Freesurfer May 2009

freesurfer@nmr.mgh.harvard.edu

81 participants
126 discussions

LGI error in make_outer_surface at 31
by Juranek, Jenifer 07 Apr '11

07 Apr '11

Hi, Encountering some difficulties with LGI on a RHEL4 box (64bit) with MATLAB v7.6.0.324 (R2008a) installed. Subject was processed under fsv405. Specific error is pasted below: Any suggestions to correct my error? Thanks, Jenifer >> reading filled volume... closing volume... ??? Undefined function or method 'fspecial' for input arguments of type 'char'. Error in ==> make_outer_surface at 31 Gaussian = fspecial('gaussian',[2 2],1); >> ERROR: make_outer_surface did not create output file 'tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Sep 24 11:51:01 CDT 2008 [jjuranek@localhost jjuranek_fsv405]$

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masking out ROIs on the surface
by Mishkin Derakhshan 07 Nov '09

07 Nov '09

Hello list, I would like to create a mask on fsaverage/surf/?h.pial that masks out the areas where the surface does not follow the cortex, but is just cutting across the mid line or across the brain stem. I know Freesurfer does this to maintain the surface toplogy, and I think it only does this in these two areas. Does a simple txt file with n vertices and a 0 or 1 value at each vertex exist somewhere? Has anyone on the list bothered to label this area manually and would be willing to share? thanks, mishkin

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Longitudinal analysis with old version
by l.gutierrez＠ion.ucl.ac.uk 11 Sep '09

11 Sep '09

Hi, We have installed the 4.0.1 version and we are starting the longitudinal analysis. I have some problems with -base flag( recon-all -base <baseid> -base-insubj <tp1subjid> -base-insubj <tp2subjid> ... -all). Should 4.0.1 version be one problem in order to do that? Many thanks Leticia >

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mri_volcluster --ERROR: you must specify a pos or neg sign with --fwhm
by PKUNWAR＠nmr.mgh.harvard.edu 26 Aug '09

26 Aug '09

Hi all, I was going through the FSFAST TUTORIAL from wiki( https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial?action=highlight&v…) I got the follwoing error during mri_volcluster, "NOT Adjusting threshold for 1-tailed test ERROR: you must specify a pos or neg sign with --fwhm" I have fwhm.dat file with 4. something vlaue. Command used, [galen:odd-v-0] (nmr-std-env) mri_volcluster --in tal.rfx.osgm/osgm/sig.nii --thmin 2 --fwhmdat tal.rfx.osgm/fwhm.dat --cwpvalthresh 0.1 --mask tal.rfx.osgm/mask.nii --fsaverage --sum tal.rfx.osgm/osgm/cluster.sum --cwsig tal.rfx.osgm/osgm/cwsig.cluster.nii --out tal.rfx.osgm/osgm/sig.cluster.nii --ocn tal.rfx.osgm/osgm/ocn.cluster.nii without --fwhmdat flag, it gave me another error "ERROR: need csd with --cwsig" will appreciate for help thanks pratap ----------------------------------- FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.1-20070927 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64 NMR Center info (/space/freesurfer exists): machine: galen SUBJECTS_DIR: /autofs/space/galen_003/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/subjects PWD: /space/galen/3/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/fb1-preproc-study/group-analysis-tut/sm-gamma-fwhm5/odd-v-0

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Multiple Comparison - Clusterwise Correction
by Devdutta W 01 Jul '09

01 Jul '09

Hi Freesurfers, More questions about this analysis. 1) Referring to the documentation, we used the following command: tksurfer fsaverage lh inflated -annot mc-z.abs.2.sig.ocn.annot -fthresh 2 -curv -gray The documentation says we should see an image as shown in Figure 1 (attached). But what we see is Figure 2 (also attached). Can somebody explain this? 2) When running the simulation does it matter what threshold we use? For example, can we use a threshold of 2 or 3 (instead of 4 as shown in documentation) when running mri_glmfit-sim? And do we have to use the same threshold while displaying the clusters after? Thanks for any help. Devdutta

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Option --fwhm with command mri_nu_correct.mni
by Ed Gronenschild 01 Jun '09

01 Jun '09

Hi I tried to use option --fwhm 0.1 with mri_nu_correct.mni and noticed that this is incorrectly interpreted as option --distance 0.1. This script reads if($#FWHM) set cmd = ($cmd -distance $FWHM); whereas this should be if($#FWHM) set cmd = ($cmd -fwhm $FWHM); Is it possible to correct the mri_nu_correct.mni script? Ed

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volume comparisons
by Samantha Clark 01 Jun '09

01 Jun '09

Hi, I was wondering if there was a way to compare t1 or t2 maps between 2 subjects using the volume brain as opposed to the surface brain. To be specific I have two brains which are T1 maps. I want to see the differences in T1's between the two brains. How would i go about doing this. I hope i am clear in my question. --sam

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FS-FAST mkanalysis GUI Bug. Please Read!
by Douglas N Greve 31 May '09

31 May '09

IMPORTANT! PLEASE READ! I am writing to let you know I have recently uncovered a bug in FSFAST. While I don't expect the bug to have widespread effects, the places where it does have an effect could be serious. I have set up the following web page to document the bug and help track what is being done to asses its impact and to fix it: surfer.nmr.mgh.harvard.edu/fswiki/FsFastGuiBug The bug has to do with contrasts configured with the mkanalysis Graphical User Interface (GUI). The bug is particularly bad for unbalanced contrasts, eg, comparing A to the AVERAGE of B and C. The contrast actually would compare A to the SUM of B and C. Please read the above wiki page for more details. If you have not used the GUI, then you are unaffected. I am currently developing tools to detect and fix these errors. If you are (or think you might) affected by this bug, please email me as I'd like to know exactly how widespread the problems really are. Finally, I apologize for the inconvenience that this will cause. doug ps. Thanks to Amitai Shenhav and Moshe Bar for bringing this to my attention. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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sulc and mid-surface
by Zhangyuanchao 30 May '09

30 May '09

Dear Mr or Ms, Thanks a lot for your previous help! In freesurfer wiki, I notice the description of 'sulc', that is how far removed a particular vertex point on a surface is from a hypothetical "mid-surface" that exists between the gyri and sulci." I am still not quite clear about sulc and how it is calculated, could you recommend me the revelant paper on how to calculated it? Thanks, Best Regards yczhang ___________________________________________________________ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/

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one more question about curvature
by Zhangyuanchao 29 May '09

29 May '09

When I compare the thickness measure among subjects, I have to resample and smooth the thickness, so that each data have the same number of vertices and which are in correspondence with one another across subjects. Now I have .curv files or .sulc files for each subject and would like to make group analysis for these datasets. To compare the curvature and sulc measures, can I follow the same procedures as above ( ie I repeat the resampling and smoothing steps as I do for thickness)? If yes, how should I choose FWHM？ By the way, could you recommend me relevant papers that calculates the following indices : k1 maximum curvature k2 minimum curvature K Gaussian = k1*k2 H Mean = 0.5*(k1+k2) C Curvedness = sqrt(0.5*(k1*k1+k2*k2)) S Sharpness = (k1 - k2)^2 BE Bending Energy = k1*k1 + k2*k2 SI Shape Index = atan((k1+k2)/(k2-k1)) FI Folding Index = |k1|*(|k1| - |k2|) .sulc, .curv So that I can get a better understanding of what the above measures reflects. Thanks a lot! yczhang ___________________________________________________________ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/

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Freesurfer May 2009