Hi all!
I've just ran the preprocessing for TRACULA analysis, with the command
"trac-all
-prep -c /home/kutato12/Desktop/dmrirc". It works everything fine, and the
output files are correct until the following command:
mri_aparc2aseg --s my_subject --annot aparc --wmparc-dmax 2 --labelwm
--hypo-a
Hi,
I have generated inner and pial surfaces using another method. However, I
am interested in computing the cortical thickness using the method
implemented in Freesurfer. My surfaces are in vtk format. I was wondering
how I can do this, if this is at all possible.
Thanks,
--
Navid Shiee
__
Dear fellow neuroimagers,
I am very excited to announce the second Nipype workshop which will
take place on 8-9 September 2012 in Magdeburg, Germany. For those who
have not heard about Nipype it is a framework which helps designing,
maintaining, sharing and executing data processing workflows. It
You will first need to register the diffusion to the anatomical with
bbregister. This will create a registration matrix ("register.dat"). You
will then need to map the cluster to the individual anatomical space
with mri_surf2surf (or mri_label2label if you are using labels). You can
then use mr
If things are significant at .001, then there is probably an
interaction, but you should also do a correction for multiple comparisons.
doug
On 05/19/2012 09:55 PM, ZhiLiangLong wrote:
> Hi Doug:
> Thank so much for your suggestions. Please find Freesufer Digest, Vol
> 99, Issue 23, Topic 1
Sorry, I got the equation exactly backwards. Try this
orig=inv(Torig)*Reg*Tmov*[32 32 15 1]';
On 05/20/2012 11:13 AM, Sinem Burcu Erdoğan wrote:
> Hi Doug;
> Thank you for your prompt reply. I have obtained Torig Tmov and Reg
> values as below:
>
> mri_info --vox2ras-tkrsegmentedanatomic.nii
>
>
Hey All,
I currently have a cortical parcellation with some unlabeled vertices in it.
I'm wondering if anybody knows how to assign a series of unlabeled vertices to
a single .label file. These vertices are copious and minute, trying to avoid
several hundred 'click, save label as..' repetition
You can try running mri_annotation2label with the --seg output. This
will create a segmentation-style output in a "volume" format such that
each vertex simply has a integer value. These unassigned vertices should
be 0s (but check by loading the output as an overlay in tksurfer). Then
run (the b
Hi everyone,
I have looked through the mailing list, and read a number of threads on using
(or rather not using) mri_convert to change the orientation of a volume, and I
have read the mri_convert help, which says about the --in_orientation and
--out_orientation flags:
"This is only to
Hi,
Sorry to re-post but I wanted to amend my questions on the basis of further
reading I have done in the forum. Ignore questions 1 to 3.
Instead
4) In a vertex wise analysis of area (using newer version of mris_preproc)
what nuisance factors are people using - does it make sense to use t
On 05/22/2012 04:18 PM, Mahinda Yogarajah wrote:
> Hi,
>
> Sorry to re-post but I wanted to amend my questions on the basis of
> further reading I have done in the forum. Ignore questions 1 to 3.
>
> Instead
>
> 4) In a vertex wise analysis of area (using newer version of
> mris_preproc)
Hi Clark, the orientation flags were not supposed to change the pixel
data, but it turns out that the out_orientation will change the pixel
data. I don't know how/when that happened.
doug
On 05/22/2012 03:56 PM, Clark Fisher wrote:
> Hi everyone,
>
> I have looked through the mailing list, an
intensity.deep and superficial are estimates of the intensity of the
bottom of the cortex (deep) and the top of the cortex (superficial).
These aren't generated by default, although we do have some tools for
doing so.
cheers
Bruce
On Tue, 22 May 2012, Douglas N Greve wrote:
>
>
> On 05/22/2012
Hi Navid,
I think mris_convert will take a .vtk file as input. Try it and see if it
works:
mris_convert lh.pial.vtk lh.pial
mris_convert lh.white.vtk lh.white
you can then use mris_thickness to calculate the thickness measures.
cheers
Bruce
On Tue, 22 May 2012, Navid Shiee wrote:
> Hi,
>
hmmm, something seems badly wrong here. You shouldn't have any vertex
indices over 150K or so. If you load that annot file onto the surface in
tksurfer does it look right? Does tksurfer complain when you try to load
it?
On Fri, 18 May 2012, Inês Violante wrote:
Hi,
It repeats this several t
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