Freesurfer October 2011

freesurfer@nmr.mgh.harvard.edu

95 participants
160 discussions

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

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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

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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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Trac-all dyld load error mac os 10.5 darwin
by Lena Palaniyappan 03 Oct '11

03 Oct '11

Dear Anastasia & Team I am running trac-all on 5.1 but my recons were processed using 4.5. I am on 10.5.8 Darwin MAcOSX I am getting the following error when @ Priors Trace/BPT trap dyld: unknown required load command 0x80000022 This error is shown right at the start of the trac-all too, but the script exits when priors are being drawn. Can you help please? I downloaded the most stable version last week. (could it still be the library dependency eror?) Cheers Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Wellcome Training Fellow | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH Ph: 0115 82 30407 This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Dimension Mismatch Error
by Michelle Umali 03 Oct '11

03 Oct '11

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

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corpus callosum segmentation
by carolina.mr 02 Oct '11

02 Oct '11

2 1

tracula bvecs bvals error
by Joana Braga Pereira 01 Oct '11

01 Oct '11

Dear Freesurfers, I'm pre-processing my DTI data with Tracula and i found the following error while running trac-all -prep -c dmrirc_H_P01: dtifit -k /home/joana/FIU/H_P01/dmri/dwi.nii.gz -m /home/joana/FIU/H_P01/dlabel/diff/aparc+aseg_mask.flt.nii.gz -r /home/joana/FIU/H_P01/dmri/bvecs -b /home/joana/FIU/H_P01/dmri/bvals -o /home/joana/FIU/H_P01/dmri/dtifit *Error: bvecs and bvals don't have the same number of entries* Linux ub029113 2.6.18-164.11.1.el5 #1 SMP Wed Jan 6 13:26:04 EST 2010 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS Although i saw a previous email reporting the same problem i wasn't able to solve it following that email's instructions... I think there is something wrong with my bvec file since dmri/bvecs.txt only contains zeros. I've tried changing bvec.txt columns to three decimals and then to 1, -1 and 0 but nothing seems to work. I've attached my bvals and bvecs files. Does anyone have any idea why this is happening? Many thanks to you all! Joana

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structure volume dti_recon vs recon_all
by Adil Javed 01 Oct '11

01 Oct '11

Hi, After running dti_recon and recon_all, I noticed that they produce different volumes of various structures for the same brain. Just trying to understand why that is? best, AJ

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Freesurfer October 2011