Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

undo pial edits only
by Torsten Ruest 04 Oct '11

04 Oct '11

Hi there, I think there is an option to remove all edits that have been incorporated using recon2 -clean. Is there a chance that I can selectively undo all incorporated pial edits (ie that have been incorporated by running "recon-all -subject TEST -autorecon2 > TEST-2.log")? Thanks very much in advance, Torsten

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Automatic correct of mislabeling around ctx- lateral orbital?
by Knut J Bjuland 04 Oct '11

04 Oct '11

Hi I have processed several subjects using recon-all. However there is problem with non-brain matter being labels as cortex around the eye ball. Are there any automatically methods to correct mislabeling of eye socket as cortex? I am having problem with mislabeling in ctx-lh-lateral orbital and ctx-rh-lateralorbital. Can I issue add any options to the recon-all? Cheers Knut J

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Re: [Freesurfer] Tool for filling
by Ed Gronenschild 04 Oct '11

04 Oct '11

Hi Bruce, I've grabbed the dev version freesurfer-Darwin-leopard-i686-dev.tar.gz (date 2 Oct 2011, 13:10) at ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ and tried mri_morphology <input vol> fill_holes 26 <output vol> but got the message that the operation "fill_holes" is not supported. Ed

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convert aparc+aseg.mgz to mni305
by Timothy Vickery 03 Oct '11

03 Oct '11

Hi, I'd like to convert a subject's aparc+aseg.mgz to mni305 (2mm) space. So, I ran the following commands (FS 5.1): (from subject's mri directory) mri_vol2vol --mov orig.mgz --tal --s $SUBNAME --o orig.mni2mm.mgz mri_label2vol --seg aparc+aseg.mgz --o aparc+aseg.mni2mm.nii.gz --reg orig.mni2mm.mgz.reg --temp orig.mni2mm.mgz The volume orig.mni2mm.mgz looks totally fine, but the aparc+aseg.mni2mm.mgz is way off -- it is shifted anterior and superior relative to the orig volume. I double-checked orig.mgz and aparc+aseg.mgz, they are totally fine and line up. I also tried this: mri_label2vol --seg aparc+aseg.mgz --o aparc+aseg.mni2mm.nii.gz --regheader orig.mgz --temp orig.mni2mm.mgz This also did not work. Can anyone point out my error? Thanks in advance, Tim

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reg-feat2anat: major failure
by Michelle Umali 03 Oct '11

03 Oct '11

Hi Freesurfers, I've run reg-feat2anat to register my FSL FEAT data to the freesurfer anatomical data. And for most subjects the registration needs a little manual editing (which sometimes includes stretching). But for a few subjects, registration is terrible, e.g. coronal is switched with horizontal or orig surfaces are completely off the FEAT brain. So I looked into my original FEAT directory and FSL's registration between example_func to standard looked fine, but example_func to highres failed. Is there a way to use Freesurfer to register example_func to high res for use in a FEAT analysis so that later reg-feat2anat works? Thanks. Michelle

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strange freeview issue
by Satrajit Ghosh 03 Oct '11

03 Oct '11

hi, we are seeing a strange freeview issue at mit and just wanted to check if anybody else has seen this. we are running natty narwhal (ubuntu 11.04). details here: https://github.com/gablab/mindhive/issues/1 cheers, satra

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Re: [Freesurfer] Dimension Mismatch Error
by Michelle Umali 03 Oct '11

03 Oct '11

Hi Doug, I've attached the mri_info output on the eccen and polar images as well as the mris_info on the lh.sphere surface Thanks. Michelle On Mon, Oct 3, 2011 at 2:38 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu>wrote: > Can you send me the result of running mri_info on > eccen/real.nii > eccen/imag.nii > polar/real.nii > polar/imag.nii > in the /usr/local/freesurfer/**subjects/retinotopy/sj12/bold/**rtopy.self.lh > directory? > > And the result of > mris_info /usr/local/freesurfer/**subjects/retinotopy/sj12/surf/** > lh.sphere > > doug > > > > > > Michelle Umali wrote: > >> Hi Doug, >> I've attached the output from running fieldsign-sess. >> >> Thanks for all your help. >> Michelle >> >> On Mon, Oct 3, 2011 at 12:59 PM, Douglas N Greve < >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu>>> >> wrote: >> >> Michelle, before you do that, can you run the offending program >> with -debug and send me the (copious) terminal output? Your anat >> should not have to be re-run. >> >> doug >> >> Michelle Umali wrote: >> >> Hi Bruce, >> Will this undo my wm and pial edits? >> >> Thanks. >> Michelle >> >> On Sat, Oct 1, 2011 at 3:37 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu >> <mailto:fischl@nmr.mgh.**harvard.edu <fischl(a)nmr.mgh.harvard.edu>> >> <mailto:fischl@nmr.mgh.**harvard.edu <fischl(a)nmr.mgh.harvard.edu> >> >> <mailto:fischl@nmr.mgh.**harvard.edu <fischl(a)nmr.mgh.harvard.edu>>>> >> wrote: >> >> try running >> >> >> recon-all -s subject -make all >> >> and leave the -dontrun off. It should bring everything up >> to date >> >> Bruce >> >> >> >> On Sat, 1 Oct 2011, Michelle Umali wrote: >> >> Dear Freesurfers, >> I'm still getting a MRISripZeros() and MRIScopyMRI Surf/src >> mismatch error >> when running fieldsign-sess. You suggested that this >> problem >> was due to the >> surfaces being out of synch. When I ran recon-all -s >> subject >> -make all >> -dontrun, I saw that several steps had not run. The data >> looked alright and >> the number of vertices matched when I ran -vno-check. >> >> The mismatch error is still occurring, and I don't know >> how to >> proceed. >> >> Please suggest steps that I should take. >> >> Thanks. >> Michelle >> >> >> >> >> >> 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<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 >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<greve(a)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> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: 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<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> >> >> >> ------------------------------**------------------------------** >> ------------ >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >

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Parallelization
by Spencer Boucher 03 Oct '11

03 Oct '11

New to Freesurfer here, but I was wondering if there is any viability to the idea of parallelizing freesurfer for running on multiple servers so as to reduce the time required to run recon-all on a single subject. Is there an aspect of the algorithm that makes this inherently infeasible? Spencer

4 3

paper related to subcortical volume in children...
by Gonzalo Rojas Costa 03 Oct '11

03 Oct '11

Hi: There exist any paper related to the subcortical volume in children (below 15 years old)?... any image database ?... Sincerely, Gonzalo Rojas Costa

1 0

Optseq2 tnullmin
by Anita Cservenka 03 Oct '11

03 Oct '11

Hi everyone, I'm using optseq2 and a tnullmin of 2 seconds to force 2 seconds between each event for my paradigm, but I get a "segmentation fault" error. Here's my command line below. I didn't specify a tnullmax, so that I would avoid any errors by specifying both. I tried other values for tnullmin like 1, which did work and 1.5, which also did not work. Ideally, the paradigm I would like to model listed in a paper that fixation was jittered 2-10 seconds between stimuli, but 2 seconds does not work for me. Do you know why this might be? Thanks. optseq2 --nsearch 1000 --nkeep 2 --pctupdate 10 --ntp 86 --tr 2 --psdwin 0 12 0.5 --ev emotion 0.5 60 --ev calm 0.5 26 --tnullmin 2 --cost eff --o emotion INFO: Setting srand48() seed to 345330 optseq2 $Id: optseq2.c,v 2.21.2.1 2011/04/21 19:50:06 greve Exp $ NoSearch = 0 nSearch = 1000 nKeep = 2 PctUpdate = 10.000000 nCB1Opt = 0 seed = 345330 Ntp = 86 TR = 2 TPreScan = 0 PSD Window = 0 12 0.5 nEvTypes = 2 EvNo Label Duration nRepsNom 1 emotion 0.500 60 2 calm 0.500 26 PctVarEvReps = 0 VarEvRepsPerCond = 0 PolyOrder = -1 tNullMax = -1 tNullMin = 2 outstem = emotion AR1 = 0 No refractory penalty Cost = eff OutStem = emotion Summary File = emotion.sum nTaskAvgs = 48 INFO: LogFile is emotion.log outstem = emotion Segmentation fault -Anita

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Freesurfer