Hi Eduardo, On 08/15/2012 04:24 PM, Eduardo Europa wrote: > Hello, > > I have two questions: > > First: > I made left hemisphere anatomical ROIs using the freesurfer cortical > parcellation atlas and fsaverage's data. However, when I convert these > ROIs from .mgz to an SPM-compatible format (.img), the LH ROIs show up > on the right. Any idea on how to resolve this problem? Use nifti instead of img. > > The ROIs I need are customized (i.e., I needed to merge some of the > areas, and did so via relabeling), but for simpler purposes let's just > say I used lh.BA44.label for now. Here are the commands I used: > > cd $FREESURFER_HOME/subjects/fsaverage > mri_label2vol --label label/lh.BA44.label --temp mri/T1.mgz --identity > --o lh.BA44.mgz > mri_convert lh.BA44.mgz lh.BA44.img > > Second: > I would like to normalize these anatomical ROIs to MNI space in SPM. > To do this I was thinking about taking fsaverage's anatomical file, > converting it to an SPM-compatible format, estimate the normalization > parameters from fsaverage's anatomical to SPM's T1 template, and then > writing those parameters to the anatomical ROIs. Therefore am I > correct in converting fsaverage's T1.mgz to .img since I am specifying > that as the template in the mri_label2vol above? If the ROIs are in fsaverage space (same as MNI305), then you can use mri_label2vol with $FREESURFER_HOME/average/mni152.register.dat to convert to mni152 space
doug > > Thanks! > > -- > Eduardo Europa > Ph.D. Student, Aphasia and Neurolinguistics Research Laboratory > President, Queer Pride Graduate Student Association > Co-Chair, Graduate Leadership Council > Member, LGBTQA Campus Advisory Network > > Northwestern University > Department of Communication Sciences and Disorders > Frances Searle Building > 2240 Campus Drive > Evanston, IL 60208-3570 > eur...@u.northwestern.edu <mailto:eur...@u.northwestern.edu> > > > > _______________________________________________ > 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
