spm not in matlab path #1256

alienx-zero · 2024-08-19T20:34:27Z

alienx-zero
Aug 19, 2024

Hi, recently I try to use clinica to preprocess t1 and then PET images.
I run the code in terminal: clinica run t1-volume /media/alex/Expansion/Data/OASIS3/PET_processing/PET_BIDS /media/alex/Expansion/Data/OASIS3/PET_processing alex
Then, I get the error:
`2024-08-19 16:29:36,814:INFO:Running pipeline for sub-OAS31447 | ses-M000
2024-08-19 16:29:36,814:INFO:Running pipeline for sub-OAS31448 | ses-M006
2024-08-19 16:29:36,815:INFO:Running pipeline for sub-OAS31449 | ses-M000
2024-08-19 16:29:36,816:INFO:Running pipeline for sub-OAS31453 | ses-M006
2024-08-19 16:29:36,816:INFO:Running pipeline for sub-OAS31450 | ses-M012
2024-08-19 16:29:36,817:INFO:Running pipeline for sub-OAS31455 | ses-M000
2024-08-19 16:29:36,820:INFO:Running pipeline for sub-OAS31456 | ses-M000
2024-08-19 16:29:36,820:INFO:Running pipeline for sub-OAS31457 | ses-M006
2024-08-19 16:29:36,822:INFO:Running pipeline for sub-OAS31458 | ses-M000
2024-08-19 16:29:36,822:INFO:Running pipeline for sub-OAS31459 | ses-M006
2024-08-19 16:29:36,824:INFO:Running pipeline for sub-OAS31460 | ses-M000
2024-08-19 16:29:36,825:INFO:Running pipeline for sub-OAS31463 | ses-M012
2024-08-19 16:29:36,826:INFO:Running pipeline for sub-OAS31464 | ses-M000
2024-08-19 16:29:36,827:INFO:Running pipeline for sub-OAS31465 | ses-M000
2024-08-19 16:29:36,828:INFO:Running pipeline for sub-OAS31466 | ses-M006
2024-08-19 16:29:38,827:INFO:Running pipeline for sub-OAS31469 | ses-M006
2024-08-19 16:29:38,838:INFO:Running pipeline for sub-OAS31471 | ses-M000
2024-08-19 16:29:38,838:INFO:Running pipeline for sub-OAS31472 | ses-M000
2024-08-19 16:29:38,839:INFO:Running pipeline for sub-OAS31473 | ses-M006
2024-08-19 16:29:38,840:INFO:Running pipeline for sub-OAS31474 | ses-M006
pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1
pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1
Traceback (most recent call last):
File "/home/alex/anaconda3/envs/clinicaEnv/bin/clinica", line 8, in
sys.exit(main())
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/cmdline.py", line 92, in main
cli()
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/decorators.py", line 33, in new_func
return f(get_current_context(), *args, **kwargs)
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/pipelines/t1_volume/t1_volume_cli.py", line 95, in cli
ctx.invoke(
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/pipelines/t1_volume_tissue_segmentation/t1_volume_tissue_segmentation_cli.py", line 70, in cli
pipeline.run(plugin="MultiProc", plugin_args={"n_procs": n_procs})
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/pipelines/engine.py", line 353, in run
raise e
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/pipelines/engine.py", line 334, in run
exec_graph = Workflow.run(self, plugin, plugin_args, update_hash)
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/nipype/pipeline/engine/workflows.py", line 638, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/nipype/pipeline/plugins/base.py", line 166, in run
self._clean_queue(jobid, graph, result=result)
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/nipype/pipeline/plugins/base.py", line 244, in _clean_queue
raise RuntimeError("".join(result["traceback"]))
RuntimeError: Traceback (most recent call last):
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 524, in run
result = self._run_interface(execute=True)
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 642, in _run_interface
return self._run_command(execute)
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 750, in _run_command
raise NodeExecutionError(
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node 2-SpmSegmentation.

Traceback (most recent call last):
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 398, in run
runtime = self._run_interface(runtime)
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/nipype/interfaces/spm/base.py", line 387, in _run_interface
results = self.mlab.run()
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 398, in run
runtime = self._run_interface(runtime)
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/nipype/interfaces/matlab.py", line 164, in _run_interface
self.raise_exception(runtime)
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 686, in raise_exception
raise RuntimeError(
RuntimeError: Command:
matlab -nodesktop -nosplash -singleCompThread -r "addpath('/tmp/tmpfjvqr6cs/t1-volume-tissue-segmentation/331bb3792fdb18145031e5fd0793b19acc097e5f/2-SpmSegmentation');pyscript_newsegment;exit"
Standard output:

                        < M A T L A B (R) >
              Copyright 1984-2023 The MathWorks, Inc.
         R2023a Update 3 (9.14.0.2286388) 64-bit (glnxa64)
                            May 25, 2023

To get started, type doc.
For product information, visit www.mathworks.com.

Executing pyscript_newsegment at 19-Aug-2024 16:32:19:
Executing pyscript_newsegment at 19-Aug-2024 16:32:19:

MATLAB Version: 9.14.0.2286388 (R2023a) Update 3
MATLAB License Number: 1147403
Operating System: Linux 5.19.0-46-generic #47~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jun 21 15:35:31 UTC 2 x86_64
Java Version: Java 1.8.0_202-b08 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode

MATLAB Version 9.14 (R2023a)
Bioinformatics Toolbox Version 4.17 (R2023a)
Curve Fitting Toolbox Version 3.9 (R2023a)
Deep Learning HDL Toolbox Version 1.5 (R2023a)
Deep Learning Toolbox Version 14.6 (R2023a)
Image Processing Toolbox Version 11.7 (R2023a)
Medical Imaging Toolbox Version 1.1 (R2023a)
Optimization Toolbox Version 9.5 (R2023a)
Parallel Computing Toolbox Version 7.8 (R2023a)
Signal Processing Toolbox Version 9.2 (R2023a)
Statistics and Machine Learning Toolbox Version 12.5 (R2023a)

Standard error:
MATLAB code threw an exception:
SPM not in matlab path
File:/tmp/tmpfjvqr6cs/t1-volume-tissue-segmentation/331bb3792fdb18145031e5fd0793b19acc097e5f/2-SpmSegmentation/pyscript_newsegment.m
Name:pyscript_newsegment
Line:7
Return code: 0
`

I already add spm into my matlab, here is the location:

which('spm')
/usr/local/MATLAB/R2023a/toolbox/spm12/spm.m
and I can call spm in matlab, but I did not why the error say SPM not in matlab path

Answered by NicolasGensollen

Aug 26, 2024

Hi @alienx-zero

Let me just try to understand. Your initial message was reporting an issue with SPM not being in the Matlab path when running the t1-volume pipeline. Theoretically, upgrading to Clinica 0.8.4 should solve this problem.
Did you end up upgrading to 0.8.4 ? Were you able to run this pipeline successfully ?

Your latest message seems to be related to another pipeline, the pet-volume pipeline, for which having correctly run t1-volume is a pre-requisite (which is why I'm checking that this was indeed successful).

If that is the case, could you show what you input folders look like (both the BIDS input folder and the CAPS folder which should contain the output of the t1-volume pip…

View full answer

alienx-zero · 2024-08-19T20:50:59Z

alienx-zero
Aug 19, 2024
Author

Any idea about this would be very helpful~

0 replies

NicolasGensollen · 2024-08-21T09:13:32Z

NicolasGensollen
Aug 21, 2024
Maintainer

Hi @alienx-zero

Thanks for reporting.
I think the issue is that you don't define the path to SPM in your "startup.m" file, but interactively, right ? At least, it seems like the SPM path is unknown when you launch the clinica pipeline.

First, could you verify that you have the environment variable SPM_HOME defined and set to the correct path ?

echo $SPM_HOME

It should print '/usr/local/MATLAB/R2023a/toolbox/spm12/' in your case.

You can then try something very simple to verify this hypothesis:
Open the script that clinica is trying to run, in your case it is /tmp/tmpfjvqr6cs/t1-volume-tissue-segmentation/331bb3792fdb18145031e5fd0793b19acc097e5f/2-SpmSegmentation/pyscript_newsegment.m, and add the following line at the top of the file:

addpath('/usr/local/MATLAB/R2023a/toolbox/spm12/')

And then try running the script:

matlab -nodesktop -nosplash -singleCompThread -r "addpath('/tmp/tmpfjvqr6cs/t1-volume-tissue-segmentation/331bb3792fdb18145031e5fd0793b19acc097e5f/2-SpmSegmentation');pyscript_newsegment;exit"

Hopefully, you shouldn't get this error and SPM should start.
If that is the case, please consider adding the addpath(...) line to your startup.m script.
If it is still not working, we would need to investigate further. An alternative solution is to rely on SPM-standalone which is becoming our recommended way to install SPM12.

Hope that helps.
Let us know how it goes!

4 replies

alienx-zero Aug 21, 2024
Author

Thanks for your response. I will try two days later. Once I tried, I will let you know the results. Hope your suggestion works.

NicolasGensollen Aug 22, 2024
Maintainer

@alienx-zero sounds good !

In the mean time I added a small fix which should ensure that the SPM path is added to Matlab when using SPM + Matlab instead of SPM standalone. I made some tests and it seems to work fine. I added this in the 0.8.4 patch release of Clinica.
So you can simply re-install clinica (using pip for example) and make sure you have the latest version:

$ clinica --version
clinica, version 0.8.4

And then try to re-run the pipeline.
Hopefully it should work 🤞

alienx-zero Aug 24, 2024
Author

Hi, the method work, but not the new problem is when I am running the script, the terminal will crash...

Showing on the figure, running the pipeline in segmentation step, it will used all the CPU and RAW in my PC, and then after one min, it will crash.....
So, do we have any parameter setting in running the pipeline, similar as the fmriprep to restrict the computing resource the code will call?

alienx-zero Aug 25, 2024
Author

I find the answer after carefully reading the contents here https://aramislab.paris.inria.fr/clinica/docs/public/latest/InteractingWithClinica/, by setting np = 3.

alienx-zero · 2024-08-25T02:00:59Z

alienx-zero
Aug 25, 2024
Author

Now, I get into new trouble. Here is the result:
`2024-08-24 21:50:49,773:WARNING:More than one run were found for subject sub-OAS30001 and session ses-M078 :

/media/alex/Expansion/Data/OASIS3/PET_processing/PET_BIDS/sub-OAS30001/ses-M078/anat/sub-OAS30001_ses-M078_run-01_T1w.nii.gz
/media/alex/Expansion/Data/OASIS3/PET_processing/PET_BIDS/sub-OAS30001/ses-M078/anat/sub-OAS30001_ses-M078_run-04_T1w.nii.gz

Clinica will proceed with the latest run available, that is

-/media/alex/Expansion/Data/OASIS3/PET_processing/PET_BIDS/sub-OAS30001/ses-M078/anat/sub-OAS30001_ses-M078_run-04_T1w.nii.gz.
2024-08-24 21:50:49,774:WARNING:More than one run were found for subject sub-OAS30002 and session ses-M078 :

/media/alex/Expansion/Data/OASIS3/PET_processing/PET_BIDS/sub-OAS30002/ses-M078/anat/sub-OAS30002_ses-M078_run-01_T1w.nii.gz
/media/alex/Expansion/Data/OASIS3/PET_processing/PET_BIDS/sub-OAS30002/ses-M078/anat/sub-OAS30002_ses-M078_run-04_T1w.nii.gz
/media/alex/Expansion/Data/OASIS3/PET_processing/PET_BIDS/sub-OAS30002/ses-M078/anat/sub-OAS30002_ses-M078_run-05_T1w.nii.gz
/media/alex/Expansion/Data/OASIS3/PET_processing/PET_BIDS/sub-OAS30002/ses-M078/anat/sub-OAS30002_ses-M078_run-02_T1w.nii.gz

Clinica will proceed with the latest run available, that is

-/media/alex/Expansion/Data/OASIS3/PET_processing/PET_BIDS/sub-OAS30002/ses-M078/anat/sub-OAS30002_ses-M078_run-05_T1w.nii.gz.
2024-08-24 21:50:49,776:WARNING:More than one run were found for subject sub-OAS30003 and session ses-M090 :

/media/alex/Expansion/Data/OASIS3/PET_processing/PET_BIDS/sub-OAS30003/ses-M090/anat/sub-OAS30003_ses-M090_run-01_T1w.nii.gz
/media/alex/Expansion/Data/OASIS3/PET_processing/PET_BIDS/sub-OAS30003/ses-M090/anat/sub-OAS30003_ses-M090_run-02_T1w.nii.gz
/media/alex/Expansion/Data/OASIS3/PET_processing/PET_BIDS/sub-OAS30003/ses-M090/anat/sub-OAS30003_ses-M090_run-08_T1w.nii.gz

Clinica will proceed with the latest run available, that is

-/media/alex/Expansion/Data/OASIS3/PET_processing/PET_BIDS/sub-OAS30003/ses-M090/anat/sub-OAS30003_ses-M090_run-08_T1w.nii.gz.
2024-08-24 21:50:49,778:WARNING:More than one run were found for subject sub-OAS30003 and session ses-M120 :

/media/alex/Expansion/Data/OASIS3/PET_processing/PET_BIDS/sub-OAS30003/ses-M120/anat/sub-OAS30003_ses-M120_run-01_T1w.nii.gz
/media/alex/Expansion/Data/OASIS3/PET_processing/PET_BIDS/sub-OAS30003/ses-M120/anat/sub-OAS30003_ses-M120_run-04_T1w.nii.gz

Clinica will proceed with the latest run available, that is

-/media/alex/Expansion/Data/OASIS3/PET_processing/PET_BIDS/sub-OAS30003/ses-M120/anat/sub-OAS30003_ses-M120_run-04_T1w.nii.gz.
2024-08-24 21:50:49,909:INFO:The pipeline will be run on the following 4 image(s):
2024-08-24 21:50:49,909:INFO: sub-OAS30001 | ses-M078,
2024-08-24 21:50:49,909:INFO: sub-OAS30002 | ses-M078,
2024-08-24 21:50:49,909:INFO: sub-OAS30003 | ses-M090, ses-M120,
2024-08-24 21:50:49,909:INFO:List available in /media/alex/work/temp/data_preprocess/pet-volume/participants.tsv
2024-08-24 21:50:49,909:INFO:The pipeline will last approximately 10 minutes per image.
2024-08-24 21:50:55,690:ERROR:Clinica could not load volumes for sub-OAS30001 | ses-M078. The image is not 3D but 4D.
Traceback (most recent call last):
File "/home/alex/anaconda3/envs/clinicaEnv/bin/clinica", line 8, in
sys.exit(main())
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/cmdline.py", line 92, in main
cli()
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/pipelines/pet_volume/pet_volume_cli.py", line 121, in cli
pipeline.run(plugin="MultiProc", plugin_args={"n_procs": n_procs})
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/pipelines/engine.py", line 353, in run
raise e
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/pipelines/engine.py", line 334, in run
exec_graph = Workflow.run(self, plugin, plugin_args, update_hash)
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/nipype/pipeline/engine/workflows.py", line 638, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/nipype/pipeline/plugins/base.py", line 166, in run
self._clean_queue(jobid, graph, result=result)
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/nipype/pipeline/plugins/base.py", line 244, in _clean_queue
raise RuntimeError("".join(result["traceback"]))
RuntimeError: Traceback (most recent call last):
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 524, in run
result = self._run_interface(execute=True)
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 642, in _run_interface
return self._run_command(execute)
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 750, in _run_command
raise NodeExecutionError(
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node init_pipeline.

Traceback (most recent call last):
File "", line 8, in init_input_node
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/utils/filemanip.py", line 167, in load_volume
raise ValueError(f"The image is not 3D but {dim}D.")
ValueError: The image is not 3D but 4D.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 398, in run
runtime = self._run_interface(runtime)
File "/home/alex/anaconda3/envs/clinicaEnv/lib/python3.10/site-packages/nipype/interfaces/utility/wrappers.py", line 142, in _run_interface
out = function_handle(**args)
File "", line 12, in init_input_node
ValueError: Clinica could not load volumes for sub-OAS30001 | ses-M078. The image is not 3D but 4D.
`
After getting the anat preprocessing result, there is error when I try to get pet preprocessing. Here is the code in terminal: '(clinicaEnv) alex@alex-MS-7D75:~$ clinica run pet-volume /media/alex/Expansion/Data/OASIS3/PET_processing/PET_BIDS /media/alex/Expansion/Data/OASIS3/PET_processing/preprocessed alex 18FAV45 cerebellumPons -tsv /media/alex/Expansion/Data/OASIS3/PET_processing/sub_oasis_list_test.tsv -wd /media/alex/work/temp/data_preprocess -np 4'

Another question is can we create the SUVR mapping for each ROI defined for whole brain? I see the default mask.nii 'pons|cerebellumPons|pons2|cerebellumPons2', they are binaried mask with one parcel. However, if I want to use AAL or schaefer, Yeo parcellations which contain multiple parcels for whole brain. If I add 'aal.nii.gz' into the pet.py, whether this whole brain mask will work?

5 replies

alienx-zero Aug 25, 2024
Author

I check the pet nifit image size, It is (256, 256, 127, 26). It shouldn't be ran successfully by the load_volume function defined in filemanip.py. So clinical can not run 4-D PET image? Only support processing 3D PET?

NicolasGensollen Aug 26, 2024
Maintainer

Hi @alienx-zero

Let me just try to understand. Your initial message was reporting an issue with SPM not being in the Matlab path when running the t1-volume pipeline. Theoretically, upgrading to Clinica 0.8.4 should solve this problem.
Did you end up upgrading to 0.8.4 ? Were you able to run this pipeline successfully ?

Your latest message seems to be related to another pipeline, the pet-volume pipeline, for which having correctly run t1-volume is a pre-requisite (which is why I'm checking that this was indeed successful).

If that is the case, could you show what you input folders look like (both the BIDS input folder and the CAPS folder which should contain the output of the t1-volume pipeline) ?

Another question is can we create the SUVR mapping for each ROI defined for whole brain? I see the default mask.nii 'pons|cerebellumPons|pons2|cerebellumPons2', they are binaried mask with one parcel. However, if I want to use AAL or schaefer, Yeo parcellations which contain multiple parcels for whole brain. If I add 'aal.nii.gz' into the pet.py, whether this whole brain mask will work?

As explained in the documentation (here and there), regional measures are computed for the AAL2, AICHA, LPBA40 and Neuromorphometrics atlases. The 'pons|cerebellumPons|pons2|cerebellumPons2' masks are used for intensity normalisation (=SUVR computation).

I check the pet nifit image size, It is (256, 256, 127, 26). It shouldn't be ran successfully by the load_volume function defined in filemanip.py. So clinical can not run 4-D PET image? Only support processing 3D PET?

Indeed, Clinica only supports 3D volumes. If you have a dynamic acquisition, you will need to perform several steps before using Clinica. For example, a simple way to do this with FSL would be to:

split the 4D volume using fslsplit
rigidly register each 3D volume to a reference volume with flirt (if it's a dynamic acquisition you may need to select some frames)
generate a new a 4D volume with your aligned images with fslmerge
finally average the (registered) 4D volume with fslmaths.

Hope this helps !
Best,

Answer selected by NicolasGensollen

alienx-zero Aug 26, 2024
Author

Thanks for your response.

To solve the issue running t1-volume, I did not upgrade my clinical version. I am still using 0.7.7. I follow your suggestion

adding the addpath(...) line to your startup.m script.

Then it works.
2. Here is an example of my BIDS input:

│   ├── ses-M078
│   │   ├── anat
│   │   │   ├── sub-OAS30986_ses-M078_run-01_T1w.json
│   │   │   ├── sub-OAS30986_ses-M078_run-01_T1w.nii.gz
│   │   │   ├── sub-OAS30986_ses-M078_run-01_T2w.json
│   │   │   ├── sub-OAS30986_ses-M078_run-01_T2w.nii.gz
│   │   │   ├── sub-OAS30986_ses-M078_run-03_T1w.json
│   │   │   ├── sub-OAS30986_ses-M078_run-03_T1w.nii.gz
│   │   │   ├── sub-OAS30986_ses-M078_run-05_T2w.json
│   │   │   └── sub-OAS30986_ses-M078_run-05_T2w.nii.gz
│   │   ├── dwi
│   │   │   ├── sub-OAS30986_ses-M078_run-01_dwi.bval
│   │   │   ├── sub-OAS30986_ses-M078_run-01_dwi.bvec
│   │   │   ├── sub-OAS30986_ses-M078_run-01_dwi.json
│   │   │   ├── sub-OAS30986_ses-M078_run-01_dwi.nii.gz
│   │   │   ├── sub-OAS30986_ses-M078_run-02_dwi.bval
│   │   │   ├── sub-OAS30986_ses-M078_run-02_dwi.bvec
│   │   │   ├── sub-OAS30986_ses-M078_run-02_dwi.json
│   │   │   └── sub-OAS30986_ses-M078_run-02_dwi.nii.gz
│   │   ├── func
│   │   │   ├── sub-OAS30986_ses-M078_task-rest_run-01_bold.json
│   │   │   ├── sub-OAS30986_ses-M078_task-rest_run-01_bold.nii.gz
│   │   │   ├── sub-OAS30986_ses-M078_task-rest_run-02_bold.json
│   │   │   └── sub-OAS30986_ses-M078_task-rest_run-02_bold.nii.gz
│   │   └── pet
│   │   ├── sub-OAS30986_ses-M078_trc-11CPIB_run-01_pet.json
│   │   ├── sub-OAS30986_ses-M078_trc-11CPIB_run-01_pet.nii.gz
│   │   └── sub-OAS30986_ses-M078_trc-11CPIB_run-01_pet.tsv
│   └── ses-M156
│   ├── anat
│   │   ├── sub-OAS30986_ses-M156_run-01_T1w.json
│   │   ├── sub-OAS30986_ses-M156_run-01_T1w.nii.gz
│   │   ├── sub-OAS30986_ses-M156_run-02_T2w.json
│   │   ├── sub-OAS30986_ses-M156_run-02_T2w.nii.gz
│   │   ├── sub-OAS30986_ses-M156_run-04_T1w.json
│   │   └── sub-OAS30986_ses-M156_run-04_T1w.nii.gz
│   ├── func
│   │   ├── sub-OAS30986_ses-M156_task-rest_run-01_bold.json
│   │   ├── sub-OAS30986_ses-M156_task-rest_run-01_bold.nii.gz
│   │   ├── sub-OAS30986_ses-M156_task-rest_run-02_bold.json
│   │   └── sub-OAS30986_ses-M156_task-rest_run-02_bold.nii.gz
│   └── pet
│   ├── sub-OAS30986_ses-M156_trc-18FAV45_run-06_pet.json
│   ├── sub-OAS30986_ses-M156_trc-18FAV45_run-06_pet.nii.gz
│   └── sub-OAS30986_ses-M156_trc-18FAV45_run-06_pet.tsv
├── sub-OAS30988
│   └── ses-M000
│   ├── anat
│   │   ├── sub-OAS30988_ses-M000_run-01_T1w.json
│   │   ├── sub-OAS30988_ses-M000_run-01_T1w.nii.gz
│   │   ├── sub-OAS30988_ses-M000_run-02_T2w.json
│   │   ├── sub-OAS30988_ses-M000_run-02_T2w.nii.gz
│   │   ├── sub-OAS30988_ses-M000_run-04_T1w.json
│   │   └── sub-OAS30988_ses-M000_run-04_T1w.nii.gz
│   ├── func
│   │   ├── sub-OAS30988_ses-M000_task-rest_run-01_bold.json
│   │   ├── sub-OAS30988_ses-M000_task-rest_run-01_bold.nii.gz
│   │   ├── sub-OAS30988_ses-M000_task-rest_run-02_bold.json
│   │   └── sub-OAS30988_ses-M000_task-rest_run-02_bold.nii.gz

Here is the CAPS folder structure:

└── sub-OAS30004
├── ses-M036
│   └── t1
│   └── spm
│   ├── dartel
│   │   └── group-alex
│   │   ├── sub-OAS30004_ses-M036_run-03_T1w_segm-csf_space-Ixi549Space_modulated-on_fwhm-8mm_probability.nii.gz
│   │   ├── sub-OAS30004_ses-M036_run-03_T1w_segm-csf_space-Ixi549Space_modulated-on_probability.nii.gz
│   │   ├── sub-OAS30004_ses-M036_run-03_T1w_segm-graymatter_space-Ixi549Space_modulated-on_fwhm-8mm_probability.nii.gz
│   │   ├── sub-OAS30004_ses-M036_run-03_T1w_segm-graymatter_space-Ixi549Space_modulated-on_probability.nii.gz
│   │   ├── sub-OAS30004_ses-M036_run-03_T1w_segm-whitematter_space-Ixi549Space_modulated-on_fwhm-8mm_probability.nii.gz
│   │   ├── sub-OAS30004_ses-M036_run-03_T1w_segm-whitematter_space-Ixi549Space_modulated-on_probability.nii.gz
│   │   └── sub-OAS30004_ses-M036_run-03_T1w_target-alex_transformation-forward_deformation.nii.gz
│   └── segmentation
│   ├── dartel_input
│   │   ├── sub-OAS30004_ses-M036_run-03_T1w_segm-csf_dartelinput.nii.gz
│   │   ├── sub-OAS30004_ses-M036_run-03_T1w_segm-graymatter_dartelinput.nii.gz
│   │   └── sub-OAS30004_ses-M036_run-03_T1w_segm-whitematter_dartelinput.nii.gz
│   ├── native_space
│   │   ├── sub-OAS30004_ses-M036_run-03_T1w_segm-csf_probability.nii.gz
│   │   ├── sub-OAS30004_ses-M036_run-03_T1w_segm-graymatter_probability.nii.gz
│   │   └── sub-OAS30004_ses-M036_run-03_T1w_segm-whitematter_probability.nii.gz
│   └── normalized_space
│   ├── sub-OAS30004_ses-M036_run-03_space-Ixi549Space_T1w.nii.gz
│   ├── sub-OAS30004_ses-M036_run-03_T1w_segm-csf_space-Ixi549Space_modulated-off_probability.nii.gz
│   ├── sub-OAS30004_ses-M036_run-03_T1w_segm-graymatter_space-Ixi549Space_modulated-off_probability.nii.gz
│   ├── sub-OAS30004_ses-M036_run-03_T1w_segm-whitematter_space-Ixi549Space_modulated-off_probability.nii.gz
│   ├── sub-OAS30004_ses-M036_run-03_T1w_target-Ixi549Space_transformation-forward_deformation.nii.gz
│   └── sub-OAS30004_ses-M036_run-03_T1w_target-Ixi549Space_transformation-inverse_deformation.nii.gz
└── ses-M036_run-03
└── t1
└── spm
└── dartel
└── group-alex
└── atlas_statistics
├── sub-OAS30004_ses-M036_run-03_T1w_segm-graymatter_space-Ixi549Space_modulated-on_probability_space-AAL2_map-graymatter_statistics.tsv
├── sub-OAS30004_ses-M036_run-03_T1w_segm-graymatter_space-Ixi549Space_modulated-on_probability_space-AICHA_map-graymatter_statistics.tsv
├── sub-OAS30004_ses-M036_run-03_T1w_segm-graymatter_space-Ixi549Space_modulated-on_probability_space-Hammers_map-graymatter_statistics.tsv
├── sub-OAS30004_ses-M036_run-03_T1w_segm-graymatter_space-Ixi549Space_modulated-on_probability_space-LPBA40_map-graymatter_statistics.tsv
└── sub-OAS30004_ses-M036_run-03_T1w_segm-graymatter_space-Ixi549Space_modulated-on_probability_space-Neuromorphometrics_map-graymatter_statistics.tsv

143 directories, 223 files

Thanks for sharing the link, I will follow this to add Yoe's parcellation into the pipeline. However, one question for this is that I can follow the https://aramislab.paris.inria.fr/clinica/docs/public/latest/Atlases/ to customize parcellation, but in the command line:

clinica run pet-volume [OPTIONS] BIDS_DIRECTORY CAPS_DIRECTORY GROUP_LABEL ACQ_LABEL
{pons|cerebellumPons|pons2|cerebellumPons2}

I did not see the parameter to use self-customize parcellation. Once I defined the parcellation in atlas.py, how can I call it when I run pet-volume to get SUVR of all regions defined by my parcellation?

Thanks for your explanation, so do you mean I just need to follow the steps you mentioned to average all 4D PET into 3D nii and replace the 4D nii with 3D nii of each subject in BIDS input?

alienx-zero Aug 28, 2024
Author

New updation, I have successfully ran the pipeline and get SUVR defined from all default parcellations. Thanks for your ideas. It helped a lot.

├── pet
│   └── preprocessing
│   └── group-alex
│   ├── atlas_statistics
│   │   ├── sub-OAS30001_ses-M078_trc-18FAV45_pet_space-AAL2_suvr-cerebellumPons_statistics.tsv
│   │   ├── sub-OAS30001_ses-M078_trc-18FAV45_pet_space-AICHA_suvr-cerebellumPons_statistics.tsv
│   │   ├── sub-OAS30001_ses-M078_trc-18FAV45_pet_space-Hammers_suvr-cerebellumPons_statistics.tsv
│   │   ├── sub-OAS30001_ses-M078_trc-18FAV45_pet_space-LPBA40_suvr-cerebellumPons_statistics.tsv
│   │   └── sub-OAS30001_ses-M078_trc-18FAV45_pet_space-Neuromorphometrics_suvr-cerebellumPons_statistics.tsv
│   ├── sub-OAS30001_ses-M078_run-04_T1w_space-Ixi549Space_brainmask.nii.gz
│   ├── sub-OAS30001_ses-M078_trc-18FAV45_pet_space-Ixi549Space_pet.nii.gz
│   ├── sub-OAS30001_ses-M078_trc-18FAV45_pet_space-Ixi549Space_suvr-cerebellumPons_mask-brain_fwhm-8mm_pet.nii.gz
│   ├── sub-OAS30001_ses-M078_trc-18FAV45_pet_space-Ixi549Space_suvr-cerebellumPons_mask-brain_pet.nii.gz
│   ├── sub-OAS30001_ses-M078_trc-18FAV45_pet_space-Ixi549Space_suvr-cerebellumPons_pet.nii.gz
│   └── sub-OAS30001_ses-M078_trc-18FAV45_pet_space-T1w_pet.nii.gz
└── t1
└── spm
├── dartel
│   └── group-alex
│   ├── sub-OAS30001_ses-M078_run-04_T1w_segm-csf_space-Ixi549Space_modulated-on_fwhm-8mm_probability.nii.gz
│   ├── sub-OAS30001_ses-M078_run-04_T1w_segm-csf_space-Ixi549Space_modulated-on_probability.nii.gz
│   ├── sub-OAS30001_ses-M078_run-04_T1w_segm-graymatter_space-Ixi549Space_modulated-on_fwhm-8mm_probability.nii.gz
│   ├── sub-OAS30001_ses-M078_run-04_T1w_segm-graymatter_space-Ixi549Space_modulated-on_probability.nii.gz
│   ├── sub-OAS30001_ses-M078_run-04_T1w_segm-whitematter_space-Ixi549Space_modulated-on_fwhm-8mm_probability.nii.gz
│   ├── sub-OAS30001_ses-M078_run-04_T1w_segm-whitematter_space-Ixi549Space_modulated-on_probability.nii.gz
│   └── sub-OAS30001_ses-M078_run-04_T1w_target-alex_transformation-forward_deformation.nii.gz
└── segmentation
├── dartel_input
│   ├── sub-OAS30001_ses-M078_run-04_T1w_segm-csf_dartelinput.nii.gz
│   ├── sub-OAS30001_ses-M078_run-04_T1w_segm-graymatter_dartelinput.nii.gz
│   └── sub-OAS30001_ses-M078_run-04_T1w_segm-whitematter_dartelinput.nii.gz
├── native_space
│   ├── sub-OAS30001_ses-M078_run-04_T1w_segm-csf_probability.nii.gz
│   ├── sub-OAS30001_ses-M078_run-04_T1w_segm-graymatter_probability.nii.gz
│   └── sub-OAS30001_ses-M078_run-04_T1w_segm-whitematter_probability.nii.gz
└── normalized_space
├── sub-OAS30001_ses-M078_run-04_space-Ixi549Space_T1w.nii.gz
├── sub-OAS30001_ses-M078_run-04_T1w_segm-csf_space-Ixi549Space_modulated-off_probability.nii.gz
├── sub-OAS30001_ses-M078_run-04_T1w_segm-graymatter_space-Ixi549Space_modulated-off_probability.nii.gz
├── sub-OAS30001_ses-M078_run-04_T1w_segm-whitematter_space-Ixi549Space_modulated-off_probability.nii.gz
├── sub-OAS30001_ses-M078_run-04_T1w_target-Ixi549Space_transformation-forward_deformation.nii.gz
└── sub-OAS30001_ses-M078_run-04_T1w_target-Ixi549Space_transformation-inverse_deformation.nii.gz

12 directories, 30 files

NicolasGensollen Aug 28, 2024
Maintainer

Happy to hear that @alienx-zero ! 👍

alienx-zero · 2024-09-05T02:52:29Z

alienx-zero
Sep 5, 2024
Author

@NicolasGensollen , hi I get a new problem, I defined the parcellation in atlas.py. However, after pet volume preprocessed, the tsv of statistics of this parcellation is still not generated,

Here is how I defined the parcellation:
`
class schaefer100_subcortex(AtlasAbstract):
def init(self):
AtlasAbstract.init(self)

@staticmethod
def get_name_atlas():
    return "schaefer100_subcortex"

@staticmethod
def get_atlas_labels():
    from os.path import join, realpath, split

    return join(
        split(realpath(__file__))[0],
        "..",
        "resources",
        "atlases",
        "atlas-schaefer100_subcortex_dseg.nii.gz",
    )

@staticmethod
def get_tsv_roi():
    from os.path import join, realpath, split

    return join(
        split(realpath(__file__))[0],
        "..",
        "resources",
        "atlases",
        "atlas-schaefer100_subcortex_dseg.tsv",
    )
    `

Here is the comments I ran in terminal:
clinica run pet-volume /media/alex/Expansion/Data/OASIS3/PET_processing/PET_BIDS /media/alex/Expansion/Data/OASIS3/PET_processing/preprocessed alex 18FAV45 cerebellumPons2 -tsv /media/alex/Expansion/Data/OASIS3/PET_processing/sub_oasis_list_batch.tsv -wd /media/alex/work/temp/data_preprocess -np 4

Any suggestions?

2 replies

alienx-zero Sep 5, 2024
Author

I fixed it by adding the name of the parcellation in T1_VOLUME_ATLASES as well...Another hint for the other new user, the parcellation.nii should be in the same resolution with built-in parcellation...Otherwise it will also raise error...

NicolasGensollen Sep 6, 2024
Maintainer

Hi @alienx-zero

There is a little piece of documentation here: https://aramislab.paris.inria.fr/clinica/docs/public/dev/Atlases/#how-to-add-a-new-volume-atlas-to-clinica

It is a bit different from what you did since the T1_VOLUME_ATLASES list was replaced with an enumeration recently. Also, it doesn't say explicitly that the parcellation should have the same resolution as the other atlases. We could clarify that indeed.

Finally, by looking at the documentation pages of t1-volume and pet-volume, I agree that there is no clear explanations saying that you can use a custom atlas and providing the link to the page above. We could totally add such an explanation.

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

spm not in matlab path #1256

{{title}}

Replies: 4 comments 11 replies

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

Select a reply

spm not in matlab path #1256

alienx-zero Aug 19, 2024

Executing pyscript_newsegment at 19-Aug-2024 16:32:19: Executing pyscript_newsegment at 19-Aug-2024 16:32:19:

MATLAB Version: 9.14.0.2286388 (R2023a) Update 3 MATLAB License Number: 1147403 Operating System: Linux 5.19.0-46-generic #47~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jun 21 15:35:31 UTC 2 x86_64 Java Version: Java 1.8.0_202-b08 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode

Replies: 4 comments · 11 replies

alienx-zero Aug 19, 2024 Author

NicolasGensollen Aug 21, 2024 Maintainer

alienx-zero Aug 21, 2024 Author

NicolasGensollen Aug 22, 2024 Maintainer

alienx-zero Aug 24, 2024 Author

alienx-zero Aug 25, 2024 Author

alienx-zero Aug 25, 2024 Author

alienx-zero Aug 25, 2024 Author

NicolasGensollen Aug 26, 2024 Maintainer

alienx-zero Aug 26, 2024 Author

alienx-zero Aug 28, 2024 Author

NicolasGensollen Aug 28, 2024 Maintainer

alienx-zero Sep 5, 2024 Author

alienx-zero Sep 5, 2024 Author

NicolasGensollen Sep 6, 2024 Maintainer

alienx-zero
Aug 19, 2024

Executing pyscript_newsegment at 19-Aug-2024 16:32:19:
Executing pyscript_newsegment at 19-Aug-2024 16:32:19:

MATLAB Version: 9.14.0.2286388 (R2023a) Update 3
MATLAB License Number: 1147403
Operating System: Linux 5.19.0-46-generic #47~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jun 21 15:35:31 UTC 2 x86_64
Java Version: Java 1.8.0_202-b08 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode

Replies: 4 comments 11 replies

alienx-zero
Aug 19, 2024
Author

NicolasGensollen
Aug 21, 2024
Maintainer

alienx-zero Aug 21, 2024
Author

NicolasGensollen Aug 22, 2024
Maintainer

alienx-zero Aug 24, 2024
Author

alienx-zero Aug 25, 2024
Author

alienx-zero
Aug 25, 2024
Author

alienx-zero Aug 25, 2024
Author

NicolasGensollen Aug 26, 2024
Maintainer

alienx-zero Aug 26, 2024
Author

alienx-zero Aug 28, 2024
Author

NicolasGensollen Aug 28, 2024
Maintainer

alienx-zero
Sep 5, 2024
Author

alienx-zero Sep 5, 2024
Author

NicolasGensollen Sep 6, 2024
Maintainer