Freesurfer January 2012

freesurfer@nmr.mgh.harvard.edu

97 participants
171 discussions

Re-generating spherical surfaces...
by Rudolph Pienaar 20 Jan '12

20 Jan '12

Hi all -- If I make changes to a subject's ?h.smoothwm, how do I re-generate the ?h.sphere surfaces? I'd like to reduce the number of mesh vertices using 'mris_decimate' on a given hemisphere, and then (re)generate a corresponding spherical surface. Thanks -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA

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MD, DO, or MD/PhD fellowship in epilepsy, brain connectomics, and cognitive neuroscience
by David Groppe 19 Jan '12

19 Jan '12

Fellowship available for work on epilepsy, brain connectomics, and cognitive neuroscience with the Comprehensive Epilepsy Center of the North Shore-LIJ Health System, NY, USA. This unique fellowship will fund an MD, DO, or MD/PhD to serve as a clinical fellow treating epilepsy patients under the mentorship of a team of experienced epileptologists and to engage in research using neuroimaging and electrophysiology to improve the diagnosis of epilepsy and to further the basic science of human brain function. More specifically, ongoing research projects include: (1) Validation of task-based and resting state fMRI and DTI measures of brain connectivity using electrical stimulation mapping and ECoG (2) Identifying areas of seizure genesis and spread using network analysis of fMRI and ECoG dynamics (3) Investigation of the neuronal dynamics underlying selective attention, language comprehension, visual object identification and auditory stream analysis. For a more detailed description about the lab and representative publications see: http://www.feinsteininstitute.org/Feinstein/Laboratory+for+Multimodal+Human… Candidates should meet the following qualifications: 1) M.D., D.O., or an M.D./Ph.D. degree, 2) Have graduated from or be currently enrolled in a New York state medical school, residency training program or fellowship. 3) Have some background in fMRI, electrophysiology, and/or data analysis using one or more of the following software packages: Matlab, FreeSurfer, FSL, AFNI This is a great opportunity for a physician-scientist to develop both as a clinician and researcher. An ideal candidate would be a neurologist, neurosurgeon or neuroradiologist with an interest in epilepsy, functional neurosurgery or functional brain mapping. This fellowship is part of the New York State ECRIP program, which offers a competitive salary and an opportunity to supplement income with clinical work. Please submit CV and short statement of interest to Dr. Ashesh Mehta at amehta(a)nshs.edu for more information. -- David Groppe, Ph.D. Postdoctoral Researcher North Shore LIJ Health System New Hyde Park, New York http://www.cogsci.ucsd.edu/~dgroppe/

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Pial extension into cerebellum
by Mahinda Yogarajah 19 Jan '12

19 Jan '12

Apologies for the repost - this may have got lost in the mail blackout ... Dear Freesurfer Experts, I have read the advice on the wiki regarding what to do when pial surfaces extend into the cerebellum. I had a few questions to clairfy things: 1) If I have made other (non-cerebellar) edits to the brainmask.mgz, and added control points can I simply do cp brainmask.mgz brain.finalsurfs.manedit.mgz edit the cerebellum voxels out on the brain.finalsurfs.manedit.mgz run recon-all -autorecon2-cp -autorecon3 -subjid name Will this then apply non-cerebellar and cerebellar edits (as well as control points) and give appropriate segmentations ? OR Do I have to make non-cerbellar edits to brainmask.mgz cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz make cerebellar edits to brain.finalsurfs.manedit.mgz run recon-all -autorecon2-cp -autorecon3 -subjid name Thanks.

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Tkmedit crashes when switching main volume
by Vy Dinh 19 Jan '12

19 Jan '12

Dear forum, Has anyone else come across this issue and resolved it? If I try to switch the main volume (after editing the vol), Tkmedit crashes with the following error message: % Bus error It happens no matter what image I select and only when I try to load a new main volume (not aux volume). I also save the main (edited) volume prior to loading a new image, so I don't know if that has any effect on tkmedit. Either way, the edited volumes have to be saved. I am currently using Freesurfer 5.1 but noticed that this also happened with the 5.0 version. Best, Vy Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh(a)rush.edu<mailto:Vy_dinh@rush.edu>

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-notalairach problem
by LAOUCHEDI MAKHLOUF 19 Jan '12

19 Jan '12

hi i have run freesurfer using -notalairach flag and i had the following message : mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 ERROR: cannot find transforms/talairach.xfm can anyone know why is it searching the transforms/talairach.xfm when we run without talairach, thanks

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Re: [Freesurfer] Freesurfer flips brains?
by Léoné, F.T.M. (Frank) 19 Jan '12

19 Jan '12

Hi Doug, Ah, I found the cause myself, which might be useful for others. It happens already in the first step, before the ones I listed: in mri_convert. I do: mri_convert struct.nii 001.mgz And it flips. This I can see because I converted the mgz back (mri_convert 001.mgz orig.nii) and then it's indeed reversed (and shifted, rotated, all rigid body transformations one can think of). Why does this happen? Is it normal for nii-files? I see that I can specify the orientation in mri_convert by doing mri_convert -in_orientation and then a three letter specification. I chose PSR and now the changes are far less severe (only a small shift still) and most importantly: no flip anymore. Do I now need to reconvert my all my surfaces? I don't hope, but I'm at least glad I have this one fixed. best, Frank ----- "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> schreef: > Van: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> > Aan: "Frank Leoné" <f.leone(a)donders.ru.nl> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Verzonden: Woensdag 18 januari 2012 18:34:31 > Onderwerp: Re: [Freesurfer] Freesurfer flips brains? > > Hi Frank, we'll need a lot more detail. Are you doing all of this in > FreeSurfer? What are your command lines? How are you evaluating > whether > volumes are flipped? > doug > > Léoné wrote: > > Dear all, > > > > I must be missing something really obvious, but it seems my brains > are flipped. What I do: > > > > - I have a highres structural scan, nii file format > > - I convert it to a surface using recon-all > > - Coregister the highres structural to the functional scan, so it is > in the voxel size and orientation as the functional scans > > - I try to bbregister the coregistered and resliced T1 with the > surface > > > > But then: hey, it doesn't fit, my low-res T1 is flipped compared to > my y surface, hence to my original T1. So is it indeed true that my T1 > might have been flipped? If so, does it make a wrong assumption on > neurological vs radiological convention, or what is going on? > > > > Thanks in advance, > > > > best, > > > > Frank > > _______________________________________________ > > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > 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.

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question about annot files and principal curvatures
by Peter Savadjiev 19 Jan '12

19 Jan '12

Hi, In order to obtain the vertices of lh.curv that belong to a specific freesurfer cortical ROI, such as 'superiortemporal', or 'superiorfrontal', etc., I use the information in lh.aparc.annot, as described for example in http://surfer.mnr.mgh.harvard.edu/fswiki/AnnotFiles/ . However, now I am interested in looking at the principal curvatures in the same cortical ROI. To obtain the principal curvatures, I use mris_curvature -max $SUBJECTS_DIR/caseXYZ/surf/lh.<some_surface> and mris_curvature -min $SUBJECTS_DIR/caseXYZ/surf/lh.<some_surface> My question is, which surface should I use in <some_surface> so that I can still identify the vertices of interest using lh.aparc.annot? In other words, how do I ensure that the output of the mris_curvature command has the surface vertices stored in the same order as lh.curv? Any help will be much appreciated! Thanks, Peter

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Re: [Freesurfer] Fw : Re: get_4dfp_dimoe problem
by LAOUCHEDI MAKHLOUF 19 Jan '12

19 Jan '12

hi everyone i want just to inform you that it is ok with my problem of the huge pathnames generated by our cluster thank you very much --- En date de : Sam 7.1.12, Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> a écrit : De: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> Objet: Re: [Freesurfer] Fw : Re: get_4dfp_dimoe problem À: "LAOUCHEDI MAKHLOUF" <laoumakhl(a)yahoo.fr> Cc: Freesurfer(a)nmr.mgh.harvard.edu Date: Samedi 7 janvier 2012, 21h28 laouchedi, the file 'endianio.c' is not a module that can be installed by the end-user. it is source code. did you install the files that i referred to in my prior email to the list? those were rebuilt using endianio.c, and are found here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86… and are named *4dfp. copy those files to your $FREESURFER_HOME/bin. n. On Fri, 2012-01-06 at 14:29 +0000, LAOUCHEDI MAKHLOUF wrote: > > > --- En date de : Ven 6.1.12, LAOUCHEDI MAKHLOUF <laoumakhl(a)yahoo.fr> a > écrit : > > De: LAOUCHEDI MAKHLOUF <laoumakhl(a)yahoo.fr> > Objet: Re: [Freesurfer] get_4dfp_dimoe problem > À: "AviSnyder" <avi(a)npg.wustl.edu> > Date: Vendredi 6 janvier 2012, 15h28 > > hi everyone > i just remind you of my problem of the file > name which was too long on our cloud; you advised us to > download the endianio.c module, we did this and we installed > it then we've run recon-all but we still have an error > message : > > $Id: imgreg_4dfp.c,v 1.4 2010/02/27 01:41:53 nicks Exp $ > Getifh: /var/spool/pbs/tmpdir/171598.gridgate.scg.nuigalway.ie/https_3a_2f_2falbalonga.cnaf.infn.it_3a9000_2ff_5f9HZFcSVMqQu-a5r7O6fQ/ws28210/.tmp/d924f86d-ff81-451c-9d0b-f655f3361f66/systemExecTask5971557784595886118/freesurfer/average/711-2B_as_mni_average_305_mnone.4dfp.ifh read error, imgfile='/var/spool/pbs/tmpdir/171598.gridgate.scg.nuigalway.ie/https_3a_2f_2falbalonga.cnaf.infn.it_3a9000_2ff_5f9HZFcSVMqQu-a5r7O6fQ/ws28210/.tmp/d924f86d-ff81-451c-9d0b-f655f3361f66/systemExecTask5971557784595886118/freesurfer/average/711-2B_as_mni_average_305_mnone.4dfp.img' > Segmentation fault > ERROR: > 'imgreg_4dfp /var/spool/pbs/tmpdir/171598.gridgate.scg.nuigalway.ie/https_3a_2f_2falbalonga.cnaf.infn.it_3a9000_2ff_5f9HZFcSVMqQu-a5r7O6fQ/ws28210/.tmp/d924f86d-ff81-451c-9d0b-f655f3361f66/systemExecTask5971557784595886118/freesurfer/average/711-2C_as_mni_average_305 /var/spool/pbs/tmpdir/171598.gridgate.scg.nuigalway.ie/https_3a_2f_2falbalonga.cnaf.infn.it_3a9000_2ff_5f9HZFcSVMqQu-a5r7O6fQ/ws28210/.tmp/d924f86d-ff81-451c-9d0b-f655f3361f66/systemExecTask5971557784595886118/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 4355' failed! status=139 > ERROR: mpr2mni305 execution aborted > > i've attached the recon-all.log contained in the scripts dir > and the log file contained in mri/transforms dir > > > thank you very much > > > > --- En date de : Mer 4.1.12, Snyder, Avi <avi(a)npg.wustl.edu> a > écrit : > > De: Snyder, Avi <avi(a)npg.wustl.edu> > Objet: Re: [Freesurfer] get_4dfp_dimoe problem > À: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> > Cc: "LAOUCHEDI MAKHLOUF" <laoumakhl(a)yahoo.fr>, > "Freesurfer(a)nmr.mgh.harvard.edu" > <Freesurfer(a)nmr.mgh.harvard.edu> > Date: Mercredi 4 janvier 2012, 1h31 > > I don't think there are any special env variables. > It may be that the environment in which FreeSurfer is > being run simply > generates huge pathnames. > A few months ago I revised the module containing > get_4dfp_dimoe() to > double the size of filename buffers. > This module (endianio.c) is attached. Theoretically, > compiling with this > revised source could fix the problem. > > Avi > ----------------------------- > On 1/3/12 6:04 PM, "Bruce Fischl" > <fischl(a)nmr.mgh.harvard.edu> wrote: > > >Hi Avi > > > >just running recon-all I think. Is there an env > variable you use to > >specify > >a tmp dir or something? > > > >thanks > >Bruce > > > >On Tue, 3 Jan 2012, Snyder, Avi wrote: > > > >> It looks like both the command (imgreg_4dfp) and > argument > >> (.../711-2B_as_mni_average_305_mask.4dfp.img) > fields are garbled. > >> Evidently, operating system paths have not been > correctly set. > >> The 4dfp suite of tools is available and probably > could be installed but > >> I'm not sure that is what is wanted. > >> I don't understand what LAOUCHEDI MAKHLOUF is > trying to do. > >> > >> AZS > >> > ----------------------------------------------------- > >> On 1/3/12 10:40 AM, "Bruce Fischl" > <fischl(a)nmr.mgh.harvard.edu> wrote: > >> > >>> this is actually not part of FreeSurfer proper, > but rather something > >>>that > >>> Avi Synder (ccd) was kind enough to contribute. > Avi: can you comment? > >>> > >>> thanks > >>> Bruce > >>> On > >>> Tue, 3 Jan 2012, LAOUCHEDI MAKHLOUF wrote: > >>> > >>>> hi everyone > >>>> we run recon-all on a cloud and we obtained this > error: > >>>> > >>>> mpr2mni305 failed, see > transforms/talairach_avi.log > >>>> > >>>> The log says the file name is too long perhaps > because of the tmp dir > >>>> file > >>>> names: > >>>> > >>>> > >>>> > >>>>get_4dfp_dimoe:/var/spool/pbs/tmpdir/169536.gridgate.scg.nuigalway.ie/h > >>>>tt > >>>> ps_3a_2f_2fwms01. > >>>> > >>>> > >>>>ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws15158/.tmp/8d3aa62d-5994-4 > >>>>7e > >>>> 5- > >>>> > >>>> > >>>>ba6d-031806ec9ffb/systemExecTask8201883777111446775/freesurfer/average/ > >>>>71 > >>>> 1- > >>>> 2B_as_mni_average_305_mask.4dfp.img filename too > long > >>>> ERROR: > >>>> > >>>>'imgreg_4dfp/var/spool/pbs/tmpdir/169536.gridgate.scg.nuigalway.ie/http > >>>>s_ > >>>> 3a_2f_2fwms01. > >>>> > >>>> > >>>>ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws15158/.tmp/8d3aa62d-5994-4 > >>>>7e > >>>> 5- > >>>> > >>>> > >>>>ba6d-031806ec9ffb/systemExecTask8201883777111446775/freesurfer/average/ > >>>>71 > >>>> 1- > >>>> 2C_as_mni_average_305 > >>>> /var/spool/pbs/tmpdir/169536.gridgate.scg.nuigalway.i > >>>> > >>>> > >>>>e/https_3a_2f_2fwms01.ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws1515 > >>>>8/ > >>>> .t > >>>> > >>>> > >>>>mp/8d3aa62d-5994-47e5-ba6d-031806ec9ffb/systemExecTask82018837771114467 > >>>>75 > >>>> /f > >>>> > reesurfer/average/711-2B_as_mni_average_305_masktalsrcimg_g11 none > >>>> talsrcimg_to_711-2C_as_mni_average_305_t4 4355' > failed! status=255 > >>>> > >>>> > >>>> knowing that it is difficult for us to do things > differently (to > >>>>change > >>>> the > >>>> path); is it possible to do something in > freesurfer to work with > >>>>thesse > >>>> filenames ? > >>>> > >>>> thanks for your help > >> > >> > >> > >> > > > > > >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. > > > > > _______________________________________________ > 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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Re: [Freesurfer] Freesurfer Digest, Vol 75, Issue 15
by Sebastian Moeller 19 Jan '12

19 Jan '12

Hi Fred, yu probably checked the following already, but on the off chance you have not... Maybe you have set X11 to 256 color mode? Start X11.app (from /Applications/Utilities) go to the X11 menu, select Preferences..., switch to the tab called output and see what is selected for Colors. If it is set to 256 Colors you have your root cause, just switch to something higher and all should be fine. best Sebastian On May 9, 2010, at 9:00 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. tksurfer/tkmedit display color fix in OSX 10.6? (Fred Dick) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 9 May 2010 15:34:35 +0100 > From: Fred Dick <fdick(a)crl.ucsd.edu> > Subject: [Freesurfer] tksurfer/tkmedit display color fix in OSX 10.6? > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <873B33F2-3339-4871-9395-1EFEEC1EFAAB(a)crl.ucsd.edu> > Content-Type: text/plain; charset="us-ascii" > > Dear all > > This is a pretty minor issue (except for figure making) - but has anyone experienced and then fixed a display problem in tksurfer/tkmedit in OSX 10.6 (possibly also 10.5) where graphics seem to be drawn only with 256 colors, thereby giving images a kind of contour-plot look? (See attached image below). [Running 10.6.3, i686-apple-darwin10-gcc-4.2.1, tksurfer 1.309 (yes, older), tkmedit v 1.330] > > I looked around the mail archives but didn't see anyone else commenting on this, but do know someone else having the same issue, so would be happy for any suggestions. > > Thanks, > Fred > > >

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Re: [Freesurfer] Freesurfer flips brains?
by Léoné, F.T.M. (Frank) 19 Jan '12

19 Jan '12

Hi Douglas, Ah, makes sense, sorry for that. I do most of the work in SPM, so: - I have a highres structural scan, nii file format - I convert it to a surface using recon-all - Coregister the highres structural to the functional scan, so it is in the voxel size and orientation as the functional scans (SPM) - I try to bbregister the coregistered and resliced T1 with the surface using something like: bbregister --s S7_FS --mov ~/Data/Exp1_Saccades_phase/S7_FS/mri/orig/flipped_rmasked_str_S2_seler20090508.nii --init-spm --reg ~/Data/Exp1_Saccades_phase/S7_FS/mri/orig/register.partial.auto.dat --t1 and view it with vglrun tkregister2 --mov /home/action/fraleo/Data/Exp1_Saccades_phase/S7_FS/mri/orig/flipped_rmasked_str_S2_seler20090508.nii --reg /home/action/fraleo/Data/Exp1_Saccades_phase/S7_FS/mri/orig/register.partial.auto.dat --surf Here you see that I already use a flipped structural scan. If I do it like this, bbregister converges to a nice and correct solution (everything aligns). If I don't, tkregister2 showms unregistered struc and func, while it is obvious it would be roughly aligned if you would flip either of them. In addition/in general: What would be the recommended way to do the coregistration etc. if you do all you analyses in SPM? Would it for example be better to coregistrate and reslice all functionals with the structural, so they are automatically aligned with the surface? Now I have a structural which is coregistered with the funcional and I realign that one, but that makes for one extra step where it can go wrong. Don't think this is related to the flip, but I also have a few alignment problems for other subjects. Thanks a lot in advance, best, Frank ----- "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> schreef: > Van: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> > Aan: "Frank Leoné" <f.leone(a)donders.ru.nl> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Verzonden: Woensdag 18 januari 2012 18:34:31 > Onderwerp: Re: [Freesurfer] Freesurfer flips brains? > > Hi Frank, we'll need a lot more detail. Are you doing all of this in > FreeSurfer? What are your command lines? How are you evaluating > whether > volumes are flipped? > doug > > Léoné wrote: > > Dear all, > > > > I must be missing something really obvious, but it seems my brains > are flipped. What I do: > > > > - I have a highres structural scan, nii file format > > - I convert it to a surface using recon-all > > - Coregister the highres structural to the functional scan, so it is > in the voxel size and orientation as the functional scans > > - I try to bbregister the coregistered and resliced T1 with the > surface > > > > But then: hey, it doesn't fit, my low-res T1 is flipped compared to > my y surface, hence to my original T1. So is it indeed true that my T1 > might have been flipped? If so, does it make a wrong assumption on > neurological vs radiological convention, or what is going on? > > > > Thanks in advance, > > > > best, > > > > Frank > > _______________________________________________ > > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > 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.

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Freesurfer January 2012