Dear List, Sorry to be unclear in my questions. I had a fundamental misunderstanding which I hope to rectify.
(1) It appears that what is called the "freesurfer" coordinate system (tkregister) is represented by subject fsaverage. 3D coordinate vectors in label files generated for any subject's scan are in RAS coordinates in the fsaverage coordinate system. Is this correct? (2) Under the assumption that (1) is true, I have plotted the vectors from label files (ROI: lh.postcentral) from fsaverage's and two subjects' scans on axial slices extracted from $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz . Since all three are in the same coordinate system, no transformation was needed. The ROI for fsaverage's label file is plotted in black and appears to follow the gray/white boundary well. The other 2 are plotted in red and green and are in the neighborhood but not the same. Is this in line with what you would expect? Regards, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- > boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Thursday, March 12, 2015 4:25 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] follow up and double check: transform RAS vectors to > talaraich > > sorry, I don't know what you've done or what you are trying to do or what the > mri_info command is related to. Can you fill in the details? > > On 03/12/2015 04:20 PM, Krieger, Donald N. wrote: > > Do the results in the attached images make sense? > > Does it make sense that the transformation was obtained: mri_info --vox2ras- > fls ? > > > > Regards, > > > > Don > > > > > > Don Krieger, Ph.D. > > Department of Neurological Surgery > > University of Pittsburgh > > > > > >> -----Original Message----- > >> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- > >> boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > >> Sent: Thursday, March 12, 2015 3:44 PM > >> To: freesurfer@nmr.mgh.harvard.edu > >> Subject: Re: [Freesurfer] follow up and double check: transform RAS > >> vectors to talaraich > >> > >> what do you want us to check? > >> > >> On 03/12/2015 03:27 PM, Krieger, Donald N. wrote: > >>> Dear List, > >>> > >>> I've done a couple of spot checks which appear to work but want to > >>> double check with you. > >>> > >>> Attached are 5 axial cuts from fsaverage's orig.mgz 5 mm apart. > >>> > >>> The "white" surface vectors are shown in black for lh.postcentral. > >>> > >>> I also put all of the CC vectors from the aseg; these show on the > >>> lower 3 cuts. > >>> > >>> I've also put in red and green the lh.postcentral "white" surface > >>> vectors from two of my scans. > >>> > >>> What do you think? > >>> > >>> Regards, > >>> > >>> Don > >>> > >>> Signature0001 > >>> > >>> Don Krieger, Ph.D. > >>> > >>> Department of Neurological Surgery > >>> > >>> Universityof Pittsburgh > >>> > >>> (412)648-9654 Office > >>> > >>> (412)521-4431 Cell/Text > >>> > >>> > >>> > >>> _______________________________________________ > >>> 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. > > > > _______________________________________________ > > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
