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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

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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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mris_divide_parcellation
by Jürgen Hänggi 17 Jan '09

17 Jan '09

Daer FS experts When using the command: mris_divide_parcellation Ego_Mean3_FineParc rh aparc.annot 100 rh_annot_100 Only some posterior brain areas (see attachment) were further divided, not the whole hemisphere. Why? Thanks 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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mris_divide_parcellation output problem solved
by Jürgen Hänggi 17 Jan '09

17 Jan '09

Dear FS experts My former problem is solved. When loading the produced annot with the GUI, the formerly reported problem disappear. 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 17 Jan '09

17 Jan '09

Dear Mr or Ms, I want to see 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. 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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GM calculation?
by Anthony 16 Jan '09

16 Jan '09

Hi all, I'm doing some analyses which involve GM volume . It might sound trivial but I wonder how could GM calculation be done in freesurfer? Is there a way to compute it based on GM between white and pial surfaces, and will the result of that approach be different from using what is given by aseg.mgz ? Thanks Anthony Get your new Email address! Grab the Email name you've always wanted before someone else does! http://mail.promotions.yahoo.com/newdomains/aa/

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template deformation error: global region empty
by Juranek, Jenifer 16 Jan '09

16 Jan '09

Just wondering if there are any suggestions for finding a work-around when the "global region of the brain empty" error message appears after executing the following command: recon-all -autorecon1 -s CIP_H0519_ERR -notal-check. The T1 image (001.mgz) looks fine. The -notal-check flag was added on the 2nd execution of recon-all due to failure at the talairach_avi stage. Same error occurs in 2/16 subjects we have recently attempted to process using freesurfer v405 on RHEL5. Many Thanks for any suggestions, Jenifer #@# Skull Stripping Fri Jan 16 12:06:43 CST 2009 /usr/local/freesurfer/subjects/CIP_H0519_ERR/mri mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz If this is incorrect, please exit with CTL-C Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=140 y=158 z=147 r=70 first estimation of the main basin volume: 1469917 voxels Looking for seedpoints 2 found in the cerebellum 6 found in the rest of the brain global maximum in x=170, y=133, z=131, Imax=255 CSF=20, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done Analyze main basin size=7426225090 voxels, voxel volume =1.000 = 7426225090 mmm3 = 7426225.152 cm3 done PostAnalyze...Basin Prior 533 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=172,y=168, z=162, r=9871 iterations GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 19890 RIGHT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=10 , nb = 1251 LEFT_CER CSF_MIN=0, CSF_intensity=3, CSF_MAX=9 , nb = 1089 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 7686 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 8289 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=6 , nb = 1575 mri_watershed Error: GLOBAL region of the brain empty ! Linux localhost.localdomain 2.6.18-8.el5 #1 SMP Fri Jan 26 14:15:14 EST 2007 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Jan 16 12:07:31 CST 2009 [jjuranek@localhost CIP_H0519_ERR]$

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