Re: multiscalebrainparcellator error locating freesurfer license

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Sebastien Tourbier

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Jan 15, 2020, 6:08:42 AM1/15/20

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Hi Ariana!

What about if you try to call multiscalebrainparcellator with following command:

docker run -it --rm \
-v $parent_dir:/bids_dir \
-v $out_dir:/output_dir \
sebastientourbier/multiscalebrainparcellator \
/bids_dir /output_dir participant --participant_label 01 \
--isotropic_resolution 1.0 \
--skip_bids_validator

On Tue, Jan 14, 2020 at 8:12 PM Ariana Familiar <af...@sas.upenn.edu> wrote:

Hello! I'm attempting to run a single subject analysis with the following command:

docker run -it --rm \
-v $parent_dir:/bids_dir \
-v $out_dir:/output_dir \
-v $FREESURFER_HOME/license.txt:/bids_dir/code/license.txt \
sebastientourbier/multiscalebrainparcellator \
/bids_dir /output_dir participant --participant_label 01 \
--isotropic_resolution 1.0 \
--skip_bids_validator

However I'm getting the following error:

Standard error:
--------------------------------------------------------------------------
ERROR: FreeSurfer license file /opt/freesurfer/license.txt not found.
If you are outside the NMR-Martinos Center,
go to http://surfer.nmr.mgh.harvard.edu/registration.html to
get a valid license file (it's free).
If you are inside the NMR-Martinos Center,
make sure to source the standard environment.
A path to an alternative license file can also be
specified with the FS_LICENSE environmental variable.
--------------------------------------------------------------------------
Return code: 255

The license.txt file is definitely in $FREESURFER_HOME & in /bids_dir/code so I'm not sure why it's not being located. I also manually made a directory /opt/freesurfer and copied the license file there but that did nothing.

I tried setting the FS_LICENSE environment variable but that did not fix it either.

Also receive an error when I use the argument in the command (even though I installed the latest version today so not sure why this argument doesn't work):

usage: multiscalebrainparcellator_bidsapp_entrypointscript [-h]

   [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]

   [--number_of_cores NUMBER_OF_CORES]

   [--isotropic_resolution ISOTROPIC_RESOLUTION]

   [--thalamic_nuclei]

   [--hippocampal_subfields]

   [--brainstem_structures]

   [--skip_bids_validator]

   [-v]

   bids_dir output_dir

   {participant}

multiscalebrainparcellator_bidsapp_entrypointscript: error: unrecognized arguments: --fs_license /Applications/freesurfer/license.txt

How can I fix this issue?

Here is the full output when I run the original command:

BIDS dataset: /bids_dir
WARNING: the specified number of cores (None) should be greater to 0
INFO: Maximal number of cores set to the maximal number of available cores (4)
Custom isotropic resolution for resampling: 1.0
Session structured dataset: False
Subjects to be analyzed: ['sub-01']
<cmp.multiscalebrainparcellator.pipelines.anatomical.anatomical.AnatomicalPipeline object at 0x7f3f69834b30>
Refresh folder WITHOUT session
INFO: New project with newly created (or overwritten) configuration file
WARNING: Configuration file overwritten !
Config file (anat) saved as /bids_dir/derivatives/sub-01_anatomical_config.ini
Config file (anat) saved as /bids_dir/derivatives/sub-01_anatomical_config.ini
Processing command:
multiscalebrainparcellator /bids_dir /output_dir sub-01 /bids_dir/derivatives/sub-01_anatomical_config.ini
###################################################################

Multi-scale Brain Parcellator 1.0.0-beta
Copyright (C) 2017-2019, Brain Communication Pathways Sinergia Consortium, Switzerland
   All rights reserved.

###################################################################
/opt/conda/lib/python2.7/site-packages/grabbit/core.py:410: UserWarning: No valid root directory found for domain 'derivatives'. Falling back on the Layout's root directory. If this isn't the intended behavior, make sure the config file for this domain includes a 'root' key.
"'root' key." % config['name'])
No session
<cmp.multiscalebrainparcellator.pipelines.anatomical.anatomical.AnatomicalPipeline object at 0x7fcc8e3af470>
Refresh folder WITHOUT session
INFO: Existing project... Loading configuration file /bids_dir/derivatives/sub-01_anatomical_config.ini
[u'sub-01']
**** Check Inputs ****
/bids_dir/derivatives/cmp/sub-01/anat/sub-01_T1w.nii.gz
Looking in /bids_dir for....
T1_file : /bids_dir/derivatives/cmp/sub-01/anat/sub-01_T1w.nii.gz
T1w available
Inputs check finished successfully.
Only anatomical data (T1) available.
parcellation_stage
/output_dir/cmp/sub-01/tmp/anatomical_pipeline/parcellation_stage
segmentation_stage
/output_dir/cmp/sub-01/tmp/anatomical_pipeline/segmentation_stage
200114-18:54:13,172 nipype.interface INFO:
**** Processing ****
Freesurfer_subjects_dir: /output_dir/freesurfer
Freesurfer_subject_id: /output_dir/freesurfer/sub-01
200114-18:54:13,850 nipype.workflow INFO:
Generated workflow graph: /output_dir/cmp/sub-01/tmp/anatomical_pipeline/graph.svg (graph2use=colored, simple_form=True).
Number of cores used: 1
200114-18:54:13,972 nipype.workflow INFO:
Workflow anatomical_pipeline settings: ['check', 'execution', 'logging', 'monitoring']
200114-18:54:14,36 nipype.workflow INFO:
Running serially.
200114-18:54:14,38 nipype.workflow INFO:
[Node] Setting-up "anatomical_pipeline.datasource" in "/output_dir/cmp/sub-01/tmp/anatomical_pipeline/datasource".
200114-18:54:14,91 nipype.workflow INFO:
[Node] Running "datasource" ("nipype.interfaces.io.DataGrabber")
200114-18:54:14,137 nipype.workflow INFO:
[Node] Finished "anatomical_pipeline.datasource".
200114-18:54:14,141 nipype.workflow INFO:
[Node] Setting-up "anatomical_pipeline.segmentation_stage.mgz_convert" in "/output_dir/cmp/sub-01/tmp/anatomical_pipeline/segmentation_stage/mgz_convert".
T1 is available
200114-18:54:14,197 nipype.workflow INFO:
[Node] Running "mgz_convert" ("nipype.interfaces.freesurfer.preprocess.MRIConvert"), a CommandLine Interface with command:
mri_convert --out_type mgz --resample_type interpolate -voxsize 1.000000 1.000000 1.000000 --input_volume /output_dir/cmp/sub-01/anat/sub-01_T1w.nii.gz --output_volume T1.mgz
200114-18:54:14,682 nipype.interface INFO:
stdout 2020-01-14T18:54:14.681884:mri_convert.bin --out_type mgz --resample_type interpolate -voxsize 1.000000 1.000000 1.000000 --input_volume /output_dir/cmp/sub-01/anat/sub-01_T1w.nii.gz --output_volume T1.mgz
200114-18:54:14,685 nipype.interface INFO:
stderr 2020-01-14T18:54:14.685078:--------------------------------------------------------------------------
200114-18:54:14,686 nipype.interface INFO:
stderr 2020-01-14T18:54:14.685078:ERROR: FreeSurfer license file /opt/freesurfer/license.txt not found.
200114-18:54:14,687 nipype.interface INFO:
stderr 2020-01-14T18:54:14.685078: If you are outside the NMR-Martinos Center,
200114-18:54:14,688 nipype.interface INFO:
stderr 2020-01-14T18:54:14.685078: go to http://surfer.nmr.mgh.harvard.edu/registration.html to
200114-18:54:14,689 nipype.interface INFO:
stderr 2020-01-14T18:54:14.685078: get a valid license file (it's free).
200114-18:54:14,691 nipype.interface INFO:
stderr 2020-01-14T18:54:14.685078: If you are inside the NMR-Martinos Center,
200114-18:54:14,692 nipype.interface INFO:
stderr 2020-01-14T18:54:14.685078: make sure to source the standard environment.
200114-18:54:14,693 nipype.interface INFO:
stderr 2020-01-14T18:54:14.685078: A path to an alternative license file can also be
200114-18:54:14,694 nipype.interface INFO:
stderr 2020-01-14T18:54:14.685078: specified with the FS_LICENSE environmental variable.
200114-18:54:14,695 nipype.interface INFO:
stderr 2020-01-14T18:54:14.685078:--------------------------------------------------------------------------
200114-18:54:14,697 nipype.interface INFO:
stdout 2020-01-14T18:54:14.697111:$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
200114-18:54:14,698 nipype.interface INFO:
stdout 2020-01-14T18:54:14.697111:reading from /output_dir/cmp/sub-01/anat/sub-01_T1w.nii.gz...
200114-18:54:14,745 nipype.workflow WARNING:
[Node] Error on "anatomical_pipeline.segmentation_stage.mgz_convert" (/output_dir/cmp/sub-01/tmp/anatomical_pipeline/segmentation_stage/mgz_convert)
200114-18:54:14,771 nipype.workflow ERROR:
Node mgz_convert failed to run on host 9585ae7d354f.
200114-18:54:14,774 nipype.workflow ERROR:
Saving crash info to /app/crash-20200114-185414-root-mgz_convert-045cac55-bcfe-45e0-857f-0c6f4f6e0d6b.txt
Traceback (most recent call last):
File "/opt/conda/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
node.run(updatehash=updatehash)
File "/opt/conda/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
result = self._run_interface(execute=True)
File "/opt/conda/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
return self._run_command(execute)
File "/opt/conda/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
result = self._interface.run(cwd=outdir)
File "/opt/conda/lib/python2.7/site-packages/nipype/interfaces/freesurfer/base.py", line 144, in run
return super(FSCommand, self).run(**inputs)
File "/opt/conda/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 511, in run
runtime = self._run_interface(runtime)
File "/opt/conda/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 898, in _run_interface
self.raise_exception(runtime)
File "/opt/conda/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 835, in raise_exception
).format(**runtime.dictcopy()))
RuntimeError: Command:
mri_convert --out_type mgz --resample_type interpolate -voxsize 1.000000 1.000000 1.000000 --input_volume /output_dir/cmp/sub-01/anat/sub-01_T1w.nii.gz --output_volume T1.mgz
Standard output:
mri_convert.bin --out_type mgz --resample_type interpolate -voxsize 1.000000 1.000000 1.000000 --input_volume /output_dir/cmp/sub-01/anat/sub-01_T1w.nii.gz --output_volume T1.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /output_dir/cmp/sub-01/anat/sub-01_T1w.nii.gz...
Standard error:
--------------------------------------------------------------------------
ERROR: FreeSurfer license file /opt/freesurfer/license.txt not found.
If you are outside the NMR-Martinos Center,
go to http://surfer.nmr.mgh.harvard.edu/registration.html to
get a valid license file (it's free).
If you are inside the NMR-Martinos Center,
make sure to source the standard environment.
A path to an alternative license file can also be
specified with the FS_LICENSE environmental variable.
--------------------------------------------------------------------------
Return code: 255

Traceback (most recent call last):
File "/opt/conda/bin/multiscalebrainparcellator", line 102, in <module>
anat_pipeline.process()
File "/opt/conda/lib/python2.7/site-packages/cmp/multiscalebrainparcellator/pipelines/anatomical/anatomical.py", line 464, in process
anat_flow.run()
File "/opt/conda/lib/python2.7/site-packages/nipype/pipeline/engine/workflows.py", line 597, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/opt/conda/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
node.run(updatehash=updatehash)
File "/opt/conda/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
result = self._run_interface(execute=True)
File "/opt/conda/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
return self._run_command(execute)
File "/opt/conda/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
result = self._interface.run(cwd=outdir)
File "/opt/conda/lib/python2.7/site-packages/nipype/interfaces/freesurfer/base.py", line 144, in run
return super(FSCommand, self).run(**inputs)
File "/opt/conda/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 511, in run
runtime = self._run_interface(runtime)
File "/opt/conda/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 898, in _run_interface
self.raise_exception(runtime)
File "/opt/conda/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 835, in raise_exception
).format(**runtime.dictcopy()))
RuntimeError: Command:
mri_convert --out_type mgz --resample_type interpolate -voxsize 1.000000 1.000000 1.000000 --input_volume /output_dir/cmp/sub-01/anat/sub-01_T1w.nii.gz --output_volume T1.mgz
Standard output:
mri_convert.bin --out_type mgz --resample_type interpolate -voxsize 1.000000 1.000000 1.000000 --input_volume /output_dir/cmp/sub-01/anat/sub-01_T1w.nii.gz --output_volume T1.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /output_dir/cmp/sub-01/anat/sub-01_T1w.nii.gz...
Standard error:
--------------------------------------------------------------------------
ERROR: FreeSurfer license file /opt/freesurfer/license.txt not found.
If you are outside the NMR-Martinos Center,
go to http://surfer.nmr.mgh.harvard.edu/registration.html to
get a valid license file (it's free).
If you are inside the NMR-Martinos Center,
make sure to source the standard environment.
A path to an alternative license file can also be
specified with the FS_LICENSE environmental variable.
--------------------------------------------------------------------------
Return code: 255

Processing with the Multi-scale Brain Parcellator BIDS App finished!

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Ariana Familiar

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Jan 15, 2020, 9:28:25 AM1/15/20

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Thanks! It worked with the following:

docker run -it --rm \
-v $parent_dir:/bids_dir \
-v $out_dir:/output_dir \
-v $FREESURFER_HOME/license.txt:/bids_dir/code/license.txt \

-v $FREESURFER_HOME/license.txt:/opt/freesurfer/license.txt \

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