The error is in the fsgd file. Can you send it to me? On 03/24/2015 05:16 PM, Elrod, Christian - SJHMC wrote: > 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 > >
-- 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
