p.s. future versions of mris_wm_volume won't need this
On Tue, 24 Jul 2007,
Morgan Hough wrote:
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
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