[Freesurfer] two questions about qdec

Hi all, I have two questions about QDEC: 1\Is there anyway to auto (not manually draw ROI) extract information (include area, the max p-value, the num of vertexes) from the significant different area? Or how can I extract the information quickly? 2\Is the coordinates in qdec belong to 'Talairach

Re: [Freesurfer] about recon-all

Okay, thanks! Best, Xiaoying 2011/4/25 Bruce Fischl > yes, I think that's a typo and should be autorecon2. Perhaps Nick can > confirm? > > > On Mon, 25 Apr 2011, Xiaoying Tang wrote: > > Hi All,I find the following content on the wikipage of freesurfer: >> >> Q. I have already skull-stripped d

Re: [Freesurfer] about recon-all

yes, I think that's a typo and should be autorecon2. Perhaps Nick can confirm? On Mon, 25 Apr 2011, Xiaoying Tang wrote: > Hi All,I find the following content on the wikipage of freesurfer: > > Q. I have already skull-stripped data. Can I submit it to recon-all? > > A: If your skull-stripped vo

[Freesurfer] about recon-all

Hi All,I find the following content on the wikipage of freesurfer: Q. I have already skull-stripped data. Can I submit it to recon-all? A: If your skull-stripped volume does not have the cerebellum, then no. If it does, then yes, however you will have to run the data a bit differently. First you

Re: [Freesurfer] Fwd: Two Volume Measurement Issues

Thanks very much Doug, I'll use this method. In case it helps anyone else, the "--supertent" option in the command provided should probably be "supratent". Tom On Mon, Apr 25, 2011 at 3:44 PM, Douglas Greve wrote: > Here are two that were suggested by anothers on the FS list: > > Winkler AM, K

Re: [Freesurfer] Fwd: Two Volume Measurement Issues

Here are two that were suggested by anothers on the FS list: Winkler AM, Kochunov P, Blangero J, Almasy L, Zilles K, Fox PT, Duggirala R, Glahn DC. Cortical thickness or grey matter volume? The importance of selecting the phenotype for imaging genetics studies. Neuroimage. 2010 Nov 15;53(3):1135-

Re: [Freesurfer] No inflated brain...

is this in tksurfer? There have been issues with video card drivers, so make sure your's are up to date. Have you been able to view any surfaces in tksurfer? On Mon, 25 Apr 2011, jim kroger wrote: > HI Bruce, thanks so much for the reply. All of the surfaces we have needed > to view to fix the

Re: [Freesurfer] No inflated brain...

HI Bruce, thanks so much for the reply. All of the surfaces we have needed to view to fix the Talairach (was OK), white matter, etc., have been there. It's only when I tried to look at the inflated brain during the WhiteMatterEdits step that something seemed to be missing. I will look at tkmedit an

[Freesurfer] Fwd: Two Volume Measurement Issues

Hello, I've been asked to obtain freesurfer volume measurements on some cases we've already run with Freesurfer for comparison to VBM measurements. Can anyone direct me to any literature or briefly share knowledge about comparing these two methods? Second question: For said analysis, I'd like to

Re: [Freesurfer] surface to native space

Hi Joost, try using mri_surf2surf, something like mri_surf2surf --sval-xyz lh.pial --reg register.dat --tval lh.pial.native --tval-xyz --hemi lh --subject subject The register.dat you can get from tkregister2 --mov orig.mgz --targ rawavg.mgz --regheader --no-edit --reg register.dat doug On

[Freesurfer] surface to native space

Hi, FS version 4.5 - goal: to transfer the ?h.pial to native ('pre-conformed') space. thus to the space of the image _before_ any FS processing. - what we have done so far: 1) if we convert the T1.mgz (from the FS mri-dir, mri_convert T1.mgz T1.nii) to nifti it coincides perfectly with the nativ

[Freesurfer] Tksurfer slow loading.....

Dear all, I met a problem when I tried to load the tksurfer...it doen't give any error, just extremely slow...I also tried the "straces -f",still very slow... FreeSurfer:~> tksurfer ben lh pial subject is ben hemi    is lh surface is pial surfer: current subjects dir: /home/virtualuser/apps/f

Re: [Freesurfer] converting surface label to volume

You can try converting it to a parcellation (mris_label2annot -- this would just be a single label parcellation), then use mri_aparc2aseg to convert the parcellation to a label. This should look better than using label2vol. doug On 4/23/11 11:07 PM, Prapti Gautam wrote: Dear freesurfers, I

Re: [Freesurfer] Fwd: error with motion correction

Hi Maryam, I don't know what is going on. Does 006/mcparams2extreg.log have anymore information? Can you run cd 110419_xu_PDM1_02_PDM/bold mcparams2extreg -mcfile 006/fmc.mcdat -northog 6 -extreg 006/mcextreg doug On 4/24/11 9:01 PM, Maryam Vaziri Pashkam wrote: Hi, I am running into troubl