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

Fellner, Marie-Christin mcfellner at gmail.com
Wed Feb 12 11:11:23 CET 2020

Hi Jonathon,

I have run into similar problems of you with nii.gz files on a PC even 
with the most recent fieldtrip version.

The problem in my case was that the subfunction load_nifit.m used 
commands that did not run using the windows command line. Downloading 
and installing git (https://git-scm.com/) and crudely changing 
load_nifit.m helped for me.

I just replaced  "cmd = sprintf('zcat %s > %s', niftifile, 
new_niftifile);" to     "cmd = sprintf(' "C:\\Program 
Files\\Git\\bin\\bash.exe " zcat -c %s > %s', niftifile, new_niftifile);"

Further change all  "  unix(sprintf('rm -f %s', niftifile)); " to   

Hope that helps!



Am 07.02.2020 um 12:00 schrieb fieldtrip-request at science.ru.nl:
> Message: 4
> Date: Thu, 6 Feb 2020 23:33:08 +0000
> From: Jonathon James Parker<parkerjo at stanford.edu>
> To:"fieldtrip at science.ru.nl"  <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] Problems with Fieldtrip MR/CT Processing Workflow
> 	on PC
> Message-ID:
> 	<BYAPR02MB575043282E5EC812196B677CAD1D0 at BYAPR02MB5750.namprd02.prod.outlook.com>
> Content-Type: text/plain; charset="windows-1252"
> 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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> ------------------------------
> Message: 5
> Date: Fri, 7 Feb 2020 08:35:23 +0000
> From: "Schoffelen, J.M. (Jan Mathijs)"<jan.schoffelen at donders.ru.nl>
> To: FieldTrip discussion list<fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Problems with Fieldtrip MR/CT Processing
> 	Workflow on PC
> Message-ID:<56E6D50D-81E1-464E-9256-221ABD935DDA at donders.ru.nl>
> Content-Type: text/plain; charset="utf-8"
> Dear Jonathon,
> Indeed, Freesurfer typically used to run only on Linux/Mac. However, rumour has it that as of Windows 10 , freesurfer might run on Windows. For this you’d need to check out the Freesurfer documentation. If you need to run the Freesurfer recon-all pipeline to extract cortical meshes and/or a surface hull, you’d need to find out how to execute this processing step yourself.
> With respect to the message you get from ft_hastoolbox: this refers to the availability (to matlab) of the relevant freesurfer code that uses Matlab (which are mainly functions related to loading Freesurfer specific file-formats into matlab for further processing). These functions in principle should work also on windows, with one possible exception, and that is the on-the-fly decompression of compressed anatomical images, which seems to be the problem that you are running into. I improved the Windows support for reading in zipped MR-images (*.nii.gz, and *.mgz) last December, and on my end it seems to work with a current version of the FieldTrip code. I should note, however, that I recently ran a training event, where several participants still did not manage to read in the zipped files on their own (Windows) laptops. This could have been due to their strange keyboard layouts (German/French/Asian etc.), but more likely this was the consequence of an interaction between Windows version, Matlab version and the students’ position in the room.
> Long story short: could you upgrade to a more recent version of the Fieldtrip code (early January onwards to be safe), and check whether your problem persists?
> Best wishes,
> Jan-Mathijs
> J.M.Schoffelen, MD PhD
> Associate PI, VIDI-fellow - PI, language in interaction
> Telephone: +31-24-3614793
> Physical location: room 00.028
> Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands

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