Hi Carina, I still don't understand what you are trying to do. It looks like you have run the individual analysis (recon-all). Have you looked at the results for the individual? Do they look ok? QDEC is for group analysis, but you should make sure that the individuals look ok first doug
On 10/23/2013 10:48 AM, carina@van-vlodrop.de wrote:
Hi Doug,
maybe I created the brain correctly with the file I mentioned.
To try if there is the problem of a wrong brain or that there is a problem just in uploading it in qdec I heard something about an "example-brain" from freesurfer.
Maybe it is possible to tell me where I can find this brain to use it for my analysis in combination with my qdec table which I can upload without problems.
Carina
----- Ursprüngliche Nachricht -----
Von: Douglas N Greve Gesendet: 21.10.13 17:13 Uhr An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Problem in final analysis
fsaverage is already part of the distribution. I don't understand from your email what the problem is. doug
On 10/21/2013 10:03 AM, carina@van-vlodrop.de wrote:
Hi Doug,
I have already run:
recon-all -s subject -qcache -target avgsubject for each subject
Is it the same file?
I am not sure if the brain is really created or if there is a problem in uploading the brain in qdec.
Is it possible to get the fsaverage brain from freesurfer to check the cause of the problem?
Thank you
Carina
----- Ursprüngliche Nachricht ----- Von: Douglas Greve Gesendet: 28.09.13 17:46 Uhr An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Problem in final analysis
Hi Carina, run
recon-all -s subject -qcache
for each subject and this will create the file
doug
On 9/28/13 5:37 AM, carina@van-vlodrop.de wrote:
Dear freesurfer community, we are conducting cortical-thickness analysis using freesurfer-4.4.0 and have been experiencing some problems with the final analysis steps. We are using the qdec. Uploading of the data table has been successful. When we try to use the “Analyze” command (design) in the qdec, we get the following error message: Error in Analyze: Couldn’t open file
/data/projects/oertelmatura/Neurodegeneration/AJ83/surf/lh.thickness.fwhm10.fsaverage.mgh
Obviously, the file was never created during preprocessing. We wonder, how to create dir/lh.thickness.fwhm10.fsaverage.mgh and would be very grateful for your comments. Yours sincerely, Carina $ bugr FREESURFER_HOME: /apps/prod/i486/freesurfer-4.4.0 Build stamp: freesurfer-Linux-centos4-stable-pub-v4.4.0 Debian version: 5.0.6 Kernel info: Linux 2.6.27.39- 1 –ql-beowulf i686 $ which surfer -> /apps/prod/i486/freesurfer-4.4.0/bin/freesurfer Used command: qdec/design/Analyze Error message: Error in Analyze: Couldn’t open file
/data/projects/oertelmatura/Neurodegeneration/AJ83/surf/lh.thikness.fwhm10.fsaverage.mgh
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