Dear all,
I must be missing something really obvious, but it seems my brains are flipped.
What I do:
- I have a highres structural scan, nii file format
- I convert it to a surface using recon-all
- Coregister the highres structural to the functional scan, so it is in the
voxel size and
Hello Doug,
Ah! this was the root of the problem. A conflict was generated with the
Stanford Vistasoft toolbox, which also contains a 'basename.m' file.
Once removed from the Matlab path list, selxavg3-sess behaves normally.
Thank you for the help!
Kind Regards,
Ivan Alvarez
PhD Student
Hi Gabriel,
have you asked the slicer folks about this?
Bruce
On Wed, 18 Jan 2012, Gabriel
Gonzalez Escamilla wrote:
Dear FS experts,
I'm trying to render the surfaces and volumetric data from FS into
3D-slicer, Because I've read on the net that is compatible with FS surfs and
images;
Hi Frank, we'll need a lot more detail. Are you doing all of this in
FreeSurfer? What are your command lines? How are you evaluating whether
volumes are flipped?
doug
Léoné wrote:
Dear all,
I must be missing something really obvious, but it seems my brains are
flipped. What I do:
- I
Hey Bruce,
Thank you for the informations.
May I ask you few additional questions?
A) In your answer to my first question you wrote you can also just look
at the map itself without
averaging over an ROI. What does this mean in reference to calculation of
the cortical thickness.
B) For my
OpenMP (depending how efficiently FreeSurfer can be parallelized) would be a
great benefit here.
I have no idea what's causing the centos4 vs. 5 results, but it might be
interesting to start collecting some performance data if enough people are
interested.
All the benchmark numbers I've
Pedro,
I've got a run going with the Intel compilers now (I'm assuming that's what
you meant?). Besides producing faster code, it will be interesting to see
whether the compilers have a noticeable result on the results.
Malcolm
On Wednesday 18 January 2012 12:14:42 Pedro Paulo de Magalhães
Dear all,
On the FS Tutorial/Diffusion the FA masked is defined as:
mri_mask $TUTORIAL_DIR/$subj/dtrecon/fa.nii \
$SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \
$TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgzand when it follows the resampling on
the CVS space I see:
mri_vol2vol --targ
mri_mask $TUTORIAL_DIR/$subj/dtrecon/fa.nii \
$SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \
$TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz
and when it follows the resampling on the CVS space I see:
mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \
--m3z
Malcolm,
I think it will be at least 10% faster. I messed with the Intel
compiler a couple years ago, but they wanted to charge a yearly fee for
its usage (mgh doesnt qualify as an academic user), so we nixed using
that compiler. also, fyi, I was unable to get the AMD compiler to build
the code
Hi,
Many thanks for your reply. Can ypu please advise me how I should calculate
the mask if I want to do the masking based upon intensity values found in the
fa image?
I tried to run (without wmparc) but it gave me error:
mri_mask $TUTORIAL_DIR/$subj/dtrecon/fa.nii \
fa-masked is a masked volume and not a segmentation file. A segmentation
file contains labels that correspond to certain anatomical areas. The
fa-masked file is the same as your fa volume but some background regions
are eliminated from it using the mask volume.
On Wed, 18 Jan 2012,
Yes, that is right.
On Wed, 18 Jan 2012, Antonella Kis wrote:
Thanks so much now I more clear. So based on my understanding when resampling
on CVS space we will use the nears interpolation if instead of the
fa-masked.mgz we have a segmentation volume such as wmparc.mgz or the
Yes, but then you would not use --reg
$TUTORIAL_DIR/$subj/dtrecon/register.dat
with mri_vol2vol.
--Lilla
On Wed, 18 Jan 2012, Antonella Kis wrote:
Finally I understood! THANKS so much Lilla!
So I can use the nearst interp if while resampling in the CVS space my input
(--mov) volume is
Is there a way to divide a surface label like V1 into equal parts (say 10
parts) either along its length or width and save each part as a separate label
? Drawing them in tkmedit is quite crude and not very accurate.
Please let me know.
Thanks
Ri
See: mris_divide_parcellation --help
On Wed, 18 Jan 2012, Ritobrato Datta wrote:
Is there a way to divide a surface label like V1 into equal parts (say 10
parts) either along its length or width and save each part as a separate
label ? Drawing them in tkmedit is quite crude and not very
Hi Ri
I wrote mris_divide_parcellation to divide up annotation units along
their primary eigenaxis. There isn't anything comparable for labels, so
you'll need to convert the label to an annotation to use it
cheers
Bruce
On Wed, 18 Jan
2012, Ritobrato Datta wrote:
Is there a way to divide a
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