Hi Doug, Just checking up on the error below.
______________________________ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana [aaf...@mgh.harvard.edu] Sent: Monday, November 16, 2015 2:14 PM To: Freesurfer support list Subject: Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR Yeah sorry, I was rerunning the preproc. Should be there now. ______________________________ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, November 16, 2015 12:48 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR When I look in hc016/msit/001/ I only see: cfg.txt f.nii mag.dat mag.nii phase.dat phase.nii Have you deleted the previous analysis? On 11/16/2015 11:41 AM, Afzal, Afsana wrote: > Hi Doug, > > Command: selxavg3-sess -s hc016 -analysis > msit.analysis.sm04.b0dc.mni305 -force > Folder: /autofs/space/lilli_002/users/DARPA-FAST > $SUBJECTS_DIR: /autofs/space/lilli_001/users/DARPA-MEG/freesurfs > > The problem might actually lie with preprocessing. > > Just looking at file sizes, the fmcpr.sm4.mni305.2mm.b0dc.nii.gz file > size for hc016 is 471kb, but it's ~46mb for other subjects. The lh and > rh files for hc016 are also pretty small compared to other subjects. > Not sure what's causing this. > > This is the preproc command I used: preproc-sess -s hc016 -surface > fsaverage lhrh -mni305 -fwhm 4 -per-run -fsd msit -nostc -b0dc -force > > Thanks for your help! > > - Afsana > ______________________________ > *Afsana Afzal* > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > ------------------------------------------------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve > [gr...@nmr.mgh.harvard.edu] > *Sent:* Friday, November 13, 2015 5:04 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR > > hmmm, not sure. Can you send me your selxavg3-sess command and the > folder your ran it from and the $SUBJECTS_DIR ? > doug > > On 11/13/15 4:16 PM, Afzal, Afsana wrote: >> Hi, >> >> I'm doing first level analysis in FSFAST and I'm consistently getting >> the following error when running fast_selxavg3(): >> >> Saving to >> /autofs/space/lilli_002/users/DARPA-FAST/hc016/msit/msit.analysis.sm04.b0dc.mni305/rho1mn.sm.nii.gz >> SmoothOnly requested, so exiting now >> >> Found 0 voxels with corrected AR1 > 0.90 >> Whitening >> Attempted to access indedge(0); index must be a positive integer or >> logical. >> >> Error in fast_histeq (line 53) >> if(indedge(end) ~= ny) indedge = [indedge ny]; end >> >> Error in fast_selxavg3 (line 640) >> [edge bincenter binmap] = fast_histeq(nrho1mn.vol(indmask), >> flac0.acfbins); >> >> >> ------------------------------------------ >> ERROR: fast_selxavg3() failed\n >> >> >> I'm only getting the error for mni305 (lh and rh analyses are >> completing without a hitch). I have re-preprocessed and attempted to >> run the analysis several times, but without any success. It's not >> clear what the error means or what's causing it. >> >> Thank you for any help, >> >> Afsana >> >> ______________________________ >> *Afsana Afzal* >> Clinical Research Coordinator >> Massachusetts General Hospital >> Division of Neurotherapeutics >> Department of Psychiatry: Neurosciences >> 149 13th St, Room 2612 >> Charlestown, MA 02129 >> Phone: 617-643-5129 >> Fax: 617-726-4078 >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list 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. 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