Dear FreeSurfers,
Due to motion I have to exclude participants from my analysis.
Is there an objective measure which could serve as a cut off value concerning
motion in the scanner? Can I find it in one of the FreeSurfer files generated
through the recon-all process?
Subjectively, one can see
Hi
I have 3 questions:
1) Does it affect the stats (or does it just affect the display) if I use
the fsaverage brain vs. the average of my subjects brains when running
mris_preproc or when simulating the cluster statistics using mri_glmfit-sim?
2) I downloaded the simulations for multiple compar
I have both. In origin, the ROI-s are 2mm volume based .nii that I convert
to FS .mgh with register.dat I obtained with bbregister.
-- In the case of label2label method I create the surface version with
mri_vol2surf (and the correspondence is perfect), and then use
mri_label2label in order to get
Hi group,
I recently reconstructed a high-resolution 3D T1-weighted structural MRI using
Freesurfer. The subject had non-metallic extensions that were tied to her head
through a series of braids. Looking at the MRI in TkMedit, I can noticeably see
pieces of the extensions above her scalp. My gr
Dear FS experts,
Is there any reference about the volume of cortical gyrus after FS cortical
parcellation in normal adult people ? I need the reference value of regional
volume base on the cortical parcellation made by FS.
Please instruct me the reference paper.
Thanks help
JLH
___
Depends on how you define "brain volume". If you're using BET, then I
assume that you are just counting the number of voxels in the mask? If
so, you can use mri_binarize and use the --count countfile to give you a
count of the voxels.
doug
On 09/22/2012 08:22 PM, Ana Arruda wrote:
>
> I've j
So you have ROIs in Colin27 space and you want to map them into your CT
space and compute average CT intensities over them? Are the ROIs
volume-based or surface-based?
doug
On 09/25/2012 05:09 AM, Garikoitz Lerma-Usabiaga wrote:
> Hi Doug,
> many thanks for your answer, I try to detail it more:
Hi Zsolt, you can use mri_annotation2label to separate the annotation
into labels, then mri_mergelabels to recombine several of them together,
then run mris_anatomical_stats on the merged label.
doug
On 09/25/2012 08:34 AM, Zsolt Cselényi wrote:
>
> Hi,
>
> I would like to find out how to pool p
Hi experts,
I want to make a new, custom-made parcellation, based on the aparc but
with much higher resolution. (I've tried mris_divide_parcellation, which
yields strip-shaped instead of isometric labels, and
mris_make_face_parcellation, which loses spatial specificity.
The wiki describes a way of
Dear all,
I met a problem while running the recon-all. I have a data with FOV=
300>256, so I add the flag -cw256 with reon-all. Then when I check the
converted data raw.mgz, I find the brain image is imperfect while some
region at the top of head is cut off. My question is, could I choose to cut
On 09/25/2012 03:09 PM, Bruce Fischl wrote:
> check the accuracy of the talairach xform
Hi
I am using Freesurfer version 5.1 with all bug fixes. I have snapshots
off all talairach xforms made through qa_tools. I have seen on a few
subjects that the talirach transformation went okay. The pial sur
try using mris_fill then to create a volume that is the filled interior
of any of the surfaces.
cheers
Bruce
On Tue, 25 Sep 2012, Fabian Schrumpf wrote:
Hi bruce,
At first I want to build a voxel-based FEM-Model based on the surfaces
freesurfer creates. For finally creating the models I want
Hi bruce,
At first I want to build a voxel-based FEM-Model based on the surfaces
freesurfer creates. For finally creating the models I want to use the MATLAB
toolbox iso2mesh. But I would also be interested in building BEM models as a
second approach.
best regards
Fabian
- Ursprüngliche
Hi EK
make sure that you don't have any control points in any voxels that
contain any GM. It looks like maybe you do in the region where you drew a
red arrow, although it's impossible to tell for sure from those images.
cheers
Bruce
On Tue, 25 Sep 2012, EK Kim wrote:
Dear all expert,
Hello
Hi Knut
can you check the accuracy of the talairach xform? And what version are
you using?
Bruce
On Tue, 25 Sep 2012, Knut J Bjuland wrote:
> Hi,
> I have calculated relative volume by dividing each volume by the
> intracranial volume and multiply it with 100. When I add the relative
> volume of
Hi Fabian
What are you trying to achieve? The easiest thing to do is to run recon-all
with the -all flag so we generate an aseg, then that can be collapsed into
different measures.
cheers
Bruce
On Tue, 25 Sep 2012, Fabian Schrumpf wrote:
> Hi folks,
>
> I successfully managed to do a brain s
Hi,
I have calculated relative volume by dividing each volume by the
intracranial volume and multiply it with 100. When I add the relative
volume of total gray matter, cortical white matter, lateral ventricle,
3rd centricle, 4th ventricle and ventral DC, I get 82-86 %. Can this be
caused by the
Hi,
I would like to find out how to pool parcellation statistics (i.e.
?.aparc.stats table entries) from several areas into a bigger one. For example:
how to get the pooled statistics for the area "parietal" which would be made up
of "superiorparietal" and "inferiorparietal" cortical structur
Hi Doug,
many thanks for your answer, I try to detail it more:
1.- bbregister is registering two Colin27 brains. First one is a 2mm found
in spm/canonical/single_subject_T1.nii, and second one is the
FS_spm_Canonical found in SurfRend distribution. It was in .COR format and
I run recon-all to have
Hi folks,
I successfully managed to do a brain segmentation using freesurfer. But the
result after mri_fill has too much detail. I'd like to do a segmentation only
dividing the brain into white matter, gray matter and csf. I suppose that I
have to alter some options when registering and alignin
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