Dear Freesurfer Experts, Could youplease clarify whether the new freesurfer stable release version 3 is compatible with SuSE Linux 10.0 (kernel 2.6.13)? Many thanks, Venkat. Dr. Venkatasubramanian, Asst. Professor of Psychiatry, National Institute of Mental Health & Neurosciences,
Hi,
I have processed some of my subjects on a previously released
dev-version (20060210). I have changed to the new stable release. Do I
need to run the -autorecon1 step again, or will -autorecon2 and -3
suffice to bring the previously run subjects up to date? (the
brainmask-volumes have been
thank you very much Bruce,
but I would still like to know if there is anyway to build an mgz image of the
grey volume segmented accordingly to ?h.aparc.annot. I hope you can help me.
thanks,
-ste
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Tue 3/14/2
Freesurfer has not been tested against SuSE Linux 10.0 here at MGH.
I would recommend using either the 32bit or 64bit centos4 freesurfer
stable release with SuSE Linux 10.0 though.
On Wed, 2006-03-15 at 00:32 -0800, Venkat subramanian wrote:
> Dear Freesurfer Experts,
>
> Could youplease clarif
Martin,
The safe option is to run -autorecon1 again for these subjects. The new
stable release is careful to keep all edits (in fact, you have to tell
it not to keep edits via the -clean flag if you don't want to retain
edits).
Manually removing the optic nerve will not decrease processing time,
I just installed the new stable release on OSX.
Installation ran smoothly and I made the changes in .cshrc. On starting
freesurfer (‘csurf’), I receive the following error:
These binaries used by csurf not found in
/Applications/freesurfer/bin: paint
This binary is not in the direct
> but I would still like to know if there is anyway to build an mgz
> image of the grey volume segmented accordingly to ?h.aparc.annot. I
> hope you can help me.
In tksurfer, you can import an annotation as a segmentation file. This
will fill the voxels between surfaces with the label in the annot
I installed the freesurfer following exactly as the instructions on the
website. When I test it, "recon-all -s bert -all" doesn't work, it runs for
a few min. and shows "flirt: Command not found.
ERROR: running flirt". When I try to use my own data, convert dicom to mgt,
"mri_convert" command show
flirt is found in the directory $FSL_DIR, where FSL_DIR is the var set
when sourcing $FREESURFER_HOME/SetUpFreeSurfer.csh. What is the output
displayed after sourcing SetUpFreeSurfer.csh? And what distribution are
you using?
What is the mri_convert command line being used?
On Wed, 2006-03-15 at
Hi, I would like to translate a label created from an average subject
inflated surface to all the subjects. How would I do that? Should I first
use mri_surf2surf to resample the average subject inflated surface to all
the other subjects? Would a label that was created on the average subject
then
Freesurfers
I was hoping someone else would do this, but well, it seems that no one
did. So I went ahead and made this myself.
Amusingly, I don't NEED to reconstruct any brains right now, so I don't
have anything to test this out with.
Please someone try it, and let me know if it is helpful.
Hi Jon,
You should use mri_label2label.
mri_label2label --help will give you usage and examples.
Jenni
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Jonathan Wisco
Sent: Wednesday, March 15, 2006 5:50 PM
To: Freesurfer
Subject: [Freesurfer] Translat
recon-all already creates such a volume. Look at aparc+aseg.mgz. You
can load it as a segmentation, same as aseg.mgz
On Wed, 15 Mar 2006, Kevin Teich wrote:
but I would still like to know if there is anyway to build an mgz
image of the grey volume segmented accordingly to ?h.aparc.annot. I
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