[Freesurfer] stats question

Hi, i read the following in a paper and would like to do the same: "At each vertex in each hemisphere, the proportion of total variance in cortical thickness (CT) accounted for by 2 linear regression models was compared: One that did not include an age-by-group interaction term, Model 1: [CT = in

[Freesurfer] question mris_preproc

Hi, freesurfer-x86_64-redhat-linux-gnu-stable5-20110522 $Id: mris_preproc,v 1.66 2012/12/06 16:06:17 mreuter Exp $ after recon-all i ran recon-all -s $subject -qcache this generates lh.area.fsaverage.mgh which only contains values 0 and higher while negative values exist for the lh.area of the

Re: [Freesurfer] cortical surface area related measures

Regarding Winkler et al.: http://brainder.org/2012/06/02/facewise-brain-cortical-surface-area-scripts-now-available/ On Aug 21, 2012 11:00 PM, "Gregory Kirk" wrote: > > Hi folks, I wanted to make sure i have everything straight w.r.t. the > surface area measures. > > as i see there are 4 ways im

Re: [Freesurfer] T-value intensity overlayed onto 2009 Destrieux Parcellations

Hi, not 100% sure what you want but perhaps this: http://brainder.org/2011/07/05/freesurfer-brains-in-arbitrary-colours is what you're looking for? -joost On Tue, Aug 14, 2012 at 11:13 PM, Douglas N Greve wrote: > Try touching ?h.orig.nofix, ie, > touch rh.orig.nofix lh.orig.nofix > > th

Re: [Freesurfer] Extraction Longitudinal Stats

Hi Martin, lot's of small changes can make a big change but from your phrasing i assume this isn't the case. what has changed? i would like to have the new (long_mris_slope) script. thanks, -joost On Tue, Jul 3, 2012 at 6:30 PM, Martin Reuter wrote: > Hi Yolanda, > > take a look at the longitu

Re: [Freesurfer] error longitudinal processing

Hi Martin, changing the dir-names and qdec table to: fsid fsid-base ISI_years Group Gender Age ICV 11298_1 11298_template 0 patient F 16 1441 11298_2 11298_template 1.83 patient F 17.92 1396 solved my problem. -joost On Sun, Jul 1, 2012 at 4:33 PM, j janssen wrote: > Hi Mar

[Freesurfer] error longitudinal processing

Hi (Martin), - version 5.1 (Ubuntu 64b) - command: long_mris_slopes --qdec ./qdec/long.qdec.table.n114.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time ISI_years --qcache fsaverage - attached: first 3 lines of qdec table containing the info for subje

Re: [Freesurfer] Freesurfer and FSL

Hi, this is not a direct comparison but at least indicates similar volumes in FSL-FIRST and Freesurfer. br J Psychiatry. 2012 Jan;200(1):30-6. hth, -joost On Sun, May 27, 2012 at 2:09 PM, Martin Reuter wrote: > Hi Ana, > > Sorry I can't help more. Have never compared fsl and FS directly. Kee

Re: [Freesurfer] lGI differences without variation in other cortical morphometric variables

Hi, I am comparing a group of patients with controls. I extracted: > cortical volume, surface area, cortical thickness and gyrification > index for each subject's lobe. > Comparisons between this variables with Total Intracranial Volume as a > covariate indicated a difference in frontal and tempor

Re: [Freesurfer] Cortical Normalization Questions

Hi Michael and others, maybe it's this one: http://bjp.rcpsych.org/content/196/5/414.1.long best, -joost On Fri, Mar 23, 2012 at 2:15 AM, Michael Harms wrote: > > Hi Jeff, > I personally like the idea of using average thickness as a covariate to > control for a reduction in "whole brain" thic

[Freesurfer] question TRACULA

Hi, TRACULA gives pathstats.txt which includes *weighted* averages, mentioned on the wiki as: "weighted average over the entire support of the path distribution". question: weighted for what (is it the probability)? thanks, -joost ___ Freesurfer mailin

[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] question on contrast matrix

FreeSurfer version: 4.5 Background: we have 6 subjects, each subject has 1 scan per site, there are 6 sites (so each subject has 6 scans). Aim: to assess whether thickness is different per site: a F-test. what we did so far: we used mri_glmfit with the following .fsdg file (here we only show th

Re: [Freesurfer] merging average cortical thickness data

Hi Tina, > (e.g. to compute a general cortical thickness average for > the inferior frontal gyrus using the pars orbitalis, pars opercularis and > pars triangularis data). instead of "merging" existing thickness-data you could create a new label that constitutes your regions of interest. somethin

[Freesurfer] mri_robust_register

Hi, - using version 4.5 in the v4.5 standard longitudinal processing stream with 2 images mri_robust_register creates halfway space transformations using the 2 time point's norm.mgz files. i would like to apply the halfway transformations (mri_convert -at) to the 2 time point's _original_ (001.m

Re: [Freesurfer] Question about cortical surface area

Hi, what's the reason that FS's default surface for measuring surface area is the white matter surface and not the pial surface? why isn't surface area measured on the intermediate surface (average of gray.and white which should be less biased by sulci and gyri, i think)? thanks, -joost > > > On

Re: [Freesurfer] Covariate for results of cortical parcellation

Hi, you could try including average cortical thickness over the entire > hemisphere as a covariate. This was Mike Harms' suggestion, and I think a > good one. why is it a good one? for cortical thickness: i'm not so sure. my 2 cents (and i may be wrong!): - controlling for intracranial volume is

[Freesurfer] surface

Hi, here's an email from Don Hagler from February 2009: It seems to me that vertex areas in the native subject space are not > meaningful. The orig surfaces should be uniformly tesselated; however, > topology correction and final surface finding should introduce complicated > and probably unint

[Freesurfer] question on tksurfer tcl

Hi, using version 4.0.5 my goal: to display in tksurfer an inflated brain with curvature and an *outlined* label, using a tcl-script. there are probably numerous ways, i did: tksurfer "subject" rh inflated -gray -tcl tksurf.tcl where tksurf.tcl contains: make_lateral_view rotate_brain_x -90

[Freesurfer] tksurfer display question

Hi, using version 4.0.5 look at the attached picture. its the result of: tksurfer code lh inflated -aparc aparc -gray i have selected one region (yellow outline). i would like to - fill this region and some other regions, *but not all regions*! - give the filled regions different color-labeling

[Freesurfer] converting modified labels from annot

Hi, using version 4.0.5. i used mri_extract_label on the aparc+aseg.mgz file to extract and convert labels into volume nifti files, which i can view and use outside FreeSurfer. works fine. however, i have manually edited some surface labels, following the instructions found here: https://surfer.

[Freesurfer] question mri_glmfit

Hi, using version 4.0.5 i ran the command: mri_glmfit --y qdec/N83_only_boys.mgh --fsgd qdec/qdec.fsgd doss --surf fsaverage lh --C qdec/diff-1-2.txt --glmdir stats/ it worked. then i did: mri_glmfit --y qdec/N83_only_boys.mgh --fsgd qdec/qdec.fsgd doss --surf fsaverage lh --C qdec/diff-1-2.tx

[Freesurfer] labels to surface

Hi, using version 4.0.5. i want to convert the lh.Medial_wall.label found in the fsaverage label subdir into a mask which consists of 1 x v vector, with value 1 inside the mask, 0 outside the mask and v=#vertices. should i follow mri_label2vol and thereafter mri_vol2surf? i guess i am looking for

[Freesurfer] localGI exits with error

Hi, i am using version 4.0.5. for two brains out of a larger study, localGI exits with errors, the error message is similar in both brains and looks like: lGI for vertex number 49901 of the outer mesh is 1.9168 lGI for vertex number 50001 of the outer mesh is 2.4523 ratio saved at 50001 lGI for v

[Freesurfer] Fwd: FindFacePath

its: ERROR: _FindFacePath: could not find path! any ideas? - the scan looks (is) crappy due to movement artifacts, which may well be the cause. best, -joost -- Forwarded message ------ From: j janssen <[EMAIL PROTECTED]> Date: Tue, Sep 16, 2008 at 2:05 PM Subject: FindFacePat

Re: [Freesurfer] Re: can not see the pial surface using tksurfer

which does this for you). > > - copy tksurfer.bin from here: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable/centos4_x86_64 > > to here: > $FREESURFER_HOME/bin > > Nick > > > On Wed, 2008-04-30 at 12:31 +0200, j janssen wrote: > &

[Freesurfer] Re: can not see the pial surface using tksurfer

Hi, i can not see the pial surface using tksurfer. i´m using Fedora core 7, 64 bits, with version: freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.3-full.tar.gz, with nvidia card. when i enter