Sorry for the delay. You should just run recon-all on $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz It will give you a wmparc.mgz which you can then use directly with the FSL output
doug On 05/26/2015 04:59 PM, Estephan J. Moana-Filho wrote: > Sorry, I thought my original post would be somehow linked to the > second one. Here it is: >> Dear Freesurfer experts, >> >> I would like to segment a WM skeleton I derived using FSL's TBSS into ROIs >> based on white matter regions as derived in the wmparc.mgz file. I thought of >> using the "fsaverage" subject, but it does not have the >> wmparc.mgz file; thus I plan to use the CVS atlas (cvs_avg35_inMNI152). My >> plan >> is to extract each relevant ROI from wmparc.mgz, transform it into a binary >> file in MNI space, then use it to mask my WM skeleton >> using fslstats. I used this example command to extract the left WM >> postcentral >> ROI: >> > mri_extract_label >> > /Applications/freesurfer/subjects/cvs_avg35_inMNI152/mri/wmparc.mgz 3022 >> > wm-lh-postcentral.mgz >> Now I need to transform the resulting file into a binary file with the same >> orientation and space as the MNI152_1mm standard brain >> ($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 > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
