Re: [Freesurfer] tkregister2 error on lion

Rito, Hi, tkregister2 works for me on lion. do tkmedit and tksurfer work? did you install XQuartz via these instructions? https://surfer.nmr.mgh.harvard.edu/fswiki/MacTksurfer Actually i dont know if it necessary for lion to install XQuartz, but that is what i am running on my lion system

[Freesurfer] applying distortion correction output from epi_reg in fsl to freesurfer

Hi Bruce, Doug, and FreeSurfer Team, We have calculated coregistrations between bold timeseries and T1 images using BBR distortion correction as implemented in the epi_reg utility in FSL5.      We would like to map our functional timeseries to surface space for connectivity analyses (analagous

[Freesurfer] Using Subcortical initial output, with fixed cortical output

Dear FreeSurfers, I am using a Linux computer with FS 5.1 Due to the known feauture in version 5.1 where Control points may adversely affect aseg but also may alter the subcortical segmentation, is it acceptable to use the initial subcortical output (before adding control points) for analysis,

Re: [Freesurfer] Using Subcortical initial output, with fixed cortical output

Hi Mark that's the way we always processed things before 5.1 and will do after 5.1, so just state what you did Bruce On Thu, 15 Nov 2012, Mark Fletcher wrote: Dear FreeSurfers, I am using a Linux computer with FS 5.1  Due to the known feauture in version 5.1 where Control points may

Re: [Freesurfer] Using Subcortical initial output, with fixed cortical output

Just wanted to mention that, in my experience at least, it isn't just that CPs in 5.1 may adversely affect the aseg, but the inclusion of CPs can actually impact the surfaces in 5.1 in places distant from the CPs themselves. So, if you are using surfaces derived from the default 5.1 recon-all,

[Freesurfer] Converting SPM2 File to FreeSurfer Space

Hi all, I'd like to convert SPM2 spmT files to FreeSurfer space. I have a Colin template brain available to help with the conversion, as well. Has anyone done this before? Any suggestions on how to do this? Many thanks in advance, Eun Young ___

Re: [Freesurfer] interpretation of vertexwise thickness, area, volume analysis

Hi, Thanks for the reply. I am using the new script and I should correct myself in that my significant volume changes do seem to correspond (although they are not completely identical) to areas where there are significant area differences (I see no significant thickness differences between my

[Freesurfer] (no subject)

Hi, I have just received this error after a recon-all subjid- ___ all : ERROR: _FindFacePath: could not find path! /home/hughp/freesurfer/subjects/B__/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces

Re: [Freesurfer] (no subject)

Hi Hugh This is fixed in the newest version. What version are you running? Bruce On Nov 15, 2012, at 6:48 PM, Hugh Pemberton hughpembert...@gmail.com wrote: Hi, I have just received this error after a recon-all subjid- ___ all : ERROR: _FindFacePath: could not find path!

Re: [Freesurfer] (no subject)

Hi Bruce, Thanks for getting back to me. In terminal window it says freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 but recon-all -version give me $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ Hugh On 16 November 2012 11:05, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi

Re: [Freesurfer] (no subject)

this is a bug in the topology fixer. Maybe Zeke or Nick can post a new version of it? Was it mris_topo_fixer that was runing or mris_fix_topology? On Fri, 16 Nov 2012, Hugh Pemberton wrote: Hi Bruce, Thanks for getting back to me. In terminal window it says

Re: [Freesurfer] (no subject)

Looks like it tried both - mris_fix_topology failed! (euler number != 2) Trying mris_topo_fixer... cp ../surf/lh.orig.nofix ../surf/lh.orig euler # = v-e+f = 2g-2: 144765 - 434289 + 289525 = 1 -- 1 holes F =2V-4: 289525 != 289530-4 (1) 2E=3F:868578 != 868575

[Freesurfer] reconall without graphics card or GPU?

Dear all, At our university, we have the option of using a high performance computing facility to run computing intensive analysis, but it doesn't have a 3D graphics card or GPU. Is it advisable to run reconall at the facility and visualise the results later on another computer? Running it on