Run recon-all on the mni152 T1 template that comes with SPM, project your VBM results to the surface of that (mri_vol2surf), binarize it if not already (mri_binarize), create a surface label (mri_cor2label with --surf option and --id 1), then use mri_label2label to map it to each subject, then use mris_anatomical_stats to compute summaries of thickness within your label.
doug On 09/04/2015 10:59 AM, Lim, Lena wrote: > > Thanks, Bruce. I ran the recon-all for all subjects before and then > did the group analysis using the mri-glmfit command and qdec. Sorry, I > don’t quite understand. What exact command do I use? > > Mri_label2label --srcsubject fsaverage --srclabel fsaverage/label/(spm > roi image file names?) --trgsubject PAC01 PAC02 PAC03…PAC70 –trglabel > PAC01 PAC02.. PAC70/label/(spm roi image file names?) --hemi lh > –regmethod surface > > How do I next do the group comparison on the ROI? > > Many thanks again, > > Lena > > *From:*freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Bruce > Fischl > *Sent:* 04 September 2015 15:25 > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Freesurfer ROI > > Hi Lena > > Sure, but you will need to run all your subjects through recon-all > first. The if the ROI is in MNI space you can use mri_label2label to > map it to our group space fsaverage. > Cheers > > Bruce > > > On Sep 4, 2015, at 9:27 AM, Lim, Lena <lena....@kcl.ac.uk > <mailto:lena....@kcl.ac.uk>> wrote: > > Sorry, I haven’t heard any replies so am re-posting this again for > help please: > > Dear Experts, > > I have 3 groups: A, PC, HC > > I did a VBM analysis in SPM and found group differences in grey > matter volume in 2 clusters: > > 1) Bilateral pre-/SMA, left middle/superior frontal gryi > > 2) left inferior/middle temporal/fusiform/inferior/middle > occipital gyri/superior/inferior posterior cerebellar lobe > > Is there any way I can use the SPM images to extract these ROI > regions to see if they differ in cortical thickness and surface > area please? > > Many thanks, > > Lena > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > 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: 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.
