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
>
>
> _______________________________________________
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> 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/

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