Re: [Freesurfer] White matter surface don't change after editing

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

Re: [Freesurfer] White matter surface don't change after editing

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) >

[Freesurfer] Question about mri_glmfit-sim

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

Re: [Freesurfer] surface based analysis for subcortical structures

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

Re: [Freesurfer] PET PVC - CSF estimation

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

Re: [Freesurfer] subject directory error: can't find subject

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

Re: [Freesurfer] ROI NumVert

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

Re: [Freesurfer] PET PVC - CSF estimation

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

Re: [Freesurfer] ROI NumVert

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

Re: [Freesurfer] ROI NumVert

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

[Freesurfer] ROI NumVert

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

Re: [Freesurfer] Fwd: question about thalamus

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

[Freesurfer] Fwd: question about thalamus

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: >

Re: [Freesurfer] Space of lh/rh.pial files does not match T1.mgz

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

Re: [Freesurfer] Using hippocampal subfields in SPM

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