Hi Bruce,
That did it. Great. The output is mm^3? Thanks again.
Cheers,
-Morgan
Bruce Fischl wrote:
oops, there should only be one --in_center on the cmd line (followed by 0 0 0 ) On Tue, 24 Jul 2007, Morgan Hough wrote:
Hi Bruce,
I try this in $subject/mri but I get the following:
mri_convert --in_center --in_center 0 0 0 aseg.mgz aseg_test.mgz
mri_convert: error converting "--in_center" to a float for --in_center flag
type mri_convert -u for usage
Do I need to set the output datatype with -odt uchar or something like that?
Cheers,
-Morgan
Bruce Fischl wrote:
okay, I think I know what's happing. Try this and see if it fixes it:
from the subject's mri dir
mri_convert --in_center --in_center 0 0 0 aseg.mg aseg_test.mgz
then run
mris_wm_volume -aseg aseg_test.mgz $subject $hemi
On Tue, 24 Jul 2007, Morgan Hough wrote:
Morning Bruce,
I just checked this on a subject you already have there. I get the same result at NMR with this subject using the dev version of mris_wm_volume from /usr/local/freesurfer/dev/bin/mris_wm_volume which I think is the best match for the binary I have.
The subject is located at NMR at /autofs/homes/010/morgan/con_2878.
Cheers,
-Morgan
Bruce Fischl wrote:
works for me. Can you drop the subjects on our site? On Tue, 24 Jul 2007, Morgan Hough wrote:
Hi Bruce,
I am afraid the zero is all the output I get. Do I need an updated mris_volume as well perhaps?
Cheers,
-Morgan
Bruce Fischl wrote: > that looks like the correct usage. Can you send the entire > screen output? > On Fri, 20 Jul 2007, Morgan Hough wrote: > >> Hi Nick, >> >> Thanks for the tool. I am getting output of 0 with >> >>> mris_wm_volume con_2304 lh >> 0 >> >> This follows the usage as I see it. Am I using this wrong? >> >> Cheers, >> >> -Morgan >> >> Nick Schmansky wrote: >>> Morgan, >>> >>> I've posted mris_wm_volume for the various platforms at this >>> location: >>> >>> >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev >>> >>> >>> Nick >>> >>> On Thu, 2007-07-19 at 17:56 +0100, Morgan Hough wrote: >>> >>>> Would it be possible to post binaries of mris_wm_volume >>>> again? I believe this is the preferred tool to calculate the >>>> total white matter volume over the current aseg output. >>>> Thanks in advance. >>>> >>>> Cheers, >>>> >>>> -Morgan >>>> >>>> _______________________________________________ >>>> 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 >> >> >>