Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

errors in recon-all -autorecon3
by Larissa Stanberry 14 Jan '11

14 Jan '11

Hi experts, I'm running the commands from recon-all -autorecon3 from a script file and I'm getting the following errors mri_segstats: unknown option --empty mri_aparc2aseg: unknown option --ribbon From the help files, mri_segstats has option --nonempty and mri_aparc2aseg has an option --new-ribbon. I suspect that the recon- all steps are slightly out of date. So what was option --empty did in mri_segstats, is it equivalent or opposite of --nonempty? Also I understand that mri_aparc2aseg --new-ribbon will by default use a ribbon.mgz file, i however have my own ribbon file which I created based on my own template. How can I feed myribbon.mgz to mri_aparc2aseg? Thanks for your help Larissa

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documentation on aseg corpus callosum segementation
by Kristine Beate Walhovd 14 Jan '11

14 Jan '11

Hi, is there any documentation on the aseg corpus callosum segmentation (the one with five subdividivisons) that I could refer to? I guess this is still the preferred cc seg in FS (not the one pased on cortical parcellation)? Thanks a lot in advance! Best, Kristine -- Kristine B Walhovd Professor University of Oslo Center for the Study of Human Cognition Department of Psychology PB 1094 Blindern 0317 Oslo Norway

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Re: [Freesurfer] overlap individual thickness map on average surface
by tulu＠ms36.hinet.net 14 Jan '11

14 Jan '11

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process with Freesurfer v4.5 and v5.0 together
by Jin Li 13 Jan '11

13 Jan '11

Dear Freesurfer experts, Our data was previously processed by Freesurfer v4.5, recently I visually checked the results and did manual correction under Freesurfer v5.0. Then ran the rest steps under Freesurfer v5.0. Here are my 2 questions. 1. Is it acceptable to run the first and second steps in previous version, then correct manually and run the rest steps in a newer version? 2. In some subjects, the pial surface was corrected, followed by a command -autorecon2-cp -autorecon3, so stages 21-31 were re-processed. In other subjects, which wm surface was corrected, stages 15-31 were re-processed, while for those with control point added, stages 12-31 were re-processed. Then is it acceptable that different stages were processed under Freesurfer v5.0 among subjects? Can I do group analysis among these subjects? Thank you in advance for any suggestion. Jin

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overlap individual thickness map on average surface
by tulu＠ms36.hinet.net 13 Jan '11

13 Jan '11

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MRI_concat
by Rita Loiotile 13 Jan '11

13 Jan '11

For a series of nifti fMRI images does it matter in what order I list the images for my input? Or does MRI_concat get the time series info from the files themselves? Sent from my iPhone

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Re: [Freesurfer] Freesurfer Digest, Vol 83, Issue 26
by Bevil R. Conway 13 Jan '11

13 Jan '11

I will be out of the country from Jan. 10 - Jan 18, 2011, and will not have access to email. For issues concerning my laboratory, please contact my lab manager, Rosa Lafer-Sousa (rlaferso(a)wellesley.edu) Thank-you and I'll be in touch when I get back. Bevil

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Continuation of my futile attempts at configuring ATI videocard driver for Freesurfer=)
by Alexander Lebedev 13 Jan '11

13 Jan '11

Dear Freesurfers, I keep fighting with my 64bit-CentOS in order to configure my videocard (ATI Radeon Sapphire HD 5750) for FS. At last I got rid of "segfault error". And now there is another error (after tkmedit command): ============================================================= X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 143 (GLX) Minor opcode of failed request: 19 (X_GLXQueryServerString) Serial number of failed request: 15 Current serial number in output stream: 15 ============================================================= I assume there is a problem with OpenGL... I have searched in archives, googled but unfortunately haven't found useful information on this topic. Do you have any idea how to solve this problem? My "xorg.conf"-file includes following: ============================================================= # Xorg configuration created by system-config-display Section "ServerLayout" Identifier "single head configuration" Screen 0 "aticonfig-Screen[0]-0" 0 0 InputDevice "Keyboard0" "CoreKeyboard" EndSection Section "Module" EndSection Section "InputDevice" Identifier "Keyboard0" Driver "kbd" Option "XkbModel" "pc105" Option "XkbLayout" "us" EndSection Section "Monitor" Identifier "aticonfig-Monitor[0]-0" Option "VendorName" "ATI Proprietary Driver" Option "ModelName" "Generic Autodetecting Monitor" Option "DPMS" "true" EndSection Section "Device" Identifier "Videocard0" Driver "vesa" EndSection Section "Device" Identifier "aticonfig-Device[0]-0" Driver "fglrx" BusID "PCI:7:0:0" EndSection Section "Screen" Identifier "Screen0" Device "Videocard0" DefaultDepth 24 SubSection "Display" Viewport 0 0 Depth 24 EndSubSection EndSection Section "Screen" Identifier "aticonfig-Screen[0]-0" Device "aticonfig-Device[0]-0" Monitor "aticonfig-Monitor[0]-0" DefaultDepth 24 SubSection "Display" Viewport 0 0 Depth 24 EndSubSection EndSection ================================================================= Thank you beforehand. -- Best Regards, Alexander Lebedev.

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Re: [Freesurfer] Freesurfer Digest, Vol 83, Issue 24
by Bevil R. Conway 12 Jan '11

12 Jan '11

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zero intensities within brainmask.mgz
by Xinian Zuo 12 Jan '11

12 Jan '11

Hi, FSers, Sorry for sending again. I am using FS5. 0 to extract brain mask for other analyses. I found there were always some zero intensities within voxels of some CSF, thus lead to a brain mask with some small holes inside after binary operation. Is there a way of filling them? Thanks! -- Xi-Nian Zuo, Ph.D of Applied Mathematics (http://lfcd.psych.ac.cn)

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