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": [
- {
- "data": {
- "text/plain": [
- "0 True\n",
- "1 True\n",
- "2 True\n",
- "3 True\n",
- "4 True\n",
- " ... \n",
- "2875 False\n",
- "2876 False\n",
- "2877 False\n",
- "2878 False\n",
- "2879 False\n",
- "Name: session, Length: 2880, dtype: bool"
- ]
- },
- "execution_count": 36,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "scanid.session == session"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 44,
- "id": "6bf6ae8c-b673-4e85-aa20-a32a9bad8ffc",
- "metadata": {
- "tags": []
- },
- "outputs": [
- {
- "data": {
- "text/plain": [
- "array([ 4, 5, 6, ..., 1437, 1438, 1439])"
- ]
- },
- "execution_count": 44,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "scanid.loc[(scanid.session == session) & scanid.fd_mask].index.values"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 29,
- "id": "abe2015a-00f4-46c1-b929-b8422571f4bf",
- "metadata": {
- "tags": []
- },
- "outputs": [
- {
- "ename": "IndexError",
- "evalue": "boolean index did not match indexed array along dimension 0; dimension is 2793 but corresponding boolean dimension is 2880",
- "output_type": "error",
- "traceback": [
- "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
- "\u001b[0;31mIndexError\u001b[0m Traceback (most recent call last)",
- "Cell \u001b[0;32mIn[29], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43mfd_mask\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mnonzero\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m[\u001b[49m\u001b[43m(\u001b[49m\u001b[43mscanid\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msession\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m==\u001b[39;49m\u001b[43m \u001b[49m\u001b[43msession\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mvalues\u001b[49m\u001b[43m]\u001b[49m\n",
- "\u001b[0;31mIndexError\u001b[0m: boolean index did not match indexed array along dimension 0; dimension is 2793 but corresponding boolean dimension is 2880"
- ]
- }
- ],
- "source": [
- "fd_mask.nonzero()[0][(scanid.session == session).values]"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 26,
- "id": "54dc67ff-c2ce-400f-b690-c0e2f48dc94e",
- "metadata": {
- "tags": []
- },
- "outputs": [
- {
- "data": {
- "text/plain": [
- "2880"
- ]
- },
- "execution_count": 26,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "len(fd_mask)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 28,
- "id": "95a33da3-2773-4936-9f9f-dcc7532c7761",
- "metadata": {
- "tags": []
- },
- "outputs": [
- {
- "data": {
- "text/plain": [
- "2880"
- ]
- },
- "execution_count": 28,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "len((scanid.session == session).values)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 20,
- "id": "7fdd01b9-3e98-4a54-b162-359fb79ae27b",
- "metadata": {
- "tags": []
- },
- "outputs": [
- {
- "data": {
- "text/plain": [
- "'24546'"
- ]
- },
- "execution_count": 20,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "subject"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 19,
- "id": "5575a0f6-ffd7-438b-b157-281473683181",
- "metadata": {
- "tags": []
- },
- "outputs": [
- {
- "data": {
- "text/plain": [
- "2880"
- ]
- },
- "execution_count": 19,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "len(scanid)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 21,
- "id": "a4154b1c-dbdf-4cb5-a863-a998ef2ff9cd",
- "metadata": {
- "tags": []
- },
- "outputs": [
- {
- "data": {
- "text/plain": [
- "array([False, False, False, ..., True, True, True])"
- ]
- },
- "execution_count": 21,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "fd_mask[(scanid.session == 1).values]"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 22,
- "id": "5f06b6ad-99ac-4b54-aa9d-0638cfb65508",
- "metadata": {
- "tags": []
- },
- "outputs": [
- {
- "data": {
- "text/plain": [
- "array([False, False, False, ..., True, True, True])"
- ]
- },
- "execution_count": 22,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "fd_mask[(scanid.session == 2).values]"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 23,
- "id": "2e0ceb6c-7bae-45b4-90a2-59fb5400fd9c",
- "metadata": {
- "tags": []
- },
- "outputs": [
- {
- "data": {
- "text/html": [
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- "\n",
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