T1 linear file not found

[Carlo Fabrizio]

Hi,

I have made a curated subset of NIFD images downloaded from LONI. I then applied the nifd-to-bids pipeline, successfully creating a BIDS folder for my images (all T1w and ses-M00, for 312 subjects). Now I would like to apply the t1-linear pipeline to preprocess the images to be ready for Deep Learning. I tried installing ANTs both from conda and from the original github repository linked in the third-party page, but I incurr in the same error.

I run t1-linear with the following call: 

clinica run t1-linear --n_procs 26 raw/bids_folder intermediate/caps_t1_linear

and I get the following:

2022-04-05 15:37:51,827:WARNING:Could not determine if intermediate/caps_t1_linear is a CAPS or BIDS directory. Clinica will assume this is a CAPS directory.
2022-04-05 15:37:52,460:INFO:The pipeline will be run on the following 312 image(s):
2022-04-05 15:37:52,460:INFO:    sub-NIFD1S0001 | ses-M00,
2022-04-05 15:37:52,460:INFO:    sub-NIFD1S0002 | ses-M00,
2022-04-05 15:37:52,460:INFO:    sub-NIFD1S0003 | ses-M00,
2022-04-05 15:37:52,460:INFO:    sub-NIFD1S0005 | ses-M00,
2022-04-05 15:37:52,460:INFO:    sub-NIFD1S0006 | ses-M00,
2022-04-05 15:37:52,460:INFO:    sub-NIFD1S0007 | ses-M00,
2022-04-05 15:37:52,460:INFO:    sub-NIFD1S0009 | ses-M00,
2022-04-05 15:37:52,460:INFO:    sub-NIFD1S0010 | ses-M00,
2022-04-05 15:37:52,460:INFO:    sub-NIFD1S0011 | ses-M00,
2022-04-05 15:37:52,461:INFO:    sub-NIFD1S0012 | ses-M00,
2022-04-05 15:37:52,461:INFO:    sub-NIFD1S0013 | ses-M00,
2022-04-05 15:37:52,461:INFO:    sub-NIFD1S0014 | ses-M00,
2022-04-05 15:37:52,461:INFO:    sub-NIFD1S0015 | ses-M00,
2022-04-05 15:37:52,461:INFO:    sub-NIFD1S0016 | ses-M00,
2022-04-05 15:37:52,461:INFO:    sub-NIFD1S0017 | ses-M00,
2022-04-05 15:37:52,461:INFO:    sub-NIFD1S0018 | ses-M00,
2022-04-05 15:37:52,461:INFO:    sub-NIFD1S0019 | ses-M00,
2022-04-05 15:37:52,461:INFO:    sub-NIFD1S0020 | ses-M00,
2022-04-05 15:37:52,461:INFO:    sub-NIFD1S0021 | ses-M00,
2022-04-05 15:37:52,461:INFO:    sub-NIFD1S0022 | ses-M00,
2022-04-05 15:37:52,461:INFO:    sub-NIFD1S0023 | ses-M00,
2022-04-05 15:37:52,461:INFO:    sub-NIFD1S0024 | ses-M00,
2022-04-05 15:37:52,461:INFO:    sub-NIFD1S0026 | ses-M00,
2022-04-05 15:37:52,461:INFO:    sub-NIFD1S0028 | ses-M00,
2022-04-05 15:37:52,462:INFO:    sub-NIFD1S0029 | ses-M00,
2022-04-05 15:37:52,462:INFO:    ...
2022-04-05 15:37:52,462:INFO:    sub-NIFD3S0012 | ses-M00,
2022-04-05 15:37:52,462:INFO:The pipeline will last approximately 6 minutes per image.
Traceback (most recent call last):
  File "/home/lab401/anaconda3/envs/clinicaEnv/bin/clinica", line 8, in <module>
    sys.exit(main())
  File "/home/lab401/anaconda3/envs/clinicaEnv/lib/python3.9/site-packages/clinica/cmdline.py", line 89, in main
    cli()
  File "/home/lab401/anaconda3/envs/clinicaEnv/lib/python3.9/site-packages/click/core.py", line 1128, in __call__
    return self.main(*args, **kwargs)
  File "/home/lab401/anaconda3/envs/clinicaEnv/lib/python3.9/site-packages/click/core.py", line 1053, in main
    rv = self.invoke(ctx)
  File "/home/lab401/anaconda3/envs/clinicaEnv/lib/python3.9/site-packages/click/core.py", line 1659, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/lab401/anaconda3/envs/clinicaEnv/lib/python3.9/site-packages/click/core.py", line 1659, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/lab401/anaconda3/envs/clinicaEnv/lib/python3.9/site-packages/click/core.py", line 1395, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/lab401/anaconda3/envs/clinicaEnv/lib/python3.9/site-packages/click/core.py", line 754, in invoke
    return __callback(*args, **kwargs)
  File "/home/lab401/anaconda3/envs/clinicaEnv/lib/python3.9/site-packages/clinica/pipelines/t1_linear/t1_linear_cli.py", line 56, in cli
    pipeline.run(plugin="MultiProc", plugin_args={"n_procs": n_procs})
  File "/home/lab401/anaconda3/envs/clinicaEnv/lib/python3.9/site-packages/clinica/pipelines/engine.py", line 288, in run
    raise e
  File "/home/lab401/anaconda3/envs/clinicaEnv/lib/python3.9/site-packages/clinica/pipelines/engine.py", line 269, in run
    exec_graph = Workflow.run(self, plugin, plugin_args, update_hash)
  File "/home/lab401/anaconda3/envs/clinicaEnv/lib/python3.9/site-packages/nipype/pipeline/engine/workflows.py", line 638, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/home/lab401/anaconda3/envs/clinicaEnv/lib/python3.9/site-packages/nipype/pipeline/plugins/base.py", line 166, in run
    self._clean_queue(jobid, graph, result=result)
  File "/home/lab401/anaconda3/envs/clinicaEnv/lib/python3.9/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/lab401/anaconda3/envs/clinicaEnv/lib/python3.9/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/home/lab401/anaconda3/envs/clinicaEnv/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 521, in run
    result = self._run_interface(execute=True)
  File "/home/lab401/anaconda3/envs/clinicaEnv/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 639, in _run_interface
    return self._run_command(execute)
  File "/home/lab401/anaconda3/envs/clinicaEnv/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 750, in _run_command
    raise NodeExecutionError(
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node n4biascorrection.

Traceback (most recent call last):
  File "/home/lab401/anaconda3/envs/clinicaEnv/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 454, in aggregate_outputs
    setattr(outputs, key, val)
  File "/home/lab401/anaconda3/envs/clinicaEnv/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 "/home/lab401/anaconda3/envs/clinicaEnv/lib/python3.9/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
    self.error(objekt, name, str(value))
  File "/home/lab401/anaconda3/envs/clinicaEnv/lib/python3.9/site-packages/traits/base_trait_handler.py", line 74, in error
    raise TraitError(
traits.trait_errors.TraitError: The 'bias_image' trait of a N4BiasFieldCorrectionOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/tmp/tmpoawpd84o/t1-linear/5e2043bd58b37366c250677ee7fb8385b4cd11f3/n4biascorrection/sub-NIFD1S0001_ses-M00_T1w_bias.nii.gz' <class 'str'> was specified.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/lab401/anaconda3/envs/clinicaEnv/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 401, in run
    outputs = self.aggregate_outputs(runtime)
  File "/home/lab401/anaconda3/envs/clinicaEnv/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 461, in aggregate_outputs
    raise FileNotFoundError(msg)
FileNotFoundError: No such file or directory '/tmp/tmpoawpd84o/t1-linear/5e2043bd58b37366c250677ee7fb8385b4cd11f3/n4biascorrection/sub-NIFD1S0001_ses-M00_T1w_bias.nii.gz' for output 'bias_image' of a N4BiasFieldCorrection interface

____________________________________

Is there something I can do?

Thanks

[Omar Rifai]

Hi Carlo,

Thank you for your interest in Clinica.

Can you  paste the content of the crash*.pklz file the error generates. For that you can use the command "nipypecli crash <crash-file-name>".

Also can you update to the latest version of Clinica if you are not already on it.

Thank you.

Omar

[Carlo Fabrizio]

Hi Omar,

thank you for your fast response.

This is the content of the crash.pklz file: 

File: /home/lab401/crash-20220405-153757-lab401-n4biascorrection.a000-b178963b-6200-4847-b047-d601d186b704.pklz
Node: t1-linear.n4biascorrection
Working directory: /tmp/tmpoawpd84o/t1-linear/5e2043bd58b37366c250677ee7fb8385b4cd11f3/n4biascorrection


Node inputs:

args = <undefined>
bias_image = <undefined>
bspline_fitting_distance = 600.0
bspline_order = <undefined>
convergence_threshold = <undefined>
copy_header = False
dimension = 3
environ = {'NSLOTS': '1'}
histogram_sharpening = <undefined>
input_image = /home/lab401/Analyses/NIFD exp/data/raw/collection1_first_t1mprage_bids/sub-NIFD1S0001/ses-M00/anat/sub-NIFD1S0001_ses-M00_T1w.nii.gz
mask_image = <undefined>
n_iterations = <undefined>
num_threads = 1
output_image = <undefined>
rescale_intensities = <undefined>
save_bias = True
shrink_factor = <undefined>
weight_image = <undefined>



Traceback:

I'm now going to update clinica, as i found out i was using version 0.5.6

I'll post updates here

Thank you

Carlo

[Carlo Fabrizio]

Hi again,

I created a new environment with clinica 0.6.0 and configured it to run t1-linear. Unfortunately, I've got a very similar error. The output is reported below:

2022-04-06 11:45:44,574:WARNING:Could not determine if /home/lab401/Analyses/NIFD exp/data/intermediate/collection1_first_t1mprage_t1_linear is a CAPS or BIDS directory. Clinica will assume this is a CAPS directory.
2022-04-06 11:45:45,293:INFO:The pipeline will be run on the following 312 image(s):
2022-04-06 11:45:45,293:INFO:    sub-NIFD1S0001 | ses-M00,
2022-04-06 11:45:45,293:INFO:    sub-NIFD1S0002 | ses-M00,
2022-04-06 11:45:45,293:INFO:    sub-NIFD1S0003 | ses-M00,
2022-04-06 11:45:45,293:INFO:    sub-NIFD1S0005 | ses-M00,
2022-04-06 11:45:45,293:INFO:    sub-NIFD1S0006 | ses-M00,
2022-04-06 11:45:45,293:INFO:    sub-NIFD1S0007 | ses-M00,
2022-04-06 11:45:45,293:INFO:    sub-NIFD1S0009 | ses-M00,
2022-04-06 11:45:45,293:INFO:    sub-NIFD1S0010 | ses-M00,
2022-04-06 11:45:45,293:INFO:    sub-NIFD1S0011 | ses-M00,
2022-04-06 11:45:45,293:INFO:    sub-NIFD1S0012 | ses-M00,
2022-04-06 11:45:45,293:INFO:    sub-NIFD1S0013 | ses-M00,
2022-04-06 11:45:45,293:INFO:    sub-NIFD1S0014 | ses-M00,
2022-04-06 11:45:45,293:INFO:    sub-NIFD1S0015 | ses-M00,
2022-04-06 11:45:45,294:INFO:    sub-NIFD1S0016 | ses-M00,
2022-04-06 11:45:45,294:INFO:    sub-NIFD1S0017 | ses-M00,
2022-04-06 11:45:45,294:INFO:    sub-NIFD1S0018 | ses-M00,
2022-04-06 11:45:45,294:INFO:    sub-NIFD1S0019 | ses-M00,
2022-04-06 11:45:45,294:INFO:    sub-NIFD1S0020 | ses-M00,
2022-04-06 11:45:45,294:INFO:    sub-NIFD1S0021 | ses-M00,
2022-04-06 11:45:45,294:INFO:    sub-NIFD1S0022 | ses-M00,
2022-04-06 11:45:45,294:INFO:    sub-NIFD1S0023 | ses-M00,
2022-04-06 11:45:45,294:INFO:    sub-NIFD1S0024 | ses-M00,
2022-04-06 11:45:45,294:INFO:    sub-NIFD1S0026 | ses-M00,
2022-04-06 11:45:45,294:INFO:    sub-NIFD1S0028 | ses-M00,
2022-04-06 11:45:45,294:INFO:    sub-NIFD1S0029 | ses-M00,
2022-04-06 11:45:45,294:INFO:    ...
2022-04-06 11:45:45,294:INFO:    sub-NIFD3S0012 | ses-M00,
2022-04-06 11:45:45,294:INFO:The pipeline will last approximately 6 minutes per image.

Traceback (most recent call last):

  File "/home/lab401/anaconda3/envs/clinica_env/bin/clinica", line 5, in <module>
    main()
  File "/home/lab401/Software/clinica-0.6.0/clinica/cmdline.py", line 89, in main
    cli()
  File "/home/lab401/anaconda3/envs/clinica_env/lib/python3.8/site-packages/click/core.py", line 1128, in __call__
    return self.main(*args, **kwargs)
  File "/home/lab401/anaconda3/envs/clinica_env/lib/python3.8/site-packages/click/core.py", line 1053, in main
    rv = self.invoke(ctx)
  File "/home/lab401/anaconda3/envs/clinica_env/lib/python3.8/site-packages/click/core.py", line 1659, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/lab401/anaconda3/envs/clinica_env/lib/python3.8/site-packages/click/core.py", line 1659, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/lab401/anaconda3/envs/clinica_env/lib/python3.8/site-packages/click/core.py", line 1395, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/lab401/anaconda3/envs/clinica_env/lib/python3.8/site-packages/click/core.py", line 754, in invoke
    return __callback(*args, **kwargs)
  File "/home/lab401/Software/clinica-0.6.0/clinica/pipelines/t1_linear/t1_linear_cli.py", line 56, in cli

    pipeline.run(plugin="MultiProc", plugin_args={"n_procs": n_procs})

  File "/home/lab401/Software/clinica-0.6.0/clinica/pipelines/engine.py", line 288, in run
    raise e
  File "/home/lab401/Software/clinica-0.6.0/clinica/pipelines/engine.py", line 269, in run

    exec_graph = Workflow.run(self, plugin, plugin_args, update_hash)

  File "/home/lab401/anaconda3/envs/clinica_env/lib/python3.8/site-packages/nipype/pipeline/engine/workflows.py", line 638, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/home/lab401/anaconda3/envs/clinica_env/lib/python3.8/site-packages/nipype/pipeline/plugins/base.py", line 166, in run
    self._clean_queue(jobid, graph, result=result)
  File "/home/lab401/anaconda3/envs/clinica_env/lib/python3.8/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/lab401/anaconda3/envs/clinica_env/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/home/lab401/anaconda3/envs/clinica_env/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 521, in run
    result = self._run_interface(execute=True)
  File "/home/lab401/anaconda3/envs/clinica_env/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 639, in _run_interface
    return self._run_command(execute)
  File "/home/lab401/anaconda3/envs/clinica_env/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 750, in _run_command

    raise NodeExecutionError(
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node n4biascorrection.

Traceback (most recent call last):

  File "/home/lab401/anaconda3/envs/clinica_env/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 454, in aggregate_outputs
    setattr(outputs, key, val)
  File "/home/lab401/anaconda3/envs/clinica_env/lib/python3.8/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate

    value = super(File, self).validate(objekt, name, value, return_pathlike=True)

  File "/home/lab401/anaconda3/envs/clinica_env/lib/python3.8/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
    self.error(objekt, name, str(value))
  File "/home/lab401/anaconda3/envs/clinica_env/lib/python3.8/site-packages/traits/base_trait_handler.py", line 74, in error
    raise TraitError(
traits.trait_errors.TraitError: The 'output_image' trait of a N4BiasFieldCorrectionOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/tmp/tmpqgduec24/t1-linear/5e2043bd58b37366c250677ee7fb8385b4cd11f3/n4biascorrection/sub-NIFD1S0001_ses-M00_T1w_corrected.nii.gz' <class 'str'> was specified.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

  File "/home/lab401/anaconda3/envs/clinica_env/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 401, in run
    outputs = self.aggregate_outputs(runtime)
  File "/home/lab401/anaconda3/envs/clinica_env/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 461, in aggregate_outputs
    raise FileNotFoundError(msg)
FileNotFoundError: No such file or directory '/tmp/tmpqgduec24/t1-linear/5e2043bd58b37366c250677ee7fb8385b4cd11f3/n4biascorrection/sub-NIFD1S0001_ses-M00_T1w_corrected.nii.gz' for output 'output_image' of a N4BiasFieldCorrection interface

[Omar Rifai]

Hi Carlo,

From the log it looks like Clinica is failing to find the the ANTs command `N4BiasFieldCorrection`. Can you please check if you are able to run the command from your terminal without passing by Clinica. For instance, you should be able to run the following command in your environment:

N4BiasFieldCorrection -i <input-niifti> -o <output-niifti>

If you are unable to find this command, the installation of ANTs must not have been successful. For reference I'm using ants 2.2.0

Regards,

Omar

On Tuesday, April 5, 2022 at 4:03:08 PM UTC+2 carlo.fa...@gmail.com wrote:

[Carlo Fabrizio]

Dear Omar,

thanks for your advice. I tried running the command you suggested and successfully got the output file. 

Now I'm a bit puzzled with how to manage the issue. It would be great if you have an idea.

Thank you,

Carlo

[Omar Rifai]

That is indeed a bit puzzling as I'm unable to reproduce the error.  In order to narrow down the scope, I have tested for sub-NIFD1S0006 - ses00.

Can you confirm this subj/session works for you with N4BiasFieldCorrection but not with Clinica ? (you can narrow the scope using the -tsv flag).

Thanks,

Omar

[Carlo Fabrizio]

I tested on sub-NIFD1S0006 - ses00 inside clinicaEnv with the following call: 

N4BiasFieldCorrection -i /home/lab401/Analyses/NIFD\ exp/data/raw/collection1_first_t1mprage_bids/sub-NIFD1S0006/ses-M00/anat/sub-NIFD1S0006_ses-M00_T1w.nii.gz -o /home/lab401/Analyses/NIFD\ exp/data/intermediate/collection1_first_t1mprage_t1_linear/prova.nii.gz

It worked perfectly.

I then tried running clinica t1-linear using the -tsv flag, but i got the same error.

The tsv file was as following:

participant_id    session_id
sub-NIFD1S0006    ses-M00

The call was as following:

clinica run t1-linear --n_procs 26 /home/lab401/Analyses/NIFD\ exp/data/raw/collection1_first_t1mprage_bids /home/lab401/Analyses/NIFD\ exp/data/intermediate/collection1_first_t1mprage_t1_linear -tsv /home/lab401/Analyses/NIFD\ exp/participants_prova.tsv

The output was as following:

2022-04-06 16:08:02,199:WARNING:Could not determine if /home/lab401/Analyses/NIFD exp/data/intermediate/collection1_first_t1mprage_t1_linear is a CAPS or BIDS directory. Clinica will assume this is a CAPS directory.
2022-04-06 16:08:02,211:INFO:The pipeline will be run on the following 1 image(s):
2022-04-06 16:08:02,211:INFO:    sub-NIFD1S0006 | ses-M00,
2022-04-06 16:08:02,211:INFO:The pipeline will last approximately 6 minutes per image.

traits.trait_errors.TraitError: The 'output_image' trait of a N4BiasFieldCorrectionOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/tmp/tmp40jcia9e/t1-linear/6da3fd5610f0f6e64691f53f828f417b9f19df1b/n4biascorrection/sub-NIFD1S0006_ses-M00_T1w_corrected.nii.gz' <class 'str'> was specified.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/lab401/anaconda3/envs/clinicaEnv/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 401, in run
    outputs = self.aggregate_outputs(runtime)
  File "/home/lab401/anaconda3/envs/clinicaEnv/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 461, in aggregate_outputs
    raise FileNotFoundError(msg)

FileNotFoundError: No such file or directory '/tmp/tmp40jcia9e/t1-linear/6da3fd5610f0f6e64691f53f828f417b9f19df1b/n4biascorrection/sub-NIFD1S0006_ses-M00_T1w_corrected.nii.gz' for output 'output_image' of a N4BiasFieldCorrection interface

_________________________________________

I know it is hard. Any clue?

Thank you very much for your responsive help.

Best regards,

Carlo

[Omar Rifai]

Hi Carlo,

From the last message you sent, it seems you have introduced space characters in your paths. This is likely a cause of error.  I couldn't find any in your initial comment so that's what puzzled me. Can you confirm that you still have an error removing the space characters from the paths?

Thanks,

Omar

[Carlo Fabrizio]

Hi Omar,

I thought I had ruled out this problem both trying to run the command inside the "NIFD exp" folder and putting the escape character "\". Renaming the folder to "NIFD_exp" did the job!

Now t1-linear ran on that single subject (sub-NIFD1S0006) but I noticed it only used 1 processor despite the --n_procs flags specifying 26 to be used. This reminds me of what was reported in the crash.pklz file:

Node inputs:

args = <undefined>
bias_image = <undefined>
bspline_fitting_distance = 600.0
bspline_order = <undefined>
convergence_threshold = <undefined>
copy_header = False
dimension = 3
environ = {'NSLOTS': '1'}
histogram_sharpening = <undefined>
input_image = /home/lab401/Analyses/NIFD exp/data/raw/collection1_first_t1mprage_bids/sub-NIFD1S0001/ses-M00/anat/sub-NIFD1S0001_ses-M00_T1w.nii.gz
mask_image = <undefined>
n_iterations = <undefined>
num_threads = 1
output_image = <undefined>
rescale_intensities = <undefined>
save_bias = True
shrink_factor = <undefined>
weight_image = <undefined>

It's not that bothering, It is still pretty fast - it just took 5 minutes to run. It is just to inform you!

Thank you very much for your help!

Have a nice day,

Carlo

[Carlo Fabrizio]

Update:

Now I'm running clinica t1-linear on all 312 subjects and multiprocessing is active. What happened before was probably due to the presence of only one subject in the tsv.

Thank you again!

[Omar Rifai]

Great ! glad it works.

Omar