Many Thanks Doug for the reply. I figured out what the problem was. It was a trivial issue. I had an empty line after my contrasts in my text file and that tripped me off. I was basically practicing doing GLM and was following the pipeline flow exactly but with my data.

Regards Koushik

________________________________________ From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, December 23, 2011 11:20 AM To: Govindarajan, Koushik Athreya Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] GLM question

Hi Koushik, it's very hard to diagnose these problems with out more detailed information (eg, the command line, the FSGD file, and the contrast). Send those along and I'll see if I can figure out what went wrong. doug

Govindarajan, Koushik Athreya wrote:

Hello group,

     I am a new user of Freesurfer and just learning to process data through the pipeline. Sorry if this is an amateur question. I was just trying to look at cortical thickness differences between a patient group and a control group. So, my fsgd file would just list the input files and the corresponding diagnosis. Now, if I were to design a contrast matrix to look at cortical thickness differences between the 2 groups, I understand that I would have only 2 regressors . So, my contrast matrix would just be [-1 1]? I tried doing that and I got a matrix read error for the contrast file. Thanks in advance for your help.

Regards Koushik

---

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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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.