Freesurfer October 2012

freesurfer@nmr.mgh.harvard.edu

119 participants
191 discussions

error: 'fast_contrastmtx' undefined near line 25 column 21
by Garlinghouse, Matthew 29 Oct '12

29 Oct '12

Dear Surfers, I was running mkcontrast-sess with Matlab and having good success. Then wanted to try Octave for ease of use on a cluster I have access to, and after browsing the listserv set the following: export FS_USE_OCTAVE=1 export FS_OCTAVE_LIB=/usr/lib64/octave export FS_OCTAVE_BIN=/usr/bin/octave However when I run mkcontrast-sess now (on the cluster and a VB ubuntu machine, both without Matlab), it runs through launching Octave and then errors out as noted below. I'm new to using Octave and wasn't sure what else I might need to set up for it to run properly? Any thoughts would be much appreciated. Best Regards, Matthew brain@neurodebian:/usr/local/freesurfer/subjects$ mkcontrast-sess -analysis test.08.lh -contrast faces_gt_objects -a 2 -c 3 INFO: Found 3 Non-Null Conditions INFO: Found 1 Delays Condition Weights: 0 1.00000000000000000000 -1.00000000000000000000 mkcontrast -anadir test.08.lh -wcond 0 1.00000000000000000000 -1.00000000000000000000 -sumconds -o test.08.lh/faces_gt_objects.mat -wdelay 1 -octave $Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $ cmtxfile test.08.lh/faces_gt_objects.mat nconds 3, wcond 0 1.00000000000000000000 -1.00000000000000000000 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau GNU Octave, version 3.2.4 Copyright (C) 2009 John W. Eaton and others. This is free software; see the source code for copying conditions. There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. For details, type `warranty'. Octave was configured for "i486-pc-linux-gnu". Additional information about Octave is available at http://www.octave.org. Please contribute if you find this software useful. For more information, visit http://www.octave.org/help-wanted.html Report bugs to <bug(a)octave.org> (but first, please read http://www.octave.org/bugs.html to learn how to write a helpful report). For information about changes from previous versions, type `news'. error: `fast_contrastmtx' undefined near line 25 column 21 ________________________________ The Nebraska Medical Center E-mail Confidentiality Disclaimer The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

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Different steps of RecommendedRecontruction on different operating systems possible?
by Thomas Fink 28 Oct '12

28 Oct '12

Dear Freesurfers, I know that differences in FS versions and operating systems can lead to different results. Thus my question: Would it be possible/advisable to run different steps of the RecommendedRecontruction on different operating systems? I would like to do talairach and control points for all my healthy subjects on a Linux based computer (Suse) and then switch to a Mac (OS X Mountain Lion) for further steps and use 5.1 on both machines. Thank you very much for your time. Thomas

3 2

make_face_parcellation ambiguous color table
by Franz Liem 26 Oct '12

26 Oct '12

Dear Freesurfers, I have performed make_face_parcellation on fsaverage (with ic5) (Darwin-leopard-i686-stable-pub-v5.1.0). I read_annotation ed the parcellation into matlab an noticed that while colortable.table has 10242 rows (as expected), length(unique(colortable.table(:,5))) produces 9834 => some entries are in the list more than once. If I grasped the procedure correctly, the entries in label are determined by colortable.table(:,5) and colortable.table(:,5) is determined by: % Column 5 is the structure ID, calculated from % R + G*2^8 + B*2^16 + flag*2^24 One example for this problem is colortable.table(43,:) and colortable.table(86,:) both read: 0 0 170 0 11141120 How are Rm G, B determined? I guess one quick fix would be to introduce flags >0. Would that affect anything else? Or, is there a way to force my own indices onto colortable.table(:,5)? (if I change this entry, save the annot and load the annot, the entry is at R + G*2^8 + B*2^16 + flag*2^24 again (I already encountered the effects of this problem a couple of months ago (2. in this post http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21189.html).) Thank you so much for your help, Franz

2 4

Retinotopy: Group map on fsaverage
by Andreas Schindler 26 Oct '12

26 Oct '12

Dear freesurfers Have you ever tried to get an average retinotopic map across all subjects on freesurfer's standard surface (fsaverage)? I obtained an individual map for each subject using the fsfast stream (mkanalysis-sess, selxavg3-sess) and plotted the results using rtview: e.g. rtview.sh --s subj1 --lh --polar --real polar/real.nii.gz --imag polar/imag.nii.gz --fsig polar/fsig.nii.gz Now for the group map, my initial idea was to sample each subject's real and imaginary component to the fsaverage surface and average them separately across subjects. However, I am not sure how I would threshold such an average map on fsaverage using rtview (i.e. what would I use as fsig.nii) given that averaging log p-values is probably not a good idea. Within each subject's rtopy.self.?/polar(or /eccen) folder the following files (and few more but probably not important here) exist: fsig.nii -> I understand this contains the unsigned log p values probably obtained via an F-test (frequency of interest) / (noise frequencies) sig.nii -> this might then be the signed counterpart of fsig.nii imag.nii -> this must contain the imaginary component of the polar angle or eccen map real.nii -> this must contain the real component of the polar angle or eccen map mag.nii -> I suppose this might contain the amplitude of the signal at the frequency of interest (i.e. the frequency the wedge / ring is traveling) However, I don't quite know what the remaining files are good for iminsig.nii minsig.nii cwmap-imag.nii cwmap-real.nii ces.nii cesmag.nii cesmagpct.nii cespct.nii cesvar.pct cesvarpct.nii For the ces* files I understand that they generally contain effect sizes / variances and are used for group analyses. However, I am not quite sure what effects they correspond to in the case of retinotopy. When browsing the web for similar problems I found the following post: > Hi Michelle, try this: > > isxconcat-sess -sf sessidlist -a rtopy.fsaverage.lh -call -o retgroup > > cd retgroup/rtopy.fsaverage.lh > > mri_glmfit --y eccen/ces.000.nii.gz --osgm --o eccen/glm.real --surface > fsaverage lh > mri_glmfit --y eccen/ces.001.nii.gz --osgm --o eccen/glm.imag --surface > fsaverage lh > mri_glmfit --y polar/ces.000.nii.gz --osgm --o polar/glm.real --surface > fsaverage lh > mri_glmfit --y polar/ces.001.nii.gz --osgm --o polar/glm.imag --surface > fsaverage lh > > mri_fieldsign --fs lh.fieldsign.mgh \ > --eccen eccen/glm.real/osgm/gamma.mgh eccen/glm.imag/osgm/gamma.mgh \ > --polar polar/glm.real/osgm/gamma.mgh polar/glm.imag/osgm/gamma.mgh \ > --s fsaverage --hemi lh --sphere --old > > tksurfer fsaverage lh inflated -aparc -ov lh.fieldsign.mgh -fthresh .5 However, as mentioned above I wonder what effect sizes are used here and why (different to rtview) there is no significance map needed to plot the data. Is there a way to use rtview for the result of a group analysis? And if yes how would I get a fsig.nii file for that? I really appreciate your help! many thanks & best wishes Andreas

2 1

Cannot save edited label
by Jürgen Hänggi 26 Oct '12

26 Oct '12

Dear FS experts I used mri_annotation2label to extract the superior frontal gyrus label from the aparc annotation. I edited (cut plane) this label in tksurfer and then tried to save it using Save Selected Label. However, the whole label is saved including also the part that I have cut away. Any idea what is going wrong here? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

2 3

recon-all crash
by Jesse Bledsoe 25 Oct '12

25 Oct '12

Hello experts, Wonder if you could help me with the following error after running "recon-all -all -subjid BT6403 -qcache": ---------- unfolding failed - restoring original position -------------------- 0581: dt=0.112000, rms=0.602 (0.000%), neg=0, invalid=766 writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is: gzip -f -c > transforms/talairach.m3z registration took 2 hours, 50 minutes and 30 seconds. /var/local/scratch/bledsoe1/ Desktop/Braintumor/BT_6403/touch/ca_register.touch: No such file or directory. bledsoe1 @ivan:~/Desktop/Braintumor/BT_6403$ Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Any suggestions are much appreciated, Jesse

1 0

znzTAGskip error using mri_em_register
by Kim, Daniel 25 Oct '12

25 Oct '12

Hello FreeSurfer users, I was finally able to compile mri_em_register successfully from source and trying to test the build with subject 'bert', I ran into this error ~/freesurfer/bin# ./mri_em_register -uns 3 -mask $SUBJECTS_DIR/bert/mri/brainmask.mgz $SUBJECTS_DIR/bert/mri/nu.mgz $FREESURFER_HOME/average/RB_all_2008-03-26.gca $SUBJECTS_DIR/bert/mri/transforms/talairach.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume /usr/local/freesurfer/subjects/bert/mri/brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer_4_5_0/freesurfer/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading '/usr/local/freesurfer/subjects/bert/mri/nu.mgz'... znzTAGskip: tag=-8454144, failed to calloc 4286513152 bytes! Cannot allocate memory Has anyone had similar error before? I'm using Ubuntu 10.04 LTS- 64 bit and I've built mri_em_register from scratch using CVS public checkout "-P dev" The test subject was through installing freesurfer 5.1.0 and also same has happened with freesurfer 4.5.0 Any help with this would be again greatly appreciated! Cheers! Danny Kim

2 2

residual after mri_glmfit
by Minjie Wu 25 Oct '12

25 Oct '12

Dear FreeSurfers, I have a question regarding mri_glmfit: Is it possible to get the residual data after mri_glmfit? Thank you very much. Minjie

2 1

mri_ca_register error
by Matt Leonard 24 Oct '12

24 Oct '12

Hello, I'm trying to run a simple recon on a single T1 dataset, and am not interested in any quantitative measures (this is just for data presentation and eventual MRI/CT co-registration). To save time, I tried to skip the CA registration step, but got the following error: #-------------------------------------- #@# CA Reg Inv Wed Oct 24 14:49:20 PDT 2012 /Applications/freesurfer/subjects/CH/mri \n mri_ca_register -invert-and-save transforms/talairach.m3z \n Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 So then I tried skipping all the steps that appear to need the talairach.m3z file, and used this command: recon-all -s CH -autorecon2 -nocanorm -nocareg -normneck -noskull-lta -nocalabel -nosegstats That gave the same error. What am I doing wrong as far as skipping the careg step? Thanks, Matt

2 1

Trac-all Error
by Franklin, Crystal G 24 Oct '12

24 Oct '12

Freesurfer, I am trying to run trac-all –prep and trac-preproc keeps exiting with errors. It keeps saying the unwrappedphasemaps must contain at least two volumes. My data only contains one phase image and 2 magnitude images. Do you know what could be causing this error or how to get around it? Thanks in advance, Crystal

2 1

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Freesurfer October 2012