Dr. Greve, Thank you for your response. I am not using a windows machine for freesurfer but a Mac with OS 10.8.5 running Freesurfer V 5.3.0. I created a new .fsgd as outlined in your previous response and am still receiving an identical error message. Is it possible that there is an error with my contrast file?
ABIDE_10k_2.mtx -1 1 1 -1 0 0 0 0 Taylor Elrod Research Assistant Human Brain Imaging Lab Barrow Neurological Institute Dignity Health St. Joseph's Hospital and Medical Center 222 West Thomas Rd Phoenix, AZ 85013 (O) 602-746-4494 (C) 804-399-8674 ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, March 23, 2015 9:32 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] GLM_Fit Question The format of the fsgd file looks ok, but I suspect that there is a platform issue. How did you create it? Under windows? You can try something like cat your.fsgd | sed 's/\\r/\\n/g' > new.your.fsgd use new.your.fsgd and see if this fixes the problem. On 03/20/2015 02:48 PM, Elrod, Christian - SJHMC wrote: > Hello Freesurfer Group, > > I have a question regarding an error that I have been receiving when > attempting to set up an analysis involving 4 groups of subjects with data > coming from 2 separate scanning sites. The error is "ERROR: gdfReadV1: Found > 7 variables, expected 1". This is how it appears in terminal when coding for > GLM_fit: > > drs-mac-pro:ABIDE_10K_2 FMRI$ mri_glmfit --y lh.ABIDE_10K_2.00.mgh --fsgd > ABIDE_10K_2.fsgd dods --C ABIDE_10k_2.mtx --surf fsaverage lh --cortex > gdfReadHeader: reading ABIDE_10K_2.fsgd > ERROR: gdfReadV1: Input line 1, subjid = 51480_out > Found 7 variables, expected. 1 > FSGDF Format Error: file = ABIDE_10K_2.fsgd, tag=Input > > > However, in the fsgd file, modeled after the example shown here ( > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V ) for 4 groups with one > co-variate, I have only established one variable (to my knowledge) and cannot > seem to figure out why I keep receiving this error. Here is a copy of the > beginning of the fsgd file that is being utilized for the mri_glmfit command: > > GroupDescriptorFile 1 > Title ABIDE_ASD_X_Age > Class ControlYoung > Class ControlOld > Class ASDYoung > Class ASDOld > Variables Site > Input 51480_out ControlYoung 1 > Input 51484_out ControlYoung 1 > Input 51485_out ControlYoung 1 > Input 50657_out ControlYoung 1 > Input 50688_out ControlYoung 1 > Input 50699_out ControlYoung 1 > Input 51333_out ControlYoung 1 > Input 10006_FSoutput ControlOld 2 > Input 10009_FSoutput ControlOld 2 > Input 10011_FSoutput ControlOld 2 > Input 10013_FSoutput ControlOld 2 > Input 10014_FSoutput ControlOld 2 > ..... > > Any help or suggestions would be greatly appreciated. > > Thanks, > Taylor Elrod > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
