ChristianGaser
commented
4 weeks ago Dear Johannes,
Answers see below ...
Von: Johannes Wiesner @. @.>> Datum: 6. Juni 2024 um 14:44:53 MESZ An: nipy/nipype @. @.>> Kopie: Christian Gaser @. @.>>, Mention @. @.>> Betreff: [nipy/nipype] nipype.interfaces.cat12.preprocess.CAT12Segment FileNotFoundError: No such file or directory '/[....]/catROIs_T1w.xml' for output 'label_rois' of a CAT12Segment interface (Issue #3654) Antwort an: nipy/nipype @. @.>>
Summary
I am running the Cat12Segment on a single T1w image. I don't want to run the surface reconstruction workflow so I set surface_and_thickness_estimation=0, and surface_measures=0.
Actual behavior
This is the error I get:
NodeExecutionError: Exception raised while executing Node cat12segment.
Traceback: Traceback (most recent call last): File "/csp-tools/anaconda3/envs/csp_wiesner_johannes/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 453, in aggregate_outputs setattr(outputs, key, val) File "/csp-tools/anaconda3/envs/csp_wiesner_johannes/lib/python3.9/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate value = super(File, self).validate(objekt, name, value, return_pathlike=True) File "/csp-tools/anaconda3/envs/csp_wiesner_johannes/lib/python3.9/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate self.error(objekt, name, str(value)) File "/csp-tools/anaconda3/envs/csp_wiesner_johannes/lib/python3.9/site-packages/traits/base_trait_handler.py", line 74, in error raise TraitError( traits.trait_errors.TraitError: The 'label_rois' trait of a CAT12SegmentOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/pandora/home/johannes.wiesner/work/testing/debug_cat12/cat12segment/label/catROIs_T1w.xml' <class 'str'> was specified.
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/csp-tools/anaconda3/envs/csp_wiesner_johannes/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 400, in run outputs = self.aggregate_outputs(runtime) File "/csp-tools/anaconda3/envs/csp_wiesner_johannes/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 460, in aggregate_outputs raise FileNotFoundError(msg) FileNotFoundError: No such file or directory '/pandora/home/johannes.wiesner/work/testing/debug_cat12/cat12segment/label/catROIs_T1w.xml' for output 'label_rois' of a CAT12Segment interface Expected behavior
Only run the VBM-process of CAT12 (aka. only output mwp1, mwp2, etc.) but don't run the surface reconstruction.
I currently have two hypotheses (please take these with a big grain of salt, I am new to CAT12) what is causing the error:
1.) If I inspect the nodes output I can see that there is /pandora/home/johannes.wiesner/work/testing/debug_cat12/cat12segment/label/catROIs_T1w.xml but not /pandora/home/johannes.wiesner/work/testing/debug_cat12/cat12segment/label/catROI_T1w.xml (s at the end!)
So the filename might have changed in later versions of CAT12? Probably @ChristianGaser https://github.com/ChristianGaser can answer this?
The filename hasn’t changed, the prefix catROI is for volume atlases, whereas catROIs is used for surface atlases. So it is correct that there is no surface ROI file but I don’t know based on the message above where such a file is requested.
The provided dataset was running (under Matlab) without surfaces and with/without ROIs but the skull-stripped input is problematic as the given skull-stripping is not really good and the further corrections are difficult.

2.) If I inspect the generated pyscript.m file I can see that even though jobs{1}.spm.tools.cat.estwrite.output.surf_measures = 0; is appropriatly set to 0 these other lines are still added:
jobs{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.neuromorphometrics = 1; jobs{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.lpba40 = 1; jobs{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.hammers = 1; jobs{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.cobra = 1; These are all volume atlases as described in the GUI. If you choose „no“ in the GUI the structure is replaced:
jobs{1}.spm.tools.cat.estwrite.output.ROImenu.noROI = struct([]);which to me looks like as if we want to extract ROI labels for these atlases even though we didn't want them in the first place? In the GUI version the equivalent would be "if user doesn't want ROI estimates, then don't open dropdown menu where user can choose atlases" (I can confirm that this happens here). So either these lines should not even exist in the first place or the values should be set to 0 if surf_measures = 0?
To keep this short ;-) Surfaces ~= Volumes Backend ~= Frontend
If you don’t need surface/thickness then simply switch it off (as you did). If you don’t need volume-based ROIs then switch them off too.
Here's the full pyscript_cat12segment.m file:
fprintf(1,'Executing %s at %s:\n',mfilename(),datestr(now)); fprintf(1,'Executing %s at %s:\n',mfilename(),datestr(now)); ver, try, %% Generated by nipype.interfaces.spm if isempty(which('spm')), throw(MException('SPMCheck:NotFound', 'SPM not in matlab path')); end [name, version] = spm('ver'); fprintf('SPM version: %s Release: %s\n',name, version); fprintf('SPM path: %s\n', which('spm')); spm('Defaults','fMRI');
if strcmp(name, 'SPM8') || strcmp(name(1:5), 'SPM12'), spm_jobman('initcfg'); spm_get_defaults('cmdline', 1); end jobs{1}.spm.tools.cat.estwrite.data = {...'/pandora/home/johannes.wiesner/work/testing/debug_cat12/cat12segment/T1w.nii,1';... }; jobs{1}.spm.tools.cat.estwrite.nproc = 1; jobs{1}.spm.tools.cat.estwrite.opts.affreg = 'mni'; jobs{1}.spm.tools.cat.estwrite.opts.biasacc = 0.5; jobs{1}.spm.tools.cat.estwrite.extopts.APP = 1070; jobs{1}.spm.tools.cat.estwrite.extopts.spm_kamap = 0; jobs{1}.spm.tools.cat.estwrite.extopts.LASstr = 0.5; jobs{1}.spm.tools.cat.estwrite.extopts.gcutstr = 2; jobs{1}.spm.tools.cat.estwrite.extopts.WMHC = 1; jobs{1}.spm.tools.cat.estwrite.extopts.vox = 1.5; jobs{1}.spm.tools.cat.estwrite.extopts.restypes.optimal(1) = 1; jobs{1}.spm.tools.cat.estwrite.extopts.restypes.optimal(2) = 0.1; jobs{1}.spm.tools.cat.estwrite.extopts.ignoreErrors = 1; jobs{1}.spm.tools.cat.estwrite.surface = 0; jobs{1}.spm.tools.cat.estwrite.output.surf_measures = 0; jobs{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.neuromorphometrics = 1; jobs{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.lpba40 = 1; jobs{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.hammers = 1; jobs{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.cobra = 1; jobs{1}.spm.tools.cat.estwrite.output.GM.native = 0; jobs{1}.spm.tools.cat.estwrite.output.GM.mod = 1; jobs{1}.spm.tools.cat.estwrite.output.GM.dartel = 0; jobs{1}.spm.tools.cat.estwrite.output.WM.native = 0; jobs{1}.spm.tools.cat.estwrite.output.WM.mod = 1; jobs{1}.spm.tools.cat.estwrite.output.WM.dartel = 0; jobs{1}.spm.tools.cat.estwrite.output.CSF.native = 0; jobs{1}.spm.tools.cat.estwrite.output.CSF.mod = 1; jobs{1}.spm.tools.cat.estwrite.output.CSF.dartel = 0; jobs{1}.spm.tools.cat.estwrite.output.label.native = 0; jobs{1}.spm.tools.cat.estwrite.output.label.warped = 1; jobs{1}.spm.tools.cat.estwrite.output.label.dartel = 0; jobs{1}.spm.tools.cat.estwrite.output.labelnative = 0; jobs{1}.spm.tools.cat.estwrite.output.bias.warped = 1; jobs{1}.spm.tools.cat.estwrite.output.las.native = 0; jobs{1}.spm.tools.cat.estwrite.output.las.warped = 1; jobs{1}.spm.tools.cat.estwrite.output.las.dartel = 0; jobs{1}.spm.tools.cat.estwrite.output.jacobianwarped = 1; jobs{1}.spm.tools.cat.estwrite.output.warps(1) = 1; jobs{1}.spm.tools.cat.estwrite.output.warps(2) = 0;
spm_jobman('run', jobs);,catch ME, fprintf(2,'MATLAB code threw an exception:\n'); fprintf(2,'%s\n',ME.message); if length(ME.stack) ~= 0, fprintf(2,'File:%s\nName:%s\nLine:%d\n',ME.stack.file,ME.stack.name,ME.stack.line);, end; end; How to replicate the behavior
Here's a python script to reproduce the error
!/usr/bin/env python3
-- coding: utf-8 --
""" Debug CAT12Segment """
import subprocess from nipype.interfaces.cat12.preprocess import CAT12Segment from nipype import Node import os
###############################################################################
Preparation: Download an anatomical files from a public available AWS-bucket
###############################################################################
download T1w image
command = """ curl \ --create-dirs https://s3.amazonaws.com/openneuro.org/ds004302/sub-02/anat/sub-02_T1w.nii.gz?versionId=93eQ.AwPcMeccJAT3sO9otYv4A_WH3Bj \ -o ./T1w.nii.gz """ subprocess.run(command,shell=True)
gunzip image to get from .nii.gz to .nii
subprocess.run("gunzip -c ./T1w.nii.gz > T1w.nii",shell=True)
get the full path to the directory where this script is being executed
script_dir = os.path.dirname(os.path.realpath(file))
get full path to both images (nipype always needs absolut paths to inputs)
image_nii = os.path.join(script_dir,'T1w.nii') image_nii_gz = os.path.join(script_dir,'T1w.nii.gz')
###############################################################################
Run CAT12Segment inside a node on one image
###############################################################################
create node
cat12segment = Node(CAT12Segment(surface_and_thickness_estimation=0, surface_measures=0), name='cat12segment')
input image (uncompressed, see nipype issue #3653). But should actually
also work for .nii.gz files
cat12segment.inputs.in_files = image_nii
set working directory of node to script directory
cat12segment.base_dir = script_dir
run the node
cat12segment.run() Platform details:
{'commit_hash': '%h', 'commit_source': 'archive substitution', 'networkx_version': '3.2.1', 'nibabel_version': '5.2.0', 'nipype_version': '1.8.6', 'numpy_version': '1.26.3', 'pkg_path': '/csp-tools/anaconda3/envs/csp_wiesner_johannes/lib/python3.9/site-packages/nipype', 'scipy_version': '1.12.0', 'sys_executable': '/csp-tools/anaconda3/envs/csp_wiesner_johannes/bin/python', 'sys_platform': 'linux', 'sys_version': '3.9.18 | packaged by conda-forge | (main, Dec 23 2023, ' '16:33:10) \n' '[GCC 12.3.0]', 'traits_version': '6.3.2'}
Execution environment
Choose one
My python environment outside container. My CAT12 version is CAT12.9 (r2560) inside an spm12/9.14 environment module that is loaded using module load spm12/9.14 in my .bashrc file. — Reply to this email directly, view it on GitHub https://github.com/nipy/nipype/issues/3654, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFKSWFRDYLZGBNE5DJTQIADZGBKT7AVCNFSM6AAAAABI4VBGFKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGMZTQMJWHE4TOOI. You are receiving this because you were mentioned.
JohannesWiesner
JailanOweda
Summary
I am running the
Cat12Segmenton a single T1w image. I don't want to run the surface reconstruction workflow so I setsurface_and_thickness_estimation=0, andsurface_measures=0.Actual behavior
This is the error I get:
Expected behavior
Only run the VBM-process of CAT12 (aka. only output mwp1, mwp2, etc.) but don't run the surface reconstruction.
I currently have two hypotheses (please take these with a big grain of salt, I am new to CAT12) what is causing the error:
1.) If I inspect the nodes output I can see that there is
/pandora/home/johannes.wiesner/work/testing/debug_cat12/cat12segment/label/catROIs_T1w.xmlbut not/pandora/home/johannes.wiesner/work/testing/debug_cat12/cat12segment/label/catROI_T1w.xml(s at the end!)So the filename might have changed in later versions of CAT12? Probably @ChristianGaser can answer this?
2.) If I inspect the generated
pyscript.mfile I can see that even thoughjobs{1}.spm.tools.cat.estwrite.output.surf_measures = 0;is appropriatly set to0these other lines are still added:which to me looks like as if we want to extract ROI labels for these atlases even though we didn't want them in the first place? In the GUI version the equivalent would be "if user doesn't want ROI estimates, then don't open dropdown menu where user can choose atlases" (I can confirm that this happens here). So either these lines should not even exist in the first place or the values should be set to
0ifsurf_measures = 0?Here's the full
pyscript_cat12segment.mfile:How to replicate the behavior
Here's a python script to reproduce the error
Platform details:
Execution environment
Choose one
module load spm12/9.14in my.bashrcfile.