Hi Bruce and others,
I completed the mri_annotation2label and mri_label2label(which used mask
created from the mri_binarize), but the result is the same as that without
mask.Here are my codes:
mri_binarize --i
Thank you Zeke, that seems to work all fine!
Best, Markus
2014-04-08 21:17 GMT+02:00 Z K zkauf...@nmr.mgh.harvard.edu:
Markus,
Thanks for pointing that out. I have added those files to the ftp link.
-Zeke
On 04/04/2014 04:16 PM, Markus Gschwind wrote:
Thank you Zeke,
What about
Allright! The only point I would like to emphasize is:
Regardless if option trilin or nearest is used I need to interpolate the
functional data to the structural image of the subject. This might be due to a
feature of the function build_sample_array in the mri_vol2surf source code.
In this
When running this :
recon-all -maskbfs -segmentation -fill -tessellate -s $SUBJECT_HighRes
mentionned on this page: http://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon
I get these :
mri_tessellate: max vertices 100 exceeded
recon-all -s Subject_12 exited with ERRORS at Thu Apr 10 11:16:42
Is it also possible to track the inflation all the way to the sphere? I was
hoping that I could take snapshots of equi-area intermediate forms as the
cortex is unfolded onto the sphere instead of stopping at the inflated cortex.
Thanks.
Date: Wed, 9 Apr 2014 08:31:46 -0400
From:
Dear all,
I want to use caudate and putamen as seed in surface to do PROBTRACK in
FSL.
For doing that, I acquired target surface which in the cortex seed
using kris_convert and label2surf script.
But I met some problems in extracting caudate and putamen in the
surface.
For creating corresponding wm segmentations to the rois derived from
mris_divide_parcellation, should mri_aparc2wmseg be used or should I follow
the steps outlined in this posting
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013471.html?
Thanks
Corinna
On Wed, Apr 9,
Use mri_aparc2aseg with the --labelwm option. Look in the recon-all.log
file for an example command line that generates wmparc.mgz
doug
On 04/10/2014 09:52 AM, Corinna Bauer wrote:
For creating corresponding wm segmentations to the rois derived from
mris_divide_parcellation, should
Hi Doug,
Following the example in recon-all.log, I tried this: mri_aparc2aseg --s
FGH_09112013 --labelwm --hypo-as-wm --rip-unknown --volmask --o
mri/wmdivided.mgz --annot aparc.split
and received and mgh Write error.mghWrite(mri/wmdivided.mgz, -1): could not
open file
On Thu, Apr 10, 2014
Please send the terminal output for mri_label2label
On 04/10/2014 02:16 AM, Rujing Zha wrote:
Hi Bruce and others,
I completed the mri_annotation2label and mri_label2label(which used
mask created from the mri_binarize), but the result is the same as
that without mask.Here are my codes:
I don't understand what the question is. If you need to interpolate,
then use --interp trilinear
doug
On 04/10/2014 04:36 AM, Joerg Pfannmoeller wrote:
Allright! The only point I would like to emphasize is:
Regardless if option trilin or nearest is used I need to interpolate the
functional
Hi Remi
I believe I upped that limit by an order of magnitude, which hopefully
would be enough? If so, Zeke can get you a new version
cheers
Bruce
On Thu, 10 Apr 2014, Remi Gau wrote:
When running this :
recon-all -maskbfs -segmentation -fill -tessellate -s $SUBJECT_HighRes
mentionned on
yes, many of our binaries take the -w n flag to write out a snapshot of
the minimization every nth step, including mris_sphere
cheers
Bruce
On Thu, 10 Apr 2014, Xuelong Zhao wrote:
Is it also possible to track the inflation all the way to the sphere? I was
hoping that
I could take
The caudate and putamen are not on the cortical surface. I'm confused as
to what you are trying to do.
On 04/10/2014 08:52 AM, gong jinnan wrote:
Dear all,
I want to use caudate and putamen as seed in surface to do PROBTRACK
in FSL.
For doing that, I acquired target surface which in the
no, I was in subjects_dir. Updated the command to this and it works now.
thanks.
mri_aparc2aseg --s FGH_09112013 --labelwm --hypo-as-wm --rip-unknown
--volmask --o FGH_09112013/mri/wmdivided.mgz --annot aparc.split
On Thu, Apr 10, 2014 at 11:24 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu
Hi Freesurfers,
Some of the Freesurfer annotations (specifically the Yeo atlases) have
multiple disconnected regions with the same label.
What's the best way to separate these annotations (or the labels produced
by mri_annotation2label) so that I can get multiple label files where each
label has
Hi
I just find out how to launch the command, it is in the terminal where
tksurfer is running, after the % sign. (I didn't understand what the tcl
window was meaning)
Best
Celine
Hi
I am sorry if my question is really basic, but I am choosing the seeds for
fsfast resting state connectivity
Post-doctoral Research Position at Columbia University
A postdoctoral research position is currently available at Columbia
University and the New York State Psychiatric Institute. Candidates must
have completed a PhD in clinical, developmental, or cognitive neuroscience,
or a related field.
Hi Andrea,
Take a look at the ?h.orig.nofix surfaces. Does it look like the wm edits
were picked up in those initial surfaces? Also, just check that the edits
to the wm.mgz were 255 and that there are no major disconnects anywhere.
-Louis
On Fri, 4 Apr 2014, Andrea Grant wrote:
I was
Hi all,
I am trying to extract vertexwise surface area values in an ascii files. For
that I am doing
mri_surf2surf --hemi ?h --srcsubject subject dir area --src_type curv
--trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv
mris_convert -c XYZ-area ?h.white XYZ-area.asc
However I am
Hi Andreas,
It is extremely different to get good registrations manually (as you
have to work in 3D and you only see 2D planes), and you'll most
certainly not be able to achieve the accuracy of an automated method
(especially not of robust_register/robust_template, which are pretty
damn
Hi Prof. Greve,
Thanks for your reply. Sorry, perhaps I have made some mistake in my
data analysis. I just want to show tractography results of basal ganglia in
surface space using FSL. Could transform fit_paths.nii.gz to surface be a brief
way?
In order to do mdi_vol2surf
Thanks for pointing this binary out- I didn't realize the user could access it
outside of recon-all.
I've
had a look at the fswiki for mris_sphere and it doesn't seem to be
complete. I used it in the following format but not sure if this is
correct:
mris_sphere -n 160 -w 20 -scale 1 lh.orig
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