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

Andrew Janke floss at apjanke.net
Wed Feb 12 12:28:15 CET 2020

What do y'all think about replacing these zcat calls with something
portable? Matlab has a gunzip() function, and the Java JRE that Matlab
ships with includes some gzip stuff in java.util.zip, so you could
accomplish this with native Matlab/Java code instead of calling out to
the system's zcat utility. I could write up a PR for this if you're

Or maybe I should send that PR directly to FreeSurfer instead of trying
to patch the copy that's included with FieldTrip?


On 2/12/20 5:11 AM, Fellner, Marie-Christin wrote:
> 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  
> "delete(niftifile);"
> Hope that helps!
> Best,
> Marie
> 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>
>> -------------- next part --------------
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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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