Dear Nick and Uri,
Thank you for your replies,
I'm not really into parallel processing and forgive me if I talk
nonsense :). From your stories I sketch the following possible
scenarios:
1. We use a sort of batch system. For instance, a Linux bash script with
10 recon-all commands or with 10 FSL
Nick and Uri: thank you for your replies,
I'm not really into parallel processing and forgive me if I talk
nonsense :). From your stories I sketch the following possible
scenarios:
1. We use a sort of batch system. For instance, a Linux bash script with
10 recon-all commands or with 10 FSL feat
Hello there,
I'm trying to resample some thickness difference maps using
mri_surf2surf. Unfortunately, I keep getting the following error:
---
[engram:Multispect] (nmr-std-env) mri_surf2surf --srcsubject 002_MEF_A \
--sval
$S
The source type is not curv but paint, so use --src_type paint. Even
better would be to use mgh, ie,
create lh.thickness_diff as an mgh instead of w (ie,
lh.thickness_diff.mgh). And then spec the output to be mgh as well. If
you use mgh, then there is no need to spec the format. The paint format
you can save individual labels by selecting the annotation unit you want
and saving it, or you can do them all using mri_annotation2label.
The vertices should be identical across the various surfaces as they all
have the same topology (except the *.nofix ones)
On Thu, 7
Dec 2006, Tao Song wr
I'll leave this for Doug. As for the label file, each annotation would be
in a different one, but I don't think it will match since there are
unknowns in the annotation and I don't think they go to a label file (do
they Doug?)
On Thu, 7 Dec 2006, T. Song wrote:
Thanks a lot, Bruce.
Another qu
Hi,
I have two questions:
1. I was wondering if the values of corpus callosum are useful
2. Why the values of the corpus callosum are included in the gray matter
data (.aparc.stat)? I need the volume/area of the corpus callosum and I
don't understand if the volume given by the stat file is the who
Hi Valentina,
If you are referring to the corpus callosum value from the *h.aparc.annot,
this region and the values associated with it are not accurate. Our
motivation in including the corpus callosum as a region of interest within
our gray matter parcellation atlas was simply as an anatomic p
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We have a SUN grid system at UCSF. I have some shell scripts for using
freesurfer on this type of grid. As said earlier, freesurfer does not
contain multi-threaded programs. Use of the grid is simply to run
multiple instances of freesurfer programs
Andries,
You are on-track with the first scenario. If you have the technical
skills and time to install the Sun Grid Engine, or PBS (which does
nearly the same thing), then the batch interface will be easy for others
to submit as many 'recon-all' instances as they want and will handle
balancing.
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