Freesurfer February 2009

freesurfer@nmr.mgh.harvard.edu

86 participants
126 discussions

eTIV
by Gabriel Go.Es. 13 Feb '09

13 Feb '09

Dear freesurfers: I have 60 subjects manual segmentated on FreeSrufer 4.0.5, i want to know if i run the recon2 or recon3 in the new FS 4.2.0, will have any problem? the diferences between versions can cause any trouble with the analisis because imcompability or something? Regards Gabriel _________________________________________________________________ Llévate Messenger en tu móvil allá donde vayas ¿A qué esperas? http://serviciosmoviles.es.msn.com/

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pial and white matter surface areas
by Al-Radaideh Ali 12 Feb '09

12 Feb '09

Dear FreeSurfer Expert, I am trying to find the surface areas of Pial surface and white matter surface. I found many files in Surf folder but not sure which is which and how t read them in a text, Excel,or matlab file. any idea please? The other thing, If I have many subjects, is there any way I can read the surface areas in a table or any text file as well. I use this command asegstats2table to group the volumes of specific structures in one table. Thanks in advance Ali 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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RE: White matter defect
by karlkarl 12 Feb '09

12 Feb '09

Hello, I sending in two more sagigital views. You mentioned it was related to the aseg. In the tutorial exmaples of defects, it always uses brainmask as a guide to fix the problem in wm.mgz, which wouldn't work in this case. Would you give some intrctions on corrction from aseg. thanks > Date: Thu, 5 Feb 2009 16:48:48 -0500 > From: fischl(a)nmr.mgh.harvard.edu > To: rememberer(a)hotmail.com > Subject: RE: [Freesurfer] white matter defect > CC: freesurfer(a)nmr.mgh.harvard.edu > > I see. The ventricles are filled in from the aseg, but if you filled in > the wm.mgz that would work as well. It may not be needed though. What does > it look like in a saggital view? > _________________________________________________________________ 新版手机MSN，满足你多彩需求！参加抢鲜体验活动，领取特色奖品！ http://mobile.msn.com.cn/

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topological defect
by Dankner, Nathan (NIH/NIMH) [F] 11 Feb '09

11 Feb '09

Hello, In many of the surfaces that I have made, a frequent error seems to center around the ventricles. The white matter segmentation often does not follow the white matter near the ventricle, leaving a circle inside the ventricle area. This seems to create a dimple on the output surface. I have attached a screenshot of the surface (the dimple is obvious) and also of a coronal and saggital slice of the wm.mgz where the error occurs. How is this best fixed? Thanks, Nathan

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exited with errors
by Dankner, Nathan (NIH/NIMH) [F] 11 Feb '09

11 Feb '09

Hello all, I have recently been running some scans with very few defects, but have been encountering a particular error message on occasion when I try to run it through autorecon2 and autorecon3 after a bit of manual correction. The error output is: MRI_fill: could not read segmentation from aseg.auto_noCC.mgz reading segmented volume aseg.auto_noCCseg.mgz... ERROR: cannot find [subject path]/aseg.auto_noCCseg.mgz No such file or directory Any suggestions as to why this is happening? Nathan

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creating label for dlpfc
by Prapti Gautam 11 Feb '09

11 Feb '09

Dear all, I am trying to measure the volume of the dorsolateral prefrontal cortex in a large group of subjects. I have created a new label that only includes the dlpfc for a subject but realised that the same label file cannot be used on another subject. Has anyone created a customised ROI for dlpfc to use in a group of large subjects or can point me in the right direction ? The only other option I know is to individually create a label file for each subject which would be very time consuming. Thanking you in advance, Prapti

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freeglut ERROR
by Lars M. Rimol 11 Feb '09

11 Feb '09

Hi, In tksurfer, when I have loaded an overlay and then try to add a color bar, I get this error message: freeglut ERROR: Function <glutBitmapCharacter> called without first calling 'glutInit' I'm using freeglut v 2.4.0. I don't know if this is caused by a bug in freeglut (I think it's the latest version). Anyone know how to fix this? Thank you! -- yours, LMR

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How to show only some parcellations
by Jürgen Hänggi 11 Feb '09

11 Feb '09

Dear FS experts Is there any possibility to show only some and not all of the parcellations of the lh.aparc.a2005s.annot annotation file? We have looked for in the archives but did not find any answer 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) 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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Error message
by Jürgen Hänggi 11 Feb '09

11 Feb '09

Dear FS experts I tried to reconstruct the surface models of a patient's brain with large anomalies (see attachment). There is a large topological defect which FS cannot fix. FS failed with the following error message: Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 169740 ambiguous faces found in tessellation segmenting defects... 87 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 10 into 0 -merging segment 26 into 0 -merging segment 61 into 3 -merging segment 39 into 31 -merging segment 0 into 36 -merging segment 45 into 37 -merging segment 53 into 37 -merging segment 56 into 37 -merging segment 64 into 54 -merging segment 69 into 66 -merging segment 72 into 70 76 defects to be corrected 0 vertices coincident reading input surface /Applications/freesurfer/subjects/altin_pre1/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.8502 (-4.4251) -vertex loglikelihood: -6.6049 (-3.3024) -normal dot loglikelihood: -3.5099 (-3.5099) -quad curv loglikelihood: -6.1072 (-3.0536) Total Loglikelihood : -25.0721 CORRECTING DEFECT 0 (vertices=29, convex hull=52) After retessellation of defect 0, euler #=-24 (121052,354507,233431) : difference with theory (-73) = -49 CORRECTING DEFECT 1 (vertices=27, convex hull=23) After retessellation of defect 1, euler #=-23 (121054,354521,233444) : difference with theory (-72) = -49 CORRECTING DEFECT 2 (vertices=48634, convex hull=6250) mris_fix_topology(4721) malloc: *** mmap(size=1417760768) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Bus error Darwin Freesurfer.local 9.6.0 Darwin Kernel Version 9.6.0: Mon Nov 24 17:37:00 PST 2008; root:xnu-1228.9.59~1/RELEASE_I386 i386 recon-all exited with ERRORS at Wed Feb 11 00:01:09 CET 2009 [Freesurfer:/Applications/freesurfer/subjects] Nicki% Any suggestions? What does bus error mean? How does I can force FS to correct this large defect? Thanks in advance 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) 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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scale factor in talairach transformations
by Cindy Eckart 10 Feb '09

10 Feb '09

Dear freesurfers, I am new in the list and will start with a hopefully not too stupid question... besides a planned cortical thickness analysis I would like to compare the volumes for some cortical parcellation areas between three groups. As far as I understood the freesurfer-procedures the brains are also stretched during the linear registration in the talairach transformation process. Is this stretching scale factor already accounted for in the volume values displayed in the aparc.statsvolume-file? Or will I have to account for potential deformations due to stretching of the brain by myself? I think it must have been already accounted for, but so far I found no specific notations in the corresponding publications... Thank you for your help and greetings from Germany Cindy ____________________________________________________________________ Psssst! Schon vom neuen WEB.DE MultiMessenger gehört? Der kann`s mit allen: http://www.produkte.web.de/messenger/?did=3123

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Freesurfer February 2009