Freesurfer December 2009

freesurfer@nmr.mgh.harvard.edu

77 participants
105 discussions

recon-all error (sample tutorial data)
by Hui J Yu 17 Dec '09

17 Dec '09

Dear freesurfer users, I have recently downloaded freesurfer (virtualbox verion) and started testing using the sample data bert. I got the following error (I also tried on my data and the same error occured). Any suggestions? ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...46 iterations mghRead: encountered error executing: 'zcat /usr/local/freesurfer/subjects/bert/mri/T1.mgz',frame -1, errno 12 mri_strip_skull: done peeling brain Brain Size = 1793357 voxels, voxel volume = 1.000 mm3 = 1793357 mmm3 = 1793.357 cm3 mri_watershed Error: read failed Linux freesurfer-virtual 2.6.28-17-generic #58-Ubuntu SMP Tue Dec 1 18:57:07 UTC 2009 i686 GNU/Linux recon-all exited with ERRORS at Thu Dec 17 17:20:18 EST 2009 Thank you. Hui Jing Yu

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Announcement: Colin dataset download
by Krish Subramaniam 17 Dec '09

17 Dec '09

Please find the download information in the following wiki-page -- http://surfer.nmr.mgh.harvard.edu/fswiki/Colin27 Thanks Krish

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lGI error (error with class.m function)
by Frédéric Andersson 17 Dec '09

17 Dec '09

Hi, I've got some troubles computing the lGI. It seems to be a trouble related to the class.m and strel.m matlab functions. Does anyone meet such problem? Thanks Frederic gray.local:andersson 11:50am [12] recon-all -s MNI_SINGLESUBJ -localGI -no-isrunning INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v4.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 INFO: SUBJECTS_DIR is /usr/remote/Darwin/freesurfer/freesurfer450/ subjects Actual FREESURFER_HOME /usr/remote/Darwin/freesurfer/freesurfer450 -rw-rw-r-- 1 andersson flat 750913 Dec 17 09:29 /usr/remote/Darwin/ freesurfer/freesurfer450/subjects/MNI_SINGLESUBJ/scripts/recon-all.log Darwin gray.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/remote/Darwin/freesurfer/freesurfer450 Previous: /usr/remote/Darwin/freesurfer/freesurfer410 /usr/remote/Darwin/freesurfer/freesurfer450/subjects/MNI_SINGLESUBJ/surf #-------------------------------------------- #@# Local Gyrification Index lh Thu Dec 17 11:50:50 CET 2009 \n mris_compute_lgi --i lh.pial \n ================= rm -Rf /usr/remote/Darwin/freesurfer/freesurfer450/subjects/ MNI_SINGLESUBJ/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /usr/remote/Darwin/freesurfer/freesurfer450/subjects/ MNI_SINGLESUBJ/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /usr/remote/Darwin/freesurfer/freesurfer450/ subjects/MNI_SINGLESUBJ/surf/tmp-mris_compute_lgi-lh.pial/ lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /usr/remote/Darwin/freesurfer/freesurfer450/ subjects/MNI_SINGLESUBJ/surf/tmp-mris_compute_lgi-lh.pial/ lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/usr/remote/Darwin/freesurfer/freesurfer450/ subjects/MNI_SINGLESUBJ/surf/tmp-mris_compute_lgi-lh.pial/ lh.pial.filled.mgz',15,'/usr/remote/Darwin/freesurfer/freesurfer450/ subjects/MNI_SINGLESUBJ/surf/tmp-mris_compute_lgi-lh.pial/lh.pial- outer'); exit ================= Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B > Copyright 1984-2007 The MathWorks, Inc. Version 7.5.0.338 (R2007b) August 9, 2007 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> reading filled volume... interactive shell interactive shell closing volume... ??? Error using ==> class The CLASS function must be called from a class constructor. Error in ==> strel>MakeArbitraryStrel at 188 se = class(se, 'strel'); Error in ==> strel at 122 se = MakeArbitraryStrel(params{:}); Error in ==> strel>MakeBallStrel at 530 se.decomposition = strel(nhood,height); Error in ==> strel at 141 se = MakeBallStrel(params{:}); Error in ==> make_outer_surface at 41 se=strel('ball',se_diameter,se_diameter); >> Frédéric ANDERSSON, PhD Ingénieur de Recherche INSERM / IFR 135 - Imagerie fonctionnelle Faculté de Médecine 10 Blvd Tonnellé Bat. Vialle - 2ème étage - Bureau 205 BP 3223 - 37032 TOURS cedex - FRANCE Tél : +33 (0) 2 47 36 61 37 / Fax: +33 (0) 2 47 36 62 07

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fsaverage to mni152
by Yigal Agam 17 Dec '09

17 Dec '09

Hi, What's the best way to convert an fsaverage volume into an MNI152 volume that can be viewed on top of a standard brain (MNI152_T1_2mm_brain.nii.gz) in fslview? Thanks, Yigal

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Graphics Card Question
by Sam Evans 17 Dec '09

17 Dec '09

Dear all I am new to FreeSurfer and would apprechiate some advice. I am about to purchase a graphics card specifically to use Free Surfer due to the nature of the desk top I have I am restricted in my choice of options. I have been recommended the ATI Radeon HD3450 and HD3470: http://accessories.euro.dell.com/sna/productdetail.aspx?c=uk&l=en&s=bsd&cs=… http://accessories.euro.dell.com/sna/productdetail.aspx?c=uk&l=en&s=bsd&cs=… Will these be up to spec for use with Free Surfer? I am planning to use these with Ubuntu. Is there anything I should know about before I take the plunge and buy them? Thanks in advance for your help Sam

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error with libtix8.1.8.4.so
by Sungeun Kim 16 Dec '09

16 Dec '09

Hello, Thank you for all help in advance. Recently, I installed the FreeSurfer ver.4.5.0 (centos4_x86_64-stable-pub-v4.5.0) on my mint 8 linux (x86_64). When I tried to run a command (recon-all) on my terminal, I didn't see any problem and all help messages were returned. But I tried to run tkmedit and tksurfer, I got an error message: "tkmedit.bin: error while loading shared libraries: libtix8.1.8.4.so: cannot open shared object file: No such file or directory" To check the dependency of tkmedit, I ran "which tkmedit' and "ldd `which tkmedit`" on a terminal. Two commands returned ..>which tkmedit /usr/local/freesurfer/bin/tkmedit ..> ldd `which tkmedit` not a dynamic executable Here is my LD_LIBRARY_PATH: ..>echo $LD_LIBRARY_PATH /lib:/usr/lib:/lib32:/usr/lib32:/usr/local/lib64:/usr/local/lib I am using freesurfer often for my research. So, any help or suggestion to resolve this issue would be really helpful to me. -- Sungeun Kim

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Re: [Freesurfer] Mris_make_face_parcellation
by Jürgen Hänggi 16 Dec '09

16 Dec '09

Hi Bruce I attached a figure that illustrates my problem. I would like to known which parcellations in the right panel (that are denoted only by numbers) are located in the fusiform gyrus parcellation shown in the left panel (aparc.a2005s). Any suggestions are welcome Thanks Jürgen On [DATE], "Bruce Fischl" <[ADDRESS]> wrote: > I guess I'm not sure what you're trying to do. If you give > mris_make_face_parcellation the sphere.reg file as input then the > triangles will be in register across subjects. > > On Wed, 16 Dec 2009, Jürgen > Hänggi wrote: > >> Hi Bruce >> >> Yes, mris_divide_parcellation produces thin stripes as parcels. I prefer the >> triangles produced by mris_make_face_parcellation. >> >> Thanks >> Regards >> Jürgen >> >> >> On [DATE], "Bruce Fischl" <[ADDRESS]> wrote: >> >>> Hi Jurgen, >>> >>> you might try using mris_divide_parcellation instead, which divides up a >>> specified set of annotation units (if you give it a configuration file). >>> >>> cheers >>> Bruce >>> On >>> Tue, 15 Dec 2009, Jürgen Hänggi wrote: >>> >>>> Dear FS experts >>>> >>>> When using mris_make_face_parcellation is it possible to restrict the face >>>> parcellation to a parcellation found in aparc.a2005s, e.g. to the >>>> precentral >>>> gyrus. >>>> >>>> Or is there another way to decide which micro-parcellation produced by >>>> mris_make_face_parcellation belong to which parcellation in aparc.a2005s? >>>> >>>> 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. >>>> --------------------------------------------------------------------------->>>> - >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >> >> >> ---------------------------------------------------------------------------- >> 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. >> ---------------------------------------------------------------------------- >> >> >> >> >> >> ---------------------------------------------------------------------------- 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. ----------------------------------------------------------------------------

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insula infarct and pial boundary understimation of gray matter
by Durazzo, Timothy 16 Dec '09

16 Dec '09

Dear Experts, Occasionally, we have patients with clear cortical or subcort. gray matter infarcts. If the infarct is large enough, in some cases the pial line bends in away from the outer boundary of viable gray matter and in toward the infarct (i.e., area of decreased contrast). In the attached power point, I show a case where there is a left (radiologic convention) rostral insula infarct and the pial line dives in toward the infarct, but the adjacent main surface line looks like it is only very slightly underestimating the white matter boundary. This occurs on six contiguous slices, but the infarct is only apparent of three. This individual was run on a 1.5T scanner and processed with FS v4.5. The area of attenuation is apparent on his raw MPR and is bright on T2, so this is not an artifact in FS. I'm reluctant to use control points or change the WM boundary because it appears to be overall correct. Is there any way to fix this? Thanks a lot. - Tim Timothy C. Durazzo, PhD Assistant Professor Department of Radiology and Biomedical Imaging University of California, San Francisco Center for Imaging of Neurodegenerative Diseases San Francisco VA Medical Center (415) 221-4810 x4157

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Saving color changes
by nlucena＠artsci.wustl.edu 15 Dec '09

15 Dec '09

I'm manually changing freesurfer's region colors in tksurfer but can't seem to save the changes. Is there a way to either save these changes, or an alternate method for replacing the default colors freesurfer uses in its cortical segmentation in a way that can be applied to each hemisphere and saved?

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[freesurfer] recon-all taking an unusually very long time
by David Qixiang Chen 15 Dec '09

15 Dec '09

Hi, We are having one scan going through recon-all that is taking way longer than ordinary. Other scans took about 20-30 hours to calculate, while this particular scan is taking 3+ days and has still not being completed. Just wondering how often something like this happens, and if there's any known problems with this sort of thing. Here's the mri_info output: Starting DICOMRead2() dcmfile = /media/HIPPO/scans/normals/C11/T1/C11_0.dcm dcmdir = /media/HIPPO/scans/normals/C11/T1 Ref Series No = 3 Found 162 files, checking for dicoms Found 160 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 1 Vs: 0 0 1 Second Sorting Counting frames nframes = 1 nslices = 160 ndcmfiles = 160 PE Dir = ROW (dicom read) Volume information for C11_0.dcm type: dicom dimensions: 256 x 256 x 160 voxel sizes: 0.9375, 0.9375, 1.0000 type: SHORT (4) fov: 240.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -80.0, zend: 80.0 TR: 11.96 msec, TE: 5.05 msec, TI: 300.00 msec, flip angle: 20.00 degrees nframes: 1 ras xform not present xform info: x_r = -1.0000, y_r = 0.0000, z_r = -0.0000, c_r = 5.3850 : x_a = 0.0000, y_a = -1.0000, z_a = -0.0000, c_a = 30.3850 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 27.4266 Orientation : ??? Primary Slice Direction: unknown voxel to ras transform: -0.9375 0.0000 -0.0000 125.3850 0.0000 -0.9375 -0.0000 150.3850 0.0000 0.0000 1.0000 -52.5734 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 0.878906 ras to voxel transform: -1.0667 0.0000 0.0000 133.7440 0.0000 -1.0667 0.0000 160.4107 -0.0000 -0.0000 1.0000 52.5734 0.0000 0.0000 0.0000 1.0000

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Freesurfer December 2009