Hi Catherine,

what does mris_preproc --version give you?

Thanks, Martin

On Jun 20, 2013, at 4:27 AM, Catherine Bois C.Bois@sms.ed.ac.uk wrote:

Hi!

I am running 5.3...Typing freesurfer into the command window leads to;

You are running this version of FreeSurfer:

freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

This should be the correct version?

Best

Quoting Martin Reuter mreuter@nmr.mgh.harvard.edu on Wed, 19 Jun 2013 20:36:10 -0400:

...

Hi Catherine,

probably you are not using 5.3. otherwise it should recognize the --qdec-long flag. You can open mris_preproc and take a look (it is a text file), there should be a "qdec-long" if you search it.

Best, Martin

On Jun 17, 2013, at 12:04 PM, Catherine Bois C.Bois@sms.ed.ac.uk wrote:

...

Dear Freesurfer experts,

I am trying to prepare my data for linear mixed modeling using the matlab add ons, with this command

mris_preproc --qdec-long qdec.table.dat --target fsaverage --hemi lh --meas thickness --out lh.thickness.mgh

However I keep getting this error message ERROR: flag --qdec-long not recognized

I am using version 5.3 and read on the release notes that qdec-long only works with unix input text files (\n newline). I thought that was the format of my textfile, and also confused as to why the wrong format of the file would make the flag unrecognized as opposed to the textfile...I was also wondering whether the -long table needs to be "shrunk" to cross-sectional format as it does in the two stage model? I have attached an excerpt of my textfile qdec, would greatly appreciate help in establishing whether it is somehow the format of the textfile that is the problem?

Thank you very much for your help,

Best Wishes,

Cathy

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-- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

--------------------------------- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129

Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu