Freesurfer

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30063 discussions

Re: [Freesurfer] segmentHA znzread failed error
by Maksimovskiy, Arkadiy 24 Oct '17

24 Oct '17

Thanks everyone! Doug- I will check the storage. If the outputs look good, is this something to worry about and rerun? Much appreciated, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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problem when run qdec
by Liu Y 24 Oct '17

24 Oct '17

Dear Experts, When I run qdec, it showed me error message, any suggestins? qdec X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 154 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 1571 Current serial number in output stream: 1572 Thanks in advance, Yawu

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mri_surf2surf failure in FS6.0
by Dongnandi 24 Oct '17

24 Oct '17

Dear Freesurfer experts, I have a binary brainmask made in volumetric space and trying to transfer it into surface space, first I use mri_vol2surf to transfer the mask into fsaverage space, then run mri_surf2surf (fs 6.0) to down sample it to fsaverage5 space. After vol2surf, some values on the vertex in fsaverage space would be less than 1 due to the interpolation, however, I find values on these vertexes (<1 in fsaverage) come to be 0 after mri_surf2surf in faverage5 space. it doesn't happen in version 5.3, how can I solve this in 6.0? Many thanks, Dong Haoming

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thickness of corpus callosum
by Vidhu Agrawal 24 Oct '17

24 Oct '17

Respected Sir, How can we measure the thickness of corpus callosum? Thank you With regards Vidhu Agarwal

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Selecting OS for image analysis
by Ramesh Babu 24 Oct '17

24 Oct '17

Dear Experts, I have purchased a new pc. I want to use for MRI and EEG analysis by using MATLAB, FSL, SPM, Fresurfer etc,. Which OS is suitable to handle these software? I have NVIDIA graphics card 610 in my system. I am using Ubuntu in another systm and little bit of experience in cent os. Thank in advance Ramesh

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surface based correlation analysis
by John Anderson 24 Oct '17

24 Oct '17

Dear Dr Doug, I want to study the relationship between PET signal measured as the mean signal of the whole cortex and gray matter volume to find regions of association between gray matter atrophy and PET signal. In this case I will need to run surface based analysis and the FSGD file must be "One Group, One Covariate" is this correct? Thanks for any suggestions/ advice! John

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Re: [Freesurfer] segmentHA znzread failed error
by Iglesias Gonzalez, Eugenio 24 Oct '17

24 Oct '17

Wow never seen that before. Does the output look OK? (segmentation and volumes) Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Maksimovskiy, Arkadiy" <AMAKSIMOVSKIY(a)mclean.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, 24 October 2017 at 14:31 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] segmentHA znzread failed error Dear Hipp. Segmentation experts, I keep getting the following error when running the segmentHA script from the Dev. Version. Wondering if this is serious or something that can be ignored, as the process keeps running to the end: Transforming points znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory threshold mask volume at 0.5 znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory threshold mask volume at 0.5 znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed Thank you for your help, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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aparcstats2table surface area
by Kasper Jessen 24 Oct '17

24 Oct '17

Hi FreeSurfer, We have extracted the surface area using aparcstats2table. 1. The ROIs extracted are by default the White Surface Area, correct? 2. Why does the WhiteSurfArea (default average) have decimals but not the surface area of the different ROIs? When taking the SUM of all the ROIs, it does not equal the WhiteSurfArea and I am thinking this must be due to the decimals? Best Regards Kasper ________________________________ Denne e-mail indeholder fortrolig information. Hvis du ikke er den rette modtager af denne e-mail eller hvis du modtager den ved en fejltagelse, beder vi dig venligst informere afsender om fejlen ved at bruge svarfunktionen. Samtidig bedes du slette e-mailen med det samme uden at videresende eller kopiere den.

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segmentHA znzread failed error
by Maksimovskiy, Arkadiy 24 Oct '17

24 Oct '17

Dear Hipp. Segmentation experts, I keep getting the following error when running the segmentHA script from the Dev. Version. Wondering if this is serious or something that can be ignored, as the process keeps running to the end: Transforming points znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory threshold mask volume at 0.5 znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed No such file or directory threshold mask volume at 0.5 znzreadInt: znzread failed No such file or directory znzreadInt: znzread failed Thank you for your help, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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[job] Program Manager for the Brain Imaging Data Structure project
by Chris Gorgolewski 23 Oct '17

23 Oct '17

Do you have great people skills and enjoy organizing events? Are you interested in helping neuroscientists exchange data in a more useful way? The Brain Imaging Data Structure project is looking for a full time Program Manager - this might be a perfect job for you! No neuroimaging experience is required, but some will come handy. This position might be especially attractive if you appreciate working in an academic environment, but prefer to avoid the stress of “publish or perish” and enjoy a competitive salary. The position is based in the legendarily sunny San Francisco Bay Area. The successful candidate will receive relocation support. More details at https://stanford.taleo.net/careersection/2/jobdetail.ftl?job=76713&lang=en#…. We will start reviewing applications on the 6th of November. Best regards, Chris Gorgolewski PS Apologies for cross posting - please forward this ad if you know someone who might be interested.

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