I was processing a particularly noisy participant which bombed out with the
following error. Looking at the data, it shouldn't make it through the
pipeline, but the error message seems more of a memory management issue. I've
pasted it below, any thoughts?
Freesurfer 5.1 (new build), Mac Pro Work
Hi Peter,
that error means that it found a gigantic topological defect - bigger
than it could hold in memory - so it's a direct consequence of the noisy
data.
cheers
Bruce
On Fri, 27 May 2011 peter.molf...@yale.edu wrote:
> I was processing a particularly noisy participant which bombed out wit
Hello all,
We are looking to develop a cerebellum atlas training set based on the
Schmahmann et al (2000) parcellation so we can automatically segment the
cerebellum based on this atlas. Does this exist already? I know Makris
and colleagues had done something similar to this, but I am not sure
Hi,
I am running Tracula on the MIT BCS cluster. The first step "-prep" finished
without error. However, during the second step "-bedp" I received the following
error messages.
ba3:~/STUT/tracula> trac-all -bedp -c ~/STUT/tracula/tracula.cfg
INFO: SUBJECTS_DIR is /users/cais/STUT/FSDATA
INFO: Dif
Hello,
I've derived a .nii.gz atlas-based volume for a specific part of the
cortical surface. I've binarized the volume and now I want to convert
the file to a .label file that I can use to identify particular
vertices in native FS space for that same subject.
This is what I have tried so f
Does anyone know how to register for the FreeSurfer Tutorial and Workshop
scheduled for September, 2011? I cannot find a link or a phone number to do
this on the Course Description page
(http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription).
Thanks!
Sarah
Sarah A. Eisenstein, Ph.D.
Pos
Dear freesurfers
I want to convert an .mgh image to NIfTY format, but even when the conversion
using "mri_convert" seems to be ok, when I try to open the nii, an error
message appears "image doesn't appear to be a valid 2D or 3D image", there is
any other way to convert an mgh image to nii?
I
I think you should send an e-mail to Allison (astevens)
On Fri, May 27, 2011 at 13:34, Eisenstein, Sarah
wrote:
> Does anyone know how to register for the FreeSurfer Tutorial and Workshop
> scheduled for September, 2011? I cannot find a link or a phone number to do
> this on the Course Descript
Nifti can only handle 32k elements in any dimension. This is a problem
for surfaces when they have upwards of 100k vertices. For our average
subject (fsaverage and derivatives), this problem is solved by reshaping
the number of vertices to be 27307x6=163842. If you are working with
fsaverage, t
It looks like your commands are correct. When you load mask.surf.nii.gz onto
the surface, does it look ok?
doug
k...@rice.edu wrote:
> Hello,
>
> I've derived a .nii.gz atlas-based volume for a specific part of the
> cortical surface. I've binarized the volume and now I want to convert
>
Registration is not open yet and that date is tentative. Once the date is
confirmed and registration open, an email will be sent out to the Course
mailing list which has a link on the top of the Course Description wiki.
Allison
On Fri, 27 May 2011, Eisenstein, Sarah wrote:
> Does anyone know ho
Dear Doug Im using :
mri_surf2surf --sval $PATH/image.mgh --tval $PATH/image.nii --reshape --s
my_avg_subject --hemi lh
and the nii output image still seems to be a not valit image, am I missign
something?
Gabriel
> Date: Fri, 27 May 2011 12:53:53 -0400
> From: gr...@nmr.mgh.harvard.edu
Hi everybody,
I just want to make sure I'm using the correct the correct syntax for
running mris_anatomical_stats for examining cortical area. Based on the
QDec Group Analysis page, my I was running the following command to
examine cortical thickness:
mris_anatomical_stats -l rh.test.label
Use mri_info to see what it reshapes it to. You can also try adding
--reshape-factor 6.
doug
Gabriel Go.Es. wrote:
> Dear Doug Im using :
>
> mri_surf2surf --sval $PATH/image.mgh --tval $PATH/image.nii --reshape
> --s my_avg_subject --hemi lh
>
> and the nii output image still seems to be a not
Hi Joakim,
I think you can remove entirely the -t option. The area will be one of
the fields in the table, regardless of this option, as it depends on the
mesh that is used to derive all other measurements except thickness. If
you specify an ?h.area file with -t, it will instead output incorre
No it doesn't look right. It is supposed to map on to the temporal
pole but doesn't do so. I don't think it's in the right space. Is
there a command we are perhaps missing to bring it to native FS space?
Best,
Kareem
Quoting Douglas N Greve :
> It looks like your commands are correct. When
Then it means that the registration is incorrect. How did you create the
reg?
k...@rice.edu wrote:
> No it doesn't look right. It is supposed to map on to the temporal
> pole but doesn't do so. I don't think it's in the right space. Is
> there a command we are perhaps missing to bring it to nat
Hmm, well I derived the volume from an FSL atlas which I exported,
binarized, then fed into the commands I listed initially. Do I need to
register the temporal pole volume to some FS space? And how would I so?
Best,
Kareem
Quoting Douglas N Greve :
> Then it means that the registration is
Yes, there's no other way for FS to know where data should go -- it has
no idea how you derived the input. You can try using bbregister with 12
DOF to register the atlas template to the FS anatomical. This will give
you a registration matrix. Check it visually to make sure that it is
reasonably
Do I feed the registration matrix into another FS command or does
bbregister use the reg matrix to transform the atlas mask into FS
anatomical space? I will try the bbregister with 12 DOF as you
recommend too.
Thank you,
Kareem
Quoting Douglas N Greve :
> Yes, there's no other way for FS
You use bbregister to compute the registration. You will need a template
for your atlas (eg, an average anatomy).
doug
On 5/27/11 7:09 PM, k...@rice.edu wrote:
> Do I feed the registration matrix into another FS command or does
> bbregister use the reg matrix to transform the atlas mask into FS
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