Hello, group,
I am running longitudinal process step by step following the wiki page of
12 differences between longitudinal and recon-all process. But some needed
files are not generated by these 12 steps, for example, brain.mgz, wm.seg.mgz,
wm.asegedit.mgz, aseg.auto_noCCseg.mgz, wm.mgz,
Hi all,
I'm having trouble using freesurfer's tksurfer program (I only get a
sliver of the brain). Here is the error info I get:
[ghidra: subjects]$ tksurfer 77059 lh pial
surfer: current subjects dir: /home/freesurfer/subjects
surfer: not in "scripts" dir ==> using cwd for session root
su
Hi Matthew,
This is the typical symptom of either not having the right OpenGL
libraries and/or not having a driver that supports the 3d stuff. That
particular chip (ES1000) seems to be an orphan as far as Linux support
goes - I haven't found a driver installation package on the ATI/AMD
si
Hello,
I am running the following command in the standard environment:
tkregister2 --targ orig.mgz --mov
/space/amaebi/35/users/ablood/DMRF_ASL/CD_DMRFASL_pat3_sess1/bold/021/fmcsm4.bhdr
--reg
/space/amaebi/35/users/ablood/DMRF_ASL/CD_DMRFASL_pat3_sess1/bold/register.dat
this command has show
Just add --regheader and it will ignore the contents of the register.adt
file
[EMAIL PROTECTED] wrote:
Hello,
I am running the following command in the standard environment:
tkregister2 --targ orig.mgz --mov
/space/amaebi/35/users/ablood/DMRF_ASL/CD_DMRFASL_pat3_sess1/bold/021/fmcsm4.bhdr
-
Hello all, I have trouble to run FreeSurfer for under one year old baby subjects, the most frequently problems are two: one is stop to run without exit in mri_fix_topology, and other one is error exit on talairach_afd: Talairach Transform:FAILED Does someone know how to solve the problem? Th
You'll probably have to do the talairach registration by hand. See the
wiki for instructions.
doug
Yuan Xu wrote:
Hello all,
I have trouble to run FreeSurfer for under one year old baby
subjects, the most frequently problems are two: one is stop to run
without exit in mri_fix_topolo
On Saturday 06 September 2008 16:50:53 asaf achiron wrote:
>
> do you have a version that can run on windows (we have it in the hospital).
>
No, sorry - FreeSurfer is Linux and Mac only. We have looked at Windows
porting (using 'cygwin') but for now there is no Windows version.
The best solution
Running children brains that are less than about 3 yrs old through FreeSurfer
is not currently supported. Other than registration issues, because of
incomplete white matter myelination at this age, T1 contrast is either all
wrong from FreeSurfer's perspective, or inconsistent).
On Monday 08 S
Hong,
If you add -help to recon-all, it has a section on longitudinal
processing. longitudinal processing assumes your timepoint 1 subject
has already been processed by the normal stream (ie, recon-all -all -s
). That will produce the files you mention.
However, we have recently made significan
Hi Yuan,
I doubt things will work if the babies are much under 1 as the gray/white
contrast will either be inverted or nonexistent. You can turn off the
talairach failure detection, but things still may not work
cheers,
Bruce
On Mon, 8 Sep
2008, Yuan Xu wrote:
Hello all,
I have
Hello,
I would be very grateful if someone could help me with a few questions I
have regarding optseq 2:
1) If presenting a given stimulus multiple times (a la repetition reduction
experiments), can Optseq2 optimize stimulus presentation and if so, what is
the command to specify the number of rep
Matt Dixon wrote:
Hello,
I would be very grateful if someone could help me with a few questions
I have regarding optseq 2:
1) If presenting a given stimulus multiple times (a la repetition
reduction experiments), can Optseq2 optimize stimulus presentation and
if so, what is the command t
Greetings,
We are using fsaverage as the template for overlaying our group fMRI
data. Which annotation file should we use for designating ROIs?
There seem to be two options: lh.aparc.a2005s.annot and
lh.aparc.annot. And which atlas is each annotation file derived from?
Thank you,
Dara
D
aparc.annot is Rahul Desikan, et al's, and a2005s is Christophe
Destriux's. Both were derived from a group of brains labeled by hand.
They are fairly different in the detail (Christophe's is very detailed).
You can use either one.
Dara Manoach wrote:
Greetings,
We are using fsaverage as the
Thanks a lot for all my helper! Some of my baby subjects are from 5 month to one year old. I tried to use tkregister2 to do the talairach registration, but it did not help. Hi Bruce, could you please tell me how can I turn off the talairach failure detection? Thanks, Yuan
recon-al -notal-check
check recon-all -help. This stuff is documented there.
cheers,
Bruce
On Mon, 8 Sep 2008,
Yuan Xu wrote:
Thanks a lot for all my helper!
Some of my baby subjects are from 5 month to one year old. I tried
to use tkregister2 to do the talairach registratio
Hi Dara,
You can certainly use either one as Doug says, but depending on your
purposes, one or the other may have some virtues. 2005 consists of
discrete sulcal and gyral labels with traditional anatomical names so
there are a lot more labels (which is why Doug describes it as very
detailed), wh
for what it's worth we label the cc now explicitly in the aseg, which is
certainly more accurate than the aparc used to be.
Thanks for the detailed answer though Carl!
Bruce
On Mon, 8 Sep 2008
[EMAIL PROTECTED] wrote:
Hi Dara,
You can certainly use either one as Doug says, but depending o
Thanks very much for the detailed info Karl (and Doug and Bruce)!
My primary ROI is ACC, so we'll probably use Aparc with the cingulate
divisions. I'll have to review the paper to see if the anatomic bases
of the divisions are described. I'm surprised, though, that there is
not an insula lab
Hi Dara,
there is an insula label in the works (*lots* of people have asked this
question). Ron: any updates on the insula label?
thanks
Bruce
On Mon, 8 Sep 2008, Dara Manoach wrote:
Thanks very much for the detailed info Karl (and Doug and Bruce)!
My primary ROI is ACC, so we'll probably
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