Sounds great, will try that! Again, thank you very much for your help! Bastian.
On 22 July 2014 01:53, Martin Reuter <mreu...@nmr.mgh.harvard.edu> wrote: > Hi Bastian, > > yes, lta are the (here rigid) transformations (dat files are deprecated). > > you can use mri_convert -at <lta> > > or mri_vol2vol for mapping images. > > I think, however, you are not interested in mapping images, but in ROI's > on the surface. > You can do the following: > > - draw/create the ROI in the base and use it on all the tp1.long.base > etc. (surfaces are in alignment). > - draw/create the ROI in the tp1.long.base and use it on all ohter time > points directly (again this works as surfaces are in alignment) > - map things non-linearly with mri_surf2surf > > You won't need the lta files for any of this. > > Best, Martin > > On 07/19/2014 01:45 AM, Bastian Cheng wrote: >> Thank you for clarification, Martin! >> >> Will do so and also try registration of base >> TP1.long etc. >> >> Does FS create registration files (.dat) for this purpose >> automatically? I found some *.lta files in the /mri/transfers folder >> of the base image but am not sure how to apply them (maybe >> tkregister2?) >> >> best regards, >> Bastian >> >> On 18 July 2014 23:00, Martin Reuter <mreu...@nmr.mgh.harvard.edu> wrote: >>> Hi Bastian, >>> >>> use the longitudinal base for it. Also, once your ROI is in that space >>> you can simply apply it in each long as they are in the same space as >>> the base. The registration of base >> TP1.long etc. probably only >>> changes results very little. >>> >>> Best, Martin >>> >>> >>> On 07/18/2014 10:45 AM, Bastian Cheng wrote: >>>> Dear Freesurfer-Experts, >>>> >>>> I am currently trying to measure Cortical Thickness of a >>>> Volume-defined ROI in a patient measured at 4 timepoints. >>>> >>>> Basically, I am interested in a ROI resulting from fMRI activation >>>> measured on Timepoint 1. >>>> I would then like to get thickness values in the same ROI for all >>>> Timepoints 1-4. >>>> >>>> I have read the instructions here: >>>> https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness >>>> this works. >>>> >>>> now, my idea is: >>>> >>>> ROI from TP1 >> register to base image of longit. recon. ("base") >>>> ROI from base >> TP1.long (from long recon) >>>> ROI from base >> TP2.long (from long recon) >>>> ROI from base >> TP3 long (from long recon) >>>> ROI from base >> TP4.long (from long recon) >>>> >>>> OR should I simpy map my ROI to fsaverage and project it back all >>>> individual timepoints? >>>> ROI from TP1 >> register to fsaverage >>>> ROI from fsaverage >> TP1 (not from long recon) >>>> ROI from fsaverage >> TP2 (not from long recon) >>>> etc. >>>> >>>> I understand that registration using the long. recon is more robust... >>>> >>>> Best regards, >>>> Bastian >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>> -- >>> Martin Reuter, Ph.D. >>> >>> Instructor in Neurology >>> Harvard Medical School >>> Assistant in Neuroscience >>> Dept. of Radiology, Massachusetts General Hospital >>> Dept. of Neurology, Massachusetts General Hospital >>> Research Affiliate >>> Computer Science and Artificial Intelligence Lab, >>> Dept. of Electrical Engineering and Computer Science, >>> Massachusetts Institute of Technology >>> >>> A.A.Martinos Center for Biomedical Imaging >>> 149 Thirteenth Street, Suite 2301 >>> Charlestown, MA 02129 >>> >>> Phone: +1-617-724-5652 >>> Email: >>> mreu...@nmr.mgh.harvard.edu >>> reu...@mit.edu >>> Web : http://reuter.mit.edu >>> >>> _______________________________________________ >>> 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 mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > -- > Martin Reuter, Ph.D. > > Instructor in Neurology > Harvard Medical School > Assistant in Neuroscience > Dept. of Radiology, Massachusetts General Hospital > Dept. of Neurology, Massachusetts General Hospital > Research Affiliate > Computer Science and Artificial Intelligence Lab, > Dept. of Electrical Engineering and Computer Science, > Massachusetts Institute of Technology > > A.A.Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, MA 02129 > > Phone: +1-617-724-5652 > Email: > mreu...@nmr.mgh.harvard.edu > reu...@mit.edu > Web : http://reuter.mit.edu > > _______________________________________________ > Freesurfer mailing list > 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
