Re: [Freesurfer] doubt regarding wm.mgz non wm voxels

won't recover from wm.mgz inaccuracies in others ones though. You might try setting wlo to above the values of the gray matter that it is including (to be passed to mri_segment and mris_make_surfaces using -seg-wlo wlo cheers Bruce On Thu, 18 Dec 2014, elisa veronese wrote: Dear FreeSurfer

Re: [Freesurfer] doubt regarding wm.mgz non wm voxels

wm.mgz inaccuracies in others ones though. You might try setting wlo to above the values of the gray matter that it is including (to be passed to mri_segment and mris_make_surfaces using -seg-wlo wlo cheers Bruce On Thu, 18 Dec 2014, elisa veronese wrote: Dear FreeSurfer users, I have

[Freesurfer] GI and CT relationship

Dear FreeSurfer users, I have a question regarding the link between cortical thickness and gyrification index: suppose I have a general decrease of cortical thickness in a lobe of the brain. Is it correct to suppose that consiquentely the gyrification index will decrease in the sulci (because of

[Freesurfer] relationship between cortical thickness and gyrification index

of the decreased curvature) and that it will increase in the gyri (because of the increased curvature)? So that probably I would not be able to measure any difference in the gyrification index of that lobe? Thank you. Best, elisa -- Elisa Veronese - PhD *Research Unit on Brain Imaging

Re: [Freesurfer] problem with gyrification index extraction

+02:00 elisa veronese dovreipensa...@gmail.com: Great, thank you Douglas, now it's not confusing :) Best, elisa 2014-10-15 16:26 GMT+02:00 Douglas Greve gr...@nmr.mgh.harvard.edu: It is a little confusing, but when you pass a map with -t lh.map, then the values in the map go

Re: [Freesurfer] problem with gyrification index extraction

is. When you then run aparcstats2table and specify thickness you get whatever is in the thickness column regardless of whether it is thickness or not. On 10/15/14 7:44 AM, elisa veronese wrote: Thank you Douglas, but I'm afraid I'm still missing the point. The -m option allows me measuring

[Freesurfer] problem with gyrification index extraction

they have nothing to do with the gyrification index. Thank you, best elisa -- Elisa Veronese - PhD *Research Unit on Brain Imaging and Neuropsychology (RUBIN)* *Inter-University Center for Behavioral Neurosciences (ICBN)University of Udine and University of Verona, ItalyICBN Website: http

[Freesurfer] exporting QDEC results

. Best, Elisa -- Elisa Veronese - PhD *Research Unit on Brain Imaging and Neuropsychology (RUBIN)* *Inter-University Center for Behavioral Neurosciences (ICBN)University of Udine and University of Verona, ItalyICBN Website: http://icbn.uniud.it/tiki-index.php http://icbn.uniud.it/tiki-index.php

[Freesurfer] mean cortical thickness on N ROIs

values obtained with the aparcstats2table? - Computing a weighted average of the 3 cortical thickness values obtained with the aparcstats2table? In this case, what would you use as weight? The area of the 3 regions? Thank you. Best, Elisa -- Elisa Veronese - PhD *Research Unit on Brain Imaging

[Freesurfer] localGI - results interpretation

the actual gyrification index? Thank you. Best, Elisa -- Elisa Veronese - PhD *Research Unit on Brain Imaging and Neuropsychology (RUBIN)* *Inter-University Center for Behavioral Neurosciences (ICBN)University of Udine and University of Verona, ItalyICBN Website: http://icbn.uniud.it/tiki

Re: [Freesurfer] localGI problems

.2127429.mgh'? y 2014-06-27 20:25 GMT+02:00 Douglas N Greve gr...@nmr.mgh.harvard.edu: #1. not a problem #2. yes, delete it doug On 06/27/2014 03:41 AM, elisa veronese wrote: Dear FS users, I'm trying the -localGI on a linux Centos machine, but I'm facing some problems: 1. should

[Freesurfer] localGI problems

, 2012 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. reading filled volume... rm: remove regular file `/tmp/tp726715349117711.load_mgh.8128471.mgh'? -- Elisa Veronese - PhD *Research Unit on Brain Imaging and Neuropsychology

Re: [Freesurfer] localGI problems

Thank you. Best, Elisa Il giorno 27/giu/2014 20:26, Douglas N Greve gr...@nmr.mgh.harvard.edu ha scritto: #1. not a problem #2. yes, delete it doug On 06/27/2014 03:41 AM, elisa veronese wrote: Dear FS users, I'm trying the -localGI on a linux Centos machine, but I'm facing some

[Freesurfer] aparc manual correction

Dear FreeSurfer users, can anybody tell me if and how it is possible to manually correct an uncorrect parcellation of the CC, i.e. if the rostrum is uncorrectly assigned to the CC_Mid_Anterior label instead of the CC_Anterior label? Thank you. Best Elisa -- Elisa Veronese - PhD *Research

[Freesurfer] FS versions

is the Freesurfer version *5.1.0 *Linux CentOS4 x86_64 When I perform the subsequent manual correction on my workstation, I use Freesurfer version *5.3.0* Linux CentOS4 x86_64 Is this correct? Should I downgrade to the 5.1.0 version also in my workstation? Thank you in advance. Regards, Elisa -- Elisa

[Freesurfer] Volume acquisition

Hi, I am a beginner in the use of Freesurfer. I was wondering if the T1w volume used as input for the recon-all has to be acquired in axial direction or not. In other words, is there a recommended acquisition direction? Thank you, Elisa -- Elisa Veronese - PhD http://www.dei.unipd.it/~verones1