Dear Freesurfer Users, We have a little problem with mri_surf2surf. Our goal is to determine the statistical data - t-test, ANOVA, for a group of subjects. So initially we made the recon-all, autorecon1,2,3 and -qcache for all subjects. After that we created the FSGD file and mris_preproc - in order to create ?h.thickness.mgh file. Now in order to initiate the mri_glmfit step we have to create the ?h.thickness.sm10.mgh file with the mri_surf2surf command.
We used this command line: mri_surf2surf --hemi lh \ --s average \ --sval lh.thickness.mgh \ --fwhm 10 \ --tval lh.thickness.sm10.mgh
and we receive the Error: – /usr/local/freesurfer/subjects/average/surf/lh.sphere.reg – could not open file
Could you please tell us where might be the mistake ? What step is needed to create the lh.sphere.reg file. Thank you very much for your help.
Best regards, Dr. Alexandru Hanganu ___________________________________
Department of Neurology, Schleswig-Holstein University Hospital, Kiel Campus Arnold-Heller-Str. 3, building no. 41 D-24105 Kiel, Germany.
did you create a subject called "average"? This is done with make_average_subject. Alternatively, we distribute an average subject called fsaverage, so you can just use that instead if you want.
doug
Alexandru Hanganu wrote:
Dear Freesurfer Users, We have a little problem with mri_surf2surf. Our goal is to determine the statistical data - t-test, ANOVA, for a group of subjects. So initially we made the recon-all, autorecon1,2,3 and -qcache for all subjects. After that we created the FSGD file and mris_preproc - in order to create ?h.thickness.mgh file. Now in order to initiate the mri_glmfit step we have to create the ?h.thickness.sm10..mgh file with the mri_surf2surf command.
We used this command line:
mri_surf2surf --hemi lh \ --s average \ --sval lh.thickness.mgh \ --fwhm 10 \ --tval lh.thickness.sm10.mgh
and we receive the Error: – /usr/local/freesurfer/subjects/average/surf/lh.sphere.reg – could not open file
Could you please tell us where might be the mistake ? What step is needed to create the lh.sphere.reg file. Thank you very much for your help.
Best regards, Dr. Alexandru Hanganu ___________________________________
Department of Neurology, Schleswig-Holstein University Hospital, Kiel Campus Arnold-Heller-Str. 3, building no. 41 D-24105 Kiel, Germany.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Doug, Thank you very much for your quick response. Following your advice, I deleted the previous "average"subject and created a new "average" subject. But now the Error is the same as it was for "fsaverage". When using the command line: mri_surf2surf --hemi lh \ --s average \ ...
or
mri_surf2surf --hemi lh \ --s fsaverage \ ...
ERROR: Option --s unknown
instead of "--s" I also tryed other command lines: --srcsubject average
I am using FS version: centos4-stable-pub-v4.0.5-full
Thank you for your help. Sincerely, Alex.
________________________________ Von: Doug Greve greve@nmr.mgh.harvard.edu An: Alexandru Hanganu hanganu.alexandru@yahoo.de CC: FS Mailing List Freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, den 18. November 2008, 19:39:04 Uhr Betreff: Re: [Freesurfer] mri_surf2surf - Error
did you create a subject called "average"? This is done with make_average_subject. Alternatively, we distribute an average subject called fsaverage, so you can just use that instead if you want.
doug
Alexandru Hanganu wrote:
Dear Freesurfer Users, We have a little problem with mri_surf2surf. Our goal is to determine the statistical data - t-test, ANOVA, for a group of subjects. So initially we made the recon-all, autorecon1,2,3 and -qcache for all subjects. After that we created the FSGD file and mris_preproc - in order to create ?h.thickness.mgh file. Now in order to initiate the mri_glmfit step we have to create the ?h.thickness.sm10..mgh file with the mri_surf2surf command.
We used this command line: mri_surf2surf --hemi lh \ --s average \ --sval lh.thickness.mgh \ --fwhm 10 \ --tval lh.thickness.sm10.mgh
and we receive the Error: – /usr/local/freesurfer/ subjects/average/surf/lh. sphere..reg – could not open fileCould you please tell us where might be the mistake ? What step is needed to create the lh.sphere.reg file. Thank you very much for your help.
Best regards, Dr. Alexandru Hanganu ___________________________________ Department of Neurology, Schleswig-Holstein University Hospital, Kiel Campus Arnold-Heller-Str. 3, building no. 41 D-24105 Kiel, Germany.
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Doug Greve