Thanks for getting back so quickly and for the clear answers. I was able to get the axial slices out by using mri_convert --split to create a .nii file. ImageJ could read that in and reslice it.
Thanks again. 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 11:27 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] newbie questions: transform RAS vectors to talaraich > vectors and view > > > On 03/12/2015 09:54 AM, Krieger, Donald N. wrote: > > > > Dear List, > > > > I have sets of vectors in RAS coordinates from many volunteers. > > > > I want to transform them into coordinates for a standard volume. > > > > (1) I presume the standard volume that makes sense to use is orig.mgz > > in $FREESURFER_HOME/subjects/fsaverage/mri. Please confirm. > > > Yes > > > > (2)I presume that I can transform the vectors contained in subject N's > > .label files to talairaich coordinates using the transform in > > $FREESURFER_HOME/subjects/subjectN/mri/transforms/talairach.xfm. > > Please confirm. > > > Yes, though it is not easy to apply yourself. If you put the xyz into a label > file, > then you can use mri_label2label. Note that the xyz have to be in an FS > coordinate system. See > http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems > > > > (3)What tool can I use to convert orig.mgz into a sequence of axial > > cuts in some standard graphics format, e.g. gif, png, tiff? > > > I don't know of one. > > > > Thanks and best regards, > > > > Don > > > > Signature0001 > > > > Don Krieger, Ph.D. > > > > Department of Neurological Surgery > > > > Universityof Pittsburgh > > > > > > > > _______________________________________________ > > 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
