On 3/13/15 10:10 AM, Krieger, Donald N. wrote: > 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? No, they are in tkregister-coordinates in the individual's conformed anatomical space (the coordinate system is defined by the way the col, row, and slice are converted into an XYZ) > (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? This is probably not correct since the labels from individuals will need to be transformed. Try using mri_label2label
> > 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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
