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
