[FieldTrip] Problems with Fieldtrip MR/CT Processing Workflow on PC

[Jonathon James Parker]

Dear Fieldtrippers:

I am working to setup my imaging analysis pipeline to co-localize my SEEG electrodes from CT with patient-specific MRIs.

I am running fieldtrip August 2019 Build with Matlab 2017a on a Windows 10 machine. I am running into some errors which I suspect are due to the freesurfer dependency.

When I run ft_hastoolbox(‘freesurfer’) it returns 1, which I don’t quite understand as I thought freesurfer was only Mac/Linux? When I look in my fieldtrip external directory there is a freesurfer folder with some matlab files in there.

Are you aware of any work-arounds that will allow me to process the CT/MR images still using fieldtrip?

The specific files I am processing are nii.gz (indentified by field trip as nifti_fsl)

When I call ft_read_mri() I get the following results:
-----
Uncompressing stan2_ct.nii.gz to /tmp/tmp2696491.nii
The system cannot find the path specified.
ERROR: could not read /tmp/tmp2696491.nii
'rm' is not recognized as an internal or external command,
operable program or batch file.
ERROR: loading stan2_ct.nii.gz as analyze
Struct contents reference from a non-struct array object.

Error in ft_read_mri (line 396)
    ndims = numel(size(tmp.vol));

Error in jpImagingPipeline (line 12)
ct = ft_read_mri(ct_filename);


Thanks in advance!

Jonathon J. Parker MD, PhD
Resident in Neurosurgery
Morgridge Endowed Postdoctoral Fellow
Maternal & Child Health Research Institute
Department of Neurosurgery
Stanford University
E: parkerjo at stanford.edu<mailto:parkerjo at stanford.edu>


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