You have a rogue non-ascii character between HM-HR10-002Rest and Group1 (between others). Make sure you create your fsgd file in a simple ascii text editor.
On 06/23/2016 01:48 AM, Jarek Rokicki wrote:
Dear Freesurfer experts,
I am trying to perform the resting state fMRI analysis as in: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthr...
I got stuck with the STEP8, when I tried to use my own fsgd file. I tried to test for two group difference, no covariance as in: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G0V
But I am getting this error: mri_glmfit --y fc.lpccseed.surf.lh/L_PCC/ces.nii.gz --wls fc.lpccseed.surf.lh/L_PCC/cesvar.nii.gz --fsgd ../glm_file.fsgd --C ../group.diff.mtx --surface fsaverage lh --glmdir my-glm.wls --nii.gz gdfRead(): reading ../glm_file.fsgd Input line 1, subjid = HM-HR10-002Rest Group1, class Input not defined FSGDF Format Error: file = ../glm_file.fsgd, tag=Input
I am testing the pipeline so just 8 subjects so far. I've checked the ces.nii.gz and cesvar.nii.gz and both of them have correct dimensions of 163842 x 1 x 1 x 8.
Thank you for your help in advance.
fsdg_file is:* GroupDescriptorFile 1 Title OSGM Class Group1 Class Group2 Input HM-HR10-002Rest Group1 Input HM-HR10-005Rest Group1 Input HM-HR10-007Rest Group1 Input HM-HR10-010Rest Group1 Input PD0001Rest Group2 Input PD0002Rest Group2 Input PD0004Rest Group2 Input PD0005Rest Group2
*mtx file is:* 1 -1
宜しくお願い致します。*
Sincerely, Jarek Rokicki, Ph.D.
Integrative Brain Imaging Center (IBIC) National Center of Neurology and Psychiatry (NCNP) /4-1-1 Ogawahigashi-chyo, Kodaira, Tokyo 187-8551 Japan/
TEL: +81-80-6628-5709
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