That is odd, not sure why. If you upload the subject we will take a look
Bruce
On Jun 8, 2011, at 5:22 PM, Wayne Su wrote:
> Anybody can help me out? What caused the middle line (both pial and wm
> boundary) shifted to right side even the wm mask is good? Please see the
> attached images. Th
Hi Alfredo
It must be a topological defect. You will need to find and correct it in the
wm.mgz
Cheers
Bruce
On Jun 8, 2011, at 7:42 PM, Alfredo Damasceno
wrote:
> Alfredo
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Hi Tracy:
You may be able to do manual tracing of the CP using FSL or 3D slicer.
best,
Alan
On Wed, Jun 8, 2011 at 3:45 PM, Tracy Butler wrote:
> Is there a good method to segment choroid plexus and calculate volume? I
> know it’s an aseg label.
>
> Thanks,
>
> Tracy
>
>
The volume should be in aseg.stats
On Wed, Jun 8, 2011 at 16:45, Tracy Butler wrote:
> Is there a good method to segment choroid plexus and calculate volume? I
> know it’s an aseg label.
>
> Thanks,
>
> Tracy
>
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Is there a good method to segment choroid plexus and calculate volume? I
know it's an aseg label.
Thanks,
Tracy
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The information i
corinna bauer wrote:
> Alright that should work. So do I use the pet.anat.nii files (from
> mri_vol2vol) as the input pet file to the mri_compute_volume_fractions?
No, use the pet volume. This does everything in the pet space.
> Also, has anyone published using this pv correction method that yo
Alright that should work. So do I use the pet.anat.nii files (from
mri_vol2vol) as the input pet file to the mri_compute_volume_fractions?
Also, has anyone published using this pv correction method that you know of?
An alternative method that I was thinking was to do something similar to the
corti
Actually, I think it only will affect the volume measurement for each
structure, so that's no good. There is not a flag to mri_segstats that
will do this. If you have a registration between your native pet data
and the FS anat, then you can use
mri_compute_volume_fractions regfile.dat pet.nii p
Hi Doug,
I'm just trying to derive the FS temporal pole label from the
annotations for each subject. However, the temporal pole label is wide
and ranging in what it actually traces. One label from one subject
might be very liberal and capture the whole temporal pole whilst
another subject'
Hi John,
mri_glmfit-sim actually runs on the GLM dir created when you run
mri_glmfit (it does not take a separate directory). It applies the
correction to all the contrasts in the GLM dir, so you just need to set
up a GLM with the contrast you want to correct.
doug
John Richey wrote:
> Dear fr
Hi Corinna,
try adding --pv mri/norm.mgz
doug
corinna bauer wrote:
> Hi all,
> I am wondering if partial volume is taken into account when
> calculating average uptake values of pet data. I know that aseg.stats
> takes partial volume into account and I am wondering if there is
> something simil
Hi Kareem, I don't understand what the problem is. Can you elaborate?
thanks
doug
k...@rice.edu wrote:
> Hello,
>
> I am deriving a cortical region of interest label from FS from a
> series of normal controls. I have tried two different methods of
> obtaining these labels to see which is more
Dear freesurfer experts,
I have a question about the conceptual use of mri_glmfit-sim. I wish to
apply permutation based cluster-correction to my between-groups results
(patients vs controls), and it is not clear to me which volume should be
the input for this type of simulation.
For example,
Hi Mike
Did you overwrite the existing FS distribution with the 5.1 version? We
do copy the shared libraries tkmedit and others need.
Can you do "ls -al" of the following 4 files and give us the
- file dates of tkmedit and tkmedit.bin in bin dir
- file dates of tkmedit and tkmedit.bin in tkt
Hi all,
I am wondering if partial volume is taken into account when calculating
average uptake values of pet data. I know that aseg.stats takes partial
volume into account and I am wondering if there is something similar in
place for pet data? From what I gather, most people when using FreeSurfer
c
Hello,
I am deriving a cortical region of interest label from FS from a
series of normal controls. I have tried two different methods of
obtaining these labels to see which is more consistent but neither are
really acceptable.
I am interested in the temporal pole label so first I did the no
Hi Elisa, sorry about that. Yes, use the
$FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat instead.
doug
Elisa Golfinopoulos wrote:
> Hi Doug,
>
> Thanks for responding to my inquiry. My version of Freesurfer (v.5)
> does not contain
>
> mni152.mni305.cor.subfov2.dat
>
> in the aver
Hi Freesurfers,
An updated Tracula tutorial data is available for download through the
following link:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data
And the tutorial to go with it can be accessed through the following link:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula
Please le
Hi,
I created a surface label from fsaverage and would like to know its coordinates
in some commonly used space, such as e.g. talairach.
The vertex 6111 coordinates look like this:
611135.2, 1.9, -27.0 0
In tksurfer the coordinates of the vertex 6111 are:
Vertex RAS: (63.48 -12.29
Hi
My PhD project focuses on developing a realistic thalamocortical model of
Alzheimer's disease (AD). One of the major components of my project is to
utilize DTI data from AD patients to build the macro-connectivity of the model.
Currently, I'm working on FSL + FreeSurfer + CAMINO to process t
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