Dear Freesurfer Folks,
I have returned to the problem of trying to extract T2 values from a T2-map using aseg & mri_segstats. When I attempt mri_segstats it only returns a small subset of the regions from aseg (see attached file). I would like to attach the T2 map but the file exceeds the 25mb limit for gmail (could I drop the file somewhere?) Could the T2 values need to be in a special format?
Thanks very much for your help.
Carl
On Thu, Dec 30, 2010 at 6:06 PM, Nick Schmansky <nicks@nmr.mgh.harvard.edu mailto:nicks@nmr.mgh.harvard.edu> wrote:
mri_segstats, for example:
mri_segstats --seg aseg.mgz \ --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \ --i T1.mgz \ --sum T1.stats
produces a text file 'T1.stats' which has stats on each aseg struct as taken from the vol T1.mgz.
n.
On Thu, 2010-12-30 at 17:52 -0500, Carl Anderson wrote:
Dear Freesurfer,
I have co-registered a map of whole brain T2-relaxation time
values to
the corresponding aseg.mgz for this subject (see attached jpegs). Does a tool exist in freesurfer to enable regional sampling of T2 values from the T2-relaxation time map based on aseg?
Thanks for any thoughts.
Hi Carl,
you can ftp it or filedrop it (both are detailed on the fs wiki site)
cheers Bruce On Tue, 15 May 2012, Carl Anderson wrote:
Dear Freesurfer Folks,
I have returned to the problem of trying to extract T2 values from a T2-map using aseg & mri_segstats. When I attempt mri_segstats it only returns a small subset of the regions from aseg (see attached file). I would like to attach the T2 map but the file exceeds the 25mb limit for gmail (could I drop the file somewhere?) Could the T2 values need to be in a special format?
Thanks very much for your help.
Carl
On Thu, Dec 30, 2010 at 6:06 PM, Nick Schmansky <nicks@nmr.mgh.harvard.edu <mailto:nicks@nmr.mgh.harvard.edu>> wrote: mri_segstats, for example: mri_segstats --seg aseg.mgz \ --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \ --i T1.mgz \ --sum T1.stats produces a text file 'T1.stats' which has stats on each aseg struct as taken from the vol T1.mgz. n. On Thu, 2010-12-30 at 17:52 -0500, Carl Anderson wrote: > Dear Freesurfer, > > > I have co-registered a map of whole brain T2-relaxation time values to > the corresponding aseg.mgz for this subject (see attached jpegs). > Does a tool exist in freesurfer to enable regional sampling of T2 > values from the T2-relaxation time map based on aseg? > > > Thanks for any thoughts. >-- <<?>>~<>~<<?>>~<>~<<?>>~<>~<<?>>~<>~<<?>>~<>~<<?>>~<>~<<?>>~<>~<<?>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfract@gmail.com; carl_anderson@hms.harvard.edu <<?>>~<>~<<?>>~<>~<<?>>~<>~<<?>>~<>~<<?>>~<>~<<?>>~<>~<<?>>~<>~<<?>>
p.s. what format is the attachment? It doesn't have an extension.... On Tue, 15 May 2012, Carl Anderson wrote:
Dear Freesurfer Folks,
I have returned to the problem of trying to extract T2 values from a T2-map using aseg & mri_segstats. When I attempt mri_segstats it only returns a small subset of the regions from aseg (see attached file). I would like to attach the T2 map but the file exceeds the 25mb limit for gmail (could I drop the file somewhere?) Could the T2 values need to be in a special format?
Thanks very much for your help.
Carl
On Thu, Dec 30, 2010 at 6:06 PM, Nick Schmansky <nicks@nmr.mgh.harvard.edu <mailto:nicks@nmr.mgh.harvard.edu>> wrote: mri_segstats, for example: mri_segstats --seg aseg.mgz \ --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \ --i T1.mgz \ --sum T1.stats produces a text file 'T1.stats' which has stats on each aseg struct as taken from the vol T1.mgz. n. On Thu, 2010-12-30 at 17:52 -0500, Carl Anderson wrote: > Dear Freesurfer, > > > I have co-registered a map of whole brain T2-relaxation time values to > the corresponding aseg.mgz for this subject (see attached jpegs). > Does a tool exist in freesurfer to enable regional sampling of T2 > values from the T2-relaxation time map based on aseg? > > > Thanks for any thoughts. >-- <<?>>~<>~<<?>>~<>~<<?>>~<>~<<?>>~<>~<<?>>~<>~<<?>>~<>~<<?>>~<>~<<?>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfract@gmail.com; carl_anderson@hms.harvard.edu <<?>>~<>~<<?>>~<>~<<?>>~<>~<<?>>~<>~<<?>>~<>~<<?>>~<>~<<?>>~<>~<<?>>
Hi Carl, those are all that are in the aseg.mgz. What more did you expect? doug
On 05/15/2012 03:44 PM, Carl Anderson wrote:
Dear Freesurfer Folks,
I have returned to the problem of trying to extract T2 values from a T2-map using aseg & mri_segstats. When I attempt mri_segstats it only returns a small subset of the regions from aseg (see attached file). I would like to attach the T2 map but the file exceeds the 25mb limit for gmail (could I drop the file somewhere?) Could the T2 values need to be in a special format?
Thanks very much for your help.
Carl
On Thu, Dec 30, 2010 at 6:06 PM, Nick Schmansky <nicks@nmr.mgh.harvard.edu mailto:nicks@nmr.mgh.harvard.edu <mailto:nicks@nmr.mgh.harvard.edu mailto:nicks@nmr.mgh.harvard.edu>> wrote:
mri_segstats, for example:
mri_segstats --seg aseg.mgz \ --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \ --i T1.mgz \ --sum T1.stats
produces a text file 'T1.stats' which has stats on each aseg struct as taken from the vol T1.mgz.
n.
On Thu, 2010-12-30 at 17:52 -0500, Carl Anderson wrote:
Dear Freesurfer,
I have co-registered a map of whole brain T2-relaxation time
values to
the corresponding aseg.mgz for this subject (see attached jpegs). Does a tool exist in freesurfer to enable regional sampling of T2 values from the T2-relaxation time map based on aseg?
Thanks for any thoughts.
-- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfract@gmail.com mailto:remfract@gmail.com; carl_anderson@hms.harvard.edu mailto:carl_anderson@hms.harvard.edu <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>
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