Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

Fwd: How to improve/fix TKMEDIT lag
by Vy Dinh 03 Jun '14

03 Jun '14

Greetings Freesurfer developers, I'm looking for ways to improve the speed of TKMEDIT for Freesurfer 5.3. Specifically, the GUI interface is abnormally slow; edits made to a voxel takes 1-2 seconds to show up on the screen. Interesting, the recon-all doesn't appear to be slow (as each subject has been processed within a 24 hr period), so I wonder if this problem has something to do with TKMEDIT's GUI & my current setup. Although I SSH into our server for data processing, here are the specs for my local workstation: Mac OSX 10.9.2 2.7 GHz Intel Core i5 Determine how many cores (Apple icon >> About this Mac >> More Info) 4 GB 1333 MHz DDR3 Server Specs: Our App servers have 4 Xeon CPUs apiece, each with 8 cores running at 2.7GHz, for a total of 32 cores (I was told that this shouldn't be the cause as the point of multi-core and multi-threading is not dependent on speed only). As well, each server has 94 GB of RAM. Our App servers mount shares via NFS from our file servers. All servers are the same version of Red Hat Linux, so there is no differences there. According to the server expert at our institution, the tkmedit does not appear to surpass a CPU *utilization* of 8*%* of a single core, so the programs running off the server should be able to utilize its maximum speed. I am working closely with our server expert to troubleshoot this issue, so any insight from the development team will be much appreciated. Thank you. Best regards, Vy Dinh MD Candidate, Class of 2017 University of Wisconsin School of Medicine and Public Health

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TRACULA statistics by mri_glmfit
by stdp82＠virgilio.it 03 Jun '14

03 Jun '14

Hi list, I'm comparing TRACULA results on three groups.I need to add age as covariate.Therefore, I I'd like to use mri_glmfit for TRACULA statistics but I'm confused on command line.Specifically, from tutorial --y inputfile can be volume or surface-based but my TRACULA results come form "tractstats2table".Please, how can I do it? Stefano

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freesurfer v5.3 TRACULA longitudinnal error
by Chung, Yoonho 02 Jun '14

02 Jun '14

Hi Anastasia I switched from FS v.5.2 to v.5.3 and I am still having this error when running TRACULA longitudinal freesurfer stream despite running with freesurfer v5.3 (both recon-all and trac-all). I am sending along the dmrirc file and the log file. Could you check what may be causing this problem? for testing subjects I am only running one subject with two timepoints. 01_V1000_2_01 # timepoint 1 01_V1000_2_02 # timepoint 2 another question I have is that in the dmrirc file, can we also define multiple bval files? (like how in the example-dmrirc long- you can set multiple bvecs.txt using 'set bveclist'? In the example, option for specifying multiple bval files is not shown. Thank you so much for your time. Best, Yoon _________________ [ychung@cns1 scripts]$ trac-all -prep -c dmrirc.long.subj1 Too many )'s. INFO: SUBJECTS_DIR is /data/napls_DTI/TSS/fs_tracula/fsrecon INFO: Diffusion root is /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI Actual FREESURFER_HOME /usr/local/packages/freesurfer-v5.3.0 trac-preproc -c /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_2_01/scripts/dmrirc.local -log /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_2_01/scripts/trac-all.log -cmd /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_2_01/scripts/trac-all.cmd ; trac-preproc -c /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_2_02/scripts/dmrirc.local -log /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_2_02/scripts/trac-all.log -cmd /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_2_02/scripts/trac-all.cmd ; trac-preproc -c /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_base/scripts/dmrirc.local -log /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_base/scripts/trac-all.log -cmd /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_base/scripts/trac-all.cmd ; ERROR: flag ; unrecognized -c /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_2_01/scripts/dmrirc.local -log /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_2_01/scripts/trac-all.log -cmd /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_2_01/scripts/trac-all.cmd ; trac-preproc -c /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_2_02/scripts/dmrirc.local -log /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_2_02/scripts/trac-all.log -cmd /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_2_02/scripts/trac-all.cmd ; trac-preproc -c /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_base/scripts/dmrirc.local -log /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_base/scripts/trac-all.log -cmd /mnt/nfs/napls_DTI/TSS/fs_tracula/DTI/01_V1000_base/scripts/trac-all.cmd ; Linux cns1.psych.yale.edu<http://cns1.psych.yale.edu/> 3.9.10-100.fc17.x86_64 #1 SMP Sun Jul 14 01:31:27 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Fri May 30 13:22:04 EDT 2014 IsRunningFile: Undefined variable.

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software for registering two flatmaps
by Anthony Dick 02 Jun '14

02 Jun '14

Hello, Can the Freesurfer software register two flatmaps that are not created in Freesurfer? Would they just need to be converted? And which program is appropriate? Anthony -- Anthony Steven Dick, Ph.D. Assistant Professor Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience Department of Psychology Florida International University Modesto A. Maidique Campus AHC4 454 11200 S.W. 8th Street Miami, FL 33199 Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879 Email: adick(a)fiu.edu Webpage: faculty.fiu.edu/~adick; Lab Webpage: http://dcn.fiu.edu Join the Society for the Study of Human Development: http://www.sshdonline.org

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Re: [Freesurfer] CUDA problem with FreeSurfer 5.3.0 on CentOS6
by Chiu, Bryan (PHTH) 02 Jun '14

02 Jun '14

Bump. Having the same problem with a similar setup.

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Queries about semi-inflated surface for overlay
by Zixuan Yang 02 Jun '14

02 Jun '14

Dear Freesurfer experts, I would like to overlay the significance map and gamma.mgh map from cortical thickness GLM on a semi-inflated surface according to one previous post in the mailing list (shown as below) by using the command (shown) under the directory of fsaverage. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-November/012445…<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-November/012445.…> mris_inflate -n <steps> lh.white lh.partially_inflated My questions are: 1) Is it right to generate semi-inflated surface under fsaverage file? Or, I need to generate a semi-inflated surface for each subject (n>500) and make an average surface? How? 2) I tried different 'n', the new generated surface while n=5, 10 or 55 didn't look different at all! Is this normal? It did look very different from lh.white though. 3) Why the generated surface can only be open using tksurfer toolbox, but not a similar command like below? tksurfer fsaverage lh inflated -overlay ./directory_path/gamma.mgh Many thanks for your attention and looking forward to your answers. Best regards, Zixuan -- Zixuan YANG Ph.D candidate Centre for Healthy Brain Ageing (CHeBA) School of Psychiatry, UNSW Medicine NPI, Euroa Centre, Barker Street, Randwick NSW 2031 AUSTRALIA T: +61 (2) 9385 0427 W: www.cheba.unsw.edu.au<http://www.cheba.unsw.edu.au/> E: z.yang(a)student.unsw.edu.au<mailto:s.reppermund@unsw.edu.au> ______________ Mailing address: University of New South Wales Randwick Campus, Building R1f 22-32 King Street, Randwick NSW 2031 Australia

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tumor mask
by Andrea Horváth 02 Jun '14

02 Jun '14

Dear Freesurfers, I would like to run recon-all on patients with brain tumors. Can I add a previously created tumor mask along with the mprage to improve the segmentation? If so, how to do it? Thank you! Andrea -- *Andrea Horváth M.D.* PhD Fellow Diagnostic Centre of Pécs horvath.andrea3(a)pte.hu

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extreme hydrocephalus -wm not recognized
by Andrea Horváth 02 Jun '14

02 Jun '14

Dear Freesurfers, I ran recon-all on a subject with extreme hydrocephalus. Registration to Talairach space and skull stripping were OK. However, a part of occipital white matter was not recognized as white matter even after adding control points and running recon-all -autorecon2-cp -autorecon3 due to the large ventricle as you can see in the attachment. What can you recommend to fix this problem? Thank you for your help! Andrea -- Dr. Horváth Andrea PhD hallgató Pécsi Diagnosztikai Központ

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Re: [Freesurfer] asegstats2table Longitudinal data.
by Victor Montal Blancafort 02 Jun '14

02 Jun '14

Thanks Martin, The provided command works! Best, Victor Hospital de Sant Pau, Barcelona

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invalid license key error
by Kristen Pammer 02 Jun '14

02 Jun '14

Hello, I have just downloaded and installed both CentOS and FreeSurfer. I am trying to run the installation tests, and a number of them do not work (e.g., tkmedit bert orig.mgz, recon etc). the error I get is as follows: ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/license.txt If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment I only recieved the license key a few days ago and copy/pasted the 3 lines exactly as sent to me. I found a thread from about a year ago, I tried to follow it through, but it didn't work. I also cannot find any other threads reporting a similar problem that follow through to a solution. Any help you could provide would be great Thanks KP

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