Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

mc-sess in freesurfer 5.0
by Luis Lafer-Sousa 29 Nov '10

29 Nov '10

We are having an issue with scripts we used in freesurfer 4.5.0 but no longer work in 5.0.0. It is the mc-sess step, and we receive: ERROR: Flag -toff unrecognized. -sf sf -df df -fsd bold -rlf ./tmp_run_list -toff 0 Done... On the wiki, that flag is still recognized. When we delete it, we then receive a "by run" or "by session" error. I suspect this has something to do with the freesurfer or AFNI update, but we do not know what the new mc-sess takes as tags since the wiki has not changed. Does anybody know how mc-sess has changed? Thank you, Luis L.S.

3 3

qdec analysis and covariates
by Roser Sala 29 Nov '10

29 Nov '10

Hi, We are doing a group analysis using qdec with two groups, and we would like to include gender and age as covariates. Which is the best option in order to perform a simple t-test (group1>group2 and group2>group1) and including the two covariates? (we would like them to have 'zero' weighting in the contrast matrix) We realized that if we include 'age' as a continous factor in the dialog, qdec is performing rather an interaction analysis than a covariate. So, would it be ok to include group and gender as fixed factors and age as nuisance, and then select the output as 'Does the average thickness accounting for gender differ between group1 and group2' (age as nuisance variable)? By checking all the possibilities this seemed the best option for us, but we would like to get a confirmation that we are doing it right. Many thanks Roser

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mri_compute_seg_overlap vs. mri_compute_overlap
by Jeff Dewey 27 Nov '10

27 Nov '10

Hi all, I'm using mri_compute_seg_overlap to calculate dice coefficients for two asegs, and the numbers look reasonable. However, for two of my comparisons, mri_compute_overlap reports zero overlapping voxels between the segmentations. Do these two commands compute overlapping voxels in a different way? Is there another reason why these two commands might report conflicting information? Thanks much for any advice, Jeff

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how to overlap two signicant regions together
by keepmoon 26 Nov '10

26 Nov '10

Dear everyone, Anyone knows how to display overlap regions of two significant changes in one image ? For example, I got the significantly different regions of thickness and curv between patients and controls. Normally we can display them seperately, but now I want to display them together so that I can see clearly where thickness and curv have the same changing regions and where just thickness changes or just curv changes. I will be very appreciated if anyone gives me some advice! Thanks! Joe

1 0

Feeding more than one MPRAGE into recon all
by Arman Eshaghi 25 Nov '10

25 Nov '10

Dear freesurfer experts, Sorry to bother the list with this question again, but I searched the archive and documentation without success. I want to feed more than one MPRAGE datasets taken independently in a single session into recon all. How should I do that? Is there any command inside freesurfer for averaging dcm files? Hoping for an answer and gratefully All the best, Arman

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Brain Segmentation Volume Without Ventricles
by Mailinglisten Lifeandbrain 25 Nov '10

25 Nov '10

Dear ladies and gentlemen, unfortunately the new version (5.0.0) does not compute the Brain Segmentation Volume Without Ventricles in the aseg.stats file any more. Is it possible to fix this problem? Kind regards, Dr. med. Jan Wagner University of Bonn Department of Epileptology Sigmund-Freud-Str. 25 53127 Bonn phone +49 (0)228-287-76140 fax +49 (0)228-287-76261 mail jan.wagner(a)ukb.uni-bonn.de

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preproc-sess error in version 5.0
by yuko YY 25 Nov '10

25 Nov '10

Hello, I recently switch to version 5, and am having a problem with preproc-sess in version 5.0. version: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 OS : Mac 10.6.5 When I ran: preproc-sess -per-session -fwhm 5 -force -surface VM20 lhrh -df sessdirfile -s VM20 -fsd bold I got the following error: %-------------------------------------------------------------------------------------------------------------------------------------------- [Yukos-iMac:sessions/VM/VMan] yuko% preproc-sess -per-session -fwhm 5 -force -surface VM20 lhrh -df sessdirfile -s VM20 -fsd bold -------------------------------------------------------------- preproc-sess logfile is log/preproc-sess.log -------------------------------------------------------------- $Id: preproc-sess,v 1.31.2.4 2010/07/26 15:55:24 greve Exp $ yuko setenv FREESURFER_HOME /Applications/freesurfer/freesurfer setenv SUBJECTS_DIR /Users/yuko/Documents/freesurfer/subjects Darwin Yukos-iMac.local 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386 /Users/yuko/Documents/FreeSurfer/sessions/VM/VMan /Applications/freesurfer/freesurfer/fsfast/bin/preproc-sess -per-session -fwhm 5 -force -surface VM20 lhrh -df sessdirfile -s VM20 -fsd bold Tue Nov 23 19:46:29 JST 2010 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain VM20 Template ----------------------------- mktemplate-sess -s VM20 -d /Users/yuko/Documents/FreeSurfer/sessions/VM -fsd bold Session: /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20 ---------------- Tue Nov 23 19:46:29 JST 2010 find: illegal option -- m find: illegal option -- a find: illegal option -- e find: illegal option -- p find: illegal option -- t find: illegal option -- h find: 1: No such file or directory ERROR: no run directories found %-------------------------------------------------------------------------------------------------------------------------------------------- I found the same error reported in msg14982, but couldn't find a solution. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14982.html Can anyone tell me what I need to do to make this work? Yuko Yotsumoto % additional info -------------------------------------------------------------------------------------------------------------------------------------------- My data are at: sessions/VM/VM20/bold/001/f.nii sessions/VM/VM20/bold/002/f.nii .. sessions/VM/VM20/bold/009/f.nii and my study directory is at: sessions/VM/VMan/ subject is at: subjects/VM20 %--------------------------------------------------------------------------------------------------------------------------------------------

2 4

"Invalid access of stack red zone"
by yuko YY 25 Nov '10

25 Nov '10

Hi, I'm having a java-related error with mkcontrast-sess. Are there any trick to get around this error? version: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 OS : Mac 10.6.5 javac 1.6.0_22 mkcontrast-sess -analysis VMfwhm5 -contrast all_null -a 1 -a 2 -a 3 -a 4 -a 5 -c 0 -rmprestim % - (error message) --------------- Invalid capturehandle provided. No capture device associated with this handle !!! Opening log file: /Users/yuko/java.log.14247 Illegal instruction % --------------------------------------- more /Users/yuko/java.log.14247 % -------------------------------- Operating System: Darwin 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386 Processor ID: x86 Family 6 Model 14 Stepping 5, GenuineIntel Host Name: Yukos-iMac.local Invalid access of stack red zone 0xb0105b2c eip=0x1fd64c % -------------------------------- Looks like a problem with java as discussed here: http://stackoverflow.com/questions/1501770/invalid-access-of-stack-red-zone… I've updated java, and got the same error. Thank you for your help! Yuko Yotsumoto

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Intracranial brain mask
by Tanner,Jared J 24 Nov '10

24 Nov '10

Hi, We want to control for intracranial volume in our analyses but we would like verify the reliability and validity of the ICV volume reported in the aseg.stats file (I know the methods reported on the WIki - http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV but haven't seen much in the way of a mask file we could look at). Is there an actual ICV mask file we can look at and load (and potentially edit)? Or, if not, is there an easy way to create an ICV mask? Thank you, Jared Tanner University of Florida

2 1

Recon-all in 7 hours
by Pedro Paulo de Magalhães Oliveira Junior 24 Nov '10

24 Nov '10

Hi, I have recently tried the recon-all process in bert dataset in the new Amazon EC2 instance with a very powerful GPU. The results are very impressive: recon-all -s bert -use-gpu -all finished in 7hours and 15 minutes. It is a useful solution when you are in a hurry to finish some cases. It's a bit pricey: US$ 2.10 / hour It's supposed to run 8 cases simultaneously, but I didn't try it. Also I tried the Small EC2 instance and it can run a recon-all case in 27-35 hours with a cost of US$ 0.085 / hour. The advantage is that you can start hundreds of instances and finish your big study in one day if you can afford it :) cheers PPJ --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile

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