hello all,
first time poster and apologize in advance if this question has been
addressed previously..
can someone provide an example script of how to use the mris_make_template
command?
I am mainly confused about what the input should be and what the output
should look like.
I've tried:
mris_
Hi All,
since the new version seems to be just around the corner, I would like to ask
nicely, if you could make sure the following functionality of
mri_motion_correct.fsl is restored? I am not sure whether this ever reached
anybody the first time I tried to send it, so I just resend it, please
Hey Bruce,
I've uploaded the data via ftp to:
transfer/incoming/EK_umn_052710.tar.gz
Please let me know if I can supply any further information. Thanks for
taking a look!
-Elias
On Thu, 2010-05-27 at 10:58 -0400, Bruce Fischl wrote:
> no idea. Can you tar and gzip the subject and put it on our
try using the aseg.auto_noCCseg.mgz as input
On Thu, 27 May 2010, Gonzalo Rojas
wrote:
Hi Bruce:
I test the command "mri_cc -aseg aseg.mgz -o test.mgz -t 5 patient", but I
get the message "mri_cc: volume
/usr/local/freesurfer/subjects/patient/mri/aseg.mgz already has CC in it"...
How c
Hi Bruce:
I test the command "mri_cc -aseg aseg.mgz -o test.mgz -t 5 patient",
but I get the message "mri_cc: volume
/usr/local/freesurfer/subjects/patient/mri/aseg.mgz already has CC in it"...
How can get the volumetry of corpus callosum in 5 sagital sliced for
example ?...
Sincerel
Hi,
I just came across a cortical parcellation issues (see attachment), which I got
when running
tksurfer M02111314 rh pial -annot aparc
There is a small-ish orange blob (belonging to the parstriangularis) seeming
to be misplaced slightly to the left onto the parsopercularis and I was
wonde
HI Andrew,
this should be generate by default by recon-all, so you should be all
set.
cheers
Bruce
On Thu, 27 May 2010, Bauer, Andrew J wrote:
> Hi,
>
> I know how to create annotation files via the "mris_ca_label" command.
> However, I'm curious as to HOW the following file is created (which
no idea. Can you tar and gzip the subject and put it on our filedrop?
thanks
Bruce
On
Thu, 27 May 2010, Elias Kersten wrote:
> One additional note: I had previously processed this subject through
> FreeSurfer version 4.0.2 without any problems. For some reason this
> problem only occurred upon
One additional note: I had previously processed this subject through
FreeSurfer version 4.0.2 without any problems. For some reason this
problem only occurred upon reprocessing with version 4.5.0. I batch
processed this subject with about 50 others, and the other subjects look
fine.
Any other su
Hi,
I know how to create annotation files via the "mris_ca_label" command. However,
I'm curious as to HOW the following file is created (which is found in the
"mri" folder of a subject), and WHEN it was created:
aparc.a2009s+aseg.mgz
I recently installed FS and I'm working only with the sample
Dear Freesurfer experts,
We are attempting to segment a template monkey brain.
The following is the command line input:
recon-all -i
/usr/local/freesurfer/subjects/template_2/mri/orig/MonkTempl_w81096_T1.nii.gz
-s template -all -notal-check -force -noaseg
It runs for a few hours and then we
Dear FS experts
One of our reviewers would like to know whether the FDR procedures as
implemented in FS on one hand and as implemented in SPM on the other hand
are comparable.
In FS, I think FDR is based on the height threshold (FDRp) and it is outside
of the random Gaussian field theory framewor
Dear all,
while I am doing my first steps using freesurfer, I am searching for a scalp
mesh, which I could use for the brainstorm toolbox. Is there a scalp mesh
produced during recon-all, which I can use for this purpose? Thanks for
every hint!
Marcel
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