Hi,
For some subjects' data, pure Csurf GUI works, while for other subjects
Csurf GUI complains, giving errors during "create surface", upon which I
have to run the command-line option "recon-all -stage1" with CC and pons
coordinates.
Is it ture, I mean the Csurf GUI is unpredictable, because of
Hi Nam,
this depends on the quality of the scans, the subject positioning, and
the quality of the MNI talairaching.
Bruce
On Wed, 5 Jan 2005, Joongnam Yang
wrote:
Hi,
For some subjects' data, pure Csurf GUI works, while for other subjects
Csurf GUI complains, giving errors during "create surfac
Nam, did the command-lines work for those same subjects for which the
GUI failed? I prefer the command-line operation, in any case.
> Hi Nam,
>
> this depends on the quality of the scans, the subject positioning, and
> the quality of the MNI talairaching.
>
> Bruce
>
> On Wed, 5 Jan 2005, J
Hi,
For another subject,
the inflated surfaces for left and right are not right after "create
surface" in csurf GUI. They are not symmetrically cut.
The brain seems to have been cut not through the midline, but
a notch toward left hemisphere.
When I looked at wm or T1 surfaces, they show that t
specify the point manually with mri_fill -c ...
On Wed, 5 Jan 2005, Joongnam
Yang wrote:
Hi,
For another subject,
the inflated surfaces for left and right are not right after "create
surface" in csurf GUI. They are not symmetrically cut.
The brain seems to have been cut not through the midline,
Hi,
Sounds like trivial questions...
(1) How do you check if the talairach.xfm is OK?
(2) Either during the command-line option of recon-all -stage 1 thru 4,
when do you use tkregister2 for registeration?
Thanks for the help.
Nam.
___
Freesurfer mail
On Wed, 5 Jan 2005, Joongnam Yang wrote:
> Hi,
>
> Sounds like trivial questions...
>
> (1) How do you check if the talairach.xfm is OK?
You load the mri/orig in tkmedit as main volume, then:
File--> Load Transform for Main Volume --> and select
SUBJECTNAME/mri/transforms/talairach.xfm *or
I parcellated a subject using parcellate_subject, and was trying to see
the labels. Doing File->Label->Import annotation and selecting
lh.aparc.annot makes tksurfer crash. Trying to convert annotations
to labels using mri_annotation2label givies a bus error. What could
be the problem? Running Max
Hi,
The man page shows the following for the AFNI motion correction binary.
3dvolreg [options] dataset
Registers each 3D sub-brick from the input dataset to the base brick.
'dataset' may contain a sub-brick selector list.
Would someone tell me how to specify "dataset"?
Is it *.img or COR-* or a
sounds like a byte ordering problem under OS/X. We'll look into it.
Bruce
On Wed, 5 Jan 2005, Rutvik Desai wrote:
I parcellated a subject using parcellate_subject, and was trying to see
the labels. Doing File->Label->Import annotation and selecting
lh.aparc.annot makes tksurfer crash. Trying to con
it's an AFNI binary, so you will need to convert to afni BRIKs to use it.
Bruce
On
Wed, 5 Jan 2005, Joongnam Yang wrote:
Hi,
The man page shows the following for the AFNI motion correction binary.
3dvolreg [options] dataset
Registers each 3D sub-brick from the input dataset to the base brick.
'da
Hi,
After I ran mri_convert, I saw the "orig" volumes.
Are the red crosses in the image significant in that the center cross should
be the center of the brain in terms of left and right hemispheres?
It is not in the center, much away from the center in my "orig" volumes.
If it has to be corrected
no, the red cross (the cursor) is by default at the center of the volume,
which is by no means necessarily the center of the brain.
Bruce
On Wed, 5 Jan
2005, Joongnam Yang wrote:
Hi,
After I ran mri_convert, I saw the "orig" volumes.
Are the red crosses in the image significant in that the cent
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