Re: [Freesurfer] volume of CSF for hemispheres

Hello Bruce, Could you please give me a link to this coordinate tutorial. I don't think I can find it. Thank you, Tanja. On Wed, Feb 16, 2011 at 5:28 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tanja, I think Doug just put up a coordinate tutorial. For each voxel in the aseg

[Freesurfer] fixing hippocampus segmentation

Dear Freesurfer users, For some of my subjects Freesurfer strongly overestimates hippocampus' volume. Is there any way to fix the segmentation of hippocampus by e.g. adding some control points (like for white matter here http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints)? Thank

Re: [Freesurfer] installation problem in ubuntu

Hi Bruce, I'm experimenting problems with the installation on Ubuntu too. There's is warning in the welcome message, it seems that something is missing: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING:

Re: [Freesurfer] installation problem in ubuntu

Please send the result of the command: uname -a On Mon, Feb 21, 2011 at 10:31, Carolina Valencia cvalen...@linkdx.com.cowrote: Hi Bruce, I'm experimenting problems with the installation on Ubuntu too. There's is warning in the welcome message, it seems that something is missing:

Re: [Freesurfer] installation problem in ubuntu

It seems you are running the 64-bit version of FreeSurfer in a 32-bit OS 2011/2/21 Carolina Valencia cvalen...@linkdx.com.co Linux cvalencia-Precision-WorkStation-T3400 2.6.35-25-generic-pae #44-Ubuntu SMP Fri Jan 21 19:01:46 UTC 2011 i686 GNU/Linux Thanks, 2011/2/21 Pedro Paulo de

Re: [Freesurfer] fixing hippocampus segmentation

Hi Tanja, Can you send us an image? Is parahippocampal white matter significantly darker than 110? Bruce On Feb 21, 2011, at 6:41 AM, Tetiana Dadakova tetian...@gmail.com wrote: Dear Freesurfer users, For some of my subjects Freesurfer strongly overestimates hippocampus' volume. Is there

Re: [Freesurfer] volume of CSF for hemispheres

Hi Tanja, type 'coordinates' into the wiki search on our page. doug On 2/21/11 4:11 AM, Tetiana Dadakova wrote: Hello Bruce, Could you please give me a link to this coordinate tutorial. I don't think I can find it. Thank you, Tanja. On Wed, Feb 16, 2011 at 5:28 PM, Bruce Fischl

[Freesurfer] mri_mask

Hello Freesurfers, I'm trying to mask the rawavg.mgz from some subjects with the brain.mgz after doing some manual segmentation corrections by using mri_mask command, I have donne it before and it always works but with this subject, the command line is excacly the same so I have no idea

Re: [Freesurfer] mri_mask

The rawavg.mgz and brain.mgz are of different sizes. You'll need to transfer one to the other. You can do this with mri_vol2vol using brain as the mov and rawavg as the target and --regheader. doug On 2/21/11 11:49 AM, Gabriel Go.Es. wrote: Hello Freesurfers, I'm trying to mask the

[Freesurfer] overlay sig.mgh onto T1 vol

Hello, Does anyone knows if is it possible to overlay the surface file sig.mgh onto a T1 vol? I tried the command: tkmedit fsaverage T1.mgz -fthresh 2 -fmax 5 -overlay qdec/rh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh (where 2 and 5 were the thresholds I used in qdec), but it seems like I

Re: [Freesurfer] overlay sig.mgh onto T1 vol

Hi Fernanda if that's a surface overlay you'll need to sample it into the volume with mri_surf2vol cheers Bruce On Mon, 21 Feb 2011, Fernanda Palhano wrote: Hello, Does anyone knows if is it possible to overlay the surface file sig.mgh onto a T1 vol? I tried the command: tkmedit

Re: [Freesurfer] installation problem in ubuntu

run this command sudo rm -rf $FREESURFER_HOME 2011/2/21 Carolina Valencia cvalen...@linkdx.com.co Thanks Pedro, How I uninstall that version to re-install the correct version? I look for some answers and try rm -rf $FREESURFER_HOME It says that I don't have permission,how I can

Re: [Freesurfer] overlay sig.mgh onto T1 vol

use tkmedit fsaverage orig.mgz -overlay teste_sig.mgz doug On 2/21/11 3:46 PM, Fernanda Palhano wrote: Hi Bruce, Thank you for the prompt reply. I tried using mri_surf2vol : mri_surf2vol --surfval qdec/g1_g2_lh_06out/lh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh --identity fsaverage

[Freesurfer] question about weighted regression analysis

So I created a weighted regression analysis to look at the effect of memory load in a particular brain region. Basically, I weighted the paradigms by a behavioral measure that reflected the number of items actually remembered (as set size was increased). As far as Doug told me there are basically

[Freesurfer] Gammafit parameters

Hi all, We are trying to use -gammafit when running the mkanalysis-sess command. In the FsFast Tutorial, the flag -gammafit 2.25 1.25 is used. Are those numbers the default? If not, what is the default? Thanks in advance. Best, Mandy Nagy ___