`numpy.AxisError: axis 1 is out of bounds for array of dimension 1` #670

andrew-yian-sun · 2023-04-23T04:28:48Z

Summary

Description of issue: using heudiconv to convert some participants' sessions ("vis") results in a numpy.AxisError: axis 1 is out of bounds for array of dimension 1 error. The same heuristic was successfully used on other participants, but I'm not seeing the difference between participant data that is successfully converted and the data that runs into the error.

commands:

time docker run --rm 
--volume /Volumes/LCproject/LC_aging/data_mri:/base nipy/heudiconv:latest 
--dicom_dir_template /base/data_BAP/{subject}_Session*{session}_*/*/* 
--outdir /base/data_BAP_BIDS 
--heuristic /base/data_BAP_BIDS/code/heuristic_postUpdate.py 
--subjects BAP120 
--ses vis 
--converter dcm2niix 
--bids 
--overwrite

command-line output:

INFO: Running heudiconv version 0.10.0 latest 0.12.2
INFO: Need to process 1 study sessions
INFO: PROCESSING STARTS: {'subject': 'BAP120', 'outdir': '/base/data_BAP_BIDS/', 'session': 'vis'}
INFO: Processing 1370 dicoms
INFO: Analyzing 1370 dicoms
/opt/miniconda-latest/lib/python3.7/site-packages/nibabel/nicom/dicomwrappers.py:536: UserWarning: Derived images found and removed
  warnings.warn("Derived images found and removed")
Traceback (most recent call last):
  File "/opt/miniconda-latest/bin/heudiconv", line 8, in <module>
    sys.exit(main())
  File "/opt/miniconda-latest/lib/python3.7/site-packages/heudiconv/cli/run.py", line 24, in main
    workflow(**kwargs)
  File "/opt/miniconda-latest/lib/python3.7/site-packages/heudiconv/main.py", line 351, in workflow
    grouping=grouping,)
  File "/opt/miniconda-latest/lib/python3.7/site-packages/heudiconv/convert.py", line 177, in prep_conversion
    custom_grouping=getattr(heuristic, 'grouping', None))
  File "/opt/miniconda-latest/lib/python3.7/site-packages/heudiconv/dicoms.py", line 202, in group_dicoms_into_seqinfos
    mwinfo = validate_dicom(filename, dcmfilter)
  File "/opt/miniconda-latest/lib/python3.7/site-packages/heudiconv/dicoms.py", line 106, in validate_dicom
    del mw.series_signature[sig]
  File "/opt/miniconda-latest/lib/python3.7/site-packages/nibabel/onetime.py", line 142, in __get__
    val = self.getter(obj)
  File "/opt/miniconda-latest/lib/python3.7/site-packages/nibabel/nicom/dicomwrappers.py", line 642, in series_signature
    signature['image_shape'] = (self.image_shape, eq)
  File "/opt/miniconda-latest/lib/python3.7/site-packages/nibabel/onetime.py", line 142, in __get__
    val = self.getter(obj)
  File "/opt/miniconda-latest/lib/python3.7/site-packages/nibabel/nicom/dicomwrappers.py", line 557, in image_shape
    frame_indices = np.delete(frame_indices, stackid_dim_idx, axis=1)
  File "<__array_function__ internals>", line 6, in delete
  File "/opt/miniconda-latest/lib/python3.7/site-packages/numpy/lib/function_base.py", line 4392, in delete
    axis = normalize_axis_index(axis, ndim)
numpy.AxisError: axis 1 is out of bounds for array of dimension 1

heuristic:

import os


def create_key(template, outtype=('nii.gz',), annotation_classes=None):
    if template is None or not template:
        raise ValueError('Template must be a valid format string')
    return template, outtype, annotation_classes


def infotodict(seqinfo):
    t1w_lowres = create_key('sub-{subject}/{session}/anat/sub-{subject}_{session}_acq-lowres_T1w')
    fmri_vis = create_key('sub-{subject}/{session}/func/sub-{subject}_{session}_task-vis_run-{item:01d}_bold')
    epi_AP_vis = create_key('sub-{subject}/{session}/fmap/sub-{subject}_{session}_acq-vis_dir-AP_epi')
    epi_PA_vis = create_key('sub-{subject}/{session}/fmap/sub-{subject}_{session}_acq-vis_dir-PA_epi')
    diff_HCPish_AP = create_key('sub-{subject}/{session}/dwi/sub-{subject}_{session}_acq-hcpish_dir-AP_dwi')
    diff_HCPish_PA = create_key('sub-{subject}/{session}/fmap/sub-{subject}_{session}_acq-hcpish_dir-PA_epi')

    info = {
        t1w_lowres: [], fmri_vis: [], epi_AP_vis: [], epi_PA_vis: [], diff_HCPish_AP: [], diff_HCPish_PA: []
        }

    for s in seqinfo:
        if 't1_mprage_low_res' == s.protocol_name:
            info[t1w_lowres].append(s.series_id)
        if 'visual_fMRI' in s.protocol_name and s.series_files == 245: # 245 ensures only full runs (not restarts) are bidsified
            info[fmri_vis].append(s.series_id)
        if 'visual_SE_EPI_Encoding_AP' in s.protocol_name:
            info[epi_AP_vis].append(s.series_id)
        if 'visual_SE_EPI_Encoding_PA' in s.protocol_name:
            info[epi_PA_vis].append(s.series_id)
        if 'diff_HCPish_AP' in s.protocol_name and 'TRACEW' not in s.image_type:
            info[diff_HCPish_AP].append(s.series_id)
        if 'diff_HCPish_PA' in s.protocol_name:
            info[diff_HCPish_PA].append(s.series_id)
    return info

Platform details:

Choose one:

Local environment

Container

Docker
tag: nipy/heudiconv:latest
image ID: 0d55d3d24064

Heudiconv version: 0.10.0

The text was updated successfully, but these errors were encountered:

yarikoptic · 2023-04-23T15:39:29Z

seems to be specifically nibabel issue, and you are using older nibabel (0.10.0). In the newer version there is newer nibabel

yoh@typhon:~$ time docker run --rm --entrypoint python nipy/heudiconv:0.10.0  -c 'import nibabel; print(nibabel.__version__)'
3.2.2
yoh@typhon:~$ time docker run --rm --entrypoint python nipy/heudiconv:latest  -c 'import nibabel; print(nibabel.__version__)'
5.0.1

so can you try with nipy/heudiconv:0.12.2 and not the outdated :latest?

andrew-yian-sun · 2023-04-23T21:29:50Z

Thanks for the suggestion - however I seemed to have run into the same error with 0.12.2 as well:

> time docker run --rm \
> --volume /Volumes/LCproject/LC_aging/data_mri:/base \
> nipy/heudiconv:0.12.2 \
> --dicom_dir_template /base/data_BAP/{subject}_Session*{session}_*/*/* \
> --outdir /base/data_BAP_BIDS \
> --heuristic /base/data_BAP_BIDS/code/heuristic_postUpdate.py \
> --subjects BAP120 \
> --ses vis \
> --converter dcm2niix \
> --bids \
> --overwrite
INFO: Running heudiconv version 0.12.2 latest 0.12.2
INFO: Need to process 1 study sessions
INFO: PROCESSING STARTS: {'subject': 'BAP120', 'outdir': '/base/data_BAP_BIDS/', 'session': 'vis'}
INFO: Processing 1370 dicoms
INFO: Analyzing 1370 dicoms
/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/nibabel/nicom/dicomwrappers.py:525: UserWarning: Derived images found and removed
  warnings.warn('Derived images found and removed')
Traceback (most recent call last):
  File "/opt/miniconda-py39_4.12.0/bin/heudiconv", line 8, in <module>
    sys.exit(main())
  File "/src/heudiconv/heudiconv/cli/run.py", line 24, in main
    workflow(**kwargs)
  File "/src/heudiconv/heudiconv/main.py", line 379, in workflow
    prep_conversion(sid,
  File "/src/heudiconv/heudiconv/convert.py", line 173, in prep_conversion
    seqinfo = group_dicoms_into_seqinfos(
  File "/src/heudiconv/heudiconv/dicoms.py", line 202, in group_dicoms_into_seqinfos
    mwinfo = validate_dicom(filename, dcmfilter)
  File "/src/heudiconv/heudiconv/dicoms.py", line 106, in validate_dicom
    del mw.series_signature[sig]
  File "/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/nibabel/onetime.py", line 142, in __get__
    val = self.getter(obj)
  File "/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/nibabel/nicom/dicomwrappers.py", line 625, in series_signature
    signature['image_shape'] = (self.image_shape, eq)
  File "/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/nibabel/onetime.py", line 142, in __get__
    val = self.getter(obj)
  File "/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/nibabel/nicom/dicomwrappers.py", line 545, in image_shape
    frame_indices = np.delete(frame_indices, stackid_dim_idx, axis=1)
  File "<__array_function__ internals>", line 200, in delete
  File "/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/numpy/lib/function_base.py", line 5136, in delete
    axis = normalize_axis_index(axis, ndim)
numpy.AxisError: axis 1 is out of bounds for array of dimension 1

yarikoptic · 2023-04-24T18:52:26Z

is there a chance you could share that DICOM publicly? privately? I think we should file the issue with nibabel -- I don't see a similar issue there.

araikes · 2023-06-28T20:51:16Z

@yarikoptic I get the same error as above using version 0.13.1 running in Singularity. All of the DICOMs are Siemens Enhanced DICOMS from the XA20 software version. dcm2niix behaves fine but nibabel doesn't like parsing the data:

singularity run --containall -B $PWD:/data /groups/adamraikes/singularity_images/heudiconv_0.13.1.sif -d /data/dicoms/{subject}/*/* -o /data/nifti/ -f convertall -s 000052 -c none
INFO: Running heudiconv version 0.13.1 latest 0.13.1
INFO: Need to process 1 study sessions
INFO: PROCESSING STARTS: {'subject': '000052', 'outdir': '/data/nifti/', 'session': None}
INFO: Processing 1187 dicoms
INFO: Analyzing 1187 dicoms
/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/nibabel/nicom/dicomwrappers.py:525: UserWarning: Derived images found and removed
  warnings.warn('Derived images found and removed')
Traceback (most recent call last):
  File "/opt/miniconda-py39_4.12.0/bin/heudiconv", line 8, in <module>
    sys.exit(main())
  File "/src/heudiconv/heudiconv/cli/run.py", line 30, in main
    workflow(**kwargs)
  File "/src/heudiconv/heudiconv/main.py", line 463, in workflow
    prep_conversion(
  File "/src/heudiconv/heudiconv/convert.py", line 216, in prep_conversion
    seqinfo = group_dicoms_into_seqinfos(
  File "/src/heudiconv/heudiconv/dicoms.py", line 283, in group_dicoms_into_seqinfos
    mwinfo = validate_dicom(filename, dcmfilter)
  File "/src/heudiconv/heudiconv/dicoms.py", line 125, in validate_dicom
    del mw.series_signature[sig]
  File "/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/nibabel/onetime.py", line 156, in __get__
    val = self.getter(obj)
  File "/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/nibabel/nicom/dicomwrappers.py", line 625, in series_signature
    signature['image_shape'] = (self.image_shape, eq)
  File "/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/nibabel/onetime.py", line 156, in __get__
    val = self.getter(obj)
  File "/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/nibabel/nicom/dicomwrappers.py", line 545, in image_shape
    frame_indices = np.delete(frame_indices, stackid_dim_idx, axis=1)
  File "<__array_function__ internals>", line 200, in delete
  File "/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/numpy/lib/function_base.py", line 5136, in delete
    axis = normalize_axis_index(axis, ndim)
numpy.AxisError: axis 1 is out of bounds for array of dimension 1

Note: The containall flag was used to rule out a conflict with nibabel installed locally. There were no differences whether running with --cleanenv, --containall, or no flag

chrisadamsonmcri · 2023-07-25T01:59:54Z

Can confirm I'm getting this error as well. Same versions. It is happening on derived TRACEW images from DWI sequences.

yarikoptic · 2023-07-25T12:51:36Z

Filed nipy/nibabel#1245 since I think the issue is to fix within nibabel.
Do you have a sample DICOM you could potentially share?
@kodiweera - do we have any TRACEW images on phantoms?

kodiweera · 2023-07-25T14:12:05Z

Not any that I'm aware of. However, I think you can derive/calculate the tracew images from dwi data. TRACEW sounds like weighting of the traces of the DTI matrix.

chrisadamsonmcri · 2023-07-25T22:27:52Z

I'm able to send one of ours as an example. As long as its not posted to be publicly accessible. Please advise where I can send.

chrisadamsonmcri · 2023-07-31T00:35:32Z

The problem is caused in this block of heudiconv/dicoms.py in MultiframeWrapper::image_shape() at line ~512

        if hasattr(first_frame, 'get') and first_frame.get([0x18, 0x9117]):
            # DWI image may include derived isotropic, ADC or trace volume
            try:
                self.frames = pydicom.Sequence(
                    frame
                    for frame in self.frames
                    if frame.MRDiffusionSequence[0].DiffusionDirectionality != 'ISOTROPIC'
                )
            except IndexError:
                # Sequence tag is found but missing items!
                raise WrapperError('Diffusion file missing information')
            except AttributeError:
                # DiffusionDirectionality tag is not required
                pass
            else:
                if n_frames != len(self.frames):
                    warnings.warn('Derived images found and removed')
                    n_frames = len(self.frames)
                    has_derived = True

For a trace image it detects all frames as derived and removes them. You are left with an empty image.

yarikoptic · 2023-08-01T18:33:52Z

eh, you really confused me with the statement of it being in heudiconv/dicoms.py since it is not there but in nibabel

❯ pwd
/home/yoh/proj/nipy/nipy-suite/nibabel
❯ git grep -n -C 3 'found and removed'
nibabel/nicom/dicomwrappers.py-522-                pass
nibabel/nicom/dicomwrappers.py-523-            else:
nibabel/nicom/dicomwrappers.py-524-                if n_frames != len(self.frames):
nibabel/nicom/dicomwrappers.py:525:                    warnings.warn('Derived images found and removed')
nibabel/nicom/dicomwrappers.py-526-                    n_frames = len(self.frames)
nibabel/nicom/dicomwrappers.py-527-                    has_derived = True
nibabel/nicom/dicomwrappers.py-528-
--

and that is why should be fixed there, thus nipy/nibabel#1245 . @kodiweera - could we collect some on phantom in coming days? (@chrisadamsonmcri we better have a public copy of it) or may be @neurolabusc has one of those tracew files somewhere among qa_ datasets?

chrisadamsonmcri · 2023-08-02T01:45:12Z

Sorry my bad.

yarikoptic · 2023-08-07T13:37:35Z

Sample tracew DICOMs were collected and available now at http://datasets.datalad.org/?dir=/dicoms/dartmouth-phantoms/Siemens-DWITrace-20230803 . But upon quick try with heudiconv - I did not reproduce this issue, so must be something special about original DICOMs.

neurolabusc · 2023-08-07T15:05:35Z

You may want to have dcm2niix ignore derived images (-i y). One should expect better derived diffusion measures (TRACE, MD, ADC, FA, etc) after processing with dwidenoise, mrdegibbs, topup and eddy. In general, BIDS treats derivatives differently than source data.

If you do ask dcm2niix to retain derived data, it will add a hint to the JSON indicating that the image has been detected as derived:

	"RawImage": false,

However, dcm2niix's derived image detection errs on the side of caution, and therefore not all derived data will be identified as such. Indeed, in many cases whether data is derived or not is in the eye of the beholder, e.g. some users only export images with NonlinearGradientCorrection and use it as their raw data, while other users export with and without this manipulation and likely consider the corrected image derived from the uncorrected image.

yarikoptic · 2023-08-09T19:25:53Z

You may want to have dcm2niix ignore derived images (-i y).

this logic happens in heudiconv before invoking dcm2niix -- we also try to sort dicoms into separate series which we then eventually give to dcm2niix.

yarikoptic · 2023-08-09T19:27:11Z

I'm able to send one of ours as an example. As long as its not posted to be publicly accessible. Please advise where I can send.

Since my attempts to reproduce on locally collected data failed, if you could share with me (yarikoptic at gmail) some way -- would be great. I will then look into fixing up nibabel for it.

yarikoptic · 2023-08-09T20:08:58Z

nevermind! I have gone through all dcm_qa repos of @neurolabusc and got one

dcm_qa_xa30/In/20_DWI_dir80_AP
INFO: Running heudiconv version 0.13.1.post7+g83c8424.d20230720 latest 0.13.1
INFO: Analyzing 1 dicoms
/home/yoh/proj/heudiconv/heudiconv-master/venvs/dev3/lib/python3.11/site-packages/nibabel/nicom/dicomwrappers.py:525: UserWarning: Derived images found and removed
  warnings.warn('Derived images found and removed')
Traceback (most recent call last):
  File "/home/yoh/proj/heudiconv/heudiconv-master/venvs/dev3/bin/heudiconv", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/yoh/proj/heudiconv/heudiconv-master/heudiconv/cli/run.py", line 30, in main
    workflow(**kwargs)
  File "/home/yoh/proj/heudiconv/heudiconv-master/heudiconv/main.py", line 394, in workflow
    study_sessions = get_study_sessions(
                     ^^^^^^^^^^^^^^^^^^^
  File "/home/yoh/proj/heudiconv/heudiconv-master/heudiconv/parser.py", line 221, in get_study_sessions
    seqinfo_dict = group_dicoms_into_seqinfos(
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/yoh/proj/heudiconv/heudiconv-master/heudiconv/dicoms.py", line 283, in group_dicoms_into_seqinfos
    mwinfo = validate_dicom(filename, dcmfilter)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/yoh/proj/heudiconv/heudiconv-master/heudiconv/dicoms.py", line 125, in validate_dicom
    del mw.series_signature[sig]
        ^^^^^^^^^^^^^^^^^^^
  File "/home/yoh/proj/heudiconv/heudiconv-master/venvs/dev3/lib/python3.11/site-packages/nibabel/onetime.py", line 156, in __get__
    val = self.getter(obj)
          ^^^^^^^^^^^^^^^^
  File "/home/yoh/proj/heudiconv/heudiconv-master/venvs/dev3/lib/python3.11/site-packages/nibabel/nicom/dicomwrappers.py", line 625, in series_signature
    signature['image_shape'] = (self.image_shape, eq)
                                ^^^^^^^^^^^^^^^^
  File "/home/yoh/proj/heudiconv/heudiconv-master/venvs/dev3/lib/python3.11/site-packages/nibabel/onetime.py", line 156, in __get__
    val = self.getter(obj)
          ^^^^^^^^^^^^^^^^
  File "/home/yoh/proj/heudiconv/heudiconv-master/venvs/dev3/lib/python3.11/site-packages/nibabel/nicom/dicomwrappers.py", line 545, in image_shape
    frame_indices = np.delete(frame_indices, stackid_dim_idx, axis=1)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/yoh/proj/heudiconv/heudiconv-master/venvs/dev3/lib/python3.11/site-packages/numpy/lib/function_base.py", line 5254, in delete
    axis = normalize_axis_index(axis, ndim)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
numpy.exceptions.AxisError: axis 1 is out of bounds for array of dimension 1

!

edit: full log with some other errors observed is at http://www.oneukrainian.com/tmp/dcm_qa_heudiconv_sweep.txt

yarikoptic · 2023-08-09T20:49:25Z

@chrisadamsonmcri I think you nailed the reason in #670 (comment) ! FWIW, if I disable that removal of isotropic images, and use "experimental" dcm2niix and check what dcm2niix assigns for BidsGuess, I get:

❯ rm -rf /tmp/out; PATH=/home/yoh/deb/gits/pkg-exppsy/dcm2niix/build/bin/:$PATH HEUDICONV_LOG_LEVEL=ERROR heudiconv --dbg -f convertall --bids -o /tmp/out --files dcm_qa_xa30/In/20_DWI_dir80_AP -s NA -ss ses1 -l ''; cat /tmp/out/.heudiconv/NA/ses-ses1/info/NA_ses-ses1.auto.txt; ls -l /tmp/out; grep -A3 Guess /tmp/out/*json
INFO: Running heudiconv version 0.13.1.post7+g83c8424.d20230720 latest 0.13.1
...
INFO: PROCESSING DONE: {'subject': 'NA', 'outdir': '/tmp/out/', 'session': 'ses1'}
{('run{item:03d}', ('nii.gz',), None): ['20-DWI_dir80_AP']}total 140
-rw------- 1 yoh yoh    364 Aug  9 16:35 CHANGES
-rw------- 1 yoh yoh    138 Aug  9 16:35 README
-rw------- 1 yoh yoh    633 Aug  9 16:35 dataset_description.json
-rw------- 1 yoh yoh    405 Aug  9 16:35 participants.json
-rw------- 1 yoh yoh     49 Aug  9 16:35 participants.tsv
-r-------- 1 yoh yoh   2881 Aug  9 16:35 run001.json
-r-------- 1 yoh yoh 111107 Aug  9 16:35 run001.nii.gz
-rw------- 1 yoh yoh    339 Aug  9 16:35 scans.json
/tmp/out/run001.json:  "BidsGuess": [
/tmp/out/run001.json-    "derived",
/tmp/out/run001.json-    "_acq-epse2_dir-AP_run-20_dwi"
/tmp/out/run001.json-],

so looks all good and legit. I guess we need to look into fixing nibabel to not overzealosly remove there since in this particular case it looks like a legit DWI (dcm_qa_xa30/In/20_DWI_dir80_AP) and not derived images right @neurolabusc ?

neurolabusc · 2023-08-09T22:27:50Z

@yarikoptic 20_DWI_dir80_AP is a derived image. This is clear in the JSON:

"ImageType": ["DERIVED", "PRIMARY", "DIFFUSION", "TRACEW"],
"RawImage": false,

The derived TRACE image is typically the geometric mean of the raw directional images. One should expect better derived diffusion measures (TRACE, MD, ADC, FA, etc) after processing with dwidenoise, mrdegibbs, topup and eddy. In general, BIDS treats derivatives differently than source data.

mitchellxh · 2024-02-07T17:09:30Z

What exactly is the fix for this? I'm experiencing the same thing.

yarikoptic · 2024-02-07T19:36:08Z

no fix yet unfortunately... I followed up on nipy/nibabel#1245

s-madhavan · 2024-02-26T21:16:13Z

Hi I'm getting the same issue. Did anyone resolving this. Running through Singularity container.

Error: numpy.exceptions.AxisError: axis 1 is out of bounds for array of dimension 1

yarikoptic · 2024-02-27T00:07:51Z

a solution is proposed by @effigies in nipy/nibabel#1245 (comment) . Those who can -- try by using patched nibabel pip install git+https://github.com/effigies/nibabel.git@fix/dicom-missing-frame-indices

yarikoptic · 2024-02-27T00:40:52Z

if you do

pip install git+https://github.com/effigies/nibabel.git@fix/dicom-missing-frame-indices
pip install pydicom

then you could test on your sample dicom using smth like python -W ignore::UserWarning -c 'import sys; f=sys.argv[1]; print(f, end=" "); from nibabel.nicom import dicomwrappers as didw; print(didw.wrapper_from_file(f).image_shape)' FILENAME

s-madhavan · 2024-02-27T00:42:59Z

@yarikoptic Thanks. I'll try that and let you know.

mitchellxh · 2024-02-27T01:20:50Z

The nipy/nibabel#1245 (comment) fix has resolved this (locally).

Would you be able to update this patch into a new heudiconv container? I'm not sure how to fix the container myself.

effigies · 2024-02-27T04:19:07Z

nibabel 5.2.1 is on PyPI.

yarikoptic · 2024-02-28T15:54:25Z

I have now merged and released

Add support for a custom seqinfo to extract from DICOMs any additional metadata desired for a heuristic #581

so you should be all set to use that docker image

❯ docker pull nipy/heudiconv
Using default tag: latest
latest: Pulling from nipy/heudiconv
09e2bc8a597c: Already exists 
119c26737198: Already exists 
55899c7a837b: Already exists 
d976abd2a5fb: Already exists 
11b5f8f00533: Already exists 
5e3ef4f14ec4: Pull complete 
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❯ docker run --rm --entrypoint /opt/miniconda-py39_4.12.0/bin/python nipy/heudiconv:master -c 'import nibabel; print(nibabel.__version__)'
5.2.1

yarikoptic mentioned this issue Jul 25, 2023

numpy.AxisError: axis 1 is out of bounds for array of dimension 1 nipy/nibabel#1245

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yarikoptic mentioned this issue Aug 9, 2023

heudiconv crashes when converting a derived ADC map from Siemens scanner #633

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2 tasks

araikes mentioned this issue Aug 30, 2023

dicominfo not reporting all information #700

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yarikoptic mentioned this issue Feb 27, 2024

Dicom to Nifti Singularity Conversion Error: numpy.exceptions.AxisError: axis 1 is out of bounds for array of dimension 1 #744

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yarikoptic closed this as completed Feb 28, 2024

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`numpy.AxisError: axis 1 is out of bounds for array of dimension 1` #670

`numpy.AxisError: axis 1 is out of bounds for array of dimension 1` #670

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numpy.AxisError: axis 1 is out of bounds for array of dimension 1 #670

numpy.AxisError: axis 1 is out of bounds for array of dimension 1 #670

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`numpy.AxisError: axis 1 is out of bounds for array of dimension 1` #670

`numpy.AxisError: axis 1 is out of bounds for array of dimension 1` #670

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