Freesurfer

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30099 discussions

?reference(s) supporting DLPFC label
by Fidel Vila 03 Jun '14

03 Jun '14

Dear FS community, I'm looking into DLPFC volume/thickness. Following advice posted before on this forum, I'm adding G_frontal_middle.label + S_frontal_inferior.label + S_frontal_middle.label from Destrieux 2009 atlas as a surrogate for DLPFC. My question is whether folks could provide reference(s) from the literature backing up this approach? Thanks for your time and help, Kev

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TRACULA: Exits with Errors, and ERROR in -qa Flag
by Shantanu Ghosh 03 Jun '14

03 Jun '14

Dear Anastasia, I wrote to the Freesurfer Listserv yesterday about the problem I am facing in running tracula, although my FS is set to version 5.3. However, I debugged some problems in the config file, and now trac-all -prep runs through all the DTI volumes, but exits with errors. Also, it does not recognize the -qa flag. What am I doing wrong? Attached is the log file, and an updated config file. Any help is highly appreciated. Thanks. Shantanu ---------------------------- Original Message ---------------------------- Subject: TRACULA: ERROR in -qa Flag From: "Shantanu Ghosh" <shantanu(a)nmr.mgh.harvard.edu> Date: Mon, June 2, 2014 6:32 pm To: freesurfer(a)nmr.mgh.harvard.edu -------------------------------------------------------------------------- Dear Anastasia and Freesurfer experts, I am trying to set up an analysis of motion parameters using the flag -q from a set of DTI Dicoms located on the Martinos cluster, but I am facing problems -- it says "ERROR: flag -qa unrecognized". My .tcshrc is set to Freesurfer5.3 and FSL. What am I doing wrong? My config file is attached and here are my commands. cd /autofs/space/glia_001/users/shantanu/dtistudy/ setenv PATH /usr/pubsw/packages/python/epd/bin:${PATH} setenv FSENV_KEEP_PROMPT setenv MNE_ROOT /usr/pubsw/packages/mne/stable setenv SUBJECTS_DIR /autofs/space/calvin_001/marvin/1/users/MRI/WMA/recons setenv FSL_DIR /usr/pubsw/packages/fsl/5.0.0 source /usr/local/freesurfer/nmr-stable53-env source /usr/pubsw/packages/mne/stable/bin/mne_setup ----My console output----- glia:shantanu[120] mynmr53 -------- freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING: /autofs/space/calvin_001/marvin/1/users/MRI/WMA/recons does not exist FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 FSFAST_HOME /usr/local/freesurfer/stable5_3_0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /autofs/space/calvin_001/marvin/1/users/MRI/WMA/recons MNI_DIR /usr/local/freesurfer/stable5_1_0/mni FSL_DIR /usr/pubsw/packages/fsl/5.0.0 MNE software location set to: /usr/pubsw/packages/mne/stable MATLAB software not available /usr/pubsw/packages/mne/stable/bin already in PATH /usr/pubsw/packages/mne/stable/lib added to LD_LIBRARY_PATH /usr/pubsw/packages/mne/stable/share/app-defaults/%N added to XUSERFILESEARCHPATH Note: Remember to set SUBJECTS_DIR and SUBJECT environment variables correctly. Note: FreeSurfer environment is needed to access tkmedit from mne_analyze. glia:shantanu[121] trac-all -qa -s 008801 -c /autofs/space/glia_001/users/shantanu/dtistudy/dticonfigfile.txt ERROR: flag -qa unrecognized -qa -s 008801 -c /autofs/space/glia_001/users/shantanu/dtistudy/dticonfigfile.txt glia:shantanu[122] Thanks in advance for all help. Shantanu -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg

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

03 Jun '14

Hi, I discovered that installing Freesurfer onto my local workstation and running Tkmedit from there has resolved my issue. It doesn't explain why tkmedit is so slow when run from our server, so if you have some ideas please let me know. Thank you all for your help. Best, Vy On Tue, Jun 3, 2014 at 12:39 PM, Vy Dinh <vydinh1(a)gmail.com> wrote: > Thank you for your reply. All of our Freesurfer commands, including > Tkmedit are run from the servers on the RedHat Machine. We use the ssh -Y > syntax (not -X), and when I tried using -X instead, it doesn't change the > speed of tkmedit. > > Additionally, I tried copying my data to another (department's) server at > our institution and running tkmedit from there. We didn't experience any > lag here, so this suggests that our department's dedicated server is > somehow dealing with tkmedit differently. However, when our server expert > checked the CPU usage, it appears that OUR department's server is using > less RAM overall (so it if anything, our data should process more > quickly.). In other words, we can't figure out how Tkmedit is utilized by > the servers differently. > > -Vy > > > On Tue, Jun 3, 2014 at 11:13 AM, dgw <dgwakeman(a)gmail.com> wrote: > >> Hi, >> >> What machine are you actually running tkmedit on? >> >> more specifically: >> You appear to be using a mac. Do you run tkmedit directly on the mac? >> >> or are you using ssh -X (or something like it to run it) on the Red Hat >> machines? >> >> Thanks, >> D >> >> >> On Tue, Jun 3, 2014 at 11:55 AM, Vy Dinh <vdinh2(a)wisc.edu> wrote: >> >>> >>> 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 >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to whom >>> it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you >>> in error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > > > -- > Vy T.U. Dinh > Research Assistant, Neurological Sciences > Rush University Medical Center > Phone: (312) 563-3853 > Fax: (312) 563-4660 > Email: Vy_dinh(a)rush.edu > > -- Vy Dinh MD Candidate, Class of 2017 University of Wisconsin School of Medicine and Public Health

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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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