Freesurfer September 2013

freesurfer@nmr.mgh.harvard.edu

124 participants
243 discussions

Brainhack 2013 Update - Registration is open, Stipend program announced
by MCLAREN, Donald 08 Sep '13

08 Sep '13

Dear colleagues, I wanted to draw your attention on the upcoming Brainhack 2013, which is being held from October 23-26 at the Centre International d'Études Pédagogiques, Sèvres, France (just outside of Paris). Registration is limited, please register to guarantee a spot (http://www. brainhack.org/?page_id=27743) * The registration page has now been separated from the abstract submission to allow for registration in advance of abstract submission. Register today while space is still available. *NEW TO BRAINHACK 2013:* (1) Abstract book listing all presented abstracts - please submit your abstract online for inclusion after you register (2) Stipend program to help defray registration fees ( http://www.brainhack.org/?page_id=40668) We have also confirmed the following "IGNITE" speakers<http://www.brainhack.org/?page_id=40630> : *Yves Burnod, PhD,<http://www.imed.jussieu.fr/en/outils/affiche_personne.php?pers_id=217> INSERM (French national Institute for Health) **Jean Daunizeau, PhD,<https://sites.google.com/site/jeandaunizeauswebsite/>l’Institut du Cerveau et de la Moelle épinière **Martin Lindquist, PhD, <http://www.biostat.jhsph.edu/~mlindqui/> Department of Biostatistics of the Johns Hopkins University Bloomberg School of Public Health. **Ziad Saad, PhD,<http://intramural.nimh.nih.gov/research/clinicians/sc_saad_z.html> US National Institutes of Mental Health Statistical and Scientific Computing Core **Gaël Varoquaux, PhD, <http://gael-varoquaux.info/> INRIA at the Neurospin **Xinian Zuo, PhD, <http://lfcd.psych.ac.cn/> Institute of Psychology, Chinese Academy of Science* Brainhack 2013 is a unique workshop with the goals of fostering interdisciplinary collaboration and open neuroscience. The structure builds from the concepts of an unconference and hackathon: The term “unconference” refers to the fact that most of the content will be dynamically created by the participants — a "hackathon" is an event where participants collaborate intensively on projects. Participants interested in neuroimaging from any discipline are welcome. Ideal participants span in range from graduate students to professors across any disciplines willing to contribute (e.g., mathematics, computer science, engineering, neuroscience, psychology, psychiatry, neurology, medicine, art, etc…). The primary requirement is a desire to work in close collaborations with people outside of your specialization in order to address neuroscience questions that are beyond the expertise of a single discipline. One should come to brainhack ready to engage into collaborative projects, and with some material (slides, ideas, data, tools) ready to start a project or a discussion panel. Brainhack will build on the successful techniques used in other unconferences to keep the meeting focused and productive. It is possible to start a project and build a team as early as today. Please have a look at the website for information on the conference and a sample of projects (from Brainhack 2012): http://www.brainhack.org The Preliminary Schedule for Brainhack 2013 is available online: http://www. brainhack.org/?page_id=27753 Registration is now open: http://www.brainhack.org/?page_id=27743 Abstract Submission is now open: http://www.brainhack.org/?page_id=40661 Stipend Application is now open: http://www.brainhack.org/?page_id=40668 Please share this with your friends and colleagues. Please do not hesitate to contact one of the members of the organizing committee if you have any questions. We look forward to seeing you in Paris. Sincerely, The Neuro Bureau

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Re: [Freesurfer] matrix ill-conditioned....
by Kayle Sawyer 08 Sep '13

08 Sep '13

Hi Doug and FreeSurfer Community, For a cortical thickness analysis, we are interested in the age-x-group interaction. We want to know if the age slope for our pathological group is different than the control group. Do we need to demean age before creating the FSGD file? I was looking at the example: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V#Contrast2group-x-age.mtx This makes it look like the FSGD does *not* need to be demeaned before examining the interaction. But Doug's email below says, "In general, you should not need to demean. For the interaction, you need to demean before computing the interaction." Do we need to subtract the mean from each age value in the FSGD file before running mri_glmfit? Thanks, -Kayle On Aug 28, 2013, at 11:39 AM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > 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. Re: Talairach Failure Detection (Bruce Fischl) > 2. Re: Recon-all error (Douglas N Greve) > 3. pial surface editing (Francesco Siciliano) > 4. Re: Talairach Failure Detection (pablo najt) > 5. Re: matrix ill-conditioned.... (Douglas N Greve) > 6. Re: Talairach Failure Detection (Bruce Fischl) > 7. Re: pb reading .annot in matlab/python (Douglas N Greve) > 8. Re: Recon-all error (pfotiad(a)nmr.mgh.harvard.edu) > 9. Re: Recon-all error (Douglas N Greve) > 10. Re: Recon-all error (pfotiad(a)nmr.mgh.harvard.edu) > 11. Re: Recon-all error (Douglas N Greve) > 12. Re: Talairach Failure Detection (pablo najt) > 13. Re: Recon-all error (pfotiad(a)nmr.mgh.harvard.edu) > 14. Re: Talairach Failure Detection (pablo najt) > 15. Re: pb reading .annot in matlab/python (Alexandre Gramfort) > 16. Re: Recon-all error (Douglas N Greve) > 17. Re: Talairach Failure Detection (Bruce Fischl) > 18. Re: pb reading .annot in matlab/python (Douglas N Greve) > 19. Re: pb reading .annot in matlab/python (Alexandre Gramfort) > 20. tutorial subject not found (leila nasehy) > 21. Otto: update freesurfer to latest version? (Otto Muzik) > 22. Re: Freesurfer dependencies (ye tian) > 23. apply a label to an overlay in tksurfer (Sarah Madsen) > 24. Re: apply a label to an overlay in tksurfer (Douglas Greve) > 25. recon-all issue (CSF seg as gray matter) (Alexandre Gramfort) > 26. Re: matrix ill-conditioned.... (Jacobs H (NP)) > 27. Thickness vertex by vertex (Giusy Chinnici) > 28. Re: recon-all issue (CSF seg as gray matter) (Bruce Fischl) > 29. Re: Thickness vertex by vertex (Bruce Fischl) > 30. Re: Thickness vertex by vertex (Avram Holmes) > 31. recon-all: 'segmentation fault' (Mark Plantz) > 32. Re: matrix ill-conditioned.... (Douglas N Greve) > 33. Longitudinal Processing Pipeline (David Tate) > 34. Re: Error message of Ubuntu 13.04 and Centos4 & Centos6 (Z K) > 35. Re: Thickness vertex by vertex (Giusy Chinnici) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 27 Aug 2013 12:08:22 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Talairach Failure Detection > To: pablo najt <pablonajt(a)hotmail.com> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <alpine.LRH.2.03.1308271207330.13629(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="iso-8859-15" > > Hi Pablo > > have you visually inspected the talairach xform to see if it is indeed > incorrect? What input format did you start with? Most of these occur > because people start with analyze, which doesn't have the direction > cosines, and so the data is oriented incorrectly > > cheers > Bruce > > > On Tue, 27 Aug 2013, pablo najt wrote: > >> Dear FS experts,I am contacting you to report an error after launching recon -all for one of my subjects (see below). I am using a >> macbook pro with snow leopard version 10.6.8.? >> >> I would greatly appreciate if you could advise me which step/s should I take to correct this. >> Thank you for your attention, >> Pablo >> >> Error:-------------------------------------------------------------------------------------------------------------------------------- >> ------------------ >> #@# Talairach Failure Detection Mon Aug 19 23:01:43 EDT 2013 >> /Users/pablonajt/subjects/tr5713/mri >> \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n >> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0554, pval=0.0034 < threshold=0.0050) >> Manual Talairach alignment may be necessary, or >> include the -notal-check flag to skip this test, >> making sure the -notal-check flag follows -all >> or -autorecon1 in the command string. >> See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach >> Darwin Pablo-Najts-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun ?7 16:33:36 PDT 2011; >> root:xnu-1504.15.3~1/RELEASE_I386 i386 >> >> recon-all -s tr5713 exited with ERRORS at Mon Aug 19 23:01:43 EDT 2013 >> >> > > ------------------------------ > > Message: 2 > Date: Tue, 27 Aug 2013 12:11:31 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Recon-all error > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <521CCFB3.2030909(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > try this instead > > recon-all -all -subjid CAA_022_struc > > On 08/27/2013 11:23 AM, pfotiad(a)nmr.mgh.harvard.edu wrote: >> Hi FS Commuity, >> >> I am using the stable version 5.3 of FS to recon-all a subject of mine, >> but the job is aborted and gives the following message: >> >> The command that I ran is: recon-all -all -subjid >> /cluster/ichresearch/Petechial/MEG/CAA_022_struc >> >> >> Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 >> Current Stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 >> INFO: SUBJECTS_DIR is /autofs/cluster/ichresearch/Petechial/MEG >> Actual FREESURFER_HOME >> /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 >> Linux eesmith 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC >> 2013 x86_64 x86_64 x86_64 GNU/Linux >> #-------------------------------------------- >> #@# MotionCor Tue Aug 27 11:09:19 EDT 2013 >> Found 2 runs >> /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/mri/orig/001.mgz >> /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/mri/orig/002.mgz >> Checking for (invalid) multi-frame inputs... >> if: Expression Syntax. >> Exit 1 >> >> Also, I tried doing the same recon-all with the stable 5.0 version and it >> runs fine. Therefore, I was wondering whether you could tell me why is >> this happening. By the way I have also attached the recon-all.log. >> >> Thank you for your time. >> >> Best, >> Panos >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > 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/ > > > > ------------------------------ > > Message: 3 > Date: Tue, 27 Aug 2013 16:13:38 +0000 > From: Francesco Siciliano <sicilia(a)nyspi.columbia.edu> > Subject: [Freesurfer] pial surface editing > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <72EB4D9B5160FC45BCD75ED55E1C8159249D9945(a)NYSPIDAG01.nyspi.local> > Content-Type: text/plain; charset="iso-8859-1" > > Hello, > > I am having a few issues with editing the pial surface in freeview. It appears as though the edits I make to the brainmask are not being taken into account when I re-run recon-all. I work on a MacBook Pro and have been using "shift+click" to delete voxels at a brush value of 1 and then saving the brainmask.mgz back into the mri folder. When making edits to the brainmask I have the brainmask highlighted. Upon clicking save, the mri folder contains both brainmask.mgz and brainmask.mgz~ (The version with a ~ seems to indicate the older version of the file based on modification time). > > Additionally, the edits that I make to brain.finalsurfs.manedit.mgz for pial surface that has extended into the cerebellum seems to not be taken into account when I re-run recon-all. I have been making a copy of brain.finalsurfs.mgz, pasting it into the mri folder, and renaming it brain.finalsurfs.manedit.mgz. I then load this volume and make edits to it according to the same specifications as the brainmask.mgz. Shouldn't I be able to see changes made to the pial surface in the brainmask.mgz from edits I make to the brain.finalsurfs.manedit.mgz after running recon-all? Neither the brainmask.mgz nor the brain.finalsurfs.mgz take into account the edits I've made on brain.finalsurfs.manedit.mgz. I'm not sure if I'm deleting voxels incorrectly or saving incorrectly. I've tried to troubleshoot several times and keep encountering similar issues. > > The version of FreeSurfer that I am working from is: freesurfer-i686-apple-darwin9.8.0-stable5-20110525 > My editing interface looks slightly different from the current version explained on the freesurfer wiki. I do not have an option to select recon-editing. Adding control points, however, has been successful. I have been using the command recon-all -autorecon2 -autorecon3 -s subj001 > > Any help getting to the bottom of this would be greatly appreciated! > > Thanks, > > Francesco Siciliano, B.A. > Research Assistant > Department of Child and Adolescent Psychiatry > The New York State Psychiatric Institute > Columbia University > 1051 Riverside Drive, Unit 74 > New York, NY 10032 > (212) 543-6155 >

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conversion from dicom to mgz
by swathy p.s 08 Sep '13

08 Sep '13

How do i convert dicom into mgz files. tried using recon-all what does subject id refer to and what is its significance.

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version 2 FS
by Anupa AV 07 Sep '13

07 Sep '13

Dear SIr, I made some analysis based on FS v.2.0. Does the Deprecated version means that the results generated by FSv.2 can't be published???

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Taking a look at QDEC/glm code
by ye tian 06 Sep '13

06 Sep '13

Dear Freesurfers, I am very curious about glm's and I would like to see how it is constructed. Would anyone please direct me to freesurfer's codes so that I can get a feeling? Thank you very much! Sincerely, Ye

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Otto: upgrade freesurfer to latest version?
by Otto Muzik 06 Sep '13

06 Sep '13

Dear All, I have posted this message before, but did not get any reply. Please help. I would like to upgrade my freesurfer distribution to the latest version - Is there an automated procedure to do this? My current version is linux-gnu-stable5-20110522 Many thanks! Otto

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arguments to mris_curvature call in -inflate2 step of recon-all
by David Romano 06 Sep '13

06 Sep '13

Hi everyone, Since they don't appear in the documentation accessible through the --help flag, I was just wondering how the flags -n, -thresh, and -distances affect the call to mris_curvature in the inflate2 step of the -autorecon2 stage of recon-all: mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ?h.inflated (as described on the webpage http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable) Thanks in advance for you help, David Romano

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ascii list of label files
by stdp82＠virgilio.it 06 Sep '13

06 Sep '13

Hi list, After mri_binarize, I'using label2surf command to trasform labels files obtained into surface files suitable for probtrackx (FSL). I do not understand how can I provide ascii list of label files for label2surf -s <surface> -o <outputsurface> -l <labels>Thanks, Stefano

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qdec_glmfit
by Yang, Daniel 06 Sep '13

06 Sep '13

Hi Freesurfer experts, Does qdec_glmfit support the option of specifying nuisance factors? Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

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new subcortical regions
by Luo,Yishan 06 Sep '13

06 Sep '13

Hello, I have run recon-all for my subject, if I want to get more subcortical segmentation, e.g., globus pallidus, medulla, pons and so on, how can I do?Can I manually draw these region on the bert image and transfer them to individual subject, like mri_label2label? Thanks. Lisa

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Freesurfer September 2013