Hi,
I am using recon-all and the norm.mgz's so far are only about half the
brain. I checked the input volumes and looked though the output to std and
everything seemed fine, so I am not sure what to do:
on machine vader
source /usr/local/freesurfer/nmr-std-env
setenv SUBJECTS_DIR /autofs/s
Is fsaverage used in recon-all processing?
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Vasanth,
When I tried to load the nu.mgz and brainmask.mgz into tkmedit it
complained that they weren't the same size. mri_info confirms this:
ukase [mri] mri_info nu.mgz
Volume information for nu.mgz
type: MGH
dimensions: 256 x 256 x 128
voxel sizes: 1., 1., 1.3300
No, it's only there for display purposes, it is not used in recon-all in
any way.
Sasha Wolosin wrote:
Is fsaverage used in recon-all processing?
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The materials in this e-mail are private and may contain Protected Health
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Hi Vasanth,
your orig.mgz hasn't been conformed. That is, it should be 1mm isotropic
in a 256^3 volume, but it's not:
mri_info /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/orig.mgz
Volume information for
/autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/orig.mgz
type:
Thanks Bruce and Jenni,
I see that I left out the conform step when going from rawavg.mgz to
orig.mgz. I was grad_unwarping the 00?.mgz's before averaging them, and I
started recon-all with the -nomc flag.
I conformed nu.mgz and it's norm.mgz is a full volume now.
Thanks,
Vasanth
On Fri,
Hi Freesurfer Help,
I am trying to get the wm.mgz file into matlab. Is there a way to change
the mgz into dicom format, or any othe matlab compatible formats?
Thanks,
Camilo
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Hi Camilo
[v,M,p] = load_mgh('wm.mgz');
will load the volume (v) into matlab, in addition to the vox2ras matrix M
and the MR parameters p. The .m file is in
$FREESURFER_HOME/matlab/load_mgh.m.
cheers,
Bruce
On Fri, 24 Mar 2006
[EMAIL PROTECTED] wrote:
Hi Freesurfer Help,
I am trying t
Or
v = MRIread('wm.mgz');
v is a struct, and v.vol will give you the volume.
Bruce Fischl wrote:
Hi Camilo
[v,M,p] = load_mgh('wm.mgz');
will load the volume (v) into matlab, in addition to the vox2ras
matrix M and the MR parameters p. The .m file is in
$FREESURFER_HOME/matlab/load_mgh.m
Hi Freesurfer help,
Thanks for the prompt response. I now am using the load_mgh function but
it is giving me the following error:
??? SWITCH expression must be a scalar or string constant.
Error in ==> load_mgh at 126
switch type
Does anyone have an idea why this is happening?
Thanks,
Camilo
did you add $FREESURFER_HOME/matlab to your matlab path? You probably
need to
On Fri, 24 Mar 2006 [EMAIL PROTECTED] wrote:
Hi Freesurfer help,
Thanks for the prompt response. I now am using the load_mgh function but
it is giving me the following error:
??? SWITCH expression must be a scalar o
Hello, I have subcortical segmentations from freesurfer. I have automatically extracted one of the segmented objects (binary). I need to get the grayscale map of the object and do not know how to register the segmented object with the original image (analyze) so it can be overlayed for masking?
you shouldn't have to register it - it will be in register. And what kind
of grayscale map do you mean?
On Fri, 24 Mar
2006, Shahabuddin Ansari wrote:
Hello,
I have subcortical segmentations from freesurfer. I have automatically
extracted one of the segmented objects (binary). I need to g
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