You can use mri_binarize with the --match option to spec the index, eg:
mri_binarize --i aseg.mgz --match 17 --o hippo.lh.nii
doug
Martin Ystad wrote:
Hi, I'd like to create binary masks in the nifti-format from each of
the subcortical segmentations in freesurfer, separately (one for
If you've reconned a subject, you can use the aparc+aseg.mgz volume.
doug
Ryan Scotton wrote:
Hi Freesurfers,
Some associates of mine are working on a pipeline that generates
cortical parcellations and we are looking to compare its measurements
to some measurements generated by the
I'm not sure. When I just tried it, it converted to .nii.gz. Maybe it
has to do with the version of fsl being used?
I'm posting this to the freesurfer listserv to see if anyone else has ideas.
Xu Cui wrote:
Thanks Kara. I tried fslmerge on my images and the result is a single
.img / .hdr
I'm trying to make a monkey template using mris_make_template. So
far, every time I run the mris_make_template, I get this error:
monkey.tif: Deflate compression support is not configured.
TiffWrite: TIFFWriteScanline returned error
___
Freesurfer
one way to do it is with mri_concat, something like
mri_concat f???.img --o f.nii.gz
if your individual volumes are f000.img f001.img etc
Kara Dyckman wrote:
I'm not sure. When I just tried it, it converted to .nii.gz. Maybe
it has to do with the version of fsl being used? I'm posting this
Which freesurfer distribution do you have?
On Fri, 2008-10-24 at 11:08 -0700, lan lin wrote:
I'm trying to make a monkey template using mris_make_template. So
far, every time I run the mris_make_template, I get this error:
monkey.tif: Deflate compression support is not configured.
Hello, I've recently started a project that involves measuring the
volume of the hippocampus and other subcortical structures, so I was
also wondering whether aseg.stats was more accurate or wmparc.stats. So
far the difference between them appears to be approximately a hundred
voxels for each
They should be exactly the same. If not, it's a bug. I just looked at a
few of mine, and they are the same.
doug
Kathy Zhang wrote:
Hello, I've recently started a project that involves measuring the
volume of the hippocampus and other subcortical structures, so I was
also wondering
You need to set up the psdwin to span the duration of a hemodynamic
response to your event as if it were presented in isolation. For a 3sec
event, you can probably use something like 24 sec (so min=0, max=24).
Since your TR=2, but your event duration is 3sec, I'd set dpsd=1 (so
that both the
