Dear Freesurfers,
I would like to map my subject thickness data to the fsaverage subject, following ROI analyses, as described under step 4: http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness Before step 4, tksurfer showed me that registration from MNI to Freesurfer space of my ROI went well!
After that I would like to get thickness data using mri_segstats (step 5). However, Freesurfer indicates that the dimensions of my segmentation image (23406 x 1 x 7) are different from the dimensions of my input image (27307 x 1 x 6), and using mri_info suggests that sth seems to have gone wrong in step 4. I have searched in the Freesurfer archives and I understood that 23406 x 1 x 7 are the correct dimension values and followed the advise to use --reshape in the fourth step. This does however not change the dimensions (it still indicates in the Freesurfer output: Reshaping 6 (nvertices = 163842) which I guess should be Reshaping 7).
Any suggestions to solve this problem of different dimensions are very much appreciated!
Best Regards,
Ruthger Righart (PhD)
Institute for Stroke and Dementia Research (ISD) Klinikum der Universität München Max-Lebsche-Platz 30 81377 Munich | Germany
Ruthger.Righart@med.uni-muenchen.de
Try adding --reshape-factor 7
doug
Righart, Ruthger Dr. wrote:
Dear Freesurfers,
I would like to map my subject thickness data to the fsaverage subject, following ROI analyses, as described under step 4: http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness Before step 4, tksurfer showed me that registration from MNI to Freesurfer space of my ROI went well!
After that I would like to get thickness data using mri_segstats (step 5). However, Freesurfer indicates that the dimensions of my segmentation image (23406 x 1 x 7) are different from the dimensions of my input image (27307 x 1 x 6), and using mri_info suggests that sth seems to have gone wrong in step 4. I have searched in the Freesurfer archives and I understood that 23406 x 1 x 7 are the correct dimension values and followed the advise to use --reshape in the fourth step. This does however not change the dimensions (it still indicates in the Freesurfer output: Reshaping 6 (nvertices = 163842) which I guess should be Reshaping 7).
Any suggestions to solve this problem of different dimensions are very much appreciated!
Best Regards,
Ruthger Righart (PhD)
Institute for Stroke and Dementia Research (ISD) Klinikum der Universität München Max-Lebsche-Platz 30 81377 Munich | Germany
Ruthger.Righart@med.uni-muenchen.de
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Righart, Ruthger Dr.