Freesurfer January 2009

freesurfer@nmr.mgh.harvard.edu

72 participants
137 discussions

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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MEMPR sequence for freesurfer analyses
by Juranek, Jenifer 15 Jan '09

15 Jan '09

Has anyone attempted an MEMPR-like sequence as described by van der Kouwe et al (2008 NeuroImage 40: 559-569) on a 3T Philips Intera? The paper utilized a 3T Siemens TRIO. Are the published sequence parameters directly transferable to a 3T Philips Intera with an 8 channel head coil and SENSE? Or is some "translation" between Siemens & Philips needed to get it to work as well as published for the Siemens? Many Thanks for any info, Jenifer

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thickness value
by Feng-Xian 15 Jan '09

15 Jan '09

Hi, I gain the cortical thickness value and other information of all ROIs for all my subjects (found in $FREESURFER_HOME/subjects/filename/stats). But, can I gain the cortical thickness value and other information of all vertices for all my subjects? I want to gain the values, not maps. Thank you 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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mri_convert failure
by Ian Malone 15 Jan '09

15 Jan '09

Hi, I'm finding that mri_convert produces a read error when trying to convert some short analyze files to mgz, invoked as the following: mri_convert -it analyze -i `pwd`/reslice/00125-003-1.img -o reslice/mni.mgz The output contains (the dimensions shown are correct): ERROR: premature end of file ERROR: Success (0) frame = 0, slice = 219, k=219, row = 155 nread = 171, nexpected = 172 fname = height = 156 width = 172 depth = 220 and: analyzeRead2(): error reading from file reslice/00125-003-1.img The file in question is 11806080 bytes. Using strace I can see that when the .img file is opened 1 byte is read from it before reading in blocks of 1024, and a final read of 383 bytes. Trying another short file (which works) this initial 1 byte read does not happen. Is this is bug? I can provide the files in question if needed. Build stamp: freesurfer-Linux-rh9-stable-pub-v4.0.3 Kernel info: Linux 2.6.21.5-smp i686 Thanks, Ian Malone

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tksurfer error
by Joshua Grant 14 Jan '09

14 Jan '09

Hello, I've run into a problem when trying to view surfaces. tkmedit works fine but tksurfer gives an error saying "Window type not found". I see that others have had this problem in the past but the solution didn't work, i.e. setenv doublebufferflag 1 tksurfer ... Also see: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00010.html I'm using a brand new quad-core machine with independent graphic memory, running Ubuntu and the CentOS 4 x86_64 V4.1.0. version of Freesurfer. Any help would be most appreciated. Joshua

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RE: [Freesurfer] reg-feat2anat failed
by Wang, Xin 14 Jan '09

14 Jan '09

Hello, Dr. Greve, I followed the steps in the tkregister2 --help: converted both example_func and orig.mgz to .img of ANALYZE format and ran the tkregister2 use -- fsl example_func2highres.mat of fsl/FEAT. The two brains are in the different views (i.e., axial view of example_func overlay on the coronal view of orig). I am still struggle with same questions as before. I appreciate any suggestion. Thank you, Xin Wang ________________________________ From: Wang, Xin Sent: Tue 1/13/2009 4:36 PM To: Douglas N Greve Cc: freesurfer Subject: RE: [Freesurfer] reg-feat2anat failed Sorry for the confusion. Let me rephase my questions. question 1: I want to use the example_func2highres.mat created by fsl/FEAT registration to register example_func and orig.mgz. Can the flag --fslregout or --fsl do it? Question 2: These numbers appear in the terminal whenever I click a point in tkregister2? What do these numbers mean? Screen: 256 257 (113,113,113), inorm = 1, mov_frame = 0 Anat: (128 126 127) ( 0.0 -1.0 2.0) 25.0000 32.7 Func: ( 31 32 21) ( 4.2 3.1 1.4) 756.0000 112.5 question 3: I can only see the middle portion of the brain in tkregister2 when I zoomed in. How can I see other parts of the target and movable pictures? Thank you, Xin Wang ________________________________ From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Tue 1/13/2009 4:19 PM To: Wang, Xin Subject: Re: [Freesurfer] reg-feat2anat failed 1) I don't know what you mean. The fslmatout is for creating an fsl mat file from a freesurfer register.dat 2. I don't know what you mean. 3. What do you mean by "moving the two images together"?

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Freesurfer January 2009