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Dear Freesurfers,
I would like to use V1 labels (created with the Hinds method) for a
ROI-based analysis on data analyzed with FSL FEAT using FSL featquery.
I have not run a full recon-all segmentation, only recon-all -s subjid
-label-v1
I need to convert the labels to nifti volumes while
hi everyone
i run recon-all on some datasets using freesurfer version
5.1. Instead of having aparc.a2009s+aseg.mgz at the end of recon-all, i had
aparc.a2005s+aseg.mgz. what to do to have the good dataset (2009 instead of
2005)
thanks
Dear FreeSurfer Experts,
I would like to down-sample the pial surface of individual subjects to have the
same number of vertices as fsaverage6. I have done so using:
mri_surf2surf --hemi lh --srcsubject 'subjectID' --sval-xyz pial --trgsubject
fsaverage6 --trgicoorder 6 --trgsurfval
Take a look at mris_decimate:
~$mris_decimate -x
Help
NAME
mris_decimate
SYNOPSIS
mris_decimate [options] input surface output surface
DESCRIPTION
This program reduces the number of triangles in a surface and
outputs
the new
Hi Christine
I think you do it the same way, just using -sval instead of -sval-xyz
(since you are mapping a scalar field instead of the coordinates).
cheeers
Bruce
On Tue,
20 Dec 2011, Ecker, Christine wrote:
Dear FreeSurfer Experts,
I would like to down-sample the pial surface of
Hi Andreia,
The XhCortexVol measures in the aseg.stats of FS v5.1 are identical to:
`mris_volume Xh.pial` - `mris_volume Xh.white`
To my knowledge, that measure is therefore simply the difference of the
volume encapsulated by the two surfaces. My point was that the surface
inaccuracies in the
Many thanks for your reply.
Unfortunately the option -sval didn't work and it is still using the old
sphere.reg file.
I was however wondering whether mri_surf2surf already sorts vertices and
hence makes them comparable. For instance, is vertex 1 on the resampled
surface the closest match to
Hi Donald,
I have a paper almost published on the longitudinal stream including
several repeatability measures (although not everything that you ask
for). Let me know if you want to take a peek at it before it goes out. I
might be able to send a pre-print version.
Best, Martin
On Tue,
Hi,
I'm trying to move a bunch of partial FOV functional images (occipital
cortex only with oblique coronal slices) into common space. For each
subject, I have a registration file (register.dat) to register
functional images to anatomicals, and I'd like to incorporate the
talairach.xfm
I think this is due to the high DOF and probably high t-value causing
the significance in matlab to be computed as 0. This gets converted to
Inf (infinity) when the -log10(p) calculation is made, then the Inf gets
set to 0 when the volume is saved. The quick fix for you is to change
Hi Andrew, use mri_vol2vol with the --tal --talres 2 or 2mm option (or
--talres 1 for 1mm isotropic) option. This will put it into an MNI305
space. So something like
mri_vol2vol --reg register.dat --mov yourvolume.nii --tal --talres 2 --o
yourvolume.mni305.nii
If you did not create the
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