-
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
-
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
Yes, if it finds it there, it will create the "2" instead of overwriting. You should not have to regenerate the average, but that should work now too.
Wen, Wei wrote:
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
You might have to delete the old cortex.label
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
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
Wen, Wei