Forwarding a previous answer from doug. I tried it before (and
recently). It does seem to work.
>>>
>>> Try running mri_annotation2label with --lobes lh.lobes.annot
>>>
>>> doug
>>>
>>>
>>> On Thu, 20 May 2010, Rudolph Pienaar wrote:
>>>
Hi all --
Is there a simple way to create a
Hi,
I am trying to downsample a 4D volume using mri_convert. However, it
seems to be killing the 4 dimension. For example, if I do
mri_convert -voxsize 4 4 4 tmp.mgz tmp444.mgz
The original volume which is 256 x 256 x 256 x 120 becomes 64 x 64 x 64.
Thanks,
Thomas
Hi,
is it possible to show all slices (or every N slices) of a volume in
freeview in a particular orientation (e.g. axial or coronal)?
Thanks,
Thomas
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yes. Thanks!
--Thomas
On Mar 18, 2010, at 10:37 AM, Ruopeng Wang wrote:
> You mean in light box (mosaic) style? No. I will put that on my
> features-to-consider list.
>
> Ruopeng
>
> On 3/18/10 10:34 AM, ythomas wrote:
>> Hi,
>>
>> is it possible to show
Hi Carrie,
I believe you just need to use the command "exit" at the end of the
tcl script to exit from tksurfer.
--Thomas
On Mar 18, 2010, at 5:43 PM, Carrie Niziolek wrote:
> Hello all,
>
> I've had great success using tcl scripts to loop over surfaces and
> overlays for a given subject. Ar
but does so in the recon-all.log file. You can find the failed subject
here:
/autofs/space/terrier_002/users/ythomas/GSP/failed_FS_subjects/
090620_JG49ZK_FS
Thanks,
Thomas
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I am a little out of the loop. Just to clarify, Marie is trying to
create an average subject out of 400+ subjects that have been run
through the freesurfer pipeline? I don't see a problem with that
(except possibly memory issues). If the subjects are from a
homogeneous population (whatever
Hi,
I am trying to run the fsfast tutorial, and I am getting the following
matlab error: Undefined function or method 'MRIwrite' for input
arguments of type 'struct'.
I ran the following commands:
nexlin7:ythomas[test_fsfast/fsfast-tutorial/my-study] pwd
/autofs/cl
Hi,
I have finished the 4.5.0 fsfast tutorial, and am wondering about the
structure-function registration part. Currently, the tutorial
recommends: fslregister-sess -s mgh-101.1. I notice that a single
register.dat is produced. How are the multiple runs being handled now?
Is only the first
Hi,
Is there an option to save snapshots in tksurfer with a white
background instead of the usual black?
Thanks,
Thomas
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The infor
Is this a preprocessed (whole brain regression, bandpass filter, etc)
rest-state volume? If so, I would suggest using the volume before the
preprocessing (which works well for me).
Thanks,
Thomas
On Jul 2, 2010, at 9:58 AM, Corey Keller wrote:
> Hi Bruce,
>
> Thanks for the info. I am trying
I believe the segmentation definitions can be found here:
http://www.cma.mgh.harvard.edu/manuals/segmentation/
--Thomas
On Aug 9, 2010, at 4:28 AM, leemon albert wrote:
> Dear Pedro, Dear Bruce,
> Dear all,
>
> In the previous discussion about VentralDC in the aseg stats file, I
> learned tha
Hi,
when we load a mri volume and a surface at the same time, such as:
freeview -v mri/norm.mgz -f surf/lh.white
should we expect to see the lh.white surface be on top of the norm.mgz
volume? I certainly do not see the surface unless I "unhighlight" the
volume.
Thanks,
Thomas
__
Hi,
when I try to load my own generated surfaces in freeview (e.g.
generated from cerebellum), I am getting the following printed errors
even though it did save out the images I want. Seems like freeview is
assuming that ?h.inflated, etc has the same dimensions as the surfaces
I am loading
Hi Guang,
the error message implies you probably do not have access to those
files or directory. You should probably ask a sysadmin to do it or if
you have admin access, you can probably do something like
sudo
The sudo command will prompt you type the root password.
--Thomas
On Aug 22,
owing command:
mri_vol2surf --regheader 090425_QF86JB_FS --mov /autofs/cluster/
con_003/users/ythomas/test_mri_vol2surf/090425_QF86JB_FS/data/
090425_QF86JB_vol2vol.nii.gz --hemi lh --projfrac .5 --trgsubject
fsaverage --o /autofs/cluster/con_003/users/ythomas/test_mri_vol2surf/
090425_QF86JB_FS
wrong (see details below)?
Thanks,
Thomas
On Sep 9, 2010, at 6:29 PM, ythomas wrote:
> Hi,
>
> I am trying to sample a volume of integers in subject's anatomical
> space to fsaverage surf. However, the output does not seem to be
> integer valued anymore even though
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