Hi Cathy,

I think the problem is when there are tabs AND spaces. Only spaces should also work. I can write some code (when I have time) that checks these things, maybe for the next release.

Best, Martin

On 05/22/2013 02:21 PM, Catherine Bois wrote:

Hi,

Thank you for your reply. I finally got it working today.thanks for your help=)! You say the qdec table should have only spaces; however they only seem to work when they are completely tab separated and not a single space? If there is accidently a space it will suddenly not work. Is there a way that can solve this problem that you can think of? It is very time consuming because suddenly it will jsut stop working and I need to start from scratch!

Quoting Martin Reuter mreuter@nmr.mgh.harvard.edu on Wed, 22 May 2013 14:08:44 -0400:

...

Hi Cathy,

it must be something else (I think). The mris_calc command looks weird ("--label " looks like the label is not passed, but a space instead, it then thinks 'mul' is a file).

qdecfinal is your qdec table? Make sure it contains only spaces to separate the fields. It should have at least these columns fsid fsid-base time

also in your command below, why are there "?" before do-label and time?

Unless you want to use the stack (within subject stack of thickness values), I would drop the --do-stack (maybe also drop do-avg or whatever else you don't need).

For debugging, I would create a directory, place a single subject there, create a new qdec table with only that subject and try again there. If it still happens , let me know.

Best, Martin

On 05/20/2013 10:25 AM, Catherine Bois wrote:

...

Dear Freesurfer experts,

I am trying to conduct the long_mris_slopes --qdec qdecfinal --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack ?do-label ?time time --qcache fsaverage command for my longitudinal processing. However I keep getting the error message:

mris_calc -o /directory/baseX/surf/lh.long.thickness-spc.fwhm0.mgh --label /directory/baseX/surf/lh.long.thickness-spc.fwhm0.mgh mul 100

mris_calc: Sorry, but I seem to have encountered an error. While accessing file 'mul',

I read online that this was due to a bug encountered in version 5.1, however I recently upgraded to version 5.3 and the error message persists. As my Long and base runs have been done in version 5.1 still, I was wondering whether in order to fix this problem the long and base runs need to be rerun with version 5.3, or whether the error I am encountering has another solution/ is caused by another problem entirely?

Thank you for your help,

Best Wishes,

Cathy

-- Martin Reuter, Ph.D. 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

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