Freesurfer June 2008

freesurfer@nmr.mgh.harvard.edu

58 participants
77 discussions

(no subject)
by Damian Jenkins 24 Jun '08

24 Jun '08

I think this may have been something that other people have figured out, and I would be grateful to know how. In the past week if I try to run autorecon-2 it fails. Running each individual command that make up autorecon-2 it would seem that the error is with the final stage (-cortribbon). The message this generates reads as: mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance avC06-1 mris_volmask.bin: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No such file or directory Linux jalapeno25.fmrib.ox.ac.uk 2.6.18-53.1.14.el5 #1 SMP Wed Mar 5 11:37:38 EST 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS How can I get around this? Thanks, Damian Dr Damian Jenkins Department of Clinical Neurology Oxford University

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cortical thickness
by Feng-Xian Yan 24 Jun '08

24 Jun '08

Hi, After I ran the qdec and analyzed my data(cortical thickness). I have two questions. First, after I display a plot of the data for a particular vertex by left-clicking on a point while holding down the Ctrl key, it shows a plot and its plot window shows this vertex's surface coordinates. What model is the surface coordinates used? Second, after analyzing the thickness, it shows the color bar's scale in p-value. How do I do to change the scale from p-value to mm? .

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conjoining labels
by Catherine Hartley 23 Jun '08

23 Jun '08

Hi, I can't seem to figure out how to save two or more labels as a conjoined single label. Thanks in advance, -Cate

2 1

GRF correction
by Catherine Hartley 23 Jun '08

23 Jun '08

Hi, I understand that there are tools under development implementing Gaussian Random Field correction for multiple comparisons. If there is a usable version available (and a brief description of how to use it), I'd like to try it out. Thanks in advance, Cate Hartley

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Talairach_avi and eTIV, version 3.0.5 vs 4.0.5
by Paul Greenberg 23 Jun '08

23 Jun '08

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white matter volume - version 3.0.5 vs 4.0.5
by Paul Greenberg 23 Jun '08

23 Jun '08

Dear Freesurfers, Is it acceptable to use the program "mris_wm_volume" from version 4.0.5 (Cent OS, x86_64) to calculate total white matter volume from data processed with version 3.0.5? Would I need to subtract any subcortical volumes such as ventricles, basal ganglia, etc, from the output of mris_wm_volume (version 4.0.5) in order to get the most accurate measurement of total white matter volume? Thanks! Paul -- Paul Greenberg, Ph.D. Radiology Department, University of California, San Diego VA San Diego Healthcare System (116A-13) 3350 La Jolla Village Drive San Diego, CA 92161 Phone: (858) 552-8585 ext. 2903 Fax: (858) 642-3836 pgreenberg(a)ucsd.edu

1 0

inorm-sess error
by Leila Reddy 23 Jun '08

23 Jun '08

Hi, I'm trying to get around the problems from my previous post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07669.html I am now trying to use mri_convert to convert from nifti to bshort using the following command: mri_convert -i rfkoch-0021-00144-000144-00.nii -it nii -o fspm2_000.bshort -ot bshort The bshort files seem to be created but then when I run inorm-sess I get the following error. The odd thing is that when I used mri_concat on exactly the same .nii files (as mentioned in my previous post) I was able to run inorm-sess with no errors... What is the difference between these two commands? The inorm error: Warning: Matrix is singular to working precision. > In fast_inorm at 196 ??? Error using ==> betainc at 35 X must be in the interval [0,1]. The exact output from the command is pasted below. Here is the output of bugr: --------------------------------------------------------------------- FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-tiger-i686-stable-pub-v3.0.5 Kernel info: Darwin 8.11.1 i386 --------------------------------------------------------------------- If anyone has any suggestions I'd be grateful to hear them! Thanks! inorm-sess -sf sessid -df sessdir -rlf runlist_inormcheck -funcstem fspm2 ------------------------------------------------ ------------------------------------------------ ------------------------------------------------ /Volumes/donnees/Imagery/imagery_data/RF005 Thu Jun 19 17:43:17 CEST 2008 Filesystem 512-blocks Used Avail Capacity Mounted on /dev/disk0s3 808067040 465870224 342196816 58% /Volumes/donnees RunList 021 ---------------------------------------------- /Volumes/donnees/Imagery/imagery_data/RF005/bold inorm -i 021/fspm2 -umask 22 -TR 2.0000 -ipr 3 -bpr 2.9999998958184 -seqname PerImg ---------------------------------------------- Log file is 021/inorm.log inorm matlab file is /tmp/inorm_21280.m ----------- Matlab file -------------- %%% ----------------- %% % matlab file to run inorm % This is a temporary file and may be deleted % /tmp/inorm_21280.m global QuitOnError; QuitOnError = 1; r = fast_inorm( '-i', '021/fspm2', '-umask', '22', '-TR', '2.0000', '-ipr', '3', '-bpr', '2.9999998958184', ' ', 'PerImg'); quit; ----------------------------------- ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display iconic, MATLAB is starting without a display. You will not be able to display graphics on the screen. < M A T L A B > Copyright 1984-2007 The MathWorks, Inc. Version 7.4.0.287 (R2007a) January 29, 2007 Warning: Duplicate directory name: /Users/lreddy/matlab. To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> $Id Parsing Arguments Checking Parameters invol 021/fspm2 firstslice 0 nslices 32 relthresh 0.750000 reportfile 021/fspm2.report meanvalfile 021/fspm2.meanval twfstem 021/fspm2.twf TR 2.000000 First Pass: Computing global mean 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 Second Pass: Segmenting 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 Warning: Matrix is singular to working precision. > In fast_inorm at 125 Warning: Matrix is singular to working precision. > In fast_inorm at 146 Warning: Matrix is singular to working precision. > In fast_inorm at 175 Warning: Matrix is singular to working precision. > In fast_inorm at 196 ??? Error using ==> betainc at 35 X must be in the interval [0,1]. Error in ==> tTest at 37 p = betainc(z,dof/2,0.5); Error in ==> fast_inorm at 223 tSigCor = tTest(s.ntp-2,tCor); >> 2008-06-19 17:43:31.661 MATLAB[21307] Process manager already initialized -- can't fully enable headless m

1 0

Reanalyzing some OASIS cases
by Martin Kavec 23 Jun '08

23 Jun '08

Hi, I would like to rerun recon-all (from the latest freesurfer) on a few cases from OASIS brains study, to get control values for my patient group. Since my computational options are rather limitted, I would like to avoid running redundant steps, which would anyway give me the same results, or to repeat possible surface editing. Anybody could please suggest me where to start the analysis or in general how to tackle this problem? Thanks in advance, Martin

1 0

cortical measures - normalised?
by Narly A Golestani 21 Jun '08

21 Jun '08

Dear all, Am I correct in thinking that the measures of cortical volume, area, and thickness, as well as subcortical volumes obtained after running the reconall pipeline (and found in the 'aparc' and 'aseg' files, respectively) are native ones? Or are they based on normalised brains, thus 'controlling' for overall brain volume differences? thanks, Narly.

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Erosion of Fill Volume/Pial Surface
by Cochrane Jamison 19 Jun '08

19 Jun '08

I have been working on getting a volume created by mris_fill from the pial surfaces exported to be used in a dipole/current density analysis software package. I have succeeded in being able to concat both halves and have gotten the volumes loaded successfully into the software, but I need a bit better resolution. My question is this: Is there a way to erode the pial surface either before or after its creation? I need maybe 0.5 - 1mm of erosion so that each sulci is a bit more defined. The surface looks great, but in order to consider the grey matter in each sulci for the dipole/current density calculation, each sulci needs to be distinct. The only way that I can think about it is by eroding the grey matter by 0.5-1mm before I use the mris_fill command. I am not sure if this is even possible, or if it is where it would need to be done. Thanks for any help. Cochrane

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Freesurfer June 2008