[Freesurfer] Two FS versions in different user accounts

Hi everyone, I'm sorry to bring this question up again, but I'm thinking to install version 5.1 in the same computer where version 5.0 is installed. However I'm thinking of installing the new one in another user account that I've created only for this porpuse. My question is, can I install

[Freesurfer] Two FS versions in different user accounts

Hi everyone, I'm sorry to bring this question up again, but I'm thinking to install version 5.1 in the same computer where version 5.0 is installed. However I'm thinking of installing the new one in another user account that I've created only for this porpuse. My question is, can I install

Re: [Freesurfer] Two FS versions in different user accounts

Hi Andreia yes, that should be fine. You really just need to change FREESURFER_HOME and the associated binary paths to use one version or the other. cheers Bruce On Fri, 27 Jan 2012, _andre...@sapo.pt wrote: > Hi everyone, > > I'm sorry to bring this question up again, but I'm thinking to inst

[Freesurfer] control point guidance

Hi guys, We are currently trying to fix some errors in the white/pial surfaces where there are thin white matter strands by using control points, and are noticing a couple things: 1) The resulting WM surface in the area of the CPs can end up too far into the GM instead. Given that, is there any

Re: [Freesurfer] control point guidance

Hi Michael, I had the same problem too. It might be because of the type of scanner you are using. I added -washu_mprage flag, it pretty much helped me (I did not had to add a lot of controls points and so on so forth. You can go through the link below. https://mail.nmr.mgh.harvard.edu/pipermail//f

[Freesurfer] how can I view and process Freesurfer files using AFNI

Hello, I ran recon all on my subjects data which went well. Now I would like to use AFNI-SUMA to view it , how do I go about doing this. Thanks, Rashmi. This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insura

Re: [Freesurfer] how can I view and process Freesurfer files using AFNI

Hello Rashmi, This is an AFNI issue. You'll have to read the SUMA manual and convert your Freesurfer files to AFNI-readable surfaces using @SUMA_Make_Spec_FS and other commands. There are too many steps to list here, but it is not too difficult once you get the hang of it. Anthony On 1/27/1

Re: [Freesurfer] control point guidance

Hi Mike it's a bit hard to state the region of effect for the control points. Essentially we go through and label voxels as control points or not based on their intensity, intensity gradient and connectivity (that is, the must be 6-connected to other control points) then build a Voronoi diagra

Re: [Freesurfer] FreeSurfer download failed

Hi all, I just wanted to bump this since I sent it out last evening. Does anyone know why I might be having trouble downloading FreeSurfer? Aaron From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Browne, Aaron N Sent: Thursday, January 26,

Re: [Freesurfer] how can I view and process Freesurfer files using AFNI

Hi Rashmi you should ask the AFNI-SUMA people :) If you want to do it in FreeSurfer, use tkmedit or freeview for volumes and tksurfer for surfaces. cheers Bruce On Fri, 27 Jan 2012, Rashmi Singh wrote: Hello,  I ran recon all on my subjects data which went well. Now I would like to use AFN

[Freesurfer] Too many levels of symbolic links

I have subjects exiting with errors and I'm not sure why. The best clue I have is a line indicating "Too many levels of symbolic links" and an inability to read lh.BA1.label. Here are the last few lines of output: SUBJECTS_DIR/Applications/freesurfer/subjects FREESURFER_HOME /Applications/

[Freesurfer] talairach_with_skull_2.lta missing

In article http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix, it is mentioned that talairach_with_skull_2.lta is created during autorecon2, and that it can be useful when troubleshooting skull-strips, however I do not find talairach_with_skull_2.lta in the mri/transforms director

Re: [Freesurfer] Too many levels of symbolic links

usually that means a symbolic link is recursive or self-referential in some way. What does ls -l /Applications/freesurfer/subjects/fsaverage return? Bruce On Fri, 27 Jan 2012, cloud.c...@me.com wrote: > I have subjects exiting with errors and I'm not sure why. The best clue I > have is a li

Re: [Freesurfer] Verifying ICV in FS5

bump :) any feedback on this would be very much appreciated. Thank you! Jeff On Mon, Jan 23, 2012 at 6:56 PM, Jeff Sadino wrote: > Hello, > > Thank you Nick, Martin, and Doug for your previous feedback about ICV. >  I have a couple more questions that I am hoping you could clarify for > me. >

Re: [Freesurfer] Verifying ICV in FS5

Hi Jeff, I am not sure about which atlas, but concerning the transforms: 4.2 and earlier: talairach_with_skull.lta later versions: talairach.xfm I am pretty convinced that the way to check as described here http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV cd $SUBJECTS_DIR/subject/mri/transforms tk