Freesurfer January 2009

freesurfer@nmr.mgh.harvard.edu

72 participants
137 discussions

Smoothing
by Rodd Pribik 20 Jan '09

20 Jan '09

Hello All, Is it possible to adjust the amount of smoothing? I am interested in making my surfaces a bit rougher. Thanks, Rodd

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Problem with lgi
by Christian Scheel 20 Jan '09

20 Jan '09

Dear all, I am trying to compute the local gyrification index but unfortunately encounter the problem below. Matlab Version (7.7.0.471 - R2008b) and also the Image Processing Toolbox are installed on my computer. As I understand 'make_outer_surface' does not find 'tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz.gz'. However when checking the surf directory I can see that tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz.gz exists. So maybe it is just a path problem? Any help is greatly appreciated! Best wishes, Christian Scheel --- Here is the output: [root@localhost christian]$ recon-all -s bert -localGI Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.1.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.1.0 INFO: SUBJECTS_DIR is /home/freesurfer/christian Actual FREESURFER_HOME /usr/local/freesurfer_410 -rw-rw-r-- 1 freesurfer freesurfer 906671 Jan 20 14:30 /home/freesurfer/christian/bert/scripts/recon-all.log Linux localhost.localdomain 2.6.9-67.ELsmp #1 SMP Fri Nov 16 12:48:03 EST 2007 i686 i686 i386 GNU/Linux INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer_410 Previous: /space/freesurfer/build/pub-releases/freesurfer /home/freesurfer/christian/bert/surf #-------------------------------------------- #@# Local Gyrification Index lh Tue Jan 20 14:43:39 CET 2009 mris_compute_lgi --i lh.pial ================= rm -Rf tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= ---------------------------------------------------------------------------- Warning: glibc 2.3.4 - Your version glibc 2.3.6 - MATLAB built using this version ---------------------------------------------------------------------------- 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 7.7.0.471 (R2008b) September 17, 2008 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> reading filled volume... zcat: tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz.gz: No such file or directory ERROR: problem reading fname ??? SWITCH expression must be a scalar or string constant. Error in ==> load_mgh at 158 switch type Error in ==> MRIread at 88 [mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly); Error in ==> make_outer_surface at 24 vol=MRIread(filled_volume); >> ERROR: make_outer_surface did not create output file 'tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux localhost.localdomain 2.6.9-67.ELsmp #1 SMP Fri Nov 16 12:48:03 EST 2007 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Tue Jan 20 14:43:55 CET 2009 [root@localhost christian]$ -- Psssst! Schon vom neuen GMX MultiMessenger gehört? Der kann`s mit allen: http://www.gmx.net/de/go/multimessenger

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topo_defect_before subject
by Sam Torrisi 20 Jan '09

20 Jan '09

Hi all- I'm doing the online tutorial and I can't find the subject topo_defect_before as instructed in http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData i've downloaded all the data except for the Feat-related stuff. Am I missing something? I apologize in advance for a potentially annoying newbie question. THANKS -Sam

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bad pial surfaces
by Derin Cobia 19 Jan '09

19 Jan '09

Any suggestions on how to correct the pial surface on this subject? The wm.mgz volume appears to be segmented properly, yet there are many 'strands' of gray matter in the left temporal lobes left outside of the pial surface. We have several like this; subjects are diagnosed with primary progressive aphasia. Thanks. -Derin

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mri_convert
by Feng-Xian 19 Jan '09

19 Jan '09

Hi, I am finished to run my subjects using recon-all and I would like to know the usage of mri_convert to convert the results of FreeSurfer into the analyze format or nifti. Some of the results of FreeSurfer are volumes (e.g. brainmask.mgz) and some of them are surfaces (e.g. lh inflated). What can I do to convert these formats to analysis format or nifti? Thanks in advance! Feng-Xian ------------------------------------------------- Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)

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A question about symmetry between two hemisphere
by carl＠nmr.mgh.harvard.edu 18 Jan '09

18 Jan '09

hi yczhang, see also my reply on Dec 2 2008 to frederic.andersson(a)univ-tours.fr re similar question -- search freesurfer archives on "comparing hemispheres" Ultimately to look at the symmetry question properly, we will need Doug's tool. In the interim, below is one, admittedly imperfect approach. Anyone else have a better suggestion in the interim? Suppose you have a cluster of thickness difference (or bold signal) in one hemisphere between 2 groups. Create your own average subject (to increase accuracy of visualization (but fs average would work as well). Then hand-draw the analogous cluster in the other hemisphere. To do so, you would need to determine the min and max values that occur in x, y, z in talairach space and additional control points as required for the cluster or region where the primary finding occurs . Then flip the sign on the x coordinates and hand draw the cluster in the opposite hemisphere, guided by the tal coodinates. Determine the variable of interest (mean thickness, mean bold signal, etc) in the "mirror" cluster. Input that variable into a glm/anova (outside of freesurfer) where side, group, variable of interest and test for whether there is a side x variable interaction, suggestive of a truly lateralized finding. Remember that the test statistic/significance level for the PRIMARY hemisphere finding is not appropriate to report as it is inherently biased (it is defined as the region where there is a significant between group difference. It is the "mirror" contra-lateral and the presence or absence of a side x variable interaction that is the focus. You might also be able to simply analyze the mirror cluster alone without putting the other side into the anova since it, unlike the primary finding cluster, is not a biased metric. best, carl >>>>>>>>>>>> no, the vertex index is essentially arbitrary and you can't use it to compare left and right. Doug had some tools for this, but I'm not sure whether they are ready for primetime yet. cheers, Bruce On Sun, 18 Jan 2009, Zhangyuanchao wrote: > Dear Expert, > > I want to exame the symmetry property of two hemispheres,for example, symmetry of cortical thickness or lgi, I want to know whether the same ID of the two hemispheres after resampling using the average pial surface corespond to the same anatomical region. > > > > For example, > > ID=1000, > For the left hemisphere, the vertex 1000 corespond to 'medial_wall'; what about the vertex 1000 on the right hemisphere? Is it also corespond to the same anatomical region "medial_wall" so that we can compare their cortical thickness of vertex 1000 on both left and right hemisphere to exame the symmetry property. > > > Thanks a lot! > yczhang > Carl E. Schwartz, M.D. Harvard Medical School Director, Developmental Neuroimaging & Psychopathology Laboratory Psychiatric Neuroscience Program Massachusetts General Hospital tel 617-726-8965 fax 617-726-4078

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Grey matter volume
by Alexa Nardelli 18 Jan '09

18 Jan '09

Hi, I was curious as to whether or not freesurfer obtains a total grey matter volume? Thanks Alexa

3 2

mris_divide_parcellation output problem
by Jürgen Hänggi 18 Jan '09

18 Jan '09

Dear FS experts I have run the following command: mris_divide_parcellation Ego_Mean3_FineParc rh aparc.annot 100 rh_annot_100 But cannot read the output file (see attachment) with tksurfer % [juergen-haenggis-mac-pro:subjects/Ego_Mean3_FineParc/label] juergenhaenggi% tksurfer Ego_Mean3_FineParc rh inflated -annot rh_annot_100 surfer: current subjects dir: /Applications/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Applications/freesurfer/subjects/Ego_Mean3_FineParc/label surfer: Reading header info from /Applications/freesurfer/subjects/Ego_Mean3_FineParc/mri/T1.mgz surfer: vertices=151401, faces=302798 could not read annot file /Applications/freesurfer/subjects/Ego_Mean3_FineParc/surf/../label/rh.rh_ann ot_100.annot No such file or directory ERROR: could not load rh_annot_100 surfer: single buffered window surfer: tkoInitWindow(Ego_Mean3_FineParc) surfer: using interface /Applications/freesurfer/lib/tcl/tksurfer.tcl Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... If I provided tksurfer the whole path to the annot file, the error still occurred. Thanks in advance Regards Juergen ---------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) 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) ----------------------------------------------------------

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A question about symmetry between two hemisphere
by Zhangyuanchao 18 Jan '09

18 Jan '09

Dear Expert, I want to exame the symmetry property of two hemispheres,for example, symmetry of cortical thickness or lgi, I want to know whether the same ID of the two hemispheres after resampling using the average pial surface corespond to the same anatomical region. For example, ID=1000, For the left hemisphere, the vertex 1000 corespond to 'medial_wall'; what about the vertex 1000 on the right hemisphere? Is it also corespond to the same anatomical region "medial_wall" so that we can compare their cortical thickness of vertex 1000 on both left and right hemisphere to exame the symmetry property. 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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Mris_divide_parcellation II
by Jürgen Hänggi 17 Jan '09

17 Jan '09

Dear FS experts Sorry, me again. If I divide the parcellations into areas of 100 mm2 only the most posterior part of the parcellations will be divided. Only with a threshold of about 500 mm2, the whole hemisphere's parcellations will be divided. Are there not enough labels resp. colors available? Thanks Regards Jürgen ---------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) 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) ----------------------------------------------------------

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Freesurfer January 2009