Freesurfer November 2018

freesurfer@nmr.mgh.harvard.edu

121 participants
189 discussions

Re: [Freesurfer] Fornix in TRACULA
by Yendiki, Anastasia 10 Nov '18

10 Nov '18

We are actively working on it, but it's a time consuming process that involves many tracts. A few months, probably. On Nov 9, 2018 4:40 AM, "Hayek, Dayana" <dayana.hayek(a)stud.uni-greifswald.de> wrote: External Email - Use Caution Dear all, In my research work, I am using Freesurfer for both grey and white matter segmentation. However, I am restricted in the white matter analysis since my studies and related to memory function and I am mainly interested in the Fornix. I read in one of the threads that TRACULA will include soon an Atlas with the Fornix. Any news regarding this issue? Do you have any timeline of the progress of this atlas? Thank you so much for your help! ------------------------------------------------------------ Dayana Hayek, MSc.-Bio, cand dr.rer.nat Universitätsmedizin Greifswald | Klinik und Poliklinik für Neurologie AG Kognitive Neurologie Ferdinand-Sauerbruch-Straße | D-17475 Greifswald [Intern: W.-Rathenau-Str. 49 | Whg. 6.5] E-Mail: dayana.hayek(a)stud.uni-greifswald.de<mailto:dayana.hayek@stud.uni-greifswald.de>

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Please join us at Coastal Coding for Reproducible Neuroimaging: 10-16 Jan 2019 in Miami, FL
by Satrajit Ghosh 10 Nov '18

10 Nov '18

External Email - Use Caution ---------- Forwarded message --------- From: Angela Laird <alaird(a)fiu.edu> Date: Fri, Nov 9, 2018 at 3:42 PM Subject: Please join us at Coastal Coding for Reproducible Neuroimaging: 10-16 Jan 2019 in Miami, FL To: Dear Colleagues, Florida International University (FIU) is hosting a Miami workshop + code sprint in January 2019 called *Coastal Coding for Reproducible Neuroimaging* : *Jan 10-12: ReproNim + Nypipe 2.0 Workshop* The goals of this workshop are two-fold. First, to enable attendees to become familiar with best practices for reproducible analysis from ReproNim. Second, to learn how to create scalable and re-executable neuroimaging workflows with the upcoming Nipype 2.0 platform. This event is targeted towards novice neuroimaging users who meet the following requirements: (1) Working knowledge of Python 3; and (2) Familiarity with scripting in at least 1 neuroimaging package (e.g., AFNI, ANTS, FSL, FreeSurfer, SPM). Advanced users are welcome to learn about the changes and hack with Nipype developers. *Jan 14-16: NiMARE Code Sprint* NiMARE (Neuroimaging Meta-Analysis Research Environment) is a new Python package for performing analyses using neuroimaging meta-analytic data. Current tools for neuroimaging meta-analyses are spread out across several packages and languages. NiMARE aims to provide a standardized interface for a broad range of algorithms, along with interfaces to open meta-analytic resources like Neurosynth, NeuroVault, and brainspell. The three-day NiMARE coding sprint will occur after the Nipype workshop, with a one-day rest period between, in which participants can enjoy Miami. At the sprint, we’ll be working to design a standard for representing meta-analytic data, to add implementations for new tools, and to improve the documentation and test coverage of the existing codebase. Anyone interested in contributing to this new package is welcome to join. *Both the workshop and code sprint will be held at FIU’s scenic Biscayne Bay Campus*, conveniently located 17 miles from the Miami International Airport (MIA) or 19 miles from the Fort Lauderdale-Hollywood International Airport (FLL). Registration costs are $125 for one event or $200 for both events. Fees cover breakfast, lunch, snacks, and plenty of coffee. *Full details can be found at:* https://coastal-coding.github.io Please feel free to forward to your colleagues! Best, Angie ***** Dr. Angie Laird, Ph.D. Professor, Department of Physics Director, Center for Imaging Science Florida International University 11200 SW 8th ST Miami, FL 33199 Office: AHC-4 Room 310 Lab: AHC-4 Room 380 http://cismri.fiu.edu http://neurolab.fiu.edu Phone: (305) 348-6737 Fax: (305) 348-6700

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myelin and thickness pvr
by Damien MARIE 10 Nov '18

10 Nov '18

External Email - Use Caution Dear freesurfer experts, I would like to replicate an analysis I did with qdec but regressing out thickness at the vertex level. It’s a myelin group contrast with age and left average myelin as nuisance factors. I used the mri_glmfit command line generated during that qdec analysis and added the pvr flag but I got that error message: ERROR: dimension mismatch between X and contrast /home/damien/bin/freesurfer6/subjects/qdec/10nov/contrasts/lh-Avg-Intercept-R1projfrac0.5.mat X has 7 cols, C has 6 cols How can I solve that, should I modify the contrast.mat? Many thanks, Damien mri_glmfit --y /home/damien/bin/freesurfer6/subjects/qdec/10nov/y.mgh --fsgd /home/damien/bin/freesurfer6/subjects/qdec/10nov/qdec.fsgd dods --glmdir /home/damien/bin/freesurfer6/subjects/qdec/10nov --surf fsaverage lh --label /home/damien/bin/freesurfer6/subjects/fsaverage/label/lh.aparc.label --C /home/damien/bin/freesurfer6/subjects/qdec/10nov/contrasts/lh-Avg-Intercept-R1projfrac0.5.mat --C /home/damien/bin/freesurfer6/subjects/qdec/10nov/contrasts/lh-Diff-ct-dys-Intercept-R1projfrac0.5.mat --pvr lh.thicknessall.fsaverage.mgh

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Desikian-Killiany and Destrieux atlas
by Miguel Ángel Rivas Fernández 09 Nov '18

09 Nov '18

External Email - Use Caution Hello Freesurfer devs, Is there available any Desikian-Killiany and Destrieux atlas template or image downloadable with all brain labels of the atlas? I would to use this image to show my results in a lab meeting? I would need somethig similar that the lookup table used in the freeview. Cheers, -- *Miguel Ángel Rivas Fernández*

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Multivariable linear regression with binary variables
by Worker, Amanda 09 Nov '18

09 Nov '18

External Email - Use Caution Hi, I am trying to run a multivariable GLM with mri_glmfit and I am currently setting up my fsgd file. I have 9 binary variables and 1 continuous variable. My understanding is that in the fsgd file, my "class" would be every possible combination of these binary variables - which is a lot (hundreds) and setting this up manually doesn't seem reasonable. Is this correct and if so could you recommend another way to run this analysis? Thanks, Amanda

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Re: [Freesurfer] Desikan Atlas in volume space (ece ulug)
by Mcnorgan, Christopher 09 Nov '18

09 Nov '18

External Email - Use Caution Hi Ece, I believe you will find a walkthrough of the steps to do exactly what you want done on my lab wiki: http://ccnlab.psy.buffalo.edu/wiki/index.php/Annotation_Coordinates Hope this helps, Chris /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/ On Nov 6, 2018, at 12:00 PM, freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote: Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@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<mailto:freesurfer-request@nmr.mgh.harvard.edu> You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu<mailto:freesurfer-owner@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. Ynt: Ynt: ?lt: Desikan Atlas in volume space (ece ulug) From: ece ulug <eceulug77(a)hotmail.com<mailto:eceulug77@hotmail.com>> Subject: [Freesurfer] Ynt: Ynt: İlt: Desikan Atlas in volume space Date: November 6, 2018 at 6:37:17 AM EST To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> External Email - Use Caution Exactly. I cannot find in this file but i found lh.aparc.label and lh.aparc.annot files in freesurfer/subjects/fsaverage/label. Actually i told in my previous message. I need coordinates for generate caudalanteriorcingulate mask in coordinate system. ________________________________ Gönderen: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>> adına freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> Gönderildi: 6 Kasım 2018 Salı 00:45 Kime: Freesurfer support list Konu: Re: [Freesurfer] Ynt: İlt: Desikan Atlas in volume space I don't think there is an lh.aparc.label file - I don't know what it would be if it existed. Maybe we can take a step back and you can let us know what you are trying to achieve? On Mon, 5 Nov 2018, ece ulug wrote: > > External Email - Use Caution > > Thanks for your reply doctor. Actually I want to access Desikan K. Atlas coordinates as x, y, z. > (each regions. for example caudalanteriorcingulate). > > > In that case, one expert said that ; the closest to what you want is probably > $FREESURFER_HOME/subjects/fsaverage/surf/lh.aparc.label. You can open it with a text editor. Then > you should cross-check with $FREESURFER_HOME/subjects/fsaverage/surf/lh.aparc.annot for the actual > labels of those vertices. The .annot file can be opened in Matlab with the read_annotation command > from FreeSurfer. > > > What do you recommend? > Ece > > ____________________________________________________________________________________________________ > Gönderen: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>> adına freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> > <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> > Gönderildi: 5 Kasım 2018 Pazartesi 20:18 > Kime: Freesurfer support list > Konu: Re: [Freesurfer] İlt: Desikan Atlas in volume space > Hi Ece > > for a given subject the Desikan parcellation is sampled into the volume > alread in the file aparc+aseg.mgz in the subject's mri dir. Is that what > you are looking for? > > cheers > Bruce > > On Mon, 5 Nov 2018, ece ulug wrote: > > > > > External Email - Use Caution > > > > Dear Experts, > > > > > > I am very beginner in Freesurfer, and I want to use 'read_annotation' > > function but i don't know what is the next step. I added the Matlab > > screenshoot. > > > > > > Additionally; 'read_curv' function don't work in Matlab. I added it. > > > > > > Thanks in advance > > > > Ece > > > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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回复： ?????? Recon-all run error
by 1013364183 09 Nov '18

09 Nov '18

External Email - Use Caution Dear Bruce Fischl: We ran two images of about 500MB, but stopped at a certain step for a few days, we would like to ask what is the reason, the attachment has a recon-all.log file at runtime. Thanks in advance yours yujunjie ------------------ 原始邮件 ------------------ 发件人: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu>; 发送时间: 2018年11月7日(星期三) 凌晨2:42 收件人: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; 主题: Re: [Freesurfer] ?????? Recon-all run error does it occur if you run it outside of recon-all? Do you have enough free ram? If so, you can filedrop us the dataset and we can try to replicate and fit ix. On Tue, 6 Nov 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear Bruce, > I found the error location in the recon-all.log folder. Here is the place where it went wrong??I > don't think it's the reason for insufficient memory.. > ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz % 4 == 0' failed.'' > This data is ok when we run with versions prior to freesurfer 6.0. But after we run the 6.0 > version and set the expert file, this error will occur.Do I need to step through the instructions to > see the problem? How should this error be solved? > > Thanks in advance > > yours yujunjie > > ------------------ ???????? ------------------ > ??????: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu>; > ????????: 2018??11??6??(??????) ????9:40 > ??????: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; > ????: Re: [Freesurfer] Recon-all run error > > that certainly looks like something is running out of ram. Can you run > the command that failed directly on the command line and see if it works? > Was anything else running on the machine at the time? We do report total > and free memory at the start of the recon in the recon-all.log file > > cheers > Bruce > On Tue, > 6 Nov 2018, 1013364183 wrote: > > > > > External Email - Use Caution > > > > Dear FS, > > When we run ??recon-all?? with a 5GB high-resolution image, core dumped appears when the > mri_convert > > command is executed. The specific errors are as follows: > > /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: 29235 Aborted (core dumped) > > mri_convert.bin "$@" > > ERROR: converting to minc > > We want to know if our high resolution image is too large for freesurfer to handle, or our > computer > > memory (64GB running memory) is limited. > > > > Thanks a lot in advance! > > yours sincerely, > > yu junjie > > > > > > > _______________________________________________ > 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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Fornix in TRACULA
by Hayek, Dayana 09 Nov '18

09 Nov '18

External Email - Use Caution Dear all, In my research work, I am using Freesurfer for both grey and white matter segmentation. However, I am restricted in the white matter analysis since my studies and related to memory function and I am mainly interested in the Fornix. I read in one of the threads that TRACULA will include soon an Atlas with the Fornix. Any news regarding this issue? Do you have any timeline of the progress of this atlas? Thank you so much for your help! ------------------------------------------------------------ Dayana Hayek, MSc.-Bio, cand dr.rer.nat Universitätsmedizin Greifswald | Klinik und Poliklinik für Neurologie AG Kognitive Neurologie Ferdinand-Sauerbruch-Straße | D-17475 Greifswald [Intern: W.-Rathenau-Str. 49 | Whg. 6.5] E-Mail: dayana.hayek(a)stud.uni-greifswald.de

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Cerelellar parcellation labels Request
by dongnandi1 09 Nov '18

09 Nov '18

External Email - Use Caution Hi Freesurfer experts, The cerebellar 7 and 17 networks parcellation cannot be downloaded. The link to cerebellar parcellation in SUIT is out of date too. so, if you can kindly share the cerebellar 17-network parcellation and their anatomy labels, I would be particularly grateful! Best wishes Fan 2018/11/08

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dcmunpack Error
by Maryam Tayebi 08 Nov '18

08 Nov '18

External Email - Use Caution Hello Freesurfer Developers, I was going to reconstruct MPRAGE images from GE 3T machine. First I used this command: *dcmunpack -src . -scanonly scan.log* It made just *scan.log* file for me. Then I used this command: *unpacksdcmdir -src /<my dicoms pathways> -targ <my output directory> -scanonly scan.log* However, it made 3 files for me; dicomdir.sumfile, parse.status and unpack.log, but they were 0 bites. Furthermore, the following message also appeared on the terminal: *ERROR: parsing /hpc/mtay316/tutorial4/practice_with_data/dicoms/ See logfile /hpc/mtay316/tutorial4/practice_with_data//unpack.log for more details* I used this command for SIEMENS data and it worked. Apparently this code just works on SIEMENS data not GE. So now what is the code that I can use for GE dcm images? 1) FREESURFER Version: freesurfer-x86_64-unknown-linux-gnu-stable6-20170118 2) Platform: Ubuntu 16.04 LTS 3) unpack.log : see attached Regards -- *Maryam Tayebi* PhD Candidate of Bioengineering Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand MSc of Medical Imaging University of Manchester, Manchester, UK

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Freesurfer November 2018