oh yeah, you're right. Unless no tal exists, in which case it's "volume
scanner".
On Thu, 22 Dec 2005 [EMAIL PROTECTED] wrote:
actually, I think it needs to be talairach coords. The next version will
use indicies (and so will be independent of the tal transform).
doug
you need to use the "
actually, I think it needs to be talairach coords. The next version will
use indicies (and so will be independent of the tal transform).
doug
> you need to use the "volume scanner coords" in tkmedit, not the indices.
>
> On Thu, 22 Dec 2005, Sven Panis wrote:
>
>> Hi surfers,
>>
>> I experience
you need to use the "volume scanner coords" in tkmedit, not the indices.
On Thu, 22 Dec 2005, Sven Panis wrote:
Hi surfers,
I experience a problem during the first step of the create surface routine : fill white
matter. Specifically, the ponscall.dat file in mri/tmp is empty and at the start
Hi surfers,
I experience a problem during the first step of the
create surface routine : fill white matter. Specifically, the ponscall.dat file
in mri/tmp is empty and at the start of step two (tessellate RH white matter)
I'm asked to confirm that "the images in .../mri/filled/COR-0 cannot
I get the following error message, when I do the 'create surface'. Images
(filled): /subjectsdir/mri/filled/COR-001 not found. wmfill first. Log
file says, could not find a valid seed for the CC. Seed point not in
structure. So I think the problem is with cutting planes.
Does CC position change
Hi Arvind,
is your problem with the talairach or the cutting planes? You can alsways
use tkregister2 to manually talairach.
Bruce
On Fri, 5 Aug
2005, Arvind Gururajan wrote:
Hello all,
This is a follow up question on this mail.
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu
Hello all,
This is a follow up question on this mail.
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00565.html
I have exactly the same problem as Margaret had mentioned, tried all the
suggestion by Tosa. My talairach fails when I do the mri_convert nu nu.mnc.
How do I generate
check out the free surfer manual, around page 31. they show pictures
and an example. use talairach or volume scanner coordinates to specify
them, not volume index as it might say in the manual. margaret
On Thu, 23 Dec 2004, Joongnam Yang wrote:
> Thanks Margaret,
>
> Is there a reference on h
Thanks Margaret,
Is there a reference on how to specify the corpus collosum and pons in the
WMFill under Preferences->Expert Preferences in csurf?
Nam.
>>> Margaret Duff <[EMAIL PROTECTED]> 12/22/04 12:10 PM >>>
i had this problem recently. try using recon-all -stage one in a terminal
window in
Hi Nam,
that means the fill failed. Can you send us the whole log file?
cheers,
Bruce
On Wed, 22
Dec 2004, Joongnam Yang wrote:
Hi all,
During "create surface" on csurf,
right after "fill white matter" is done, as soon as "tesselate RH white
matter" starts,
an error message comes up, which is
ima
i had this problem recently. try using recon-all -stage one in a terminal
window instead of process volume in csurf. or specify the corpus collosum
and pons in the WMFill tab under Preferences->Expert Preferences in csurf.
it probably cant find where to segment. you might want to check the
archi
Hi all,
During "create surface" on csurf,
right after "fill white matter" is done, as soon as "tesselate RH white
matter" starts,
an error message comes up, which is
images filled:
somedirectory/mri/filled/COR-001...not found, wmfill first.
I checked the directory of /mri/filled, which d
Hi, Margaret:
If you have downloaded the freesurfer release, everything should be
included (including
MNI software).I guess that the script "recon-all" is not written in
the out-dated
documentation.
You can do the talairach using the script "talairach2" or line-by-line
as follows:
$ set
yes, that is incorrect. If there is no talalairach you need to enter the
"volume scanner" coords from tkmedit (you can turn them on under
view->information).
cheers,
Bruce
On Mon, 6 Dec 2004, Margaret Duff wrote:
in the manual it says if the talairach coordinates are not available,
enter the x,y
in the manual it says if the talairach coordinates are not available,
enter the x,y,z locations from the volume index in the cursor area. is
this not true anymore? thanks, margaret
On Mon, 6 Dec 2004, Bruce Fischl
wrote:
> Hi Margaret,
>
> the points need to be specified in talairach coords -
Hi Margaret,
the points need to be specified in talairach coords - it looks like you
are using voxels coords.
Bruce
On Mon, 6 Dec 2004, Margaret Duff wrote:
Hi, I tried to manually set the cutting planes, but I was unable to get
the create surface to run. My subjects info is at
/space/troy/1/u
hi, just to clarify, running this from the command line will create
talairach coordinates or do you need to download the additional mni
software? and, is this step included in the process volume command when
using the csurf interface? thanks, margaret
On Mon, 6 Dec 2004, Yasunari
Tosa wrote:
Hi, Margaret
The head is tilted almost 10 degrees. This makes it difficult to cut
the brain into two.
You really need the talairach transform or any other transform to
straighten up the head to
find the cutting planes.
I just copied your volume and ran recon-all -stage1 and "mri_fill"
created
Hi, I tried to manually set the cutting planes, but I was unable to get
the create surface to run. My subjects info is at
/space/troy/1/users/FREESURFER/SM2S4_freesurfer and I tried to specify
coordinates (121 90 139) for the CC and (131 159 118) for the pons. I
used the manuals troubleshooting
Hi Margaret,
if no talairach.xfm exists, then the fill may still find the cc and pons,
but it might not. You can always specify them manually be finding a
sagittal slice in which the cc is disconnected and a horizontal slice above
the cerebellar peduncles where the pons is disconnected.
cheers,
Hi,
The identity matrix did not work as you found. If you have a good
talairach.xfm, it should work better.
You can try specifying the seed corpus callosum position:
Seed point options in Talairach coordinates (RAS):
-C- the Talairach coords of the seed for the corpus
callosum
Alte
So, even though it says it will substitute the identity matrix for the
transform, I still need a transform or it won't work? Is the only way
to create a transform with that separate MNI software? Thanks, Margaret
On
Wed, 1 Dec 2004, Yasunari Tosa wrote:
> Hi,
>
> The log says that it could not
Hi,
The log says that it could not find
$subject/mri/transforms/talairach.xfm for this volume.
Tosa
Margaret Duff wrote:
The log file is below. And at the end it says command finished, not that
something went wrong. I am not sure about the cutting planes or how to
specify them manually. Thanks
The log file is below. And at the end it says command finished, not that
something went wrong. I am not sure about the cutting planes or how to
specify them manually. Thanks for your help. Margaret
/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255
-rval 80 -ccmask -T 1
Hi Margaret,
we need more information than that. Can you send us log files from trying
to run mri_fill? Is it finding the cutting planes? Have you tried
specifying them manually?
cheers,
Bruce
On Tue, 30 Nov 2004, Margaret Duff wrote:
Hi, I keep getting an error message after I run Create Surfa
Hi, I keep getting an error message after I run Create Surface. It is
similar to questions found in the archive but those solutions did not work
and this problem did not occur for the first 2 brains I reconstructed. I
get an alert that the Images (filled): /subjectsdir/mri/filled/COR-001 not
fou
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