Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

Non-FDR Multiple Corrections for Volume?
by Dave Brohawn 01 Apr '09

01 Apr '09

Hello, I am curious if there are non-FDR multiple comparison correction options available for volume data? I am guessing monte carlos are possible to run for volumetric data, though I am not sure what the input file would be. It wouldn't be the mgh file made from mris_preproc, but what command could create a similar concatenated file using volume data that could produce an input file for the monte carlos? Thanks, Dave Brohawn

1 0

Non-FDR Multiple Corrections for Volume?
by Dave Brohawn 01 Apr '09

01 Apr '09

1 0

tksurfer error
by Elisa Dell'Oglio 01 Apr '09

01 Apr '09

Hi all, I am running freesurfer on CentOS (5.2-x86_64). I get the folowing error when I launch tksurfer: surfer: ### redraw failed: no gl window open. The result is that no surface is shown. Any advice on how to solve the problem? Thanks, Elisa

2 3

Command works in optseq, not optseq2
by Dan Dillon 31 Mar '09

31 Mar '09

Dear FreeSurfers, I'm having a little trouble getting something that works in optseq to work in optseq2. Here's what' is going on . . . when I run this command, things work fine and I get 6 nice sequences: optseq -ntp 170 -TR 3 -npercond 4 4 4 4 4 4 -tpercond 17 17 17 17 17 17 -label NgReal NgLook NgPhoto NuReal NuLook NuPhoto -nsessions 6 -nruns 1 -timewindow 20 -prestim 4 -nsearch 50 -o OptseqTEST However, when I run this command (i.e., my best translation of the previous command into optseq2), I get an error saying that all my schedules are ill-conditioned and I need more scan time or fewer repetitions: optseq2 --ntp 170 --tr 3 --psdwin 0 20 1 --ev NgReal 17 4 --ev NgLook 17 4 --ev NgPhoto 17 4 --ev NuReal 17 4 --ev NuLook 17 4 --ev NuPhoto 17 4 --nsearch 100 --nkeep 6 --o Optseq2TEST Is this a substantive difference between optseq and optseq2 or did I make a mistake with my optseq2 command? Also, I'm assuming there is a reason why I should use optseq2 rather than optseq, but I don't know what it is. Can someone clue me in? Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: <mailto:dillon@wjh.harvard.edu> dillon(a)wjh.harvard.edu

2 1

GM in ROIs
by Kelly Silva 31 Mar '09

31 Mar '09

Hello, Can I calculate GM in ROIs that I have done? How can I do that? Thanks and regards, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

2 1

selxavg3-sess error: matrix is singular to working precision
by Jeremy Elman 30 Mar '09

30 Mar '09

Hello all, I am trying to run a first level analysis on a subject with selxavg3-sess but keep running into the same error. The dof file is created, but that is it. Any ideas what might be causing this? Below is the error given. Thank you very much for your help, Jeremy [jelman@psych118 functional]$ selxavg3-sess -s LDR001-1 -analysis LDR-fmcsm4-rec -------------------------------------------------------------- selxavg3-sess logfile is /mtl/LDR/functional/log/selxavg3-sess-bold-LDR-fmcsm4-rec-090326144433.log -------------------------------------------------------------- ------------------------------------------- /mtl/LDR/functional/LDR001-1 Thu Mar 26 14:44:35 PDT 2009 anadir = /mtl/LDR/functional/LDR001-1/bold/LDR-fmcsm4-rec ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2008 The MathWorks, Inc. Version 7.6.0.324 (R2008a) February 10, 2008 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> $Id: fast_selxavg3.m,v 1.55.2.6 2008/05/14 20:01:35 greve Exp $ outtop = /mtl/LDR/functional Extension format = nii UseFloat = 0 INFO: acfbins is not set, setting to 10 INFO: mask is not set, setting to brain 1 old-v-new.mat Loaded /mtl/LDR/functional/LDR001-1/bold/007/ldr_paradigm.par as a par4 file. nruns = 2 autostimdur = 1 outanadir = /mtl/LDR/functional/LDR001-1/bold/LDR-fmcsm4-rec Found 155793/475136 (32.8) voxels in mask Creating Design Matrix Loaded /mtl/LDR/functional/LDR001-1/bold/007/ldr_paradigm.par as a par4 file. Warning: Matrix is singular to working precision. > In fast_selxavg3 at 208 Loaded /mtl/LDR/functional/LDR001-1/bold/011/ldr_paradigm.par as a par4 file. Warning: Matrix is singular to working precision. > In fast_selxavg3 at 208 ntptot = 364, nX = 14, DOF = 350 ??? Error using ==> svd Input to SVD must not contain NaN or Inf. Error in ==> cond at 40 s = svd(A); Error in ==> fast_selxavg3 at 239 XCond = cond(XtX); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n

2 1

active volume of surface-based analysis
by Wang, Xin 30 Mar '09

30 Mar '09

Hello, Freesurfer group, In the tutorial of surface-based fMRI analysis, the active volume are calculated from the entire depth of an given active vertex. I do not think it is the best way to measure it since no all activities occupy the entire depth of cortex. A logical way to get accurate active volume is measuring the active verities of multiple planes (e.g., at 0.1 mm distance) and then constructing the active volume from activity on these planes. A option (similar as --projfrac_max) can project the sum of all planes on the surface, and 3D active volume can be viewed in tkmedit. Does Freesurfer currently have commands to achieve something like this procedure? I am looking forward to hearing from you ASAP. Thanks, Xin

2 1

GM
by Kelly Silva 30 Mar '09

30 Mar '09

Hello, How can I calculate the GM using the FSL? Thanks, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

4 3

Incorrect correspondence in the aparc+aseg.mgz volume?
by Ryan Scotton 30 Mar '09

30 Mar '09

Hi FreeSurfers, After a months of QC'ing FreeSurfer results, my team and I are now working toward end stage analysis of our cortical thickness data. All along, we have been aiming to make improvements in the wm.mgz volume so that we can assure that the white matter and gray matter surfaces are as accurate as possible. This was under the assumption that if the white matter and gray matter surfaces are accurate, then the voxel-wise representation of the white and gray matter in the aparc+aseg.mgz file would be accurate. However, in almost all of our cases, the aparc+aseg.mgz segmentation looks very bad. The bad aparc+aseg.mgz representation of what seem to be accurate white and gray matter segmentations in the wm.mgz file is leading us to believe that the cortical correspondences created after template mapping are wrong. Does anyone else have an explanation for such a discrepancy? Is this a common problem and if so, is there any way to remedy this situation? Thanks, Ryan

3 11

sulcal width
by Prapti Gautam 30 Mar '09

30 Mar '09

Dear Freesurfers, Is there a reliable way to measure sulcal widths from T1 images using Freeesurfer? I have found information on sulcal curvatures and depth but not on width measurement and am wondering if it is possible to do so. Thanks, Prapti

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