Freesurfer December 2015

freesurfer@nmr.mgh.harvard.edu

115 participants
187 discussions

Merge both hemispheres in cortical parcellations
by Carme Uribe Codesal 17 Dec '15

17 Dec '15

Dear FreeSurfer users, I've been looking for an appropiate way to merge both hemispheres in the Desikan parcellations but I can't find it in the list. Which formula do I need to use to consider, for example, the bilateral posterior cingulate as an only measure (not lh and rh separated)? I'm not sure if I can just add them in a mean... Thank you very much for your help! Carme

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Position Available: Director of Machine Learning Core
by Thomas, Adam (NIH/NIMH) [E] 17 Dec '15

17 Dec '15

The NIMH is starting up a Machine Learning core facility and needs a director. Apply now! Title 42 Staff Scientist / Director Machine Learning Core National Institute of Mental Health, National Institutes of Health Department of Health and Human Services, Bethesda, MD The National Institute of Mental Health (NIMH), a major research component of the National Institutes of Health (NIH), and the Department of Health and Human Services (DHHS), is seeking exceptional candidates for the Director position in the Division of Intramural Research Programs (DIRP) of the newly created Machine Learning Core (MLC). The NIMH DIRP represents one of the largest concentrations of neuroimaging researchers in the world with experts in cognitive neuroscience, mental health, neurological disorders, functional MRI methods and technology, DTI, high field imaging, parallel imaging, spectroscopy, and molecular imaging, among others. The NIH also hosts a world class high performance computing cluster with 20,000+ computing nodes and over a petabyte of storage (http://hpc.nih.gov <http://hpc.nih.gov/>). The new Machine Learning Core will be responsible for developing, facilitating, and supporting machine learning approaches to analyzing human neuroimaging data collected within the NIMH IRP as well as the currently growing number of functional and anatomic imaging databases worldwide. The MLC will also be responsible for assisting investigators in their own research for the search for biomarkers to help diagnose mental health and neurologic disorders in individual subjects. Lastly, MLC will provide extensive education and outreach efforts to help NIMH IRP investigators learn more about machine learning approaches and effectively collaborate with machine learning experts. Candidates must have a Ph.D. in a STEM discipline, post doctoral experience in machine learning approaches, and a passion for applying computational analysis to imaging data towards the goal of deriving biomarkers. Skill and experience in fMRI and MRI acquisition and analysis methods will be considered very favorably. The director’s role will include hiring and supervising junior machine learning specialists, maintain the core’s budget, managing an educational series focused on machine learning for NIMH IRP staff, developing novel and generally useful machine learning approaches, and providing support to investigators in machine learning analyses. Salary will be commensurate with education and experience. Application deadline is March 1, 2016. Applicants should send curriculum vitae and three letters of recommendation to: Peter A. Bandettini, Ph.D. MLCORE-JOBSEARCH(a)mail.nih.gov bandettini(a)nih.gov Building 10, Room 1D80 10 Center Drive Bethesda, MD 20892-1148, 301-402-1333 TTY: MD Relay Operator at 1-800-735-2258. The National Institutes of Health is an equal opportunity employer. http://bit.ly/Machine_Learning_Core_Director

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Fwd: error in long_mri_slopes
by Nabin Koirala 17 Dec '15

17 Dec '15

Hi all, I am doing longitudinal analysis (recon-all) and while running the long_mri_slopes using the following command, I am getting different errors for each run and its driving me crazy. The command I am running : long_mris_slopes --qdec ./qdec/long.qdec.Sub_7_t0t1.dat --meas thickness --hemi lh --do-avg --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd /home/nk/freesurfer/subjects/ I could not make any sense as the errors as they are different every time and sometimes it gets completed aswel. The various errors are : ERROR 1 : mri_convert splitting qcache stack did not work? ERROR 1 : mris_label_calc intersect did not work? ERROR 1 : mri_glmfit did not work? These are for the same subject and for the same hemisphere. And once it completed for left hemisphere but threw similar error for right hemisphere. Your suggestions would be very much appreciated. PS This is not only for one subject but for most of them. Thank you. Regards, Nabin

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freeview automatization not working nicely
by BAUTISTA-PERPINYA Maximilià 17 Dec '15

17 Dec '15

Hi FS experts, I have an script (screenshots.txt) that takes screenshots of freeview of several scans: It looks like this: -v scan1/mri/T1.mgz ; -v scan1/mri/aparc+aseg.mgz:colormap=lut:opacity=0.2 ; -viewport sagittal -slice 80 127 127 -ss sag1_scan1 ; -v scan2/mri/T1.mgz ; -v scan2/mri/aparc+aseg.mgz:colormap=lut:opacity=0.2 ; -viewport sagittal -slice 80 127 127 -ss sag1_scan2 ; ... and so on Then I run freeview -cmd screenshots.txt and it gives me this error: MRIread failed: Unable to read from /home/freesurfer/Desktop/test005/subjects/; This path is my cwd. The scan folders (scan1, scan2, and so on) are contained within the above mentioned cwd, but the cwd is not mentioned in the script. I tried specifying the complete path (/home/freesurfer/Desktop/test005/subjects/scan1 and so on) but gives the same error. As well, the only output from this is the screenshot from the last scan (sag1_scan2 in this case). The other ones before are missing. Anybody knows a way around this? Any help would be much appreciated Best regards, Max Bautista btw: --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: CentOS release 6.7 (Final) Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64 ---------------------------------------------------------------------

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Tracula: trac-all prep badly formed if error
by Katherine Damme 17 Dec '15

17 Dec '15

Hello Everyone! I am getting a badly formed number error in my trac-all any ideas?

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Display NV-GLX error
by Chuck Theobald 16 Dec '15

16 Dec '15

When trying to run the Display command, I get the following messages and no imaging of the .mnc file. machine7 ~ $ Display /home/research/bamlab/ATLAS/001/antsreg/data/coronalspace/rois/drawn/l_hip.mnc Xlib: extension "NV-GLX" missing on display "localhost:11.0". Could not get requested colour_map_mode(0), got(1,256) Xlib: extension "NV-GLX" missing on display "localhost:11.0". Could not get requested colour_map_mode(0), got(1,256) Inputting /home/research/bamlab/ATLAS/001/antsreg/data/coronalspace/rois/drawn/l_hip.mnc. Objects input. Xlib: extension "NV-GLX" missing on display "localhost:11.0". Could not get requested colour_map_mode(0), got(1,256) G_draw_pixels(): cannot draw rgb pixels in colour map mode. G_draw_pixels(): cannot draw rgb pixels in colour map mode. G_draw_pixels(): cannot draw rgb pixels in colour map mode. G_draw_pixels(): cannot draw rgb pixels in colour map mode. G_draw_pixels(): cannot draw rgb pixels in colour map mode. G_draw_pixels(): cannot draw rgb pixels in colour map mode. G_draw_pixels(): cannot draw rgb pixels in colour map mode. G_draw_pixels(): cannot draw rgb pixels in colour map mode. G_draw_pixels(): cannot draw rgb pixels in colour map mode. When using version 5.3.0, I get: chuck@ong7 ~ $ Display /home/research/bamlab/ATLAS/001/antsreg/data/coronalspace/rois/drawn/l_hip.mnc Xlib: extension "NV-GLX" missing on display "localhost:11.0". Xlib: extension "NV-GLX" missing on display "localhost:11.0". Inputting /home/research/bamlab/ATLAS/001/antsreg/data/coronalspace/rois/drawn/l_hip.mnc. Objects input. Xlib: extension "NV-GLX" missing on display "localhost:11.0". and the output windows appear as in the attached image. Is this normal behavior? If not, how can I get rid of the nv-glx errors? Thanks, T-- Chuck Theobald System Administrator The Robert and Beverly Lewis Center for Neuroimaging University of Oregon P: 541-346-0343 F: 541-346-0345

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Recon Error
by Hamel, Maura K. 16 Dec '15

16 Dec '15

Hi Freesurfer experts, I’m looking for some help with some recons I tried running yesterday for about 60 subjects. The command I submitted was: recon-all -i /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS53/${subject}/MPRAGE/0*/001.mgz -s ${subject} -all I have attached the log files, and I’m hoping you can explain the error I received and what I need to do fix it. Thanks in advance for your help! FREESURFER_HOME: /usr/local/freesurfer/stable6 Build stamp: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151208 RedHat release: CentOS release 6.7 (Final) Kernel info: Linux 4.1.8-1.el6.elrepo.x86_64 x86_64 NMR Center info (/space/freesurfer exists): machine: tyra SUBJECTS_DIR: /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS60 PWD: /autofs/cluster/maury/users/gcoombs/College_Risk ssh tyra setenv SUBJECTS_DIR /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS60 cd /autofs/cluster/maury/users/gcoombs/College_Risk Best, Maura Hamel Clinical Research Coordinator Psychiatric Neuroimaging Research Program Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th St, Room 2602A Charlestown, MA 02129 Phone: 617-643-4441 Fax: 617-726-4078

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wm-hypointensities label on MS subjects
by Guido Orlando Pascariello 16 Dec '15

16 Dec '15

Hi FS Experts: I've been using T1 data from MS subjects in order to try to identify lesion volume using wm-hypointensities label from aseg. I wonder if there is any tool which uses T2-flair sequence to the same goal? I'll be grateful if you can help Being all for now, I await a reply Guido PASCARIELLO Facultad de Ingeniería - Universidad Nacional de Entre Ríos Argentina

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R: Re: R: Re: FDR in FS-FAST
by stdp82＠virgilio.it 16 Dec '15

16 Dec '15

I have run mri_fdr --help but I obtained this warning: /Applications/freesurfer/bin/mri_fdr: Permission denied. I would also ask you if is possible to threshold the FDR map (p<0.05), eliminating clusters < 5 voxels. Thanks Stefano >----Messaggio originale---- >Da: greve(a)nmr.mgh.harvard.edu >Data: 11-dic-2015 20.23 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: FDR in FS-FAST > >$FREESURFER_HOME/bin > >On 12/11/15 2:08 PM, stdp82(a)virgilio.it wrote: >> Thanks, in which folder I should put this file? >> >> Stefano >> >> >>> ----Messaggio originale---- >>> Da: greve(a)nmr.mgh.harvard.edu >>> Data: 7-dic-2015 19.23 >>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>> Ogg: Re: [Freesurfer] FDR in FS-FAST >>> >>> >>> >>> On 12/07/2015 08:35 AM, stdp82(a)virgilio.it wrote: >>>> Hi list, >>>> I have two concerns, please: >>>> 1) It is possible to apply FDR correction on rs-fMRI seed based >>>> analysis by FS-FAST? If yes, I can I do it? >>> try this binary >>> ftp://surfer.nmr.mgh.harvard. edu/transfer/outgoing/flat/greve/mri_fdr >>>> 2) I have apply the FS guidelines and I have used Montecarlo >>>> correction with threshold at 1.3 but in the within group analysis >> the >>>> clusters are very large. In the guide I read examples with a >> threshold >>>> at 3. Is there a specific reason? >>> There is not a hard-and-fast criteria for the voxel-wise threshold. 3 >> is >>> fine as is 1.3 >>>> Thanks >>>> >>>> Stefano >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: ftp://surfer.nmr.mgh.harvard. >> edu/transfer/outgoing/flat/greve/ >>> _______________________________________________ >>> 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 >> >> > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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example #PBS Torque script for FreeSurfer on a HPC cluster & multithreading question
by Riphagen Joost (NP) 16 Dec '15

16 Dec '15

Dear all, I'm learning how to work with Freesurfer on a #PBS/Torque HPC cluster. There is enough documentation about using #PBS, but I have not been able to find anything on the net about how to process multiple subjects in FS in this environment. If somebody is willing to share an example script that would be most helpful. Am I right in thinking that by using the "-itkthreads" flag FS can make use of multiple threads but not use multiple cores ? The nodes use two Xeon processors with 8 cores and 16 threads per CPU and have 64 GB per node. I have to book per node so the more I can use it the better. Regards Joost Riphagen

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Freesurfer December 2015