Freesurfer

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30088 discussions

Freeview: Load multiples overlays for one surface
by Emanuel Alvaredo 07 Sep '18

07 Sep '18

External Email - Use Caution Hi! I would like from command line to open one surface with multiple ovelays. For example, intead of this ......-f surf/lh.inflated:overlay=surf/lh.sulc surf/lh.inflated:overlay=surf/lh.thickness:overlay_threshold=1,5 I would like to do something like that -f surf/lh.inflated:overlay=surf/lh.sulc,overlay=surf/lh.thickness:overlay_threshold=1,5 is this possible? Thanks!

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recon-all error
by Song, Da-Yea 07 Sep '18

07 Sep '18

External Email - Use Caution Hello, I'm running some subjects through recon-all but have noticed that some error out (terminate the job) within seconds of starting. Any suggestions would be really appreciated. Here is the recon-all.cmd error message: #--------------------------------- # New invocation of recon-all Fri Sep 7 09:34:58 EDT 2018 mri_convert /g5/dcn/freesurfer/MPRAGE/PS070/001 /g5/dcn/freesurfer/subjects/PS070/mri/orig/001.mgz #-------------------------------------------- #@# MotionCor Fri Sep 7 09:35:30 EDT 2018 cp /g5/dcn/freesurfer/subjects/PS070/mri/orig/001.mgz /g5/dcn/freesurfer /subjects/PS070/mri/rawavg.mgz mri_convert /g5/dcn/freesurfer/subjects/PS070/mri/rawavg.mgz /g5/dcn/freesurfer /subjects/PS070/mri/orig.mgz --conform mri_add_xform_to_header -c /g5/dcn/freesurfer /subjects/PS070/mri/transforms/talairach.xfm /g5/dcn/freesurfer /subjects/PS070/mri/orig.mgz /g5/dcn/freesurfer /subjects/PS070/mri/orig.mgz #-------------------------------------------- #@# Talairach Fri Sep 7 09:35:44 EDT 2018 mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 #--------------------------------- # New invocation of recon-all Fri Sep 7 09:36:58 EDT 2018 #--------------------------------- # New invocation of recon-all Fri Sep 7 09:37:03 EDT 2018 #--------------------------------- # New invocation of recon-all Fri Sep 7 09:39:43 EDT 2018 #--------------------------------- # New invocation of recon-all Fri Sep 7 09:39:47 EDT 2018 #--------------------------------- # New invocation of recon-all Fri Sep 7 09:42:58 EDT 2018 #--------------------------------- # New invocation of recon-all Fri Sep 7 09:43:02 EDT 2018 Best, Da-yea ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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FsPalm patch
by Tom Parker 07 Sep '18

07 Sep '18

External Email - Use Caution Dear Freesurfer developers, I am attempting to download the FsPalm patch (https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm <https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm>) using: the link described in the wiki - ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/PALM <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/PALM> However, there appears to be no directory at that location. Please can you inform me how to install the FsPalm patch? Many thanks

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FS6.0-dev (Jun27, 2018) Hippocampal subfield Matlab runtime Java error
by Sean Ma 07 Sep '18

07 Sep '18

External Email - Use Caution Hi Eugenio, I'd like to report a Matlab runtime Java error when running the Hippocampal subfield on FS6.0-dev (Jun 27, 2018) after a successful completion of `recon-all`. Matlab 2014b runtime has been successfully expanded at /MCRv84. The error I've encountered follows. Any suggestions on how I can overcome this error? Thanks for your pointers! Best, Sean Ma University of Michigan ================================== [tehsheng@b-fmri FS6results]$ segmentHA_T1.sh b30002_02712 #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Mon Jul 2 15:16:41 EDT 2018 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/opt/freesurfer6/MCRv84//runtime/glnxa64:/opt/freesurfer6/MCRv84//bin/glnxa64:/opt/freesurfer6/MCRv84//sys/os/glnxa64::/opt/freesurfer6/MCRv84//sys/opengl/lib/glnxa64: Error using checkRequiredMCRProducts (line 25) Java exception occurred: java.lang.NullPointerException at com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:56) at com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:49) at com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.executeTask(InstalledProductFactory.java:193) at com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.access$200(InstalledProductFactory.java:108) at com.mathworks.install.InstalledProductFactory.getInstalledProducts(InstalledProductFactory.java:67) Error in deployrc (line 9) Error in matlabrc (line 238) @#@FSTIME 2018:07:02:15:16:41 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 32.59 S 0.39 U 5.00 P 16% M 205368 F 82 R 43627 W 0 c 54 w 1963 I 24008 O 82888 L 0.00 0.07 0.89 @#@FSLOADPOST 2018:07:02:15:17:13 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 0.15 0.11 0.87 Linux b-fmri.edu 2.6.32-696.28.1.el6.x86_64 #1 SMP Thu Apr 26 04:27:41 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux T1 hippocampal subfields exited with ERRORS at Mon Jul 2 15:17:13 EDT 2018 For more details, see the log file /mnt/blab/Sean_Working/FS6results/b30002_02712/scripts/hippocampal-subfields-T1.log

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longitudinal hippocampal aseg editing
by Rebecca Ray 07 Sep '18

07 Sep '18

External Email - Use Caution I have 2 time points on 60 subjects with most being in some form of AD. There are considerable differences in hippocampal volume between time points. I edited the raw images before making the template. I then had to edit the aseg template image and there were still problems on the -long images. I tried to edit and rerun autorecon2-noaseg and autorecon3 and it does not appear to be keeping my edits. What am I doing wrong? Rebecca

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Re: [Freesurfer] Did not find any volume info. Warning: MatrixInverse failed
by Sofia Rodriguez Penuela 07 Sep '18

07 Sep '18

External Email - Use Caution Thanks for your quick answer Ruopeng. They are loaded with the same command and we check that the freeview's build time is the same in both computers: _Version 2.0_ _Build Jan 18 2017 16:48:55_ _Copyright (c) 2016_ Do you know what else can happen? Thanks --- Sofía Rodríguez Peñuela, Técnico de Laboratorio. Laboratorio de Neurociencia Funcional Departamento de Fisiología, Anatomía y Biología Celular. Universidad Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - España - Movil: 627273085 Email: srodpen(a)upo.es http://www.upo.es/neuroaging/es/ El 2018-09-06 18:00, freesurfer-request(a)nmr.mgh.harvard.edu escribió: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > Today's Topics: > > 1. Data Analyst Position - Child Mind Institute (New York) > (Suk Jun Hong) > 2. Re: Did not find any volume info. Warning: MatrixInverse > failed (Ruopeng Wang) > 3. Using the new Thalamus tool (Erik O'Hanlon) > 4. Parcellations (e.g., labels for Brodmann Areas) for > Connectome Workbench? (Dinicola, Lauren) > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 6 Sep 2018 14:52:13 +0000 > From: Suk Jun Hong <SukJun.Hong(a)childmind.org> > Subject: [Freesurfer] Data Analyst Position - Child Mind Institute > (New York) > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <AD459B82-DE8C-4200-8C08-95A81D6A66FC(a)childmind.org> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > The Child Mind Institute is seeking a Data Analyst to support a collaborative study with Dr. Amy Roy at Fordham University. The Data Analyst?s role is to assist with the analysis of functional MRI data, as well as reporting results. In particular, the work includes: 1) preprocessing of a large fMRI dataset and implementing quality assurance protocols, 2) maintaining the database and imaging processing pipeline; 3) supporting post-doctoral researchers by implementing novel analytic methods; and 4) training graduate and undergraduate students in how to preprocess and analyze resting state and task-based functional MRI data. > > Reporting to Dr. Suk Jun Hong and the Director of the Center for the Developing Brain, this is a full-time position, primarily located at the CMI headquarters (101 E 56th St, New York, NY 10022). > > Responsibilities: > Implementation, execution, and maintenance of fMRI imaging analysis pipelines > Conduct neuroanatomical profile analyses as well as analyses of resting-state functional MRI data using novel software packages and neuroinformatic platforms > Develop graphs, reports, and presentations of project results > Training undergraduate and graduate students in data analysis theory and implementation > Perform basic statistical analyses for projects and reports > > Qualifications: > Master?s degree in neuroscience, computer science, mathematics, statistics or related areas is preferred > Extensive neuroimaging experience in fMRI analysis and proficiency with one or more packages (e.g. FreeSurfer, AFNI, FSL, Workbench or SPM) > Programming experience in one or more languages (e.g., Python, Matlab, R or similar platforms is required) > Significant prior neuroimaging experience with more imaging and/or simulation modalities (e.g., DTI, EEG, MEG, TMS etc.) is a plus, but not required > A passion for the applying computational methods to understand clinical conditions. > > If you are interested in the positions, please apply to > https://workforcenow.adp.com/mascsr/default/mdf/recruitment/recruitment.htm… > > Thank you! > > -------------------------- > Suk-Jun Hong, PhD > Postdoc, Center for the Developing Brain > Child Mind Institute >

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Parcellations (e.g., labels for Brodmann Areas) for Connectome Workbench?
by Dinicola, Lauren 06 Sep '18

06 Sep '18

Hi all, I have been searching for the Freesurfer label or annot files for fsaverage in the formats compatible with Connectome Workbench and have not yet found them. Are these available? If not, is there a way to convert all the BA labels to then convert them to borders for viewing on fsaverage? I tried mris_convert -annot but was unsuccessful opening the output files. Thank you very much for any help. Lauren

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Unknown Region_Stats
by Song, Da-Yea 06 Sep '18

06 Sep '18

External Email - Use Caution Hello, I read on the website FAQ that "if you use the values in the ?h.aparac.stats, it already factors out the 'unknown' region, so you don't have to do it yourself". Is there a way to view stats (ex. thickness, area, volume) for these unknown regions? Thank you, Dayea ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Did not find any volume info. Warning: MatrixInverse failed
by Sofia Rodriguez Penuela 06 Sep '18

06 Sep '18

External Email - Use Caution Hello team! We are trying to load the same set of images with Freeview on two different computers. One of the computers, load the images correctly (see attached image 1). On the other computer the surfaces are shown misaligned (see attached image 2). When we try to load surfaces after loading a volume the Command Console shows the following error:"DID NOT FIND ANY VOLUME INFO. WARNING: MATRIXINVERSE FAILED". This happens with all subjects in this computer. Freesurfer (v6.0) and Freeview are updated correctly. In both computers there are Ubuntu 16.04. Why Freeview didn´t find any volume info in this computer? Can you help us to solve this problem? Thank you. -- Sofía Rodríguez Peñuela, Técnico de Laboratorio. Laboratorio de Neurociencia Funcional Departamento de Fisiología, Anatomía y Biología Celular. Universidad Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - España - Movil: 627273085 Email: srodpen(a)upo.es http://www.upo.es/neuroaging/es/

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LGI without Matlab license?
by Thomas, Adam (NIH/NIMH) [E] 06 Sep '18

06 Sep '18

External Email - Use Caution We’d like to calculate the Local Gyrification Index (LGI) on several thousand scans, but our HPC cluster does not have the necessary Matlab licenses to do this in a reasonable amount of time. Has anyone managed to compile the LGI code such that it could be run without a Matlab license? Or is anyone working on this? Our HPC staff tried to compile it, but did not succeed. Ref: https://surfer.nmr.mgh.harvard.edu/fswiki/LGI Best Regards, -Adam Thomas

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