Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Seeing the Results in the Original Space
by Maedeh Khalilian 10 Sep '18

10 Sep '18

External Email - Use Caution Dear FreeSurfer Experts, How can i have the results of FreeSurfer in its original space? The results have rotation and also the axial and the coronal images are replaced with each other. Thanks in advance Best regards, Maedeh

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Question on subcortical segmentation
by limiyu 09 Sep '18

09 Sep '18

External Email - Use Caution Dear freesurfer developers Execuse me, I have a problem on subcortical segmentation, about how to output a segmentation which has the same shape with the input MRI image. The input shape of my MRI image is 197*233*189 and I run <recon-all -i mysubject.nii.gz -s bert -all>. Then Freesurfer output files in different foders such as 'label', 'mri', 'scripts' and so on. In the folder called 'mri', there are files about segmentation. and I convert the 'aseg.mgz' file into .nii.gz file by using <mri_convert> After that I load the .nii.gz file into MATLAB, so that I could compare the result with a mannual segmentation with shape of 197*233*189. However the shape of .nii.gz file converted from aseg.mgz is 256*256*256. But what I expect is the shape with 197*233*189 (the same shape with the imput MRI image). Then what should I do? Because I run Freesurfer on a server without GUI, the Graphical User Interface, so the freeview will not work. So could you please give me some help on how to solve the problem using command line? Looking forward to your reply Thank you Mingyuan Liu

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How to display two overlays and its overlap in freeview?
by Fred Sampedro 08 Sep '18

08 Sep '18

External Email - Use Caution Dear FS experts, How could I use freeview to overlay two unrelated significance maps (say sig1.mgh and sig2.mgh) on fsaverage? I would like to display sig1.mgh with a red colorbar, sig2.mgh with a blue one, and its intersection/overlap in purple. Basically, I would like to produce the following figure (attached), also available at: http://pysurfer.github.com/auto_examples/plot_fmri_conjunction.html I am well aware this question has been asked several times in this archive (a recent one being https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41621.html) However, I have struggled to implement and adapt all suggestions in those threads without success. Clearly, being a recent FS user, I am probably missing some very basic concepts regarding LUT tables, annots and common FS commands. Could anyone please provide some exact commands to replicate this figure (same colors, same everything)? (please including LUT files and freeview/tksurfer commands/instructions). Thanks a lot in advance! Fred

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About FreeSurfer source code
by Renew Andrade 08 Sep '18

08 Sep '18

External Email - Use Caution Dear community: I was curious about how the software is made and I decided to write an email to Dr. Bruce Fischl who answered all of the questions I asked, but he gave me the input to ask these questions also in FreeSurfer Community. I first asked the programming language of the software(I didn’t know that it was even open source). He says its mostly C but also some Matlab and C++. I am concerned with the long preprocessing time of raw T1 data so if anyone has some insights about which is the longest part and how faster it can get with nowadays hardware of course share with us. I think perhaps if some of the code of C were translated to C++ may be it could be faster. Although I don’t know how faster in fact but it could be a start. It should be easier if there were someone with clear head picture of time processing in different parts of the program in different hardware specifics. I know there is an entry in FreeSurfer wiki but I’m talking of an exchange of experiences with different machines with the same version of the software. May be I am going too far on my expectations. It would be nice to have a thread where we all shared our knowledge about how to improve performance. May be programming language translation is a bit of a lazy start and a change in some of the algorithms is the what we should encourage. Sincerely, Andrade.

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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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