should be the same as when you use --regheader with tkregister
On 02/09/2018 11:24 PM, Rita Elena Loiotile wrote: > Hi, > > I just noticed that when I open my volume file in tksurfer using > --overlay it gives a better volume to surface mapping than when I do > mri_vol2surf. Do you know what .dat file is used implicitly when > tksurfer is called with a volume overlay? It also seems to work well > when the subject is fsaverage and when it is 32k_fs_LR. Thank you. > > On Wed, Apr 5, 2017 at 9:54 AM, Douglas Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > If you have a 3mm MNI152 space, then you should run bbregister to > fsaverage to create a new register.dat file. Alternatively, you > can register it directly to 32k_fs_LR and cut out the middle man > (make sure to use --9 to account for scaling). Please ignore my > comment about fsaverage. In that case it was actually fine. > > > > On 4/4/17 9:40 PM, Rita Elena Loiotile wrote: >> Hi Doug, >> >> Thanks for the email. It is in 3mm space, so I guess I should >> reslice. Can you please clarify the comment about fsaverage? >> Does the --mni152reg flag not apply to that subject? I'm not >> sure what you mean about the inclusion indicating ambiguity. >> >> Thanks again, >> Rita >> >> On Tue, Apr 4, 2017 at 9:21 PM, Douglas Greve >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> The --mni152reg flag is only appropriate if the mov file is >> in the 2mm mni152 space. The inclusion of fsaverage as the >> source subject indicates some ambiguity about this >> >> >> On 4/3/17 1:56 PM, Rita Elena Loiotile wrote: >>> Hi, >>> >>> I'm trying to compare analyses that I've done entirely on >>> the surface to analyses I've done in the volume. I'm >>> comparing the analyses by projecting the volume analyses to >>> the surface (HCP's 32k_fs_LR). >>> >>> The commands I'm using are: >>> mri_vol2surf --mov $niftiFile --mni152reg --hemi ${hemi} >>> --projfrac-max 0 1 0.2 --o ${giftiFile}.$hemi.gii; >>> mri_surf2surf --srcsubject fsaverage --srcsurfval >>> ${giftiFile}.$hemi.gii --trgsubject 32k_fs_LR --trgsurfval >>> ${giftiFile}.$hemi.gii --hemi ${hemi};It seems that the FSL >>> volumes look identical to the surface analysis, when mapped. >>> (Our surface analysis is mainly FSL-based, so this makes sense.) >>> The SPM mapping, however, looks very odd. It isn't just that >>> the intensity differs, but the localization of high >>> intensity areas also varies. It seems that everything is >>> shifted a bit superior and, possibly, posterior to the true >>> location (as seen on the surface analysis). >>> I'm wondering if I'm doing anything obviously wrong in my >>> command usage. The brains were normalized to the MNI ICBM >>> 152 template in SPM. I *think* it's suitable to use the >>> -mni152reg flag in the command. >>> >>> I can attach pictures of the comparison if you'd like. >>> >>> Thanks in advance, >>> Rita >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> _______________________________________________ Freesurfer >> mailing list Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <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 >> <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 mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <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 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
