[Freesurfer] problem when run qdec

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:

[Freesurfer] aparcstats2table surface area

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

Re: [Freesurfer] mri_surf2surf failure in FS6.0

Hi dong, sorry for the delay. What is your mri_vol2surf command line? On 10/20/17 4:44 AM, Dongnandi wrote: 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

Re: [Freesurfer] Selecting OS for image analysis

Hi Ramesh, Freesurfer is built and developed mainly on centos machines, but ubuntu works fine as well. Here’s some more info: https://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements best Andrew On Oct 17, 2017, at 7:04 AM, Ramesh Babu

[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

Re: [Freesurfer] segmentHA znzread failed error

some times the compression/decompression routines will store intermediate files in /tmp or /scratch or somewhere else. If its target location fills up, then you can get errors, so check the disk space in those locations On 10/24/17 9:34 AM, Iglesias Gonzalez, Eugenio wrote: Wow never seen

Re: [Freesurfer] surface based correlation analysis

That sounds right, yes On 10/24/2017 10:54 AM, John Anderson wrote: > 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

Re: [Freesurfer] mri_surf2surf failure in FS6.0

Hi Doug, Thanks very much for your reply. The mri_vol2surf command line i used is: mri_vol2surf --mov brainmask.nii.gz --reg bbregister.dof6.dat --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi ${hemi} --o brainmask.fsaverage.${hemi}.nii.gz --noreshape --cortex --surfreg

[Freesurfer] surface based correlation analysis

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

Re: [Freesurfer] segmentHA znzread failed error

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:

Re: [Freesurfer] aparcstats2table surface area

On 10/24/17 2:37 AM, Kasper Jessen wrote: Hi FreeSurfer, We have extracted the surface area using aparcstats2table. 1.The ROIs extracted are by default the White Surface Area, correct? Correct. 2.Why does the WhiteSurfArea (default average) have decimals but not the surface area of

Re: [Freesurfer] thickness of corpus callosum

people have used the medial axis for this I believe. Not sure we have any code around for it anymore, although we once did. You basically compute the medial axis, then for each point on it you should have the radius of the largest inscribed circle as the thickness cheers Bruce On Tue, 24 Oct

Re: [Freesurfer] problem when run qdec

Hi Yawu, Seems like a graphics driver issue. Does running "glxinfo" give the same error? What OS are you using? Andrew > On Oct 24, 2017, at 3:36 AM, Liu Y wrote: > > Dear Experts, > When I run qdec, it showed me error message, any suggestins? > qdec > X Error of failed

Re: [Freesurfer] segmentHA znzread failed error

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

Re: [Freesurfer] problem when run qdec

I noticed that a hided message saying the system crashed. I reboot the computer, then it worked. Thanks, Yawu 2017年10月24日 20:34，"Hoopes, Andrew" 写道： > Hi Yawu, > > Seems like a graphics driver issue. Does running "glxinfo" give the same > error? What OS are you using? >

Re: [Freesurfer] segmentHA znzread failed error

I verified that it is not a storage issue. Let me know if znzreadInt is important. Thank again, arkadiy From: "Maksimovskiy, Arkadiy" Date: Tuesday, October 24, 2017 at 1:37 PM To: "Freesurfer@nmr.mgh.harvard.edu" Subject: Re:

Re: [Freesurfer] segmentHA znzread failed error

Sorry for another question, but it seems that even when I open out the output, it produces the following: amaksimovskiy% freeview -v nu.mgz -v lh.hippoAmygLabels-T1.v20.mgz:colormap=lut -v rh.hippoAmygLabels-T1.v20.mgz:colormap=lut znzreadInt: znzread failed znzreadInt: znzread failed