Re: [Freesurfer] WM ROIs: Using wmparc.mgz from cvs_avg35_inMNI152 atlas
Sorry, I thought my original post would be somehow linked to the second one. Here it is: Dear Freesurfer experts, I would like to segment a WM skeleton I derived using FSL's TBSS into ROIs based on white matter regions as derived in the wmparc.mgz file. I thought of using the fsaverage subject, but it does not have the wmparc.mgz file; thus I plan to use the CVS atlas (cvs_avg35_inMNI152). My plan is to extract each relevant ROI from wmparc.mgz, transform it into a binary file in MNI space, then use it to mask my WM skeleton using fslstats. I used this example command to extract the left WM postcentral ROI: mri_extract_label /Applications/freesurfer/subjects/cvs_avg35_inMNI152/mri/wmparc.mgz 3022 wm-lh-postcentral.mgz Now I need to transform the resulting file into a binary file with the same orientation and space as the MNI152_1mm standard brain ($FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz) before using it with fslstats. Could you please point to me the commands in order to achieve this? Thank you. Estephan J. Moana-Filho, DDS, MS, PhD Clinical Assistant Professor TMD and Orofacial Pain Division U of MN School of Dentistry ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] WM ROIs: Using wmparc.mgz from cvs_avg35_inMNI152 atlas
Any suggestions? I've perused the freesurfer mailing list and couldn't find any advice specifically to this question. Estephan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] WM ROIs: Using wmparc.mgz from cvs_avg35_inMNI152 atlas
Dear Freesurfer experts, I would like to segment a WM skeleton I derived using FSL's TBSS into ROIs based on white matter regions as derived in the wmparc.mgz file. I thought of using the fsaverage subject, but it does not have the wmparc.mgz file; thus I plan to use the CVS atlas (cvs_avg35_inMNI152). My plan is to extract each relevant ROI from wmparc.mgz, transform it into a binary file in MNI space, then use it to mask my WM skeleton using fslstats. I used this example command to extract the left WM postcentral ROI: mri_extract_label /Applications/freesurfer/subjects/cvs_avg35_inMNI152/mri/wmparc.mgz 3022 wm-lh-postcentral.mgz Now I need to transform the resulting file into a binary file with the same orientation and space as the MNI152_1mm standard brain ($FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz) before using it with fslstats. Could you please point to me the commands in order to achieve this? Thank you. Estephan J. Moana-Filho, DDS, MS, PhD Clinical Assistant Professor TMD and Orofacial Pain Division U of MN School of Dentistry ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
