds" + "# run func_preproc+denoise\n", + "This takes about 4 hours and depends on the hires HCP wrapper, but not the headmodel.\n", + "Example command:\n", + "`./func_preproc+denoise_ME-fMRI_wrapper.sh /data/EDB/TMSpilot/liston sub-24704 15`" ] }, { "cell_type": "code", - "execution_count": null, - "id": "5f8689c0-daef-415a-b67b-8c001bce0d03", + "execution_count": 53, + "id": "fcb600fa-8066-49b5-89ec-2a33cfc0f1f2", "metadata": {}, "outputs": [], "source": [ - "/data/MLDSST/nielsond/target_test/other_repos/Liston-Laboratory-MultiEchofMRI-Pipeline/MultiEchofMRI-Pipeline/func_vol2surf.sh sub-24546 /data/EDB/TMSpilot/liston /data/MLDSST/nielsond/target_test/other_repos/Liston-Laboratory-MultiEchofMRI-Pipeline/MultiEchofMRI-Pipeline /data/MLDSST/nielsond/target_test/other_repos/Liston-Laboratory-MultiEchofMRI-Pipeline/MultiEchofMRI-Pipeline/config/CiftiList.txt 1" + "func_script_path = (liston_scripts_dir / 'func_preproc+denoise_ME-fMRI_wrapper.sh').as_posix()\n", + "\n", + "\n", + "swarm_cmd_dir = liston_dir/'swarm/swarm_cmds'\n", + "swarm_cmd_dir.mkdir(exist_ok=True, parents=True)\n", + "swarm_log_dir = liston_dir/'swarm/swarm_log'\n", + "swarm_log_dir.mkdir(exist_ok=True, parents=True)" ] }, { @@ -842,8 +828,8 @@ "id": "9dd2a090-c89d-48be-b507-50285d682536", "metadata": {}, "source": [ - "### smooth the data and do subcortical smoothing\n", - "cd /data/MLDSST/nielsond/target_test/other_repos/Liston-Laboratory-MultiEchofMRI-Pipeline/Res0urces/; matlab -nodesktop -nosplash -r \"pfm_example_use; exit\"" + "### smooth the data and do subcortical regression\n", + "This is pretty quick (< 1 hour) and depends on the func_preproc+denoise" ] }, { @@ -855,31 +841,7 @@ }, "outputs": [], "source": [ - "smooth_script_path = '/data/MLDSST/nielsond/target_test/other_repos/Liston-Laboratory-MultiEchofMRI-Pipeline/MultiEchofMRI-Pipeline/func_smooth_subcort_concat.sh'\n", - "medir=\"/data/MLDSST/nielsond/target_test/other_repos/Liston-Laboratory-MultiEchofMRI-Pipeline/MultiEchofMRI-Pipeline\"\n" - ] - }, - { - "cell_type": "code", - "execution_count": 26, - "id": "84ef91c4-48bf-4f42-94c9-a0e23b493022", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/plain": [ - "PosixPath('/data/EDB/TMSpilot/liston')" - ] - }, - "execution_count": 26, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "liston_dir" + "smooth_script_path = (liston_scripts_dir /'func_smooth_subcort_concat.sh').as_posix()" ] }, { @@ -897,7 +859,7 @@ " cmd = [\n", " 'bash',\n", " smooth_script_path,\n", - " medir,\n", + " liston_scripts_dir.as_posix(),\n", " f'sub-{sub}',\n", " liston_dir.as_posix(),\n", " ]\n", @@ -972,19 +934,6 @@ "split_subjs = ['247183', '24740', '24742', '245461', '245462']" ] }, - { - "cell_type": "code", - "execution_count": 3, - "id": "1864e0db-3556-4c35-88d0-342850d37ae6", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "data_dir = Path('/data/EDB/TMSpilot/liston/')\n", - "fd_thresh = 0.3" - ] - }, { "cell_type": "code", "execution_count": 4, @@ -1008,7 +957,7 @@ "source": [ "jobs = []\n", "for subject in subjects: #['24563', '24573', '24704', '24718', '24740', '24742']:\n", - " sub_concat_dir = data_dir / f'sub-{subject}/func/rest/ConcatenatedCiftis'\n", + " sub_concat_dir = liston_dir / f'sub-{subject}/func/rest/ConcatenatedCiftis'\n", " fd = sio.loadmat(sub_concat_dir / 'FD.mat')['FD'].squeeze()\n", " scanid = sio.loadmat(sub_concat_dir / 'ScanIdx.mat')['ScanIdx'].squeeze()\n", " scanid = pd.DataFrame(scanid, columns=['session', 'run'])\n", @@ -1025,10 +974,13 @@ " concat_nii = sub_concat_dir / f'Rest_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing{smoothing}.dtseries.nii'\n", " \n", " for session in [1,2]:\n", + " for nruns in ['all']:\n", + " concat_nii = sub_concat_dir / f'Rest_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing{smoothing}.dtseries.nii'\n", + "\n", + " for session in [1]:\n", " ses_concat_dir = sub_concat_dir.parent / f'session_{session}/concatenated'\n", " ses_concat_dir.mkdir(exist_ok=True, parents=True)\n", " if nruns == 'all':\n", - " continue\n", " ses_concat_name = concat_nii.parts[-1].replace('Rest_', f'Rest_session-{session}_')\n", " elif nruns == 2:\n", " ses_concat_name = concat_nii.parts[-1].replace('Rest_', f'Rest_session-{session}_2runs+')\n", @@ -1041,7 +993,6 @@ " concat_nii.as_posix(),\n", " ]\n", " if nruns == 'all':\n", - " continue\n", " if subject in split_subjs:\n", " if session == 1:\n", " cmd += (' '.join([f'-column {trn + 1}' for trn in scanid.loc[(scanid.run < 4) & scanid.fd_mask].index.values])).split(' ')\n", @@ -1050,6 +1001,7 @@ " else:\n", " cmd += (' '.join([f'-column {trn + 1}' for trn in scanid.loc[(scanid.session == session) & scanid.fd_mask].index.values])).split(' ')\n", "\n", + "\n", " elif nruns == 2:\n", " if subject in split_subjs:\n", " if session == 1:\n", @@ -1139,28512 +1091,6 @@ "source": [ "Parallel(n_jobs=20, verbose=10)(jobs)" ] - }, - { - "cell_type": "code", - "execution_count": 36, - "id": "fd1b456b-fa8a-4752-9e86-ebe11d10cdfc", - "metadata": { - "tags": [] - }, - "outputs": [ - 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} - ], - "source": [ - "cmds" - ] - }, - { - "cell_type": "code", - "execution_count": 189, - "id": "4fc0f041-7823-4bbe-b23b-7165298fd6af", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/plain": [ - "(460, 82428)" - ] - }, - "execution_count": 189, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "nb.load(ses_concat_out).shape" - ] - }, - { - "cell_type": "code", - "execution_count": 179, - "id": "71b83b5a-a7d4-4e78-a085-68547f8344bf", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/plain": [ - "5770" - ] - }, - "execution_count": 179, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "subprocess.run(cmd)" - ] - }, - { - "cell_type": "markdown", - "id": "e60611b2-0df7-45cf-a598-7daed0d2a82f", - "metadata": {}, - "source": [ - "## Make FSLR images, Dconn for separate sessions, run template matching" - ] - }, - { - "cell_type": "code", - "execution_count": 74, - "id": "f8c50f71-9e81-4e01-b93a-6d080cd4814f", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "def create_fslr32k_sample(subject, datadir, medir, hcpdir, session=1, run=1, overwrite=False):\n", - " \"\"\"\n", - " Create actual fslr32k space examples from \n", - " Session and run default to 1 because we only need to make a single sample image in order to run the transformation.\n", - " \"\"\"\n", - " subdir = datadir / f'sub-{subject}'\n", - " \n", - " \n", - " rundir = subdir / f'func/rest/session_{session}/run_{run}'\n", - " acpc_rest = rundir / 'Rest_OCME+MEICA+MGTR.nii.gz'\n", - " ocifti_rest = rundir / 'Rest_OCME+MEICA+MGTR.dtseries.nii'\n", - " nonlin_rest = rundir / 'Rest_OCME+MEICA+MGTR_nonlin.nii.gz'\n", - " rois = hcpdir / 'global/templates/91282_Greyordinates/Atlas_ROIs.2.nii.gz'\n", - " mni152_2mm = medir / 'Res0urces/FSL/MNI152_T1_2mm.nii.gz'\n", - " \n", - " warp = subdir / 'anat/MNINonLinear/xfms/acpc_dc2standard.nii.gz' \n", - " \n", - " if not nonlin_rest.exists() or overwrite:\n", - " # create a functional volume in MNI space\n", - " cmd = [\n", - " 'applywarp',\n", - " '-i',\n", - " acpc_rest.as_posix(),\n", - " '-r',\n", - " mni152_2mm.as_posix(),\n", - " '-o',\n", - " nonlin_rest.as_posix(),\n", - " '-w',\n", - " warp.as_posix(),\n", - " '--interp=trilinear'\n", - " ]\n", - " subprocess.run(cmd, check=True)\n", - " # # trim all but first TR to save space\n", - "\n", - " # cmd = [\n", - " # 'fslroi',\n", - " # nonlin_rest,\n", - " # nonlin_rest,\n", - " # '0', \n", - " # '1'\n", - " # ]\n", - " # subprocess.run(cmd, check=True)\n", - "\n", - " left_metric = rundir / 'lh.32k_fs_LR.shape.gii'\n", - " right_metric = rundir / 'rh.32k_fs_LR.shape.gii'\n", - " if not (left_metric.exists() & right_metric.exists()) or overwrite:\n", - "\n", - " # split out giftis\n", - " cmd = [\n", - " 'wb_command',\n", - " '-cifti-separate',\n", - " ocifti_rest.as_posix(),\n", - " 'COLUMN',\n", - " '-metric',\n", - " 'CORTEX_LEFT',\n", - " left_metric.as_posix(),\n", - " '-metric',\n", - " 'CORTEX_RIGHT',\n", - " right_metric.as_posix()\n", - " ]\n", - " subprocess.run(cmd, check=True)\n", - "\n", - "\n", - " # create a cifti that's actually in fslr\n", - " tr_file = rundir / 'TR.txt'\n", - " tr = float(tr_file.read_text().strip())\n", - " fslr_cifti_example = rundir / 'Rest_OCME+MEICA+MGTR_fsLR32k.dtseries.nii'\n", - " left_roi = subdir / f'anat/MNINonLinear/fsaverage_LR32k/sub-{subject}.L.atlasroi.32k_fs_LR.shape.gii'\n", - " right_roi = subdir / f'anat/MNINonLinear/fsaverage_LR32k/sub-{subject}.R.atlasroi.32k_fs_LR.shape.gii'\n", - " if not fslr_cifti_example.exists() or overwrite:\n", - " cmd = [\n", - " 'wb_command',\n", - " '-cifti-create-dense-timeseries',\n", - " fslr_cifti_example.as_posix(),\n", - " '-volume',\n", - " nonlin_rest.as_posix(),\n", - " rois.as_posix(),\n", - " '-left-metric',\n", - " left_metric.as_posix(),\n", - " '-roi-left',\n", - " left_roi.as_posix(),\n", - " '-right-metric',\n", - " right_metric.as_posix(),\n", - " '-roi-right',\n", - " right_roi.as_posix(),\n", - " '-timestep',\n", - " str(tr)\n", - " ]\n", - " subprocess.run(cmd, check=True)\n", - " return fslr_cifti_example\n", - "\n", - "def _nlresample_wrapper(acpc_t1w, source_cifti, fslr_example, warp, standard, outpath, overwrite=False):\n", - " if not Path(outpath).exists() or overwrite:\n", - " cmd = [\n", - " 'wb_command',\n", - " '-cifti-resample',\n", - " source_cifti.as_posix(),\n", - " 'COLUMN',\n", - " fslr_example.as_posix(),\n", - " 'COLUMN',\n", - " 'ADAP_BARY_AREA',\n", - " 'TRILINEAR',\n", - " outpath.as_posix(),\n", - " '-warpfield',\n", - " warp.as_posix(),\n", - " '-fnirt',\n", - " acpc_t1w.as_posix()\n", - " ]\n", - " subprocess.run(cmd, check=True)\n", - " return outpath\n", - "\n", - "def resample_procced_to_realfslr32(subject, smoothing, datadir, medir, hcpdir, overwrite=False):\n", - " datadir = Path(datadir)\n", - " medir = Path(medir)\n", - " hcpdir = Path(hcpdir)\n", - " subdir = datadir / f'sub-{subject}'\n", - " fslr_example = create_fslr32k_sample(subject, datadir, medir, hcpdir, overwrite=False)\n", - " acpc_t1w = subdir / 'anat/T1w/T1w_acpc_dc_restore.nii.gz'\n", - " warp = subdir / 'anat/MNINonLinear/xfms/acpc_dc2standard.nii.gz'\n", - " mni152_2mm = medir / 'Res0urces/FSL/MNI152_T1_2mm.nii.gz'\n", - " catted_dir = subdir / 'func/rest/ConcatenatedCiftis'\n", - " procd_cifti = catted_dir / f'Rest_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing{smoothing}.dtseries.nii'\n", - " fslr_procd_cifti = catted_dir / f'Rest_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing{smoothing}_fslr32k.dtseries.nii'\n", - " \n", - " _ = _nlresample_wrapper(acpc_t1w, procd_cifti, fslr_example, warp, mni152_2mm, fslr_procd_cifti, overwrite=overwrite)\n", - " return fslr_procd_cifti" - ] - }, - { - "cell_type": "code", - "execution_count": 75, - "id": "af221a42-ab6e-4962-a943-5d0f0953aef2", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "subjects = ['24563','24546', '245461', '245462', '24573', '24704', '24718', '247183', '24740', '24742']\n", - "datadir = Path('/data/EDB/TMSpilot/liston')\n", - "medir = Path('/data/MLDSST/nielsond/target_test/other_repos/Liston-Laboratory-MultiEchofMRI-Pipeline/')\n", - "hcpdir = Path('/data/MLDSST/nielsond/target_test/other_repos/HCPpipelines')\n", - "fd_thresh = 0.3" - ] - }, - { - "cell_type": "code", - "execution_count": 76, - "id": "e6a69d24-0169-460e-b26a-365c44263953", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "swarm_cmd_dir = datadir/'swarm/swarm_cmds'\n", - "swarm_cmd_dir.mkdir(exist_ok=True, parents=True)\n", - "swarm_log_dir = datadir/'swarm/swarm_log'\n", - "swarm_log_dir.mkdir(exist_ok=True, parents=True)" - ] - }, - { - "cell_type": "code", - "execution_count": 77, - "id": "b19adc9a-ede4-4f29-b273-323199fc807a", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "20\n" - ] - } - ], - "source": [ - "jobs = []\n", - "for subject in subjects:\n", - " for smoothing in [2.55, 5]:\n", - " jobs.append(delayed(resample_procced_to_realfslr32)(subject, smoothing, datadir, medir, hcpdir, overwrite=True))\n", - " #resample_procced_to_realfslr32(subject, smoothing, datadir, medir, hcpdir, overwrite=True)\n", - "print(len(jobs))\n" - ] - }, - { - "cell_type": "code", - "execution_count": 78, - "id": "009f4939-e061-47b8-8a26-e420934fd1dc", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "[Parallel(n_jobs=14)]: Using backend LokyBackend with 14 concurrent workers.\n", - "[Parallel(n_jobs=14)]: Done 2 out of 20 | elapsed: 32.3s remaining: 4.8min\n", - "[Parallel(n_jobs=14)]: Done 5 out of 20 | elapsed: 44.9s remaining: 2.2min\n", - "[Parallel(n_jobs=14)]: Done 8 out of 20 | elapsed: 49.4s remaining: 1.2min\n", - "[Parallel(n_jobs=14)]: Done 11 out of 20 | elapsed: 1.4min remaining: 1.2min\n", - "[Parallel(n_jobs=14)]: Done 14 out of 20 | elapsed: 1.6min remaining: 40.7s\n", - "\n", - "SEVERE: error closing compressed file '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/Rest_OCME+MEICA+MGTR_nonlin.nii.gz'\n", - "Method: virtual caret::ZFileImpl::~ZFileImpl()\n", - "Location: CaretBinaryFile.cxx:276\n", - "\n", - "\n", - "While running:\n", - "/usr/local/apps/connectome-workbench/1.5.0/workbench/bin_rh_linux64/../exe_rh_linux64/wb_command -cifti-create-dense-timeseries /data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/Rest_OCME+MEICA+MGTR_fsLR32k.dtseries.nii -volume /data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/Rest_OCME+MEICA+MGTR_nonlin.nii.gz /data/MLDSST/nielsond/target_test/other_repos/HCPpipelines/global/templates/91282_Greyordinates/Atlas_ROIs.2.nii.gz -left-metric /data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/lh.32k_fs_LR.shape.gii -roi-left /data/EDB/TMSpilot/liston/sub-24740/anat/MNINonLinear/fsaverage_LR32k/sub-24740.L.atlasroi.32k_fs_LR.shape.gii -right-metric /data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/rh.32k_fs_LR.shape.gii -roi-right /data/EDB/TMSpilot/liston/sub-24740/anat/MNINonLinear/fsaverage_LR32k/sub-24740.R.atlasroi.32k_fs_LR.shape.gii -timestep 2.5\n", - "\n", - "ERROR: error while reading from nifti file '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/Rest_OCME+MEICA+MGTR_nonlin.nii.gz'\n", - "\n", - "[Parallel(n_jobs=14)]: Done 17 out of 20 | elapsed: 3.5min remaining: 37.0s\n", - "[Parallel(n_jobs=14)]: Done 20 out of 20 | elapsed: 3.5min remaining: 0.0s\n" - ] - }, - { - "ename": "CalledProcessError", - "evalue": "Command '['wb_command', '-cifti-create-dense-timeseries', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/Rest_OCME+MEICA+MGTR_fsLR32k.dtseries.nii', '-volume', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/Rest_OCME+MEICA+MGTR_nonlin.nii.gz', '/data/MLDSST/nielsond/target_test/other_repos/HCPpipelines/global/templates/91282_Greyordinates/Atlas_ROIs.2.nii.gz', '-left-metric', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/lh.32k_fs_LR.shape.gii', '-roi-left', '/data/EDB/TMSpilot/liston/sub-24740/anat/MNINonLinear/fsaverage_LR32k/sub-24740.L.atlasroi.32k_fs_LR.shape.gii', '-right-metric', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/rh.32k_fs_LR.shape.gii', '-roi-right', '/data/EDB/TMSpilot/liston/sub-24740/anat/MNINonLinear/fsaverage_LR32k/sub-24740.R.atlasroi.32k_fs_LR.shape.gii', '-timestep', '2.5']' returned non-zero exit status 255.", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31m_RemoteTraceback\u001b[0m Traceback (most recent call last)", - "\u001b[0;31m_RemoteTraceback\u001b[0m: \n\"\"\"\nTraceback (most recent call last):\n File \"/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/externals/loky/process_executor.py\", line 428, in _process_worker\n r = call_item()\n File \"/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/externals/loky/process_executor.py\", line 275, in __call__\n return self.fn(*self.args, **self.kwargs)\n File \"/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/_parallel_backends.py\", line 620, in __call__\n return self.func(*args, **kwargs)\n File \"/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/parallel.py\", line 288, in __call__\n return [func(*args, **kwargs)\n File \"/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/parallel.py\", line 288, in \n return [func(*args, **kwargs)\n File \"/tmp/ipykernel_600570/1202779090.py\", line 117, in resample_procced_to_realfslr32\n File \"/tmp/ipykernel_600570/1202779090.py\", line 89, in create_fslr32k_sample\n File \"/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/subprocess.py\", line 528, in run\n raise CalledProcessError(retcode, process.args,\nsubprocess.CalledProcessError: Command '['wb_command', '-cifti-create-dense-timeseries', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/Rest_OCME+MEICA+MGTR_fsLR32k.dtseries.nii', '-volume', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/Rest_OCME+MEICA+MGTR_nonlin.nii.gz', '/data/MLDSST/nielsond/target_test/other_repos/HCPpipelines/global/templates/91282_Greyordinates/Atlas_ROIs.2.nii.gz', '-left-metric', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/lh.32k_fs_LR.shape.gii', '-roi-left', '/data/EDB/TMSpilot/liston/sub-24740/anat/MNINonLinear/fsaverage_LR32k/sub-24740.L.atlasroi.32k_fs_LR.shape.gii', '-right-metric', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/rh.32k_fs_LR.shape.gii', '-roi-right', '/data/EDB/TMSpilot/liston/sub-24740/anat/MNINonLinear/fsaverage_LR32k/sub-24740.R.atlasroi.32k_fs_LR.shape.gii', '-timestep', '2.5']' returned non-zero exit status 255.\n\"\"\"", - "\nThe above exception was the direct cause of the following exception:\n", - "\u001b[0;31mCalledProcessError\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[78], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m res \u001b[38;5;241m=\u001b[39m \u001b[43mParallel\u001b[49m\u001b[43m(\u001b[49m\u001b[43mn_jobs\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m14\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mverbose\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m10\u001b[39;49m\u001b[43m)\u001b[49m\u001b[43m(\u001b[49m\u001b[43mjobs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/parallel.py:1098\u001b[0m, in \u001b[0;36mParallel.__call__\u001b[0;34m(self, iterable)\u001b[0m\n\u001b[1;32m 1095\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_iterating \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mFalse\u001b[39;00m\n\u001b[1;32m 1097\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_backend\u001b[38;5;241m.\u001b[39mretrieval_context():\n\u001b[0;32m-> 1098\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mretrieve\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1099\u001b[0m \u001b[38;5;66;03m# Make sure that we get a last message telling us we are done\u001b[39;00m\n\u001b[1;32m 1100\u001b[0m elapsed_time \u001b[38;5;241m=\u001b[39m time\u001b[38;5;241m.\u001b[39mtime() \u001b[38;5;241m-\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_start_time\n", - "File \u001b[0;32m/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/parallel.py:975\u001b[0m, in \u001b[0;36mParallel.retrieve\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 973\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 974\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mgetattr\u001b[39m(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_backend, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124msupports_timeout\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;28;01mFalse\u001b[39;00m):\n\u001b[0;32m--> 975\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_output\u001b[38;5;241m.\u001b[39mextend(\u001b[43mjob\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget\u001b[49m\u001b[43m(\u001b[49m\u001b[43mtimeout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mtimeout\u001b[49m\u001b[43m)\u001b[49m)\n\u001b[1;32m 976\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 977\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_output\u001b[38;5;241m.\u001b[39mextend(job\u001b[38;5;241m.\u001b[39mget())\n", - "File \u001b[0;32m/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/_parallel_backends.py:567\u001b[0m, in \u001b[0;36mLokyBackend.wrap_future_result\u001b[0;34m(future, timeout)\u001b[0m\n\u001b[1;32m 564\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"Wrapper for Future.result to implement the same behaviour as\u001b[39;00m\n\u001b[1;32m 565\u001b[0m \u001b[38;5;124;03mAsyncResults.get from multiprocessing.\"\"\"\u001b[39;00m\n\u001b[1;32m 566\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 567\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfuture\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mresult\u001b[49m\u001b[43m(\u001b[49m\u001b[43mtimeout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtimeout\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 568\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m CfTimeoutError \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 569\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTimeoutError\u001b[39;00m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01me\u001b[39;00m\n", - "File \u001b[0;32m/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/concurrent/futures/_base.py:439\u001b[0m, in \u001b[0;36mFuture.result\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m 437\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m CancelledError()\n\u001b[1;32m 438\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_state \u001b[38;5;241m==\u001b[39m FINISHED:\n\u001b[0;32m--> 439\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m__get_result\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 441\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_condition\u001b[38;5;241m.\u001b[39mwait(timeout)\n\u001b[1;32m 443\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_state \u001b[38;5;129;01min\u001b[39;00m [CANCELLED, CANCELLED_AND_NOTIFIED]:\n", - "File \u001b[0;32m/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/concurrent/futures/_base.py:391\u001b[0m, in \u001b[0;36mFuture.__get_result\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 389\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_exception:\n\u001b[1;32m 390\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 391\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_exception\n\u001b[1;32m 392\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 393\u001b[0m \u001b[38;5;66;03m# Break a reference cycle with the exception in self._exception\u001b[39;00m\n\u001b[1;32m 394\u001b[0m \u001b[38;5;28mself\u001b[39m \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n", - "\u001b[0;31mCalledProcessError\u001b[0m: Command '['wb_command', '-cifti-create-dense-timeseries', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/Rest_OCME+MEICA+MGTR_fsLR32k.dtseries.nii', '-volume', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/Rest_OCME+MEICA+MGTR_nonlin.nii.gz', '/data/MLDSST/nielsond/target_test/other_repos/HCPpipelines/global/templates/91282_Greyordinates/Atlas_ROIs.2.nii.gz', '-left-metric', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/lh.32k_fs_LR.shape.gii', '-roi-left', '/data/EDB/TMSpilot/liston/sub-24740/anat/MNINonLinear/fsaverage_LR32k/sub-24740.L.atlasroi.32k_fs_LR.shape.gii', '-right-metric', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/rh.32k_fs_LR.shape.gii', '-roi-right', '/data/EDB/TMSpilot/liston/sub-24740/anat/MNINonLinear/fsaverage_LR32k/sub-24740.R.atlasroi.32k_fs_LR.shape.gii', '-timestep', '2.5']' returned non-zero exit status 255." - ] - } - ], - "source": [ - "res = Parallel(n_jobs=14, verbose=10)(jobs)" - ] - }, - { - "cell_type": "code", - "execution_count": 82, - "id": "03c3b2d5-e0f5-4067-bf67-cad9d4d544a9", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/plain": [ - "[True,\n", - " True,\n", - " True,\n", - " True,\n", - " True,\n", - " True,\n", - " True,\n", - " True,\n", - " True,\n", - " True,\n", - " True,\n", - " True,\n", - " True,\n", - " True]" - ] - }, - "execution_count": 82, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "[rr.exists() for rr in res]" - ] - }, - { - "cell_type": "code", - "execution_count": 17, - "id": "f438b8ca-b91c-40d5-bc40-710ed30e12e1", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "subject='sub-24563'\n", - "smoothing=2.55\n", - "\n", - "concat_dir = data_dir / f'{subject}/func/rest/ConcatenatedCiftis'\n", - "fd_thresh = 0.3" - ] - }, - { - "cell_type": "code", - "execution_count": 18, - "id": "9db1bdac-5b1a-431d-b79d-a89c91304df8", - "metadata": {}, - "outputs": [], - "source": [ - "concat_nii = sorted(data_dir.glob(f'{subject}/func/rest/ConcatenatedCiftis/Rest_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing{smoothing}.dtseries.nii'))[0]\n", - "fd = sio.loadmat(sorted(data_dir.glob(f'{subject}/func/rest/ConcatenatedCiftis/FD.mat'))[0])['FD'].squeeze()\n", - "scanid = sio.loadmat(sorted(data_dir.glob(f'{subject}/func/rest/ConcatenatedCiftis/ScanIdx.mat'))[0])['ScanIdx'].squeeze()" - ] - }, - { - "cell_type": "code", - "execution_count": 19, - "id": "2994ff79-c42d-427b-9164-c4abc19dd846", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/plain": [ - "array([[1, 1],\n", - " [1, 1],\n", - " [1, 1],\n", - " ...,\n", - " [2, 2],\n", - " [2, 2],\n", - " [2, 2]], dtype=uint8)" - ] - }, - "execution_count": 19, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "scanid" - ] - }, - { - "cell_type": "code", - "execution_count": 22, - "id": "6bc0d832-927f-4c14-bab9-1b213eac1886", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/plain": [ - "PosixPath('/data/EDB/TMSpilot/liston/24563/func/rest/ConcatenatedCiftis/FD.mat')" - ] - }, - "execution_count": 22, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "concat_dir / 'FD.mat'" - ] - }, - { - "cell_type": "code", - "execution_count": 29, - "id": "be995978-b038-46c4-a508-8ca2d48e4e34", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/plain": [ - "'247183'" - ] - }, - "execution_count": 29, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "subject" - ] - }, - { - "cell_type": "code", - "execution_count": 30, - "id": "92035d0c-dcbc-4d1b-8e67-39461e0cb1a8", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/plain": [ - "array([[1, 1],\n", - " [1, 1],\n", - " [1, 1],\n", - " ...,\n", - " [1, 6],\n", - " [1, 6],\n", - " [1, 6]], dtype=uint8)" - ] - }, - "execution_count": 30, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "scanid" - ] - }, - { - "cell_type": "code", - "execution_count": 12, - "id": "e89cd388-d897-4286-abbc-f2d3495756b0", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "split_subjs = ['247183', '24740', '24742']" - ] - }, - { - "cell_type": "code", - "execution_count": 125, - "id": "198a4bcc-2d9a-4279-b876-8d7ab0842982", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/plain": [ - "['24563', '24573', '24704', '24718', '247183', '24740', '24742']" - ] - }, - "execution_count": 125, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "subjects" - ] - }, - { - "cell_type": "code", - "execution_count": 126, - "id": "9232944b-908b-49d4-be2a-794b19e41268", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "cmds = []\n", - "for subject in ['24563', '24573', '24704', '24718', '24740', '24742']:\n", - " concat_dir = data_dir / f'sub-{subject}/func/rest/ConcatenatedCiftis'\n", - "\n", - " fd = sio.loadmat((concat_dir / 'FD.mat').as_posix())['FD'].squeeze()\n", - " scanid = sio.loadmat((concat_dir / 'ScanIdx.mat').as_posix())['ScanIdx'].squeeze()\n", - " for session in [1,2]:\n", - " weights = (fd < fd_thresh).astype(int)\n", - " # deal with 247183\n", - " if subject in split_subjs:\n", - " if session == 1:\n", - " weights[scanid[:, 1] > 3] = 0\n", - " else:\n", - " weights[scanid[:, 1] <= 3] = 0\n", - " else:\n", - " # 0 weights for session mask\n", - " weights[scanid[:, 0] != session] = 0\n", - " dconn_sess_dir = data_dir / f'sub-{subject}/func/rest/session_{session}/conn'\n", - " dconn_sess_dir.mkdir(exist_ok=True, parents=True)\n", - "\n", - " weight_file = dconn_sess_dir / 'weights.txt'\n", - " weight_file.write_text(' ' .join(list(weights.astype(int).astype(str))) + '\\n')\n", - " for smoothing in [2.55, 5]:\n", - " concat_nii = concat_dir / f'Rest_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing{smoothing}_fslr32k.dtseries.nii'\n", - "\n", - " dconn_res = dconn_sess_dir / concat_nii.parts[-1].replace(\"Rest\", f\"Rest_session-{session}\").replace('.dtseries', '.dconn')\n", - " cmd = [\n", - " 'wb_command',\n", - " '-cifti-correlation',\n", - " concat_nii.as_posix(),\n", - " dconn_res.as_posix(),\n", - " '-weights',\n", - " weight_file.as_posix(),\n", - " '-mem-limit',\n", - " '100'\n", - " ]\n", - " cmds.append(' '.join(cmd))" - ] - }, - { - "cell_type": "code", - "execution_count": 84, - "id": "aa010a96-27ac-427d-91c0-0ad67212aa85", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['10892803']\n" - ] - } - ], - "source": [ - "if len(cmds) > 0:\n", - " swarm_cmd_file = swarm_cmd_dir / 'liston_dconn'\n", - " swarm_cmd_file.write_text('\\n'.join(cmds))\n", - " run_name = 'liston_dconn'\n", - " jobid = ! swarm -f {swarm_cmd_file} -g 140 -t 22 --gres=lscratch:200 --module matlab,freesurfer/6.0,fsl,simnibs/4.0,connectome-workbench,openblas --time 4:00:00 --logdir {swarm_log_dir} --job-name {run_name} --partition quick,norm\n", - " print(jobid)" - ] - }, - { - "cell_type": "code", - "execution_count": 86, - "id": "90297b96-d8dc-4836-8fa3-0151aa48a9c6", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "template_matching_script_path = Path('/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh')" - ] - }, - { - "cell_type": "code", - "execution_count": 93, - "id": "03a12f33-62ae-4e76-a5b4-81e02ebce707", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "cmds = []\n", - "for subject in subjects:\n", - " concat_dir = data_dir / f'sub-{subject}/func/rest/ConcatenatedCiftis'\n", - "\n", - " fd = sio.loadmat((concat_dir / 'FD.mat').as_posix())['FD'].squeeze()\n", - " scanid = sio.loadmat((concat_dir / 'ScanIdx.mat').as_posix())['ScanIdx'].squeeze()\n", - " for session in [1,2]:\n", - " weights = (fd < fd_thresh).astype(int)\n", - " # deal with 247183\n", - " if subject == '247183':\n", - " if session == 1:\n", - " weights[scanid[:, 1] > 3] = 0\n", - " else:\n", - " weights[scanid[:, 1] <= 3] = 0\n", - " else:\n", - " # 0 weights for session mask\n", - " weights[scanid[:, 0] != session] = 0\n", - " dconn_sess_dir = data_dir / f'sub-{subject}/func/rest/session_{session}/conn'\n", - " dconn_sess_dir.mkdir(exist_ok=True, parents=True)\n", - "\n", - " weight_file = dconn_sess_dir / 'weights.txt'\n", - " weight_file.write_text(' ' .join(list(weights.astype(int).astype(str))) + '\\n')\n", - " for smoothing in [2.55, 5]:\n", - " concat_nii = concat_dir / f'Rest_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing{smoothing}_fslr32k.dtseries.nii'\n", - "\n", - " dconn_res = dconn_sess_dir / concat_nii.parts[-1].replace(\"Rest\", f\"Rest_session-{session}\").replace('.dtseries', '.dconn')\n", - " template_matching_dir = dconn_sess_dir.parent / f'template_matching_smoothing-{smoothing}'\n", - " template_matching_dir.mkdir(exist_ok=True)\n", - " if dconn_res.exists():\n", - " cmd = [\n", - " template_matching_script_path.as_posix(),\n", - " template_matching_script_path.parent.as_posix(),\n", - " dconn_res.as_posix(),\n", - " template_matching_dir.as_posix()\n", - " ]\n", - " cmds.append(' '.join(cmd))\n" - ] - }, - { - "cell_type": "code", - "execution_count": 94, - "id": "66f4131e-bc34-4d59-a298-9b397a7cd649", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/plain": [ - "['/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh /data/MLDSST/nielsond/target_test/other_repos/template_matching_container /data/EDB/TMSpilot/liston/sub-24563/func/rest/session_1/conn/Rest_session-1_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing2.55_fslr32k.dconn.nii /data/EDB/TMSpilot/liston/sub-24563/func/rest/session_1/template_matching_smoothing-2.55',\n", - " '/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh /data/MLDSST/nielsond/target_test/other_repos/template_matching_container /data/EDB/TMSpilot/liston/sub-24563/func/rest/session_1/conn/Rest_session-1_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing5_fslr32k.dconn.nii /data/EDB/TMSpilot/liston/sub-24563/func/rest/session_1/template_matching_smoothing-5',\n", - " '/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh /data/MLDSST/nielsond/target_test/other_repos/template_matching_container /data/EDB/TMSpilot/liston/sub-24563/func/rest/session_2/conn/Rest_session-2_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing2.55_fslr32k.dconn.nii /data/EDB/TMSpilot/liston/sub-24563/func/rest/session_2/template_matching_smoothing-2.55',\n", - " '/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh /data/MLDSST/nielsond/target_test/other_repos/template_matching_container /data/EDB/TMSpilot/liston/sub-24563/func/rest/session_2/conn/Rest_session-2_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing5_fslr32k.dconn.nii /data/EDB/TMSpilot/liston/sub-24563/func/rest/session_2/template_matching_smoothing-5',\n", - " '/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh /data/MLDSST/nielsond/target_test/other_repos/template_matching_container /data/EDB/TMSpilot/liston/sub-24573/func/rest/session_1/conn/Rest_session-1_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing2.55_fslr32k.dconn.nii /data/EDB/TMSpilot/liston/sub-24573/func/rest/session_1/template_matching_smoothing-2.55',\n", - " '/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh /data/MLDSST/nielsond/target_test/other_repos/template_matching_container /data/EDB/TMSpilot/liston/sub-24573/func/rest/session_1/conn/Rest_session-1_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing5_fslr32k.dconn.nii /data/EDB/TMSpilot/liston/sub-24573/func/rest/session_1/template_matching_smoothing-5',\n", - " '/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh /data/MLDSST/nielsond/target_test/other_repos/template_matching_container /data/EDB/TMSpilot/liston/sub-24573/func/rest/session_2/conn/Rest_session-2_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing2.55_fslr32k.dconn.nii /data/EDB/TMSpilot/liston/sub-24573/func/rest/session_2/template_matching_smoothing-2.55',\n", - " '/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh /data/MLDSST/nielsond/target_test/other_repos/template_matching_container /data/EDB/TMSpilot/liston/sub-24573/func/rest/session_2/conn/Rest_session-2_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing5_fslr32k.dconn.nii /data/EDB/TMSpilot/liston/sub-24573/func/rest/session_2/template_matching_smoothing-5',\n", - " '/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh /data/MLDSST/nielsond/target_test/other_repos/template_matching_container /data/EDB/TMSpilot/liston/sub-24704/func/rest/session_1/conn/Rest_session-1_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing2.55_fslr32k.dconn.nii /data/EDB/TMSpilot/liston/sub-24704/func/rest/session_1/template_matching_smoothing-2.55',\n", - " '/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh /data/MLDSST/nielsond/target_test/other_repos/template_matching_container /data/EDB/TMSpilot/liston/sub-24704/func/rest/session_1/conn/Rest_session-1_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing5_fslr32k.dconn.nii /data/EDB/TMSpilot/liston/sub-24704/func/rest/session_1/template_matching_smoothing-5',\n", - " '/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh /data/MLDSST/nielsond/target_test/other_repos/template_matching_container /data/EDB/TMSpilot/liston/sub-24704/func/rest/session_2/conn/Rest_session-2_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing2.55_fslr32k.dconn.nii /data/EDB/TMSpilot/liston/sub-24704/func/rest/session_2/template_matching_smoothing-2.55',\n", - " '/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh /data/MLDSST/nielsond/target_test/other_repos/template_matching_container /data/EDB/TMSpilot/liston/sub-24704/func/rest/session_2/conn/Rest_session-2_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing5_fslr32k.dconn.nii /data/EDB/TMSpilot/liston/sub-24704/func/rest/session_2/template_matching_smoothing-5',\n", - " '/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh /data/MLDSST/nielsond/target_test/other_repos/template_matching_container /data/EDB/TMSpilot/liston/sub-24718/func/rest/session_1/conn/Rest_session-1_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing2.55_fslr32k.dconn.nii /data/EDB/TMSpilot/liston/sub-24718/func/rest/session_1/template_matching_smoothing-2.55',\n", - " '/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh /data/MLDSST/nielsond/target_test/other_repos/template_matching_container /data/EDB/TMSpilot/liston/sub-24718/func/rest/session_1/conn/Rest_session-1_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing5_fslr32k.dconn.nii /data/EDB/TMSpilot/liston/sub-24718/func/rest/session_1/template_matching_smoothing-5',\n", - " '/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh /data/MLDSST/nielsond/target_test/other_repos/template_matching_container /data/EDB/TMSpilot/liston/sub-24718/func/rest/session_2/conn/Rest_session-2_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing2.55_fslr32k.dconn.nii /data/EDB/TMSpilot/liston/sub-24718/func/rest/session_2/template_matching_smoothing-2.55',\n", - " '/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh /data/MLDSST/nielsond/target_test/other_repos/template_matching_container /data/EDB/TMSpilot/liston/sub-24718/func/rest/session_2/conn/Rest_session-2_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing5_fslr32k.dconn.nii /data/EDB/TMSpilot/liston/sub-24718/func/rest/session_2/template_matching_smoothing-5',\n", - " '/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh /data/MLDSST/nielsond/target_test/other_repos/template_matching_container /data/EDB/TMSpilot/liston/sub-247183/func/rest/session_1/conn/Rest_session-1_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing2.55_fslr32k.dconn.nii /data/EDB/TMSpilot/liston/sub-247183/func/rest/session_1/template_matching_smoothing-2.55',\n", - " '/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh /data/MLDSST/nielsond/target_test/other_repos/template_matching_container /data/EDB/TMSpilot/liston/sub-247183/func/rest/session_1/conn/Rest_session-1_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing5_fslr32k.dconn.nii /data/EDB/TMSpilot/liston/sub-247183/func/rest/session_1/template_matching_smoothing-5',\n", - " '/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh /data/MLDSST/nielsond/target_test/other_repos/template_matching_container /data/EDB/TMSpilot/liston/sub-247183/func/rest/session_2/conn/Rest_session-2_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing2.55_fslr32k.dconn.nii /data/EDB/TMSpilot/liston/sub-247183/func/rest/session_2/template_matching_smoothing-2.55',\n", - " '/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh /data/MLDSST/nielsond/target_test/other_repos/template_matching_container /data/EDB/TMSpilot/liston/sub-247183/func/rest/session_2/conn/Rest_session-2_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing5_fslr32k.dconn.nii /data/EDB/TMSpilot/liston/sub-247183/func/rest/session_2/template_matching_smoothing-5',\n", - " '/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh /data/MLDSST/nielsond/target_test/other_repos/template_matching_container /data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/conn/Rest_session-1_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing2.55_fslr32k.dconn.nii /data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/template_matching_smoothing-2.55',\n", - " '/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh /data/MLDSST/nielsond/target_test/other_repos/template_matching_container /data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/conn/Rest_session-1_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing5_fslr32k.dconn.nii /data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/template_matching_smoothing-5',\n", - " '/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh /data/MLDSST/nielsond/target_test/other_repos/template_matching_container /data/EDB/TMSpilot/liston/sub-24740/func/rest/session_2/conn/Rest_session-2_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing2.55_fslr32k.dconn.nii /data/EDB/TMSpilot/liston/sub-24740/func/rest/session_2/template_matching_smoothing-2.55',\n", - " '/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh /data/MLDSST/nielsond/target_test/other_repos/template_matching_container /data/EDB/TMSpilot/liston/sub-24740/func/rest/session_2/conn/Rest_session-2_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing5_fslr32k.dconn.nii /data/EDB/TMSpilot/liston/sub-24740/func/rest/session_2/template_matching_smoothing-5',\n", - " '/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh /data/MLDSST/nielsond/target_test/other_repos/template_matching_container /data/EDB/TMSpilot/liston/sub-24742/func/rest/session_1/conn/Rest_session-1_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing2.55_fslr32k.dconn.nii /data/EDB/TMSpilot/liston/sub-24742/func/rest/session_1/template_matching_smoothing-2.55',\n", - " '/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh /data/MLDSST/nielsond/target_test/other_repos/template_matching_container /data/EDB/TMSpilot/liston/sub-24742/func/rest/session_1/conn/Rest_session-1_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing5_fslr32k.dconn.nii /data/EDB/TMSpilot/liston/sub-24742/func/rest/session_1/template_matching_smoothing-5',\n", - " '/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh /data/MLDSST/nielsond/target_test/other_repos/template_matching_container /data/EDB/TMSpilot/liston/sub-24742/func/rest/session_2/conn/Rest_session-2_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing2.55_fslr32k.dconn.nii /data/EDB/TMSpilot/liston/sub-24742/func/rest/session_2/template_matching_smoothing-2.55',\n", - " '/data/MLDSST/nielsond/target_test/other_repos/template_matching_container/run_once_biowulf.sh /data/MLDSST/nielsond/target_test/other_repos/template_matching_container /data/EDB/TMSpilot/liston/sub-24742/func/rest/session_2/conn/Rest_session-2_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing5_fslr32k.dconn.nii /data/EDB/TMSpilot/liston/sub-24742/func/rest/session_2/template_matching_smoothing-5']" - ] - }, - "execution_count": 94, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "cmds" - ] - }, - { - "cell_type": "code", - "execution_count": 96, - "id": "b342e8cc-a125-455c-9925-54986680db39", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "['10894961']\n" - ] - } - ], - "source": [ - "if len(cmds) > 0:\n", - " swarm_cmd_file = swarm_cmd_dir / 'template_matching'\n", - " swarm_cmd_file.write_text('\\n'.join(cmds))\n", - " run_name = 'template_matching'\n", - " jobid = ! swarm -f {swarm_cmd_file} -g 140 -t 22 --gres=lscratch:200 --module singularity --time 4:00:00 --logdir {swarm_log_dir} --job-name {run_name} --partition quick,norm\n", - " print(jobid)" - ] - }, - { - "cell_type": "code", - "execution_count": 28, - "id": "471f8dab-a81a-4929-9120-9b39e426f245", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "AverageSBref ConcatenatedCiftis session_1\n" - ] - } - ], - "source": [ - "!ls /data/EDB/TMSpilot/liston/sub-247183/func/rest/" - ] - }, - { - "cell_type": "code", - "execution_count": 60, - "id": "605aa875-0f60-4bca-ab12-9681a118d6b2", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/plain": [ - "PosixPath('/data/EDB/TMSpilot/liston')" - ] - }, - "execution_count": 60, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "data_dir" - ] - }, - { - "cell_type": "code", - "execution_count": 50, - "id": "137bf060-be39-4674-812a-c0d28b8b7482", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/plain": [ - "'Rest_session-1_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing2.55.dconn.nii'" - ] - }, - "execution_count": 50, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "concat_nii = sorted(data_dir.glob(f'{subject}/func/rest/ConcatenatedCiftis/Rest_OCME+MEICA+MGTR_Concatenated+SubcortRegression+SpatialSmoothing{smoothing}.dtseries.nii'))[0]\n", - "fd = sio.loadmat(sorted(data_dir.glob(f'{subject}/func/rest/ConcatenatedCiftis/FD.mat'))[0])['FD'].squeeze()\n", - "scanid = sio.loadmat(sorted(data_dir.glob(f'{subject}/func/rest/ConcatenatedCiftis/ScanIdx.mat'))[0])['ScanIdx'].squeeze()" - ] - }, - { - "cell_type": "code", - "execution_count": 35, - "id": "11a467e2-bb4e-4dbf-bdf9-191fade91540", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/plain": [ - "(960, 82428)" - ] - }, - "execution_count": 35, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "nb.load(concat_nii[0]).shape" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "371c68d4-9618-4336-b01f-2a88809bcb85", - "metadata": {}, - "outputs": [], - "source": [] - }, - { - "cell_type": "markdown", - "id": "412b1393-82f5-4beb-8439-c8a22ec9e684", - "metadata": {}, - "source": [ - "'/data/MLDSST/nielsond/target_test/data/cornell/" - ] } ], "metadata": {