Freesurfer May 2010

freesurfer@nmr.mgh.harvard.edu

98 participants
145 discussions

fixing cortical parcellation
by Esther Walton 27 May '10

27 May '10

Hi, I just came across a cortical parcellation issues (see attachment), which I got when running tksurfer M02111314 rh pial -annot aparc There is a small-ish orange blob (belonging to the parstriangularis) seeming to be misplaced slightly to the left onto the parsopercularis and I was wondering what ways there are to fix it. I look up the freesurfer wiki, but couldn't really find anything about this. I mean this wouldn't work with control points or the like, right? Thanks for your help, Esther _________________________________________________________________ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:…

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Cortical parcellation-related
by Bauer, Andrew J 27 May '10

27 May '10

Hi, I know how to create annotation files via the "mris_ca_label" command. However, I'm curious as to HOW the following file is created (which is found in the "mri" folder of a subject), and WHEN it was created: aparc.a2009s+aseg.mgz I recently installed FS and I'm working only with the sample "bert" folder. Thus there are a lot of files pre-created, and I'm wondering how some were created. I'd like to end up with an "aparc.a2009s+aseg.mgz" file for each subject, but I don't know how to go from cortical parcellation annotation files to a volume form with the parcellation mapped onto it. Just to let you know, ultimately I'd like to convert the volume with cortical parcellation into an AFNI BRIK. Apologies in advance if my question seems confusing. Please advise! And please let me know if you need any further information. Thanks. -- AJB

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color wheel woes
by Chris Said 27 May '10

27 May '10

Hi, I know that there have been questions about the color wheel in the past, and that future versions of tksurfer will resolve some of the issues. But in the meantime, I was wondering if I could get some help with the existing version: (1) Does anybody have access to good images of the color wheel or RYGB wheel, for use in displaying eccentricity and polar angle maps? Or alternatively, if someone just has a list of the RGB values for these wheels, I could make the images of the wheels myself (and can give them to anyone else who might want them). (2) In the Configure Overlay panel, changing the the offset has an effect on non-complex data, but it has no effect on complex data. Does anybody know how to change the offset for complex data? Thanks very much for your help. Chris

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mac installation problems
by Ed Vessel 26 May '10

26 May '10

Hi folks - I just installed Freesurfer on my Mac (OSX 10.5.8, quad-core intel xeon). The environment variables appear to be set up properly. >source ~/.tcshrc -------- freesurfer-Darwin-leopard-ppc-stable-pub-v4.5.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /CBI/bin/fsldir However, when I try to run some of the programs, I encounter errors: >tkmedit bert orig.mgz X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 128 (Apple-DRI) Minor opcode of failed request: 1 () Serial number of failed request: 16 Current serial number in output stream: 16 [nothing loads] >qdec dyld: Library not loaded: /sw/lib/libtiff.3.dylib Referenced from: /Applications/freesurfer/lib/vtk/lib/ libvtkVolumeRendering.5.0.dylib Reason: image not found Trace/BPT trap [nothing loads] >tksurfer bert rh pial surfer: current subjects dir: /Applications/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Network/Servers/TESLA.CBI.FAS.NYU.EDU/Volumes/data1/Home/ vessel surfer: Reading header info from /Applications/freesurfer/subjects/ bert/mri/T1.mgz surfer: vertices=131860, faces=263716 WARNING: No colortable found! surfer: single buffered window surfer: tkoInitWindow(bert) Received X error! Error code : 1 Request code : 128 Minor code : 1 Error text : 'BadRequest (invalid request code or no such operation)' surfer: using interface /Applications/freesurfer/lib/tcl/tksurfer.tcl [does continue to load properly] So, it looks like perhaps I'm having some issues with X, and perhaps the tk libraries. Do you have any suggestions on what I might need to do? X version: XQuartz 2.1.6 (xorg-server 1.4.2-apple33) thanks, Ed -- Ed Vessel Center for Brain Imaging New York University ed.vessel(a)nyu.edu 4 Washington Place, Rm. 156 New York, NY 10003 http://www.cns.nyu.edu/~vessel (212) 998-8217

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Gyral region centroids?
by Dankner, Nathan (NIH/NIMH) [F] 26 May '10

26 May '10

Hi all, I am looking to get the centroids of the Desikan parcellation gyral regions to calculate distance. Any ideas on how to go about doing this? Thanks, Nathan

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Recon failing during topology correction
by Michael Waskom 26 May '10

26 May '10

Hi, all, We have a recon that is failing during topology correction. Here's the history or what's happened: --first run through the recon-all -all pipeline went fine --control points were added and pial edits were made for quality control --a second recon was run with --autorecon3-cp --autorecon3 During the second recon, the process gets stuck for a long time in topology correction and eventually crashes. We've tried it twice, and it crashes on the same defect. Here's info from the bugr script: Debian version: 5.0 Kernel info: Linux 2.6.28-18-generic x86_64 recon-all log is attached. Any ideas? Thanks! Mike

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missing gaussian curvature file
by Ana Catarino 26 May '10

26 May '10

Hello, I was trying to run a qdec analysis on Gaussian curvature and got the following error message: Error in Analyze: Couldn't open file $SUBJECTS_DIR/AS1/surf/lh.white.K.fwhm10.avgsubject.mgh I get the same error message on mean curvature analysis. Any ideas? Thanks, Ana Catarino

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Doubt about GM and thickness
by Kelly Silva 26 May '10

26 May '10

Hello, I'm doing regression analyses with cortical thickness at the level of voxel. Should I correct the total GM volume by introducing this parameter as a confounding variable? Shoud I include the intracranial volume as an additional nuisance variable? If positive, I assume that these variables can only be introduced as covariates if they differ between groups. Am I correct? I saw in one message that we should not corret for thickness. Why not? Thanks in advance and best regards, Kelly

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3mm slices?
by Mishkin Derakhshan 25 May '10

25 May '10

Hi, I'm wondering if anyone has looked at the accuracy/reproducibility of cortical thickness measurements using 3mm slice data. I found the Han 2006 paper in NeuroImage comparing different sequences, but it doesn't compare different slice thicknesses. If not, does anyone have anecdotal experience using 3mm slices? thanks, mishkin

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brainmask and wm correction
by Deniz Ozgen 25 May '10

25 May '10

Hello all, I am new to FreeSurfer and still trying to understand how things work. I am currently trying to understand how the manual correction works. Following the online tutorials I was able to fix the brainmask and wm.mgz, and also add control points in the wm so that low intensity wm is also included in the segmentation. In the tutorials it is suggested to run the FreeSurfer after doing the brainmask correction by recon-all -autorecon2 -subjid <subject name> After the wm control point addition, the tutorial says that "run the program with -autorecon2-cp" Is it possible to do brainmask correction, white matter edits and control points in one session and run the FreeSurfer again to fix all this at once? Is there a different command for this? I apologize if this has been answered before. Thanks a lot. Deniz.

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Freesurfer May 2010