Freesurfer

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30089 discussions

recon-all for multiple subjects
by Anupa AV 10 Sep '13

10 Sep '13

Dear Sir, I'd like to know the command lines for running recon-all for multiple datasets. Can you please help me on that? I've tried using the following command lines cd /home/john/Anu (where I kept all the .nii files) for x in * do recon-all -i SZ*.nii -s $x -all done But this is not working

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Issue running Longitudnal Analysis
by Ray, Siddharth 09 Sep '13

09 Sep '13

Hi all, I was trying to run freesurfer longitudinal analysis for my subjects at 2 time points and when I ran the pre_proc step it gave me an error that file 'lh/rh.thickness is missing'. Here is what I have done. 1) Run the Freesurfer till CA Normalize stage (till norm.mgz stage). 2) Created unbiased template - log file showed 'exited without error' (and it looks fine) 3) Run longitudinal processing - log file showed 'exited without error' , but when I closely looked at the file there was following error: #@# Talairach Failure Detection Wed Sep 4 14:22:01 CDT 2013 /work/02510/sray2/Free_Sub/FS_output/54062.long.54062_59467/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0124, pval=0.0000 < threshold=0.0050) Do you where is I am doing wrong. Why is the log file showing 'exited without error' if there was an error at Talairach Detection. Please let me know. Thanks, -Siddharth

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Recon-all ceases working after mri_nu_correct.mni ...
by Amy Bilderbeck 09 Sep '13

09 Sep '13

Dear FreeSurfer community, My recon-all commands have stopped working, when previously they (usually) completed just fine. I am not sure at what level the problem is at. I'm working off the Jalapeno cluster at FMRIB, where FreeSurfer is centrally installed. I run a configuration script to get started (. $FREESURFER_HOME/SetUpFreeSurfer.sh) and then define my subjects directory (SUBJECTS_DIR=~/scratch/my_fs_subjects). I then run recon-all commands e.g. fsl_sub -q verylong.q recon-all -s SubjectXXX -i T1_biascorr.nii.gz -all This previously worked. I now within minutes get a log file with no obvious error message, but which ends #-------------------------------------------- #@# Talairach Wed Aug 28 15:38:06 BST 2013 /home/fs0/amyb/scratch/Enigma_bipolar/FSURFER_OUTPUT/BF_subject10/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux jalapeno04.fmrib.ox.ac.uk 2.6.32-358.14.1.el6.x86_64 #1 SMP Mon Jun 17 15:54:20 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s SubjectXXX exited with ERRORS at Wed Aug 28 15:38:13 BST 2013 We are using FreeSurfer version 5.3.0. After reading some of the archive I've checked that nu_correct is indeed stored in the freesurfer directory mni/bin/nu_correct. Any tips? Thanks and warm regards, Amy Dr. Amy Bilderbeck From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of ye tian Sent: 09 August 2013 21:05 To: Douglas N Greve Cc: Freesurfer Subject: Re: [Freesurfer] Qdec and one discrete variable Dear Doug, Thank you very much! Sincerely, Ye On Thu, Aug 8, 2013 at 4:46 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>> wrote: Try adding a carriage return after TM doug On 08/08/2013 05:30 PM, ye tian wrote: Dear Doug, It is a mac. I made the meditation.levels file using emacs. emacs meditation.levels --> type "Normal" (level1) --> hit enter --> type "TM" (level2) --> save file Thank you very much! Sincerely, Ye On Thu, Aug 8, 2013 at 4:22 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>>> wrote: How did you create the levels file? Eg, did you use a windows computer? Or did you use msword or some other word processor. If not, can you send the levels file? On 08/08/2013 03:49 PM, ye tian wrote: > Dear freesurfers, > > I am experimenting qdec with one of my discrete variables. Besides > qdec.table.dat file, I do have a .levels file with the two levels of > the variable (say level1 and level2). However, I keep getting the > following error message: > > Reading discrete factor levels from config file > /$SUBJECTS_DIR/qdec/meditation.levels > level1 > done. > ERROR: /$SUBJECTS_DIR/qdec/meditation.levels is invalid. Must have at > least two levels. > Error loading the data table. > > Is there something that I have missed in the declaration of the variable? > > Thank you very much! > > Sincerely, > Ye > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@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<mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358<tel:617-724-2358> <tel:617-724-2358<tel:617-724-2358>> Fax: 617-726-7422<tel:617-726-7422> <tel:617-726-7422<tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358<tel:617-724-2358> Fax: 617-726-7422<tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Segmentation edits
by krista kelly 09 Sep '13

09 Sep '13

Hi all, I am doing cortical thickness and surface area analyses and had a few questions regarding editing the borders. 1) Is it reasonable to edit every (big and small) error that I find? Basically, how much a difference would it make in terms of the surface area and cortical thickness values if I did not edit the smaller errors? 2) If the skull hasn't been completely stripped, but is not designated as either white or gray matter, do I need to adjust the thresholding for extracting the brain and re-extract? The only situation in which I feel this would be a problem is when doing whole brain analyses. 3) Would it make a difference to the data if I initially ran recon-all using freesurfer version 5.0 and then, after editing the segmentations/labels/skullstripping, reran autorecon 2,or 3 using freesurfer version 5.1? If anyone could answer any or all of these questions that would be great! Krista

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Tkmed in VirtualBox and wm parcelation
by Martin Kavec 09 Sep '13

09 Sep '13

Hi all, I have two questions: 1. Does tkmedit, or freeview work under VirtualBox 2. Is it possible to parcelate white matter in freesurfer? Thanks, Martin Sent from my iPad

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Cortical labels for WM seeding
by Sean Hatton 09 Sep '13

09 Sep '13

Hello FS Gurus, I would like to export FS labels as seed regions for deterministic tractography in TrackVis (probabilistic is not appropriate in this investigation). I run mri_label2vol with “--proj abs -4 0 .1” to try and grow the label into the WM and exclude GM. While I get a biologically plausible ROIs and plenty of good streamlines, I do get some stray streamlines that jump across the sulci into adjacent gyri which (I have read) is an artefact of seeding from GM. Have I got the right approach? Should I create an inverse intracranial volume mask as an exclusion mask? Something else? Kind regards, Sean Hatton Brain & Mind Research Institute University of Sydney, Australia.

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cluster threshold
by Yang, Daniel 09 Sep '13

09 Sep '13

Hi FreeSurfer Experts, On this page (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons) it says: "In particular, thresholds of 1.3, 2, 2.3, 3, 3.3 and 4, corresponding to p-values of 0.05, 0.01, 0.005, 0.001, 0.0005 and 0.0001, which are common thresholds." I am wondering how these thresholds were computed. In my own computation, I found z-value to be the following, but neither one-sided nor two-sided matches the thresholds of 1.3, …, 4 as shown above? one-sided: p-value=0.0500, z-value=1.6 p-value=0.0100, z-value=2.3 p-value=0.0050, z-value=2.6 p-value=0.0010, z-value=3.1 p-value=0.0005, z-value=3.3 p-value=0.0001, z-value=3.7 two-sided: p-value=0.0500, z-value=2.0 p-value=0.0100, z-value=2.6 p-value=0.0050, z-value=2.8 p-value=0.0010, z-value=3.3 p-value=0.0005, z-value=3.5 p-value=0.0001, z-value=3.9 Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

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Re: [Freesurfer] apply fnirt transformation on a surface
by Shani Ben Amitay 09 Sep '13

09 Sep '13

Sorry to bug again with this issue when converting the freesurfer surface to GIFTI using mris_convert the surface is shifted in space. Does anyone know how to transform it to freesurfer space? Thanks! Shani On Tue, Sep 3, 2013 at 12:34 PM, Saad Jbabdi <saad(a)fmrib.ox.ac.uk> wrote: > You need to convert your surface file into a format that workbench > understand (GIFTI): > > mris_convert lh.whiteinraw lh.whiteinraw.surf.gii > > Cheers > Saad > > > On 3 Sep 2013, at 10:57, Shani Ben Amitay <shani.holzer(a)gmail.com> wrote: > > Thank you! > Still somehow I haven't manage to make it work when I ran the suggested > command I get an error saying : > ERROR, Command Failed: Parse Error while reading lh.whiteinraw: error > occurred while parsing element line number: 1 column number: 1. > Any advise? > > Thanks again > > Shani > > > > On Mon, Sep 2, 2013 at 10:18 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > >> thanks Matt >> Bruce >> On Mon, 2 Sep 2013, Glasser, Matthew wrote: >> >> > Hi Bruce, >> > >> > Connectome Workbench commandline utilities can do this with FSL warp >> > fields: >> > >> > wb_command -surface-apply-warpfield >> > >> > One needs to use the inverse warp as the <warpfield> argument and the >> > forward warp as the -fnirt <forward-warp>. >> > >> > Peace, >> > >> > Matt. >> > >> > On 9/2/13 11:19 AM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: >> > >> >> A veritable game of telephone! Thanks Jesper. Matt? >> >> >> >> On Mon, 2 Sep 2013, Jesper Andersson wrote: >> >> >> >>> Hi guys, >> >>> I didn't think we had any tools for doing that, and said so much on >> the >> >>> FSL >> >>> mailbase. But apparently the WashU people has something that does just >> >>> that >> >>> for you. I think the best person to contact about the details is Matt >> >>> Glasser. >> >>> >> >>> J >> >>> >> >>> On 2 Sep 2013, at 15:58, Saad Jbabdi <saad(a)FMRIB.OX.AC.UK> >> >>> wrote: >> >>> >> >>> Hi In Probtrackx, this is done internally. >> >>> If you just want to transform the vertex coordinates, then I think >> >>> you'll need to play with the FNIRT source code - I've CC'd Jesper who >> >>> knows better. >> >>> >> >>> Cheers, >> >>> Saad >> >>> >> >>> >> >>> >> >>> On 2 Sep 2013, at 15:56, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> >>> wrote: >> >>> >> >>> you might check on the FSL list. I think I've seen some >> >>> traffic indicating that there are some tools for doing >> >>> this. I'l cc Saad as he might know >> >>> >> >>> cheers >> >>> Bruce >> >>> >> >>> >> >>> On Mon, 2 Sep 2013, Douglas Greve wrote: >> >>> >> >>> Hi Shani, I don't think you can apply a FNIRT >> >>> transform to a surface. >> >>> doug >> >>> On 9/2/13 8:20 AM, Shani Ben Amitay wrote: >> >>> Dear freesurfer people, >> >>> Any idea whether I can apply transformation >> >>> that was calculated by fsl >> >>> fnirt on the white/pial surfaces calculated >> >>> using the freesurfer >> >>> stream? >> >>> Thanks! >> >>> Shani >> >>> _______________________________________________ >> >>> Freesurfer mailing list >> >>> Freesurfer(a)nmr.mgh.harvard.edu >> >>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>> >> >>> >> >>> >> >>> The information in this e-mail is intended only for the >> >>> person to whom it is >> >>> addressed. If you believe this e-mail was sent to you in >> >>> error and the e-mail >> >>> contains patient information, please contact the Partners >> >>> Compliance HelpLine at >> >>> http://www.partners.org/complianceline . If the e-mail was >> >>> sent to you in error >> >>> but does not contain patient information, please contact >> >>> the sender and properly >> >>> dispose of the e-mail. >> >>> >> >>> >> >>> >> >>> -- >> >>> Saad Jbabdi >> >>> University of Oxford, FMRIB Centre >> >>> >> >>> JR Hospital, Headington, OX3 9DU, UK >> >>> (+44)1865-222466 (fax 717) >> >>> www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi >> >>> >> >>> >> >>> >> > >> > >> > ________________________________ >> > The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. If you >> are not the intended recipient, be advised that any unauthorized use, >> disclosure, copying or the taking of any action in reliance on the contents >> of this information is strictly prohibited. If you have received this email >> in error, please immediately notify the sender via telephone or return mail. >> > >> > >> > >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > > -- > Saad Jbabdi > University of Oxford, FMRIB Centre > > JR Hospital, Headington, OX3 9DU, UK > (+44)1865-222466 (fax 717) > www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi > >

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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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