Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

aseg.stats data output
by shi yao wang 10 Aug '16

10 Aug '16

Dear FS experts: How can I only out put the volume value in the aseg.stats file? I applied following command: but it will produce a table with lots of values such as brainsegvol, brainsegvolnotvent, which I donot want to use. thanks asegstats2table --subjects 004 021 040 067 080 092 \ --segno 11 17 18 \ --tablefile aseg.vol.table

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query about the "normal range" in aseg.stats
by shi yao wang 10 Aug '16

10 Aug '16

Dear FS experts: I noticed that there is a "normal Range" results in the aseg.stats table. I am wondering how can I consider of this normal range? is that based on population or what. thanks Lawrence Emory University

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resample structural ROI in functional space?
by Kami Koldewyn 10 Aug '16

10 Aug '16

Hi All, I have a set of ROIs that were created in structural space, currently saved as volume masks. I would like to transform these into functional space, re-sampled to the functional resolution. Can anyone suggest a good way to do this? -kami Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565 Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor. This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s), you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office.

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Registration of low-resolution EPI time series to CVS MNI (avoiding resampling)
by Heidi Grohn 10 Aug '16

10 Aug '16

Hi Freesurfer (FS) users, I am a new user in the world of FS and I am trying to normalize rsfMRI EPI series to CVS MNI space. I would like to do it without resampling the EPI images to 1*1*1mm3 resolution. I've registered EPI series to FS T1 space by using following command (after bbregister), with --no-resample flag, after which the resolution of the EPI images did not change. mri_vol2vol --mov EPI.nii.gz --targ ...subject/mri/wmparc.mgz --interp trilinear --o EPI_in_FS_T1_space.mgz --reg EPI_in_FS_T1_space.dat --no-resample --no-save-reg After that I used the following command to apply normalization to CVS MNI, but I cannot find any similar option to maintain the low resolution. Output is always on 1*1*1mm3 resolution. applyMorph --template ../cvs_avg35_inMNI152/mri/norm.mgz --transform ..subject/cvs_mni/combined_tocvs_avg35_inMNI152_elreg_afteraseg-norm.tm3d \vol EPI_in_FS_T1_space.mgz EPI_in_MNI.mgz trilinear In summary, how would I maintain the resolution of the EPI images after normalization? By the way, I am using Freesurfer 5.3. Your help is very much appreciated, Thanks, Heidi %%%%%%%%%%%%%%%% Heidi Gröhn, PhD CMRR University of Minnesota %%%%%%%%%%%%%%%%

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mri_glmfit-sim problem
by miracle ozzoude 10 Aug '16

10 Aug '16

Hello FreeSurfer experts, I am running surfaced based analysis using ROI approach. My mris_preproc, mri_surf2surf and mri_glmfit worked as expected. Since i restricted the region i built my own monte carlo "mri_mcsim --o roianalysis/average/mult-comp-cor/fsaverage/rh/rightmaskforcomp --base mc-z --surface fsaverage rh --nreps 10000 --label 2mask" which worked. However, when I wanted to run the mri_glmfit-sim using this command line " mri-glmfit-sim --glmdir rh.score.glmdir --cache-dir roianalysis/average/mult-comp-cor --cache-label rightmaskforcomp --cache 2 pos --cwpvalthresh 0.05 --2spaces" i got an error "setenv SUBJECTS_DIR users/paul/desktop/roianalysis FREESURFER_HOME/ applications/freesurfer original mri_glmfit command line ............ DoSim = 0 UseCache = 1 dopoll = 1 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 17.292581 ERROR: cannot find roianalysis/average/mult-comp-cor/fsaverage/rh/rightmaskforcomp/fwhm17/pos/th20/mc.z.csd" I looked into roianalysis/........./fwhm17/pos/th20/mc.z.csd and it does exist. I saw a post like this on the forum but it wasn't answered. How can I direct it to my simulation on my subjectfolder (i.e., desktop/roianalysis/......)? Thanks Paul

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white and gray matter masks
by John Anderson 10 Aug '16

10 Aug '16

2 1

New way of installing and running Freesurfer - containers
by Chris Filo Gorgolewski 09 Aug '16

09 Aug '16

Dear all, I have created a Docker image with Freesurfer distribution (and all required dependencies). Features: - Only requires Docker to run (works on Linux, Mac and Windows - does not suffer from the VirtualBox bug <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42474.html> ) - understands BIDS <http://bids.neuroimaging.io/> formatted datasets - performs recon-all on all subjects - allows you to run each subject independently (and potentially in parallel) - automatically performs longitudinal analysis when multiple sessions are detected - creates custom group level template for your study - can be easily converted to a Singularity <http://singularity.lbl.gov/> image using docker2singularity <https://github.com/chrisfilo/docker2singularity> tool and run on your local HPC/cluster You can find more information here: https://github.com/BIDS-Apps/freesurfer Please let me know what do you think! Best, Chris

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Postdoctoral Position in Infant MRI Analysis at UNC-Chapel Hill
by gangli 09 Aug '16

09 Aug '16

Postdoctoral research associate positions are available in the Department of Radiology and Biomedical Research Imaging Center at the University of North Carolina at Chapel Hill (UNC-Chapel Hill). Our current focuses are to better understand the dynamic and critical early brain development in both health and disease, via multimodal neuroimaging analysis. The successful candidate will support our efforts either in advancing neuroimaging analysis technologies or in neuroscience applications. We are seeking highly motivated individuals who have extensive research experience in neuroimaging analysis (e.g., structural, diffusion or functional MRI) and demonstrated academic excellence, including publications in first-class journals and conferences. The candidate should have a Ph.D. (or equivalent) in Neuroscience, Computer Science, Applied Mathematics/Statistics, Electrical Engineering, Biomedical Engineering, or related fields. Good command of programming tools including Matlab, C++, Linux, and scripting are necessary to carry out the research work in this group. The successful candidate will be part of a diverse group including neuroscientists, radiologists, psychologists, physicists, biostatistician, and computer scientists, and will build upon the group's extensive foundation on neuroimaging analysis. If interested, please email resume to Dr. Gang Li (gang_li(a)med.unc.edu) For more information, please visit: http://www.unc.edu/~gangl/contact.html.

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Re: [Freesurfer] brain mask and T1 are not the same size
by Isabelle Deschamps 09 Aug '16

09 Aug '16

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Error running hippocampal segmentation with FS6
by Lauri Tuominen 09 Aug '16

09 Aug '16

Dear freesurfers, I tried running hippocampal segmentation using the Dev version 6 on launchpad. I get the following error message: I ran the recon-all command yesterday and it worked fine. Cheers! Lauri Tuominen INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20160805 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20160809 INFO: SUBJECTS_DIR is /autofs/space/colbert_001/users/ljt22/Feargen2/SUBJECTS_DIR Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6 -rw-rw-r-- 1 ljt22 dinahgp 490999 Aug 9 09:26 /autofs/space/colbert_001/users/ljt22/Feargen2/SUBJECTS_DIR/iaon/scripts/recon-all.log Linux compute-0-57 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux `/autofs/cluster/freesurfer/centos6_x86_64/stable6/bin/recon-all' -> `/autofs/space/colbert_001/users/ljt22/Feargen2/SUBJECTS_DIR/iaon/scripts/recon-all.local-copy' #-------------------------------------------- #@# Hippocampal Subfields processing (T2 only) left Tue Aug 9 13:11:58 EDT 2016 /usr/local/freesurfer/stable6/bin/segmentSF_T2.sh /usr/local/freesurfer/stable6/MCRv80 /usr/local/freesurfer/stable6 iaon /autofs/space/colbert_001/users/ljt22/Feargen2/SUBJECTS_DIR /autofs/space/colbert_001/users/ljt22/Feargen2/subjects/iaon/anat/012/T2.mgz left T2_analysis2 See log file: /autofs/space/colbert_001/users/ljt22/Feargen2/SUBJECTS_DIR/iaon/scripts/hippocampal-subfields-T2.log ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64: Warning: application is running on a locale different from the original platform locale. Error using segmentSubjectT1_autoEstimateAlveusML Too many input arguments. MATLAB:TooManyInputs Warning: Unable to open display 'localhost:48.0'. You will not be able to display graphics on the screen. #-------------------------------------------- #@# Hippocampal Subfields processing (T2 only) right Tue Aug 9 13:12:06 EDT 2016 /usr/local/freesurfer/stable6/bin/segmentSF_T2.sh /usr/local/freesurfer/stable6/MCRv80 /usr/local/freesurfer/stable6 iaon /autofs/space/colbert_001/users/ljt22/Feargen2/SUBJECTS_DIR /autofs/space/colbert_001/users/ljt22/Feargen2/subjects/iaon/anat/012/T2.mgz right T2_analysis2 See log file: /autofs/space/colbert_001/users/ljt22/Feargen2/SUBJECTS_DIR/iaon/scripts/hippocampal-subfields-T2.log ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threa/pbs/ljt22/pbsjob_59.o12129908

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