Can you send us specific coordinates of things to look at?
> On Oct 24, 2016, at 10:44 PM, Cong <3110103...@zju.edu.cn> wrote:
>
> Hi Dear Bruce
> I have uploaded a subject named Cong2Bruce.zip through ftp. I can’t fix
> it by myself. Could you help me how to use expert options to get corre
Hi Dear Bruce
I have uploaded a subject named Cong2Bruce.zip through ftp. I can’t fix
it by myself. Could you help me how to use expert options to get correct white
matter and gray matter surface. Thank you very much.
Best Wished
Cong Chen
> Date: Tue, 20 Sep 2016 10:45:30 -0400 (EDT)
> F
Hi FreeSurfer experts,
I am currently performing some cortical thickness comparisons in my group
of subjects and using
mri_glmfit-sim --glmdir my_dir --cache 2.3010 --cwpalthresh 0.05 --2spaces
found some clusters that have significantly different cortical thickness
values,
Given Eklund et al PNA
The cache is not set up for volume-based analysis. There are two options:
1. use gaussian random fields (--grf instead of --cache). If you want to
use this option, let me know as I have recently made some changes to it
that make it more accurate
2. use permutation (--perm 5000 1.3 pos). This me
Hi Adam, it might depend on which version you are running. I've been
working on it over the last year and made some changes related to
choroid plexus. The version that I have now does not merge CP with CSF.
You can check in your analysis by running
cd gtmdir/aux
mri_binarize --i seg.nii.gz --m
Try setting SUBJECTS_DIR to the full path rather than just ./
On 10/21/2016 03:03 PM, Russ, Brian (NIH/NIMH) [E] wrote:
> Hi,
>
> I’m attempting to use FreeSurfer to create a set of surface and flat maps for
> use with some macaque data. Using a number of programs prior to FreeSurfer I
> have
It would depend on how big the ROI is to begin with. Do you know that we
have our own interhemispheric analysis that might be better for this?
Check out
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 10/24/2016 12:33 PM, Daya P wrote:
> Hi Bruce,
>
> I drew ROIs on an initial subject and th
Hi,
Just want to bump this to the top now that the weekend is over!
Thanks for any insights about the CSF estimation,
Adam
On Fri, Oct 21, 2016 at 1:03 PM, Adam Martersteck
wrote:
> Thanks for replying Doug,
>
> Yes, I would like to use my own mask if the choroid plexus is included but
> *only
Hi Bruce,
I drew ROIs on an initial subject and then after registering all other
subjects to the initial one, used mri_label2label to map the ROIs from the
initial subject to subsequent ones.
I am interested in looking at asymmetry between left and right regions.
I had two concerns, one that the
Hi Daiana
yes, that is to be expected given the nonlinear nature of the cross-subject
registration. It shouldn't bias things, although you'll need to give us
more details if you want a more definitive answer.
cheers
Bruce
On Mon, 24 Oct 2016, Daya P wrote:
Hi All,
My question is about us
Hi All,
My question is about using mri_label2label. When mapping the labels from
one subject to another the number of vertices of each ROI is different. Is
that something to be expected?
How much of a difference does a number of vertices of 50 compare to 40 have
on measures like thickness, grey m
I don't think we have anything yet that will do this for the thalamus. If
you have highres data that is full brain T1 you can analyze it in its
native space in the upcoming 6.0
On Mon, 24 Oct 2016, Dorsa Haji Ghaffari
wrote:
So what I understand is that we can do the segmentation using the
So what I understand is that we can do the segmentation using the whole
brain MRI and then use the higher contrast MRI to refine the thalamus
segmentation? if so, can you explain more about it?
Thank you
Dorsa
On Thu, Oct 20, 2016 at 12:20 PM, Bruce Fischl
wrote:
> no, you need full brain cove
Hi Bastian
Hmm, if everything looks right when you view things inside FreeSurfer then
it is goiong to be hard for us to help you as the issue sounds like it is a
3D slicer one. Have you contacted them? You can use mri_info to look at the
headers and the ras2vox matrices. Typically this is a pro
Dear Mike,
You can use the files ending in FSvoxelSpace.mgz for this. Or, when you use
mri_convert, add the flags -rt nearest (for nearest neighbor interpolation) and
-rl [targetFile] (resample like target file).
Cheers
Eugenio
Juan Eugenio Iglesias
Translational Imaging Group
University Colleg
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