Freesurfer

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30083 discussions

AFNI /freesurfer aseg files problem
by Liat Levita 28 Jul '08

28 Jul '08

Hello, I wonder if anyone using AFNI converted freesurfer files has come across this problem (or can tell me if I making an error somewhere that I am just not seeing right now). I posted the same question on the AFNI board but haven't gotten feedback as yet. Here is the problem: After using freesurfer to get subcortical segmentations, I converted the resulting freesurfer files to AFNI format, which was fine - I had no problems doing that. However, when I try use these subcortical segmentation data files (subjectID_aseg_m_at3+tlrc) as masks to pull put PSC signal from each region of interest, I am getting an odd effect of right versus left; whereby left clusters output is fine ( voxel numbers are correct after 3dmaskave), but for the left it is very wrong. I have checked that the labels of the ROIs I am using are correct on AFNI GUI and they are. (code and output below) I am a bit at a loss; any help will be much appreciated. Liat AFNI Code used --------------- Foreach subj (xxx) foreach cluster (18 54) 3dmaskave -q -mask ${subj}_aseg_m_at3+tlrc -mrange ${cluster} ${cluster} \ "${subj}_all_runs_pscA_at3+tlrc" > ${subj}_fsROI_PSC_cluster_${cluster}.1D end end Output (get the same odd voxel output from all right hand side of the brain freesurfer generated ROIs) ------------------- *For cluster 18 Left Amygdala ++ 3dmaskave: AFNI version=AFNI_2008_02_01_1144 (Jul 3 2008) [32-bit] +++ 37 voxels survive the mask *For cluster 54 Right Amygdala ++ 3dmaskave: AFNI version=AFNI_2008_02_01_1144 (Jul 3 2008) [32-bit] +++ 200 voxels survive the mask

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Hippo-Amyg defs
by Juranek, Jenifer 28 Jul '08

28 Jul '08

Hi, Is any documentation available for describing the anatomical landmarks for demarcation of amygdala and hippocampus used by aseg? Many Thanks, Jenifer

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recon-all crash on talairach_afd
by Rudolph Pienaar 28 Jul '08

28 Jul '08

Hi - I'm a non-power freesurfer user in as much as I usually just run recon-all and rarely deal with individual steps. This usually addresses >90% of my FS needs. :-) I've been running some recons lately that fail very early on with talairach_afd... If anyone has some advice, I'd be really happy. I've appended the recon-all.log file to this email, but in a nutshell the error report is: Fri Jul 25 16:43:30 EDT 2008 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Fri Jul 25 16:43:31 EDT 2008 /autofs/space/kaos_005/users/dicom/postproc/2680228390711/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0083, pval=0.0000 < threshold=0.0050) Linux node0352 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:28:26 CDT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Jul 25 16:43:32 EDT 2008 -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA

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PhD position / Post-doctoral Position in Magnetic Resonance Imaging
by Thomas Stephan 28 Jul '08

28 Jul '08

On behalf of Prof. Martin Dichgans: The Imaging in Stroke and Dementia programme at the Department of Neurology, Klinikum Großhadern, Ludwig-Maximilians-University, Munich invites applications for a full-time PhD position / Post-doctoral Position in Magnetic Resonance Imaging The focus of our research programme is on translational approaches to explore the neural correlates of cognitive and behavioural dysfunctions in vascular cognitive impairment. An ongoing longitudinal study involving more than 250 patients with a genetic variant of stroke and VCI grants access to a unique resource of multimodal MR imaging data (FA-and MD maps from DTI, 3DT1, FLAIR etc. available) and comprehensive neuropsychological test results (see www.neurogenetik.de and publication record). We are increasingly interested in voxel-based-morphometry (VBM) and more advanced techniques to explore structure-function relationships. There is direct access to several MR scanners operating at 1.5 to 3.0 Tesla. Research activities are embedded in a center of highly productive MR imaging research groups at Campus Großhadern. Applicants should have a background in MRI analysis techniques (FSL, SPM, Matlab etc.), programming and statistics. Interest in clinical neuroscience and cognitive function would be appreciated. Applicants will have the opportunity to pursue their own projects. The position is funded for 3 years with an option to renew. Salary will be based on qualifications with provision for bonuses. The position is available Fall 2008. To apply please send a CV and the names of 2 referees to Prof. Martin Dichgans, e-mail: martin.dichgans(a)med.uni-muenchen.de or phone: ++49-89-7095-6670. Prof. Dr. med. Martin Dichgans Neurologische Klinik Ludwig-Maximilians-Universität München Marchioninistr. 15, 81377 München Tel.: +49 (089) 7095-3670 (or: -6670) Fax: +49 (089) 7095-6679

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Cortical Thickness
by Al-Radaideh Ali 27 Jul '08

27 Jul '08

Hello, I am Ali Al-Radaideh from the University of Nottingham. I used freesurfer on one set of my MRI data ( MP-RAGE 1mm isotropic resolution) and finished the recon-all step. I was able to display the thickness map but unfortunately I could not be able to find any file that gives me a quantitative measure of cortical thickness, as my intention is to measure the cortical thickness using freesurfer. Would it be possible to advice me on that, please? Best regards Ali Al-Radaideh PhD student Sir Peter Mansfied MR Centre The University of Nottingham,UK This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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AW: Freesurfer Digest, Vol 53, Issue 23
by Steinmann, Iris 25 Jul '08

25 Jul '08

Hi, I load Version 4.0,5, and it works!!!!!!!!!!!!! Thanks!!! Yet, I just have another question now: Is it possible to conduct a conjunction analysis like implemented in SPM5? If not, is it valid to simply take the p-maps in the surface space and compute the pooled dependent p-values according to Heller et. al 2007 (NeuroImage 37 1178-1185), and if so are there Matlab readers for the p-map files? thanks, schüss -----Ursprüngliche Nachricht----- Von: freesurfer-bounces(a)nmr.mgh.harvard.edu im Auftrag von freesurfer-request(a)nmr.mgh.harvard.edu Gesendet: Mi 23.07.2008 23:31 An: freesurfer(a)nmr.mgh.harvard.edu Betreff: Freesurfer Digest, Vol 53, Issue 23 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Version 4.0.4 (Tricia Merkley) 2. AW: [Fsdev] Re: [Freesurfer] Talairach Coordinates (Steinmann, Iris) 3. Vertex information lookup (P?draig Kitterick) 4. qdec ERROR: Rendering vtkXOpenGLRenderWindow (Juranek, Jenifer ) 5. tkmedit problem with XQuartz-2.3.0 (Martin Kavec) 6. Re: qdec ERROR: Rendering vtkXOpenGLRenderWindow (Nick Schmansky) 7. Re: tkmedit problem with XQuartz-2.3.0 (Nick Schmansky) 8. RE: qdec ERROR: Rendering vtkXOpenGLRenderWindow (Juranek, Jenifer ) 9. RE: qdec ERROR: Rendering vtkXOpenGLRenderWindow (Nick Schmansky) 10. Re: tkmedit problem with XQuartz-2.3.0 (Martin Kavec) ---------------------------------------------------------------------- Message: 1 Date: Tue, 22 Jul 2008 14:59:54 -0700 (PDT) From: Tricia Merkley <tmerkle22(a)yahoo.com> Subject: [Freesurfer] Version 4.0.4 To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <858531.40896.qm(a)web52007.mail.re2.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" We ran several subjects using version 4.0.4 and now need to reinstall freesurfer to finish the processing. Is there a linux centos4, 32 bit version available somewhere? Thanks, Tricia Merkley

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tkmedit reconstruction to perpendicular axes of ROIs
by Aaron Shmookler 25 Jul '08

25 Jul '08

Is it possible to reconstruct an MRI such that the images in tkmedit are perpendicular to the axis of a particular region such as in my ROI the temporal pole? As I see them the tkmedit MRIs are oblique slices with the dorsal regions appearing caudally on the tksurfer (volumetric) images relative to the ventral regions.

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Version 4.0.4
by Tricia Merkley 24 Jul '08

24 Jul '08

We ran several subjects using version 4.0.4 and now need to reinstall freesurfer to finish the processing. Is there a linux centos4, 32 bit version available somewhere? Thanks, Tricia Merkley

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Compute individual statistics (selxavg3)
by Balaji Goparaju 24 Jul '08

24 Jul '08

Hi Doug and all, There is another problem when i try the individual statistics, I use the command selxavg3-sess -analysis LD-analysis -s LD-functional and i am getting an error: ERROR: cannot find volume matching /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold/006/mcextreg ERROR: loading nonpar reg /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold/006/mcextreg ------------------------------------------ ERROR: fast_selxavg3() failed\n so i was wondering if the problem was because the software is not creating the file, or if there was any other way i could make freesurfer create the file. Thank you for any help!

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qdec ERROR: Rendering vtkXOpenGLRenderWindow
by Juranek, Jenifer 23 Jul '08

23 Jul '08

Hi, Running Freesurfer v405 on RHEL5. Tried to launch qdec from the command prompt. While the splash screen did appear with the inflated brain surface, the qdec interface did not appear (even after 10min). When I tried to CTRL-C the terminal window, the following error message appeared: [jjuranek@sph3053 subjects]$ qdec & ERROR: In /usr/pubsw/packages/vtk/5.0.4/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, line 219 vtkXOpenGLRenderWindow (0x7e06290): Could not find a decent visual [jjuranek@sph3053 subjects]$ ps -ef | grep qdec jjuranek 32682 32579 0 10:45 pts/11 00:00:00 /bin/tcsh -ef /usr/local/freesurfer/bin/qdec jjuranek 32687 32682 0 10:45 pts/11 00:00:00 qdec.bin jjuranek 32763 9505 0 11:13 pts/1 00:00:00 grep qdec [jjuranek@sph3053 subjects]$ kill -1 32687 Any ideas how to fix? Thanks, Jenifer

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