Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30064 discussions

Freeview aborts under centos6
by Markus Gschwind 15 Sep '17

15 Sep '17

Dear experts, I am installing freeusrfer on our cluster which is running Centos6. [gschwind@login1 ~]$ uname -a Linux login1.cluster 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Apr 11 17:13:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Freeview aborts without any other complaint. [gschwind@login1 ~]$ freeview Abort When running freeview.bin it complains about a libraries error: [gschwind@login1 ~]$ freeview.bin freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: cannot open shared object file: No such file or directory I searched the archives and found this info to be given, [gschwind@login1 ~]$ ls -l $FREESURFER_HOME/lib/vtk/lib/ vtk-5.6/*libvtkverdict* -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6 -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6.0 I then integrated this into bashrc export LD_LIBRARY_PATH=$FREESURFER_HOME/lib/vtk/lib/vtk-5.6 however, the problem persists. Any help is highly appreciated! Thanks you! Markus

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Repronim Training Workshop on Reproducible Research Nov 10-11 before SFN
by Satrajit Ghosh 14 Sep '17

14 Sep '17

*ReproNim Training Workshop: Nov 10 full day - Nov 11 morning - George Washington** University* *Register and information at:* https://tinyurl.com/repronim-sfn17 *Purpose:* The issue of lack of reproducibility has been described in several scientific domains for several years, raising concerns specifically in the life science community. ReproNim has developed a curriculum ( http://www.reproducibleimaging.org/#trai... <http://www.reproducibleimaging.org/#training>) that will give the students the information, tools and practices to perform repeatable and efficient research. This training workshop will introduce material on the critical aspects of reproducible brain imaging and will orient attendees using a hands on and practical experience to conduct neuroimaging analyses with the next generation of tools. By the end of this course, the student will be aware of training materials and concepts necessary to perform reproducible research in neuroimaging. The student will be able to reuse these materials to conduct local workshops and training and be able to customize the training for their specific scenario. *Prerequisites:* If you are a student, postdoc or researcher in life science who directly works with neuroimaging data - or wish to work with these data, and you have some basic computational background, this training workshop is for you. For instance, you should have already done either some R, or Python, or Matlab or Shell scripting, or have used standard neuroimaging tools (SPM, FSL, Afni, FreeSurfer, etc) and be engaged in neuroimaging research projects. You should have already completed a neuroimaging analysis or know how to do one. *Logistics:* *Location:* George Washington University, Marvin Center, Room 402-404 https://events-venues.gwu.edu/meeting-ro... <https://events-venues.gwu.edu/meeting-rooms> *Dates:* November 10-11, 2017. *Costs:* Free - but space is limited - please apply for approval. *Schedule:* Friday November 10th: 8:30-9am: Introduction to the course and participants "setup" 9am-10:45: Reproducibility Basics (Module 0) 10:45-11am : Coffee break 11am-12:45 : FAIR data (Module 1) 12:45-2pm : Lunch+coffee 2pm-3:45: Data Processing (Module 2) 3:45-4pm: coffee break 4pm-5:45pm: Statistics for reproducible analyses (Module 3) 5:45-6:15: Questions and answers and feedback session Saturday November 11th: 9am-12pm: The Re-executable Micro Publication Challenge During this time, we will propose a small challenge around producing an entirely re-executable neuroimaging analysis from fetching data to producing statistical results. This will also be a time with close interactions with neuroimaging experts in data handling and analysis. 12pm-12:30: Closing session: feedback and future: "become a trainer". Weekly online office hours will be held prior to the workshop. Registered attendees will receive information via email. *Modules:* *Module 0 - Reproducibility Basics:* Friday Nov. 10. 9am-10:45am. This module guides through three somewhat independent topics, which are in the heart of establishing and efficiently using common generic resources: command line shell, version control systems (for code and data), and distribution package managers. Gaining additional skills in any of those topics could help you to not only become more efficient in your day-to-day research activities, but also would lay foundation in establishing habits to make your work actually more reproducible. *Module 1 - FAIR Data:* Friday Nov. 10. 11am-12:45. This module provides an overview of strategies for making research outputs available through the web, with an emphasis on data. It introduces concepts such persistent identifiers, linked data, the semantic web and the FAIR principles. It is designed for those with little to no familiarity with these concepts. More technical discussions can be found in the reference materials. *Module 2 - Data Processing:* Friday Nov. 10. 2pm-3:45pm. This module teaches you to perform reproducible analysis, how to preserve the information, and how to share data and code with others. We will show an example framework for reproducible analysis, how to annotate, harmonize, clean, and version brain imaging data, how to create and maintain reproducible computational environments for analysis and use dataflow tools to capture provenance and perform efficient analyses (docker) and other tools. *Module 3 - Statistics:* Friday 4am-5:45 The goal of this module is to teach brain imagers about the statistical aspects of reproducibility. This module should give you a critical eye on most of the current literature and the knowledge to do solid work, understand exactly what is a p-value and its limitation to represent evidence for results, practical notion of power and associated tools, etc. *Instructors:* J. Bates, S. Ghosh, J. Grethe, Y. Halchenko, C. Haselgrove, S. Hodge, D. Jarecka, D. Keator, D. Kennedy, M. Martone, N. Nichols, S. Padhy, JB Poline, N. Preuss, M. Travers *This workshop is brought to you by ReproNim: A center for Reproducible Neuroimaging **Computation NIH-NIBIB P41 EB019936*

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control point and aseg edit
by miracle ozzoude 14 Sep '17

14 Sep '17

I used the expert option for control points and manually edited the aseg.presurf.mgz. Which is the proper flag to use in other to incorporate the respective changes? a) recon-all -autorecon2-cp -autorecon2-noaseg -autorecon3 -expert -parallel -openmp 8 -bigventricles -3T -time or b) recon-all -autorecon2-cp -autorecon3 -expert -parallel -openmp 8 -bigventricles -3T -time Thanks. Best, Paul

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Using FreeSurfer5.3 via VirtualBox
by Ledesma, Jason 14 Sep '17

14 Sep '17

To whom it may concern, How does one access the files in a shared folder when using FreeSurfer5.3 via VirtualBox on a windows unit? I have not had success with the "sudo mount -t vboxsf <shared_folder_name> /media/<shared_folder_name>" command which I have seen on several forums. Furthermore, I continually receive a warning which states that the "...VirtualBox Guest Additions do not appear to be available on this virtual machine, and shared folders cannot be used with them...", however I have inserted the Guest Additions CD image from the devices menu as the warning requests. Thanks. Sincerely, Jason Ledesma Staff Research Associate Phone: 1(424)571-7755 E-mail: jason.ledesma(a)labiomed.org<mailto:jason.ledesma@labiomed.org> ________________________________ LA BioMed Warning: This email (and any attachments) is intended for the use of the person to which it is addressed. It may contain information that is privileged and confidential. As the recipient, you are obligated to maintain it in a safe, secure and confidential manner. Unauthorized disclosure or failure to maintain confidentiality may subject you to governmental penalties. Should you not be the intended recipient, please notify us by return email, and delete this message from your computer at once. ________________________________

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adding volumes of seperated parts of one structure?
by Benjamin Luerweg 14 Sep '17

14 Sep '17

dear all, what do you think about adding the volumes of seperated parts of one structure to a complete volume? e.g. the corpus callosum or also cingulate gyrus. is it ok to get the complete volume value by just adding the volumes of the seperated parts? beside that, am i right that wmparc parts of e.g. insula is just the white matter volume? would it be ok to add the volume of the aparc equivalent as the grey matter volume part? kind regards, ben luerweg

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what does the CSF label describe?
by Benjamin Luerweg 14 Sep '17

14 Sep '17

dear all, i already tried to find out what the label CSF stands for.. but beside realizing that its not a common/regular part of the ventricle system i couldn’t get any other informations regarding the meaning? of the CSF label. i tried to find out whats it about by using freeview (screenshot (black part)) anyone any idea? kind regards, b. luerweg doctoral student

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Re: [Freesurfer] lobes volume (WM and GM)
by Gonzalo Rojas Costa 14 Sep '17

14 Sep '17

Hi Douglas: By removing --rip-unknown I got the same results... Why ?... Sincerely, Gonzalo Rojas Costa > Date: Tue, 12 Sep 2017 12:33:11 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] lobes volume (WM and GM) > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <d547d519-c2fd-980d-3021-2c5fd44620a3(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > Try removing the --rip-unknown > > > On 09/12/2017 11:09 AM, Gonzalo Rojas Costa wrote: >> Hi: >> >> I created the following script (for freesurfer 5.3.0) to compute the >> lobes volume (including GM and WM). >> >> mri_annotation2label --subject pac --hemi rh --lobesStrict lobulos >> --seg lobulos --stat lobulos >> mri_annotation2label --subject pac --hemi lh --lobesStrict lobulos >> --seg lobulos --stat lobulos >> mris_anatomical_stats -a lobulos -f pac.lobulos.rh pac rh >> mris_anatomical_stats -a lobulos -f pac.lobulos.lh pac lh >> mri_aparc2aseg --s pac --labelwm --hypo-as-wm --rip-unknown >> --volmask --o $SUBJECTS_DIR/pac/mri/lobulitos.mgz --annot lobulos >> --wmparc-dmax 20 >> mri_segstats --seg $SUBJECTS_DIR/pac/mri/lobulitos.mgz --ctab >> /usr/local/freesurfer/LobulesColorLUT.txt --excludeid 0 --sum >> $i.lobulo.aseg.sum --id 1001 1004 1005 1006 2001 2004 2005 2006 3001 >> 3004 3005 3006 4001 4004 4005 4006 251 252 253 254 255 >> >> But, I didn't got the complete WM volume for each lobe (frontal lobe >> for example... see red arrow in attached image)... why ?... Any >> solution ?... >> >> Sincerely, >> >> >> Gonzalo Rojas Costa >> Laboratory for Advanced Medical Image Processing >> Department of Radiology >> Cl?nica las Condes >> Lo Fontecilla 441, Las Condes, Santiago, Chile. >> Tel: 56-2-2105170 >> Cel: 56-9-97771785 >> www.clc.cl >> http://www.aribrain.info >> https://scholar.google.com/citations?user=LO7LZ3oAAAAJ >> https://www.researchgate.net/profile/Gonzalo_Rojas2 >> https://cl.linkedin.com/in/gonzalorojascosta >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Cluster-Defining Threshold of p=0.025
by Douglas N Greve 14 Sep '17

14 Sep '17

Andy, please remember to post to the FS list, thanks. As for your question, this is a bug in mri_glmfit-sim that hard codes the allowable thresholds. I've attached a version that should work with 1.6. On 09/14/2017 10:06 AM, Jahn, Andrew wrote: > Thanks again; I was able to create new simulation tables. However, > when I run mri_glmfit-sim, I get the following error: > > foreach dir (results_Directory) > mri_glmfit-sim \ > --glmdir {$dir} \ > --mczsim 1.6 abs \ > --cwp 0.05 \ > --2spaces > end > > ERROR: thresh = 1.6, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 > > > I get this error even though I have the tables located in > $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhm10/abs. > Is there something I'm missing? > > > Best, > > -Andy > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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mri_convert: line 3: 38445 Segmentation fault
by M Janani 14 Sep '17

14 Sep '17

Hi Team, Am getting segmentation error during the reconstruction process. Please help in resolving the error. I have attached log for reference. Thanks, Janani ::DISCLAIMER:: ---------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. ----------------------------------------------------------------------------------------------------------------------------------------------------

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correcting defect
by Meng Li 14 Sep '17

14 Sep '17

Hi all, I tried to use FreeSurfer version 6.0.0 to process fifteen subjects, but half of the subjects was stuck at the ‘Correcting Defect’ step. However, when I changed to FreeSurfer version 5.3.0, the ‘Correcting defect’ step finished successfully. Is it possibility that the unsuccessful ‘Correcting Defect’ step is caused by the different versions of Freesurefer? In addition, when I added the flag -parallel -openmp 30 based on the version 6.0.0, the recon-all –all runtime still need 20+ hours. It seems that the parallel processing did not reduce the processing time. I wonder why the parallel processing did’t save time? Any help would be greatly appreciated. Meng

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