Hi Freesurfer Community,
I sent this message to the mailinglist a little bit ago. It never showed up in my mailbox, although it seems to have posted on the mailinglist website. Anyway, on the chance that it didn't mail out properly, I thought I'd resend it, as I still havent been able to figure out what I'm doing wrong.
Thanks! Emily
---------- Forwarded message ---------- From: Emily Cooper ecooper@uchicago.edu Date: Mar 9, 2007 2:27 PM Subject: mris_convert To: freesurfer@nmr.mgh.harvard.edu
Hi,
I have a question about using mris_convert to convert .asc to .mgh. I have a .mgh file I made with mri_vol2surf (target subject as fsaverage). I convert it to .asc using this command:
mris_convert -c 010.onerun.space.intval.lh.fsave.mgh /home/ecooper/subjects/fsaverage/surf/lh.white lh.010mg2txt.asc
then I try to convert it from .asc to .mgh using this command:
mris_convert -c lh.010mg2txt.asc /home/ecooper/subjects/fsaverage/surf/lh.white lh.010mg2txt2mg.mgh
but when I try to load the new .mgh (lh.010mg2txt2mg.mgh) in tksurfer as an overlay:
tksurfer fsaverage lh inflated &
I get this error:
% Loading tal xfm file /home/ecooper/subjects/fsaverage/surf/../mri/transforms/talairach.xfm MRIalloc: could not allocate 443 slices Cannot allocate memory
From the documentation of mris_convert, it seems that
lh.010mg2txt2mg.mgh should be identical to the original .mgh (010.onerun.space.intval.lh.fsave.mgh). Is mris_convert unable to convert .asc to .mgh? Or is there something wrong with my commands?
Thanks for your time! Emily
Sorry, fell thru the cracks the first time. Which version of freesurfer are you using? The stable versions do not allow writing of mgh files from mris_convert. I've put a new version here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_convert
See if that works
doug
Emily Cooper wrote:
Hi Freesurfer Community,
I sent this message to the mailinglist a little bit ago. It never showed up in my mailbox, although it seems to have posted on the mailinglist website. Anyway, on the chance that it didn't mail out properly, I thought I'd resend it, as I still havent been able to figure out what I'm doing wrong.
Thanks! Emily
---------- Forwarded message ---------- From: Emily Cooper ecooper@uchicago.edu Date: Mar 9, 2007 2:27 PM Subject: mris_convert To: freesurfer@nmr.mgh.harvard.edu
Hi,
I have a question about using mris_convert to convert .asc to .mgh. I have a .mgh file I made with mri_vol2surf (target subject as fsaverage). I convert it to .asc using this command:
mris_convert -c 010.onerun.space.intval.lh.fsave.mgh tkregister2/ /home/ecooper/subjects/fsaverage/surf/lh.white lh.010mg2txt.asc
then I try to convert it from .asc to .mgh using this command:
mris_convert -c lh.010mg2txt.asc /home/ecooper/subjects/fsaverage/surf/lh.white lh.010mg2txt2mg.mgh
but when I try to load the new .mgh (lh.010mg2txt2mg.mgh) in tksurfer as an overlay:
tksurfer fsaverage lh inflated &
I get this error:
% Loading tal xfm file /home/ecooper/subjects/fsaverage/surf/../mri/transforms/talairach.xfm MRIalloc: could not allocate 443 slices Cannot allocate memory
From the documentation of mris_convert, it seems that
lh.010mg2txt2mg.mgh should be identical to the original .mgh (010.onerun.space.intval.lh.fsave.mgh). Is mris_convert unable to convert .asc to .mgh? Or is there something wrong with my commands?
Thanks for your time! Emily _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
That version seems to do the trick! Thanks!
Emily
On 3/20/07, Doug Greve greve@nmr.mgh.harvard.edu wrote:
Sorry, fell thru the cracks the first time. Which version of freesurfer are you using? The stable versions do not allow writing of mgh files from mris_convert. I've put a new version here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_convert
See if that works
doug
Emily Cooper wrote:
Hi Freesurfer Community,
I sent this message to the mailinglist a little bit ago. It never showed up in my mailbox, although it seems to have posted on the mailinglist website. Anyway, on the chance that it didn't mail out properly, I thought I'd resend it, as I still havent been able to figure out what I'm doing wrong.
Thanks! Emily
---------- Forwarded message ---------- From: Emily Cooper ecooper@uchicago.edu Date: Mar 9, 2007 2:27 PM Subject: mris_convert To: freesurfer@nmr.mgh.harvard.edu
Hi,
I have a question about using mris_convert to convert .asc to .mgh. I have a .mgh file I made with mri_vol2surf (target subject as fsaverage). I convert it to .asc using this command:
mris_convert -c 010.onerun.space.intval.lh.fsave.mgh tkregister2/ /home/ecooper/subjects/fsaverage/surf/lh.white lh.010mg2txt.asc
then I try to convert it from .asc to .mgh using this command:
mris_convert -c lh.010mg2txt.asc /home/ecooper/subjects/fsaverage/surf/lh.white lh.010mg2txt2mg.mgh
but when I try to load the new .mgh (lh.010mg2txt2mg.mgh) in tksurfer as an overlay:
tksurfer fsaverage lh inflated &
I get this error:
% Loading tal xfm file /home/ecooper/subjects/fsaverage/surf/../mri/transforms/talairach.xfm MRIalloc: could not allocate 443 slices Cannot allocate memory
From the documentation of mris_convert, it seems that
lh.010mg2txt2mg.mgh should be identical to the original .mgh (010.onerun.space.intval.lh.fsave.mgh). Is mris_convert unable to convert .asc to .mgh? Or is there something wrong with my commands?
Thanks for your time! Emily _______________________________________________ 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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
Emily Cooper