-
Hi Doug,
Perhaps it was this: after "make_cortex_label" instead of replacing the original "lh.cortex.label" with this newly generated one, it creates "lh.cortex2.label". I renamed this "lh.cortex2.label" into "lh.cortex.label" and so far so good.
Perhaps we need to regenerate the average anyway in such case. I will let you know if there is any problem even after regenerating the "average".
Many thanks Doug for your help!
Wei Wen
Wen, Wei wrote:
Hi Doug,
I ran make_cortex_label (that went through) for my average subject which was mas_average and tried qdec again but still the same message:
mri_glmfit: could not parse 149955th line in /home/wei/working/tmp/ThicknessTest/mas_average/label/lh.cortex.label ERROR reading /home/wei/working/tmp/ThicknessTest/mas_average/label/lh.cortex.label Error in Analyze: command failed: mri_glmfit --y /home/wei/working/tmp/ThicknessTest/qdec/lh_thickness_sex_10/y.mgh --fsgd /home/wei/working/tmp/ThicknessTest/qdec/lh_thickness_sex_10/qdec.fsgd --glmdir /home/wei/working/tmp/ThicknessTest/qdec/lh_thickness_sex_10 --surf mas_average lh --label /home/wei/working/tmp/ThicknessTest/mas_average/label/lh.cortex.label --C /home/wei/working/tmp/ThicknessTest/qdec/lh_thickness_sex_10/contrasts/Avg-Intercept-thickness.mat --C /home/wei/working/tmp/ThicknessTest/qdec/lh_thickness_sex_10/contrasts/Diff-Female-Male-Intercept-thickness.mat
I am now rerunning the average step and see what will happen next.
Wei Wen
Doug Greve wrote:
I think you can just run make_cortex_label for your average subject.
Wen, Wei wrote:
Thanks Doug.
Do I need to rerun everything or at least rerun the average step? I went straight into qdec but the same error message appears (after replacing the old mri-mergelabels with the one just downloaded.
Wei Wen
Doug Greve wrote:
This may be a problem with the way that the unix tail command is implemented in newer OSs. Try copying this file:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_mergelabels
into $FREESURFER_HOME/bin
doug
Wen, Wei wrote:
Hi
FOrgot to attach the file of lh.cortex.label with my last email. Here it is.
My error message is the same as Sky's: see http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07271.html
Looked like there was no solution for it at the time (April 17th, 2008), what about now please?
"mri_glmfit: could not parse 149955th line in /home/wei/working/tmp/ThicknessTest/mas_average/label/lh.cortex.label"
here I have attached the file for you to have a look. Also, I got the same error message while trying to load that file using tksurfer. I am using your latest version: 4.0.3.
Many thanks and regards,
Wei Wen
_______________________________________________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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting