Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

new GPU binaries
by Nick Schmansky 25 Oct '10

25 Oct '10

Freesurfanados and GPU fans, We (namely Richard) have fixed some of the problems with the existing freesurfer gpu binaries, which were the result of building against cuda 3.0 on our build platforms, which seemed to be incompatible with 3.1. We've built against 3.1, although now i see nvidia has come out with 3.2, but i've tested against that and they seem to work. So you can get the binary tarball here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86… and here for the 32b linux: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86… copy the extracted contents of those tarball into your freesurfer/bin dir. The binaries are: mri_ca_register_cuda mri_em_register_cuda mris_fix_topology_cuda mris_flatten_cuda mris_inflate_cuda mris_sphere_cuda mri_vol2vol_cuda No doubt people will encounter problems, so let us know. But hopefully you will see a dramatic reduction in the runtime of the subcortical segmentation stage (mri_ca_register). Also, to remind people, Richard is targeting our gpu development for the Fermi class of gpu card, which has better memory management which leads to better performance of some algorithms, so if you're buying new hardware, be sure to spec that class of card (see nvidia site). Nick

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question about using lta file from mri_robust_register
by Mehul Sampat 23 Oct '10

23 Oct '10

Hi Folks, I am trying to troubleshoot an issue and I have not been able to find a solution yet. Here is what I am trying to do: 1. I used mri_robust_register to register a t1-weighted image to a t2-image. mri_robust_register works very well and i also got an lta file (t1-to-t2.lta) 2. now i also have the wm-mask from the freesurfer output. this was created using: mri_binarize --i aparc+aseg.mgz --wm --o t1-wm-mask-fs.mgz 3. Then I take the wm-mask to native space using: mri_convert -rl orig/001.mgz t1-wm-mask-fs.mgz t1-wm-mask-ns.nii 4. Finally, I want to apply the t1 white matter mask to the t2 image using the lta file generated in step 1. for this I use: mri_convert --apply_transform t1-to-t2.lta t1-wm-mask-ns.nii t1-to-t2.nii step 1-3 work fine. but when i try to apply the transform in the last step, the output is zeros. The output of mri_robust_register in step 1 is fine. Does mri_robust_register use mri_convert to apply the transform and create the output image ? Or am I making some error ? thanks Mehul

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Re: [Freesurfer] Nifti surface to FreeSurfer surface
by Nick Schmansky 22 Oct '10

22 Oct '10

use mri_binarize to set each brain voxel value to the same value (maybe bet does this), then use something like: mri_tesselate mybrainmask.nii.gz 127 mybrainmask.surf where '127' happens to be voxel value used in the binarization. n. On Fri, 2010-10-22 at 15:08 -0600, Alexander Hunold wrote: > Dear experts, > > > > I got BEM surfaces out of the BET tool from the FSL package. The > surface files are in nifti format (*.nii.gz). > Now I wonder if there is any opportunity to convert nifti surfaces to > FreeSurfer surface in surf format (*.surf)? > > I appreciate any hint. > > Thank you so much in advance. > > > > Sincerely, > > Alexander > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Nifti surface to FreeSurfer surface
by Alexander Hunold 22 Oct '10

22 Oct '10

Dear experts, I got BEM surfaces out of the BET tool from the FSL package. The surface files are in nifti format (*.nii.gz). Now I wonder if there is any opportunity to convert nifti surfaces to FreeSurfer surface in surf format (*.surf)? I appreciate any hint. Thank you so much in advance. Sincerely, Alexander

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Talairach coordinates for Desikan gyral regions
by Robustelli, Briana (NIH/NIMH) [F] 22 Oct '10

22 Oct '10

Hi all, We are trying to depict spatial relations of each of the Desikan et. al (2006) gyral regions in a separate 3-D graph. To do this we need every regions' center Talairach coordinates in common space, not in relation to any particular group or subject. Is there a way to do this using Freesurfer? Thank you. Briana

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Freeview and Mac OS 10.6 - Snow Leopard
by Andreas Schindler 22 Oct '10

22 Oct '10

Dear Freesurfers Does anyone know if freeview already works on Mac OS Snow Leopard or when it will be patched? best wishes Andreas

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Postdoctoral Fellowship in multimodal developmental neuroimaging
by Michels Lars 22 Oct '10

22 Oct '10

Postdoctoral Fellowship in multimodal developmental neuroimaging Applications are invited for a 2-years postdoctoral fellowship in the human multimodal neuroimaging project "Linking the major system markers for typical and atypical brain development: a multimodal imaging and spectroscopy study" (http://www.zihp.uzh.ch/1610.php#45) funded by the Zürich Institute of Human Physiology. This study will investigate the major physiological markers of brain development, using a combination of advanced magnetic resonance imaging (e.g., functional MRI) and MR-spectroscopy methods. The initial phase of the study will establish baseline neurotransmitter levels, cerebral blood flow (e.g., perfusion MRI) and EEG frequency and power at rest across a range of age groups. Examining the interactions between these markers and the changes they demonstrate with age and hormone levels will allow to better understanding the global and regional processes underlying brain maturation. The later phases will investigate changes in these physiological markers with (a) cognitive tasks and (b) attention deficit hyperactivity disorder (ADHD). The starting date of the position is January 2011. The successful applicant will have a PhD research background in Cognitive Neuroscience, Neurophysiology, Psychology, Neuropsychology, or related fields. Fluency in English, good oral and written German, and the ability to work within a multidisciplinary team are essential. Applicants should be experienced at conducting fMRI and/or EEG studies and be familiar with analysis software, such as SPM/Matlab, BrainVoyager and/or FSL. Experience with stimulus presentation software (such as Presentation), UNIX, and programming languages a plus. Salaries are in accordance with the Swiss National Research Foundation (starting at around 80'000 CHF p.a.). APPLICATION INSTRUCTIONS: To apply by e-mail (max 5 MB), please send a curriculum vitae, a personal statement describing research interests, 3 letters of recommendations, and up to 5 article reprints/preprints to: Dr Lars Michels lars.michels(a)kispi.uzh.ch MR-Zentrum University Children's Hospital Steinwiesstrasse 75 Zürich 8032 Switzerland Reviews of applications will begin on the 7th of November and will continue until the positions are filled.

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Symbolic links generated
by Stephan Gerhard 21 Oct '10

21 Oct '10

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 fsaverage/ lh.EC_average/ and rh.EC_average/. How can I avoid this behaviour? Thanks, Stephan

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exiting with errors
by Nathan Dankner 21 Oct '10

21 Oct '10

Hi all, I've run into a recurring error with some scans that I am running. It is duplicated below: ncopen: filename "./tmp.mri_nu_correct.mni.8091/0/nu1_residue.mnc": Not a netCD$ miopen: MINC package entry point nu_estimate_np_and_em: crashed while running mincmath (termination status=768) nu_correct: crashed while running nu_estimate_np_and_em (termination status=768) ERROR: nu_correct This is occuring very early in autorecon1. Any idea what's going wrong? Thanks, Nathan

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recon-all using cuda
by Jordi Delgado 20 Oct '10

20 Oct '10

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 and PCI Express 2.0 suport. The SDK examples runs perfect but when I run the following script: export FREESURFER_HOME=/home/neuro/freesurfer source /home/neuro/freesurfer/SetUpFreeSurfer.sh export SUBJECTS_DIR=/home/neuro/proc/OutPBS_GPU recon-all -all -force -i /home/neuro/orig/ACR_103/ACR_103_0002 -s ACR_103 -qcache *-use-cuda* I obtain the following error message: *** glibc detected *** mri_em_register: malloc(): memory corruption: 0x00000000315dfdc0 *** ======= Backtrace: ========= /lib64/libc.so.6[0x3304072fae] /lib64/libc.so.6(__libc_calloc+0xcd)[0x330407495d] mri_em_register[0x42efad] mri_em_register[0x40e80d] /lib64/libc.so.6(__libc_start_main+0xf4)[0x330401d994] mri_em_register(__gxx_personality_v0+0x16a)[0x40b16a] ======= Memory map: ======== 00400000-00b55000 r-xp 00400000 00:00 0 00b55000-00c54000 ---p 00b55000 00:00 0 00c54000-02627000 rwxp 00c54000 00:00 0 1ef6f000-3c61e000 rwxp 1ef6f000 00:00 0 [heap] 3303c00000-3303c1c000 r-xp 00000000 08:03 79331333 /lib64/ld-2.5.so 3303c1c000-3303e1b000 ---p 3303c1c000 00:00 0 3303e1b000-3303e1c000 r-xp 0001b000 08:03 79331333 /lib64/ld-2.5.so 3303e1c000-3303e1d000 rwxp 0001c000 08:03 79331333 /lib64/ld-2.5.so 3304000000-330414e000 r-xp 00000000 08:03 79331340 /lib64/libc-2.5.so 330414e000-330434d000 ---p 0014e000 08:03 79331340 /lib64/libc-2.5.so 330434d000-3304351000 r-xp 0014d000 08:03 79331340 /lib64/libc-2.5.so 3304351000-3304352000 rwxp 00151000 08:03 79331340 /lib64/libc-2.5.so 3304352000-3304357000 rwxp 3304352000 00:00 0 3304400000-3304402000 r-xp 00000000 08:03 79331344 /lib64/libdl-2.5.so 3304402000-3304602000 ---p 00002000 08:03 79331344 /lib64/libdl-2.5.so 3304602000-3304603000 r-xp 00002000 08:03 79331344 /lib64/libdl-2.5.so 3304603000-3304604000 rwxp 00003000 08:03 79331344 /lib64/libdl-2.5.so 3304800000-3304882000 r-xp 00000000 08:03 79331372 /lib64/libm-2.5.so 3304882000-3304a81000 ---p 00082000 08:03 79331372 /lib64/libm-2.5.so 3304a81000-3304a82000 r-xp 00081000 08:03 79331372 /lib64/libm-2.5.so 3304a82000-3304a83000 rwxp 00082000 08:03 79331372 /lib64/libm-2.5.so 3304c00000-3304c16000 r-xp 00000000 08:03 79331354 /lib64/libpthread-2.5.so 3304c16000-3304e15000 ---p 00016000 08:03 79331354 /lib64/libpthread-2.5.so 3304e15000-3304e16000 r-xp 00015000 08:03 79331354 /lib64/libpthread-2.5.so 3304e16000-3304e17000 rwxp 00016000 08:03 79331354 /lib64/libpthread-2.5.so 3304e17000-3304e1b000 rwxp 3304e17000 00:00 0 3305000000-3305014000 r-xp 00000000 08:03 12817044 /usr/lib64/libz.so.1.2.3 3305014000-3305213000 ---p 00014000 08:03 12817044 /usr/lib64/libz.so.1.2.3 3305213000-3305214000 rwxp 00013000 08:03 12817044 /usr/lib64/libz.so.1.2.3 3306400000-3306409000 r-xp 00000000 08:03 79331382 /lib64/libcrypt-2.5.so 3306409000-3306608000 ---p 00009000 08:03 79331382 /lib64/libcrypt-2.5.so 3306608000-3306609000 r-xp 00008000 08:03 79331382 /lib64/libcrypt-2.5.so 3306609000-330660a000 rwxp 00009000 08:03 79331382 /lib64/libcrypt-2.5.so 330660a000-3306638000 rwxp 330660a000 00:00 0 3309c00000-3309c0d000 r-xp 00000000 08:03 79331394 /lib64/libgcc_s-4.1.2-20080825.so.1 3309c0d000-3309e0d000 ---p 0000d000 08:03 79331394 /lib64/libgcc_s-4.1.2-20080825.so.1 3309e0d000-3309e0e000 rwxp 0000d000 08:03 79331394 /lib64/libgcc_s-4.1.2-20080825.so.1 330b400000-330b4e6000 r-xp 00000000 08:03 12824478 /usr/lib64/libstdc++.so.6.0.8 330b4e6000-330b6e5000 ---p 000e6000 08:03 12824478 /usr/lib64/libstdc++.so.6.0.8 330b6e5000-330b6eb000 r-xp 000e5000 08:03 12824478 /usr/lib64/libstdc++.so.6.0.8 330b6eb000-330b6ee000 rwxp 000eb000 08:03 12824478 /usr/lib64/libstdc++.so.6.0.8 330b6ee000-330b700000 rwxp 330b6ee000 00:00 0 2b2d46aaa000-2b2d46aad000 rwxp 2b2d46aaa000 00:00 0 2b2d46ab9000-2b2d47f2e000 rwxp 2b2d46ab9000 00:00 0 2b2d48000000-2b2d48021000 rwxp 2b2d48000000 00:00 0 2b2d48021000-2b2d4c000000 ---p 2b2d48021000 00:00 0 7fff73ffe000-7fff741f2000 rwxp 7fffffe0a000 00:00 0 [stack] ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0 [vdso] I attached the output log of the execution. Any idea will be apreciated! Thank you in advance!! -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona Tel: +34 93 586 82 32 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html

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