Hi,
Summary of what happened:
I tried to transform a surface based image into volume space using nipype’s freesurfer.Surface2VolumeTransform in a nipype container. But running that function failed unfortunately because the command mri_surf2vol could not be found. I noticed that also in the terminal within that container it looks like no mri_surf2vol was on the PATH.
It is nice to have all fMRI analysis toolboxes integrated in this one nipype container. It is just a pity that some of the FreeSurfer functionality appears not to be available in the container.
Currently I am running some of the FreeSurfer commands outside the container in a different environment. This solution is not exactly ideal. How can I use all of FreeSurfer with the nipype image?
A few thoughts come to mind:
- Install a different FreeSurfer manually inside Docker (a bit annoying because FreeSurfer is supposed to already be there and the two installations might not play nice with each other)
- Perhaps -v mount an existing installation from outside and run the container (not sure if this would actually work)
Command used (and if a helper script was used, a link to the helper script or the command generated):
import nipype.interfaces.freesurfer as fs
import os
opj = os.path.join
sub_id = 'sub-sid000005'
hemi = 'lh'
surf2vol = fs.Surface2VolTransform()
surf2vol.inputs.source_file = opj(
fs_dir, sub_id, 'surf/%s.wang15_mplbl.mgz' % hemi)
surf2vol.inputs.transformed_file = opj(
fmriprep_dir, sub_id, 'rois/%s_wang15_mplbl.nii.gz')
surf2vol.inputs.template_file = opj(
fmriprep_dir, sub_id,
'func/%s_task-movie_run-3_space-T1w_boldref.nii.gz' % sub_id)
surf2vol.inputs.reg_file = opj(
fs_dir, sub_id, 'stats/%s_register.dat' % sub_id)
surf2vol.inputs.subjects_dir = fs_dir
surf2vol.inputs.projfrac = .1
surf2vol.inputs.hemi = hemi
surf2vol.run()
Version:
nipype 1.8.6.dev0
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Environment (Docker, Singularity, custom installation):
I am using this nipype Docker image.
Data formatted according to a validatable standard? Please provide the output of the validator:
BIDS validation successful
Relevant log outputs (up to 20 lines):
---------------------------------------------------------------------------
OSError Traceback (most recent call last)
Cell In[12], line 20
17 surf2vol.inputs.projfrac = .1
18 surf2vol.inputs.hemi = hemi
---> 20 surf2vol.run()
File /src/nipype/nipype/interfaces/freesurfer/base.py:149, in FSCommand.run(self, **inputs)
147 self.inputs.subjects_dir = inputs["subjects_dir"]
148 self._subjects_dir_update()
--> 149 return super(FSCommand, self).run(**inputs)
File /src/nipype/nipype/interfaces/base/core.py:398, in BaseInterface.run(self, cwd, ignore_exception, **inputs)
396 # Run interface
397 runtime = self._pre_run_hook(runtime)
--> 398 runtime = self._run_interface(runtime)
399 runtime = self._post_run_hook(runtime)
400 # Collect outputs
File /src/nipype/nipype/interfaces/base/core.py:753, in CommandLine._run_interface(self, runtime, correct_return_codes)
750 cmd_path = which(executable_name, env=runtime.environ)
752 if cmd_path is None:
--> 753 raise IOError(
754 'No command "%s" found on host %s. Please check that the '
755 "corresponding package is installed."
756 % (executable_name, runtime.hostname)
757 )
759 runtime.command_path = cmd_path
760 runtime.dependencies = (
761 get_dependencies(executable_name, runtime.environ)
762 if self._ldd
763 else ""
764 )
OSError: No command "mri_surf2vol" found on host b32ee0851ce9. Please check that the corresponding package is installed.
Any ideas?
Cheers,
Michael