Hi,
I have produced retinotopic maps using the FS-Fast retinotopy
processing stream for individual subjects. I was wondering if anyone
has advice regarding how to average these retinotopic maps across
subjects, in order to produce a group average retinotopic map?
(something surface-based would be
you can do this "manually" in tksurfer using the custom-fill tool. Not
sure if there is any commandline way to do it.
Bruce
On Wed, 31 Mar 2010, Dankner,
Nathan (NIH/NIMH) [F] wrote:
> Hi All,
>
> I'm sure this information is on the website somewhere, but I had a hard time
> finding it. Is the
use mris_label2annot, like this:
set cmd=(mris_label2annot \
--s $s \
--hemi $h \
--ctab $SUBJECTS_DIR/scripts/colortable.txt \
--l $h.oasis.chubs.ifc.label \
--l $h.oasis.chubs.ipc.label \
-
Hi All,
I'm sure this information is on the website somewhere, but I had a hard time
finding it. Is there a way to consolidate 2 or more labels into one
annotation? I am attempting to load two cluster labels onto the difference map
in qdec for the purposes of making a figure, but I cannot loa
Hello, Bruce,
I'd like to send you this subject data, could you please let me know where I
can drop it?
Thanks!
Guang
> Date: Wed, 31 Mar 2010 08:44:42 -0400
> From: fis...@nmr.mgh.harvard.edu
> To: freesurfer...@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] FW:
Hey my brother .. For the love of God Let this nonsense in the Writing Well,
help me ..
I was stuck in Turkey .. My only wish for it from you, on that ..
Harvard.edu end of an e-mail address is ending as I want .. But unfortunately I
can not get such an e-mail address .. Please help me on this
Hi,
To run bbregister outside of the recon stream, I tried:
setenv SUBJECTS_DIR /autofs/space/brownie_003/users/gcoombs/SUBJECTS_DIR
cd $SUBJECTS_DIR
bbregister --mov mri/nu.mgz --int ../mni305.cor.mgz --reg
mri/transforms/talairachTEST.xfm --init-spm --t1 --s amac_TEST --tmp ./TEMP
but when I t
Hi Becca,
try putting the -s first:
mri_label_volume -s HRDEVtest.txt mri/test/mgz 1 2
cheers
Bruce
On Wed, 31 Mar 2010,
Rebecca Dautoff wrote:
> I have hand drawn labels that I want to find volumes for. I used
> mri_label2vol to create a .mgz mask of the label and am now using
> mri_label_
I have hand drawn labels that I want to find volumes for. I used
mri_label2vol to create a .mgz mask of the label and am now using
mri_label_volume to extract the volumes. it looks like the -s flag should
output in a spreadsheet (I am assuming similar to asegstats2table) but i
cant seem to get an o
Hi Guang,
hard to say from just images, but it looks like those voxels are a lot
darker than the rest of the gray matter. Did you visualize the surfaces?
They may be voxels that contain a bunch of csf - if you look at them in
another plane you could tell.
cheers,
Bruce
On Wed, 31 Mar 2010, G
recon-all -s subjid -make qcache
should work
On Wed, 2010-03-31 at 10:49 -0400, Hui J Yu wrote:
> Dear freesurfer users,
>
> After running recon-all for all subjects, I started running qcache
> using the following commands:
>
> (in the subject directory)
> foreach i (*)
> recon-all -s $i -qcac
Dear freesurfer users,
After running recon-all for all subjects, I started running qcache using the
following commands:
(in the subject directory)
foreach i (*)
recon-all -s $i -qcache
end
However, the process was terminated/stopped. Is there a way to resume the
process (like what you will ha
Hi Guang,
yes, it looks like the segmentation didn't do a great job on your data.
if you send us the orig.mgz we'll take a look (or the individual runs
00?.mgz in the orig dir if you have more than one). You could copy the SPM
results to wm.mgz and proceed from there I think, or you can use the
13 matches
Mail list logo
