Hi,
We're getting the following error from recon-all:
command line:
pbsubmit -m etanski -c 'recon-all -s DODASD012 -all -i
/cluster/archive/300/siemens/TrioTim-35006-20120718-151622-227000/391000-15-01.dcm
-mail etan...@nmr.mgh.harvard.edu'
output:
...
...
mri_binarize --i
Hi,
Is it possible in matlab to get the volume index coordinates
corresponding to specific MNI coordiates?
Thanks,
Yigal
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The
Hi,
Is it possible to restrict FDR correction to gray matter in tkmedit?
Thanks
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Hi,
Is it possible to export a functional volume from individual brain space
to mni152, so it can be overlaid on the standard mni152 brain in fslview?
Thanks,
Yigal
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Hi,
There are some holes in fsaverage lh cingulate labels in the a2005s
annotation. For example, vertex 16631, between the cingulate gyrus and
sulcus is part of the superior frontal gyrus label. Same with vertices
20390 and 141081. Is that an error? This is a problem for us because it
creates
How do I convert between the two coordinate systems?
Yigal
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Hi,
Is it possible to convert a .w file to another format?
Thanks,
Yigal
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Hi,
Can you add comments to a paradigm file?
Thanks,
Yigal
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Hi,
In surface-based analysis, is it possible to create an ROI label that is
a circle of a certain radius around a given vertex?
Thanks,
Yigal
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Thanks, Doug. Also, how can this be done from an individual brain to
mni152? Do I need to use fsaverage as an intermediate?
Yigal
Douglas N Greve wrote:
Use $FREESURFER_HOME/average/mni152.register.dat and mri_vol2vol with
--inv
Yigal Agam wrote:
Hi,
What's the best way to convert
Hi,
What's the best way to convert an fsaverage volume into an MNI152 volume
that can be viewed on top of a standard brain
(MNI152_T1_2mm_brain.nii.gz) in fslview?
Thanks,
Yigal
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Hi all,
Is there a way to convert results that I have on fsaverage to average7?
I need to do that to be compatible with some average7 results that go
into the same paper. When I use mri_surf2surf, activation is displaced.
Any advice would be appreciated.
This is what I've done:
How about when viewing an mni152 volume in tkmedit - what should I use
as overlay-reg?
Douglas N Greve wrote:
you don't need to invert it, just use as is.
doug
Yigal Agam wrote:
Hi,
Does mni152.register.dat map from fsaverage to mni152 or vice versa?
Specifically, I'm using an fsaverage
Hi,
Does mni152.register.dat map from fsaverage to mni152 or vice versa?
Specifically, I'm using an fsaverage surface that I want to project onto
mni152 volume using surf2vol. Should I invert the matrix?
Thanks,
Yigal
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Hi,
I'm getting an NAN value for some surfaces but not for others. Any
ideas? Both surfaces below were generated using an identical process.
[yi...@schnook sph_sm20]$ pwd
/autofs/space/ventzl_001/users/SUBJECTS_DIR/mano010/bold/EMexec3/sph_sm20
[yi...@schnook sph_sm20]$ mris_fwhm --i
Hi,
When I run mri_surfcluster on a surface with 12 timepoints, how do I
know when each of the reported clusters occurred?
Thanks,
Yigal
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Hi,
I'm trying to convert corical thickness maps into a common space and
getting this error. Any ideas?
mri_surf2surf --srcsubject mano002_new --trgsubject fsaverage --hemi lh
--srcsurfval lh.thickness --trgsurfval
Hi,
If I have volume data in MNI subject space (produced using --tal option
in mri_vol2vol), how do I project it onto the surface in the same
subject space? There does not seem to be an equivalent tal option in
mri_vol2surf.
Thanks,
Yigal
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tksurfer fsaverage lh inflated
surfer: current subjects dir: /autofs/space/ventzl_001/users/SUBJECTS_DIR
surfer: not in scripts dir == using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /autofs/space/schnook_001/users/yigal/projects/functional
surfer: Reading
Hi,
I'm trying to use a TCL script that runs through every time point in a
surface. I'm using the following commands:
set gaLinkedVars(ftimepoint) 0 (or 1, 2, etc)
SendLinkedVarGroup overlay
But tksurfer is always showing point 0 (doesn't advance in time).
Similar TCL commands for fthresh
Hi,
Of all the files that selxavg3 generates inside the contrast folder,
only three are described in the wiki: ces.nii, cesvar.nii, and sig.nii.
Does anyone know the other files below represent? Also, which files are
used for subsequent group analyses?
cesmag.nii
fsig.nii
minsig.nii
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