Freesurfer June 2020

freesurfer@nmr.mgh.harvard.edu

91 participants
130 discussions

Freesurfer 5.3.0 recon-all failure
by Ian 23 Jun '20

23 Jun '20

External Email - Use Caution Hey guys. I have need to run recon-all from freesurfer 5.3.0. When I do I get this error: INFO: SUBJECTS_DIR is /execute Actual FREESURFER_HOME /usr/local/freesurfer Linux ca9b4aef337a 5.3.0-59-generic #53~18.04.1-Ubuntu SMP Thu Jun 4 14:58:26 UTC 2020 x86_64 GNU/Linux Can't locate MNI/Startup.pm in @INC (you may need to install the MNI::Startup module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.28.1 /usr/local/share/perl/5.28.1 /usr/lib/x86_64-linux-gnu/perl5/5.28 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.28 /usr/share/perl/5.28 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /usr/local/freesurfer/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /usr/local/freesurfer/mni/bin/nu_correct line 37. Could you advise please? Thanks, Ian -- *Ian Hardingham*

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PhD Position - Early MRI and childhood outcomes - Liggins Institute, Auckland
by Eleanor Kennedy 22 Jun '20

22 Jun '20

External Email - Use Caution Hello, We are seeking a PhD candidate at the Liggins Institute, University of Auckland with Prof Jane Harding. Research at the Liggins Institute focuses on early life determinants of long-term health and covers a broad range of disciplines from basic science through to clinical trials and translational research. Project Description: MRI is increasingly being used in preterm newborns to assess early brain injury and brain maturation, but its relationship to later development is unclear. We plan to determine the relationship between early MRI and later development in children who as babies took part in clinical trials of additional nutrition, or of magnesium sulphate administration to prevent cerebral palsy. If early MRI is predictive of particular problems such as cerebral palsy, it could be used in the future to identify babies at risk and allow early intervention. The project will involve neonatal MRI (DTI, fMRI and structural scans). Assessments of children at two years of age for cognitive, language, motor and executive function. We are looking for candidates with a degree in a health, psychology or education-related discipline and some experience with MRI analysis. For more information, see the Find a Thesis entry here: https://www.findathesis.auckland.ac.nz/research-entry/10464530 Thanks, Eleanor Kennedy Research Fellow Liggins Institute DDI +64 9 923 6701 Ext 86701 E eleanor.kennedy(a)auckland.ac.nz<mailto:eleanor.kennedy@auckland.ac.nz> W www.liggins.auckland.ac.nz<http://www.liggins.auckland.ac.nz/> A The University of Auckland, Building 503, Level 2, 85 Park Road, Auckland P Private Bag 92019, Auckland 1142, NZ [Liggins Logo Colour_small]

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Re: [Freesurfer] How to make surface cuts / flatmaps. Alternative for tksurfer in 2020?
by Chris Klink 22 Jun '20

22 Jun '20

External Email - Use Caution Someone messaged me that in the latsest FS7 we can now do this in Freeview. Awesome! I don't think a lot of people know about this. Spread the word! -- Chris Klink (sent from a phone)

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Re: [Freesurfer] QDEC analyses
by xunzhang_hmrrc 22 Jun '20

22 Jun '20

External Email - Use Caution Thanks for your timely response. To assess the two group differences in cortical thickness, whole-brain vertex-wise analyses were performed using the graphical user interface of FreeSurfer known as QDEC. We used a general linear model to compare the thickness between the patients and healthy controls with age and sex as covariates. The Monte Carlo Null-Z Simulation was conducted to control for multiple comparisons (cluster-wise corrected P< 0.05). But, as we all know, QDEC analyses have always be done for the two hemispheres separately, so the multiple comparisons are also conducted for two hemispheres separately, which, the reviewer assumed, is different from multiple comparisons for the whole brain? So, could you please provide some perspective and citation about the validation for such design of QDEC (i.e., the right and left hemisphere were tested separately)? ------------------ Original ------------------ From: "Douglas N. Greve"<dgreve(a)mgh.harvard.edu>; Date: Mon, Jun 22, 2020 10:17 AM To: "freesurfer"<freesurfer(a)nmr.mgh.harvard.edu>; Subject: Re: [Freesurfer] QDEC analyses How you did you do your analysis? As an exploratory/map-based analysis? Or as an ROI analysis? How did you correct for multiple comparisons? Generally, in a map-based analysis, the correction for multiple comparisons incorporates the fact that there are two hemispheres being tested. On 6/20/2020 10:04 PM, xunzhang_hmrrc wrote:         External Email - Use Caution        Hello Freesurfer developers, Recently, I have used QDEC of freesurfer 6.0.0 to examine the cortical thickness differences between two groups, and the manuscript has been submitted to a journal. One reviewer raised a question -"The manuscript stated that the right and left hemisphere were tested separately. Could the authors provide an explanation for this? I assume that testing over 68 (all ROIs) vs testing separately left and right (34 ROIs) would have an effect?" Unfornately, I don't know how to responde to this reviewer, so I would like to ask for your help. I just followed the tutorials of QDEC (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysisV6.0) and I found QDEC analyses have always be done for the two hemispheres separately. So, could you please provide some perspective and citation about the validation for such design of QDEC? Thank you in advance for your assistance, Best regards, Xun _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] recon-all for macaque brain
by Minqing Jiang 22 Jun '20

22 Jun '20

External Email - Use Caution Dear Chris and Douglas, Thank you for the help! I would try the hires and precon_all. One more quesion, now I have a much better recon result from adult macaque brain. But when I performed MRI in 1 years old macaque. Recon-all barely can generate result, either with error or very bad segmentation. We are using TI 1100ms, TR3000/TE3.29 and FOV 128*128. Is there any way to segment young monkeys better? Thanks again. bests, Minqing Hi Minqing Jiang, Getting a macaque brain through Freesurfer requires a bit of manual tinkering. We have a description of how we do it on GitHub: https://github.com/VisionandCognition/NHP-Freesurfer There's also precon_all (https://github.com/recoveringyank/precon_all) which I haven't personally used yet, but I've seen results and it looks very promising! ?Good luck! Chris

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Recon-all error output
by Frank Chau 22 Jun '20

22 Jun '20

External Email - Use Caution Dear Freesurfer experts, I ran Recon-all on a batch of subject. Only one Recon-all error results were generated which the process just last for few minutes. There just 2 mgz file in mri folder of the subject output directory were generated. I re-run recon-all on the same subject, same result was got again. May I know the cause of this error? I upload the output result, log history and the T1.nii to the following share link, please feel free the check them: <https://www.dropbox.com/sh/lhbzct444n8ek8z/AADbtfyYEBNWZ4yYXPw7ejmwa?dl=0> https://www.dropbox.com/sh/lhbzct444n8ek8z/AADbtfyYEBNWZ4yYXPw7ejmwa?dl=0 Thank you. Regards Frank --------------------------- FRANK C Y CHAU Research assistant Division of Neurology Department of Medicine Tel: +852 6340 2553 Fax: 2872 5828 E-mail : cyfrank(a)hku.hk<mailto:cyfrank@hku.hk> Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong

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Error with -qcache
by Mateus Aranha 22 Jun '20

22 Jun '20

External Email - Use Caution Dear FS team, I'm running -qcache on my subjects before group analysis and I get the following error for 2 of the subjects: ERROR: number of vertices in /home/neuroimagen7/Desktop/SoccerPlayers/ReconFiles/recon_T1/edits/ANON0266_recon_T1/surf/lh.thickness does not match surface (139424,138940) ERROR: reading curvature file The remaining subjects are fine! Thank you! Mateus

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Re: [Freesurfer] Freeview - Load custom overlay from terminal
by Loucao, Ricardo 22 Jun '20

22 Jun '20

External Email - Use Caution Hi Ruopeng, You were correct - for some reason the version I built was 2.0. I’ve downloaded a built version of freesurfer v7.1.0 and now I can successfully use the flag. Another question if I may: is there a way to toggle the “clear lower”/“clear higher” option also from the terminal? Thank you in advance! Best regards, Ricardo Date: Thu, 18 Jun 2020 13:28:56 +0000 From: "Wang, Ruopeng" <RWANG4(a)mgh.harvard.edu<mailto:RWANG4@mgh.harvard.edu>> Subject: Re: [Freesurfer] Freeview - Load custom overlay from terminal To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <FE2C8592-CFC2-41FD-9BB0-B4763CA86185(a)mgh.harvard.edu<mailto:FE2C8592-CFC2-41FD-9BB0-B4763CA86185@mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" Hi Ricardo, The way you use the flag is correct. But have you made sure that you were actually running the latest version that you built? You can check freeview?s build time from About menu. Best, Ruopeng Date: Thu, 18 Jun 2020 08:15:44 +0000 From: "Loucao, Ricardo" <r.loucao(a)fz-juelich.de<mailto:r.loucao@fz-juelich.de>> Subject: [Freesurfer] Freeview - Load custom overlay from terminal To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <25D279E0-2256-47B0-B05A-1F470A1B3089(a)fz-juelich.de<mailto:25D279E0-2256-47B0-B05A-1F470A1B3089@fz-juelich.de>> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Dear FS experts, I?m trying to load a surface with a custom overlay directly from the terminal using the sub-option ?overlay_custom? but it returns ?Unrecognized sub-option flag ?overlay_custom??. I checked the source code on GitHub and found the flag to be present and implemented. I also built the freeview app from the GitHub (as it could be that my version did not have that sub-option) but I got the same return message. Upon inspecting the code further, I figured the way this flag works is via quadruplets of the form ?val, r, g, b?. However, I also noticed that this return message comes when the overlay_custom sub-option is empty (freeview/MainWindow.cpp: line 3484). It seems to me like I might be using the flag improperly. Here?s an example of how I am using it: ?:overlay_custom=0.85,255,0,0,0.875,0,255,255,0.90,0,0,255? Do you have any hints for me on how to deal with this? Thank you very much in advance! Best regards, Ricardo ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Re: [Freesurfer] recon-all for macaque brain
by Chris Klink 22 Jun '20

22 Jun '20

External Email - Use Caution Hi Minqing Jiang, Getting a macaque brain through Freesurfer requires a bit of manual tinkering. We have a description of how we do it on GitHub: https://github.com/VisionandCognition/NHP-Freesurfer There's also precon_all (https://github.com/recoveringyank/precon_all) which I haven't personally used yet, but I've seen results and it looks very promising! Good luck! Chris

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How to make surface cuts / flatmaps. Alternative for tksurfer in 2020?
by Chris Klink 22 Jun '20

22 Jun '20

External Email - Use Caution How do people create flatmaps these days? It's getting more and more of a hassle to work with tksurfer (won't work on 64bit only Mac, throws tcl & tix errors on Linux in Freesurfer 7). I'm currently running tksurfer on Linux in FS6, that I basically only keep around for that purpose. I read on the mailing list that tkmedit and tksurfer are pretty much deprecated, but I've looked in Freeview and can't find a way to make cuts there. I must be missing something? Is there some other way of doing it? Should I dive into pycortex' Blender based approach? What are the options in 2020? Best, Chris

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Freesurfer June 2020