[Freesurfer] brain stem volume

Dear Freesurfers, I am curious as to how accurate the brain stem and ventral DC volumes are? In particular, how does FS decide where to stop in the inferior direction, i.e. where does it draw the junction between brain stem and spinal cord? Are there FS options to segment the brain stem any fur

Re: [Freesurfer] brain stem volume

Hi Thomas, we segment the brainstem as far inferior as our training set goes. You can look at the CMA papers to see what landmark they use for the inferior border, sorry I'm not sure what it is. cheers Bruce On Wed, 20 Oct 2010, Thesen, Thomas wrote: > Dear Freesurfers, > > I am curious as

[Freesurfer] Symbolic links generated

Hi Freesurfer Team, I am running Freesurfer 5.0 on Ubuntu 64-bit. I want to change the SUBJECTS_DIR environment variable to point to an other location than inside the FREESURFER_HOME/subjects folder. When I do so, and run the recon-all command, 3 symbolic linked folders are generated for fsaverag

[Freesurfer] recon-all using cuda

Hi FS experts, I'm currently testing FS v5 with cuda support. I'm using Centos 5.5 x86_64 on a DELL XPS with 4GB RAM, Intel Core 2 Extreme Processor QX9650 @ 3.67GHz and three GPUS Geforce 9800 GT. Every GPU has 512 GDDR3 memory, 256-BIT Memory Bus, 112 Stream Processing Units, 2x 400MHz RAMDACs

Re: [Freesurfer] Error with mris_volmask.bin

Hi Nick, Thank you for your fast answer. I downloaded yesterday the version5 and I was trying to execute the whole process with the new one. It's running now, and I will tell you if it finishes without errors. Thank you. Jordi. On Mon, Oct 18, 2010 at 4:26 PM, Nick Schmansky wrote: > is it pos

Re: [Freesurfer] Retinotopic mapping of only polar data]

Oh, I see now. I did not read your subject line carefully. You have to have both eccen and polar to run the retinotopy. One way around it is to just copy the polar data and call it eccen. This is a bit of an annoyance, I'll try to fix it in the next version. doug f.le...@donders.ru.nl wrote: >

Re: [Freesurfer] fs450 Longitudinal edits, varied data, and other questions

Hi Jeff, On Tue, 2010-10-19 at 13:40 -1000, Jeff Sadino wrote: > Thank you for your feedback on my previous question regarding the > surface area measurement. We found it very helpful to move forward. > > > I am beginning (again) to do longitudinal processing using fs4.5.0, > but I just want t

Re: [Freesurfer] recon-all using cuda

On Wed, 2010-10-20 at 16:18 +0200, Jordi Delgado wrote: > *** glibc detected *** mri_em_register: malloc(): memory corruption: > 0x315dfdc0 *** > === Backtrace: = > /lib64/libc.so.6[0x3304072fae] > /lib64/libc.so.6(__libc_calloc+0xcd)[0x330407495d] > mri_em_register[0x42efad]