Freesurfer September 2009

freesurfer@nmr.mgh.harvard.edu

85 participants
131 discussions

Averaging Labels
by David Brang 09 Sep '09

09 Sep '09

Hi, I’m trying to average 2 labels together, but haven’t seen any script out there that does this. Essentially we used ROI localizer tasks to create individual labels for each of our subjects. For visualization purposes, we created an average brain, and used mri_label2label to map each individual subjects’ label onto the group brain. But, now I’m not sure how to create an average of these labels. Thanks! David Brang

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Autoredraw in TKSurfer
by Pedro Paulo de Magalhães Oliveira Junior 09 Sep '09

09 Sep '09

Some people asked me how to enable Auto Redraw in TKSurfer in the virtual machine distribution of FreeSurfer. A video tutorial was placed in YouTube: http://www.youtube.com/watch?v=9573UYJxlok ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.2 www.Netfilter.com.br --- Novo Netfilter Small Business

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Temporal lobe surface problem
by Chris Adamson 09 Sep '09

09 Sep '09

Everyone, I am having problems with Freesurfer not seemingly appreciating the WM/GM boundary in the temporal lobe. I have attached a screenshot of the problem area which is in the bottom right of the pic. A large portion of the grey matter is outside the pial surface and the inner boundary does not extend to the edge of the white matter. I have checked the white matter segmentation and edited the aseg volume to correct this problem but after running recon-all again I get the same result. Any ideas? Chris. -- Dr Christopher Adamson, PhD (Melb.), B Software Engineering (Hons., Monash) Research Officer Developmental and Functional Brain Imaging, Critical Care and Neurosciences Murdoch Childrens Research Institute The Royal Children’s Hospital Flemington Road Parkville Victoria 3052 Australia T 9345 4306 M XXXX XXX XXX E chris.adamson(a)mcri.edu.au www.mcri.edu.au

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Big lesion
by Lemkaddem Alia 09 Sep '09

09 Sep '09

Hi, One of our subjects has a big lesion in the left hemisphere, which appears on the MRI. Because of this, I obtain a big whole in the cortical parcellation. I have already tried: - To correct the WM mask. - Used control points to fix intensity normalization. Please have a look at the images that I have attached. The lesion is very big and it's very hard to tell where the WM is. Thankful for all the help I can get, Alia

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The error about recon-all -s subjid -autorecon1
by QQ Liu 09 Sep '09

09 Sep '09

Hi all, In order to find the debug of the problem which occurred when I run recon-all -s subjid -all, I run recon-all -s subjid -autorecon1 for a try. Then there is a another error message to report as follows: ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...40 iterations mghRead: encountered error executing: 'zcat /usr/local/freesurfer/subjects/am03/mri/T1.mgz',frame -1, errno 12 mri_strip_skull: done peeling brain Brain Size = 1657531 voxels, voxel volume = 1.000 mm3 = 1657531 mmm3 = 1657.531 cm3 mri_watershed Error: read failed Linux qq-desktop 2.6.28-15-generic #51-Ubuntu SMP Mon Aug 31 13:33:16 UTC 2009 i686 GNU/Linux recon-all exited with ERRORS at Wed Sep 9 15:08:15 CST 2009 I'm confused that when running -all the first step passed. And the test of bert all passed. Is there anything wrong with the conerted data of our raw data? Thanks a lot in advance. -- Best wishes. Q.Q Liu +8613426232824 qqliu16(a)gmail.com

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The image display window cannot show up in the top
by QQ Liu 08 Sep '09

08 Sep '09

Hi all, When I use tkmedit and tksurfer to view the volume or surface, the image display window just fleets once. I click the tag and it doesn't show up either. What's more, the menus of tkmedit don't response when I click them, besides the menu of "Edit". I just use the test commands as follows: tkmedit bert orig.mgz tksurfer bert rh pial Thanks. -- Best wishes. Q.Q Liu +8613426232824 qqliu16(a)gmail.com

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problem with intensity normalization control points
by Ritobrato Datta 08 Sep '09

08 Sep '09

Hello All, I followed the steps in exercise C in the following page http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints and added control points manually and then saved the Control Points by File > Save Control Points Then I ran recon-all -autorecon2-cp -autorecon3 -s <subjid> After completion, I opened the viewer to check if it is implemented by tkmedit <subjid> brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white But saw that the image where I added the control points didnt get converted to a continuous line. I have attached a figure as an illustration. What am I doing wrong ? Thanks Ri

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tksurfer: "can't find talairach file"
by Philipp Klein 08 Sep '09

08 Sep '09

Hello, I installed version 4.50 of freesurfer on a Ubuntu 8.10 system, the tests listed in the wiki all run well. Starting tksurfer with other data a warning is shown in the terminal (the talairach.xfm can't be found), but the program starts after that. As far as we can judge after a quick examination, everything is working fine, it's just the warning. Another issue is the warning concerning the missing colortable. Hope anyone can help. Greetings Philipp ps: the terminal output: >>> /usr/local/freesurfer/subjects/FS_spm_CanonicalBrain/mri/T1$ tksurfer FS_spm_CanonicalBrain rh pial surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer/subjects/FS_spm_CanonicalBrain/mri/T1 can't find talairach file '/usr/local/freesurfer/subjects/FS_spm_CanonicalBrain/mri/T1/COR-.info/../transforms/talairach.xfm' surfer: Reading header info from /usr/local/freesurfer/subjects/FS_spm_CanonicalBrain/mri/T1/COR-.info surfer: vertices=171090, faces=342176 can't find talairach file '/usr/local/freesurfer/subjects/FS_spm_CanonicalBrain/surf/../mri/orig/COR-.info/../transforms/talairach.xfm' WARNING: No colortable found! surfer: single buffered window surfer: tkoInitWindow(FS_spm_CanonicalBrain) surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % surfer: dmin=0.1820, vno=121693, x=60.0832, y=26.3634, z=-18.3935 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 121693 marked (curv=0.000000, stat=0.000000) x = (60.1, 26.4, -18.4), n = (0.7, -0.1, -0.8). surfer: dmin=0.8543, vno=79701, x=72.6551, y=-6.2425, z=-27.2842 % surfer: curv=0.000000, fs=0.000000 <<< It has to be added, that COR-.info isn't a folder at all, so the path can't be correct.

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The error maessage about recon-all
by QQ Liu 08 Sep '09

08 Sep '09

Hi all, When I run the FreeSurfer with one scan images(128) of a subject, I am getting the error message as follows: Segmentation fault ERROR: mri_ca_register with non-zero status 139 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Fri Sep 4 23:59:54 CST 2009 /usr/local/freesurfer/subjects/am01/mri mri_ca_register -invert-and-save transforms/talairach.m3z 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 Linux qq-desktop 2.6.28-15-generic #51-Ubuntu SMP Mon Aug 31 13:33:16 UTC 2009 i686 GNU/Linux recon-all exited with ERRORS at Fri Sep 4 23:59:54 CST 2009 The commond used is "recon-all -s subjid -all". Can you give some tips to solve this question? Thanks in advance. -- 祝好！刘倩倩 13426232824 qqliu16(a)gmail.com -- 祝好！刘倩倩 13426232824 qqliu16(a)gmail.com

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postdoctoral position at The University of Chicago (on behalf of Dr. Steven Small)
by Anthony Dick 08 Sep '09

08 Sep '09

A 2-3 year post-doctoral position is available at the Human Neuroscience Laboratory of The University of Chicago (www.humanneuroscience.org) The ideal candidate should be interested in the study of the neural basis of language and/or neural plasticity characterized by changes in brain networks during learning or recovery from injury (primarily stroke). Candidates should have a background in psychology, neuroscience, computational biology, and/or communication sciences and disorders. Prior experience with fMRI is desirable but not obligatory. Experience with multivariate statistics/structural equation modeling, EEG/MEG, TMS, behavioral experimental methods, or neuroinformatics would also be advantageous. Applicants should email their CV and a statement of research interests to Professor Steven Small (small(a)uchicago.edu) -- Anthony Steven Dick, Ph.D. Post-Doctoral Fellow Human Neuroscience Laboratory Department of Neurology The University of Chicago 5841 S. Maryland Ave. MC-2030 Chicago, IL 60637 Phone: (773)-834-7770 Email: adick(a)uchicago.edu Web: http://home.uchicago.edu/~adick/

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Freesurfer September 2009