Hi Cate,
there is a section on the wiki about troubleshooting the skullstripping.
Try some of those recommendations first (mostly changing the preflooding
height). If the cerebellum is messed up, then the aseg probably won't work
well which can hurt the whole processing stream.
cheers,
Bruce
You can start with that one and fix it by hand (which is a hassle). We
are working on ways to make the talairach more robust. BTW, if you run
tkregister2 again after fixing it, you should not include the
--regheader as that will ignore your previous edits.
doug
Chacko Cherian wrote:
Yes,It
Yes,It is perfectly fine with the --regheader
optionmwhich means no problem with geometry info.
But how do I fix the talairach.xfm?
Thanks a lot!
Chacko.
--- Doug Greve <[EMAIL PROTECTED]> wrote:
> I mean to just load the orig.mgz into tkmedit and
> see if it is oriented
> correctly. Assuming t
I mean to just load the orig.mgz into tkmedit and see if it is oriented
correctly. Assuming that it is oriented correctly, then it sounds like
the talairach transform is messed up pretty badly. When you run
tkregister2, try adding --regheader. This will ignore the info in the
talairaach.xfm fil
It has the problem in tkmedit,after I load the
transform..i checked brainmask.img and T1.img after
loading the transform and they had this problem..The
header and geometry info look fine..
--- Doug Greve <[EMAIL PROTECTED]> wrote:
> That means that the geometry info in the file is
> messed up. W
That means that the geometry info in the file is messed up. Where did
the data come from? Are the dicoms messed up too?
Chacko Cherian wrote:
No, It has the same problem in tkmedit too.
--- Doug Greve <[EMAIL PROTECTED]> wrote:
Does it view correctly in tkmedit?
Chacko Cherian wrote:
No, It has the same problem in tkmedit too.
--- Doug Greve <[EMAIL PROTECTED]> wrote:
> Does it view correctly in tkmedit?
>
> Chacko Cherian wrote:
>
> >Hello ALL,
> >
> >Has anybody had trouble with tkregister2..I loaded
> the
> >transform and the coronal and horizontal views are
> >mixed up
Does it view correctly in tkmedit?
Chacko Cherian wrote:
Hello ALL,
Has anybody had trouble with tkregister2..I loaded the
transform and the coronal and horizontal views are
mixed up.Coronal view of the subject is coupled with
the horizontal view of the talairach volume.
Thanks in advance
Reg
You should simply try to align the images, don't worry about what's in
the matrix.
Chacko Cherian wrote:
Hello all,
To rectify the talairach transform, I am editing
brainmask.mgz using tkregister2 and aligning the
subject and talairach volume.
THank you.
Chacko.
What are you trying to r
jorge luis wrote:
I computed the region areas by adding the areas of the
triangular faces inside these regions using the
spherical coordinates of the vertexs and the Heron
formula for the triangle area.
On fsaverage? If so, then you will need to take into account the effect
that I descri
Hi,
I ran autorecon1 on a group of data consisting of a single set of mprage
DICOMs per subject, acquired on a Siemens Allegra 3T scanner. Several of
the brainmask.mgz images had large portions of the brainstem and cerebellum
removed. A couple had portions of the neck which were not removed. Th
I've noticed that the gray matter volume output from mris_anatomical_stats
(lh) vs. mris_volume (lh.pial) differs. Am I missing something? Do I
need to run mris_volume for a different surface? Thanks.
-Derin
> sure. Tell us what platform and Nick can post it for you
> On Mon, 5 Feb 2007,
> Der
Derin,
mris_wm_volume for 32bit centos is on the website:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist
It's gzipped, so to install, after downloading and copying to your
$FREESURFER_HOME/bin, type:
gunzip mris_wm_volume.gz
chmod a+z mris_wm_volume
Typing 'mris_wm_volume' without args gives
Hello ALL,
Has anybody had trouble with tkregister2..I loaded the
transform and the coronal and horizontal views are
mixed up.Coronal view of the subject is coupled with
the horizontal view of the talairach volume.
Thanks in advance
Regards,
Chacko.
__
Hello all,
To rectify the talairach transform, I am editing
brainmask.mgz using tkregister2 and aligning the
subject and talairach volume.
THank you.
Chacko.
What are you trying to register?
>
>
>
> Chacko Cherian wrote:
>
> >Hello All,
> >
> >After making changes using tkregister2 the
I computed the region areas by adding the areas of the
triangular faces inside these regions using the
spherical coordinates of the vertexs and the Heron
formula for the triangle area.
Another thing:
Should I use the sig.mgh file resulted from the
mri_glm estimation as the input to the
mri_surf
How did you get the 15 mm^2 regions? And how did you know that they are
15mm^2? There are some complications with using the raw vertex areas on
fsaverage. The total surface area of the average will be wrong
(inevitable with the way that fsaverage is computed). However, there is
a correction, an
CentOS 4 (32-bit). Thanks!
-Derin
> sure. Tell us what platform and Nick can post it for you
> On Mon, 5 Feb 2007,
> Derin Cobia wrote:
>
>> Is there any way I can get mris_wm_volume? If not, what's the next best
>> thing? Can I use the aseg.stats estimates?
>>
>> -Derin
>>
>>>
>>> I have not
What are you trying to register?
Chacko Cherian wrote:
Hello All,
After making changes using tkregister2 the input
registration matrix changes.IS there an 'optimum'
input registration matrix that i should try to get.I
notice that the closer the values(last column of the
input reg matrix) a
Hello all
I have made deep changes in 9 regions of a left
hemisfere of a subject surface after maped it onto
the fsaverage subject sphere. The changes were made to
have areas close to 15 mm^2. I computed the areas by
add the areas of the faces inside the regions
(computed using the vertexes sphe
sure. Tell us what platform and Nick can post it for you
On Mon, 5 Feb 2007,
Derin Cobia wrote:
Is there any way I can get mris_wm_volume? If not, what's the next best
thing? Can I use the aseg.stats estimates?
-Derin
I have not implemented it in recon-all yet.
doug
On Fri, 2 Feb 20
Is there any way I can get mris_wm_volume? If not, what's the next best
thing? Can I use the aseg.stats estimates?
-Derin
>
> I have not implemented it in recon-all yet.
>
> doug
>
>
>
>
> On Fri, 2 Feb 2007, Bruce Fischl wrote:
>
>> you would need to add in whatever subcortical components you
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