Hi Paul,
thanks for your reply. I think the problem is that after editing the aseg.mgz
and rerunning -autorecon2-noaseg it doesn't update the aparc+aseg.mgz, so the
surfaces still cross.
Cheers, Clara
- Ursprüngliche Mail -
Von: silve...@gmx.com
An: freesurfer@nmr.mgh.harvard.edu
Hi FS experts,
In order to start FS I am sourcing the following script routinely:
#!/bin/tcsh
setenv FREESURFER_HOME /usr/local/freesurfer/stable5_3_0
setenv USE_STABLE5_3_0
setenv LD_LIBRARY_PATH /usr/lib64/GLoverride:/usr/lib/GLoverride
setenv FSENV_KEEP_PROMPT
setenv SUBJECTS_DIR
Perfect. Thanks Bruce!
On Thu, Apr 23, 2015 at 6:46 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
Hi Michael
you can use label2patch for this.
cheers
Bruce
On Wed, 22 Apr 2015, Michael Waskom wrote:
Hi Freesurfers,
Is there a way to generate patch files from surfaces outside of
Thank you. Much appreciated.
Cheers,
PB
On Wed, Apr 22, 2015 at 6:25 PM Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
yes, it is available with the FreeSurfer source code, which you can
download
doug
On 04/22/2015 04:30 PM, Patrick Beukema wrote:
Hi,
Is it possible to get the source
The version of freesurfer installed in /usr/local/freesurfer/stable5_3_0
is the same as the release and does not change, so it will not have the
updates.
The version of freesurfer installed in /usr/local/freesurfer/dev is
updated nightly and contains the updates to Tracula and the dmri_group
Have you tried these steps: http://wiki.centos.org/TipsAndTricks/NTFS
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fatma Zribi
[zribi.fa...@gmail.com]
Sent: Thursday, April 23, 2015 9:14 AM
To:
Hi André,
Could you send the command that you ran to produce this ouput? Also (just to
check), do you have permissions to read the b0_brain.nii.gz file, and is it
here:
/Applications/freesurfer/subjects/HC001/b0_brain.nii.gz
Thanks,
Lee
On Thu, 23 Apr 2015, André Schmidt wrote:
Dear Lee,
Hi,
We are working on the analysis step of a project, in which we are interested in
the brain activation pattern in response to five different body part movement.
We have done a group analysis using FSL (N=10), to see the average activation
pattern for each body part.
However, we are having
I don't think you want noaseg. Why not try autorecon2-cp so it starts
after the aseg but uses it?
cheers
Bruce
On Thu, 23 Apr 2015, Clara Kuehn wrote:
Hi Paul,
thanks for your reply. I think the problem is that after editing the aseg.mgz
and rerunning -autorecon2-noaseg it doesn't update
How do you draw the structure names that are present in aseg.stats and
aparc.stats files on Desikin Killiany or Destrieux Atlas?
For example, I want to draw lh_bankssts, rh_cunueus and lh_fusiform on
any suitable atlas with color scale corresponding to some result from my
study.
Are there any
Dear all,
Hi,
When i open freeview the images at the center of the screen dont let me see
an opne dialog,
for example when i want to add surface, the opening dialog go behind them
and i cant access the dialog.
Kind Regards
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Hi everybody,
I installed CentOS 6.6 in a machine without using internet connexion.
Everything is fine. I would like now to install Freesurfer and Tracula
mounting a NTFS partition from an external hard disk. also I note that I
can not copy Freesurfer in a FAT32 partition.
Actually I'm not sure
I would think autorecon2-cp autorecon3 would be fine, but maybe Martin can
comment?
On Wed, 22 Apr 2015, prasser
wrote:
Repost.Thanks.
On Mon, 20 Apr 2015 16:35:29 -0700 pras...@zoho.com wrote
Thank you again for your reply.
For editing aseg.mgz, as mentioned in
Hi Michael
you can use label2patch for this.
cheers
Bruce
On Wed, 22 Apr 2015, Michael Waskom wrote:
Hi Freesurfers,
Is there a way to generate patch files from surfaces outside of tksurfer? I'm
specifically
hoping that there is some tool that will allow me to use a label file to
define
no, sorry
Bruce
On Wed, 22 Apr 2015, Jon Alan Wieser wrote:
Dear freesurfer experts.
is it possible for tkmedit to display volumes in neuroscience format (R is R)
rather than
radiologic format (R is L)?
Thanks
Jon
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Freesurfer mailing list
Hi Noa
you need to look at the defects and fix the giant ones (e.g. wm connected
to skull or cerebellum). This is documented on the wiki - you need to
visualize the defects on the lh.inflated.nofix or lh.orig.nofix and either
add cps or edit the wm
cheers
Bruce
On Wed, 22 Apr 2015, Golan,
I think noaseg is a bit different as it will not use the aseg in
downstream processing. From the help:
-noaseg
Skips subcortical segmentation steps (same as -nosubcortseg), and does
not use aseg.presurf.mgz for inorm2, wm segmentation, or filling.
Use this flag for brains that do not support
For the approach below you need to edit both the aseg.mgz and brainmask.mgz and run -autorecon-pialfor each hemishphere individually.
Just make sure you keep a copy of the unedited brainmask.mgz and aseg.mgz so you can do both hemispheres.
Also, I think-autorecon2-noaseg andautorecon2-cp
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