Hello Bruce, I took a look at the file with freeview and I can't identify anything peculiar about the data. The file is named Indices_oob.nii and has been uploaded to /transfer/incoming on the FTP file exchange server. Thank you for your swift reply and in advance for your time.
Best regards, Edgar Busovaca On Tue, Mar 24, 2015 at 5:34 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Edgar > > the LINE SEARCH thing is not a real problem. I've never seen "indices out > of bounds" before though. Is there anything strange about your dataset? > Does freeview display it properly (that is, are what freeview thinks the > RAS dirs the correct anatomical ones)? If you upload the dataset we'll see > if we can replicate and fix the problem > > cheers > Bruce > > On Tue, 24 Mar 2015, Edgar Busovaca wrote: > > Dear Freesurfer users, >> I have attempted to process a subject (.nii type input) through recon-all >> -all, but for some reason the processing gambit is terminated early ( >> during >> the skullstrip). >> >> During skullstripping the following warning appears twice: >> >> IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR >> RETURN OF LINE SEARCH: INFO=3 POSSIBLE CAUSES FUNCTION OR GRADIENT ARE >> INCORRECT OR INCORRECT TOLERANCESoutof WuasiNewtonEMA: 007: -log(p) = >> 10341.8 tol 0.000010 >> >> following the skullstrip step in ***********WATERSHED******** the >> following >> appears: >> >> mri_watershed Error: indices out of bounds >> >> >> Oddly, this particular subject failed where the rest of the data set >> successfully completed recon-all -all. >> >> >> >> As a reference I am running freesurfer 5.1 >> Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 >> RedHat release: CentOS release 6.5 (Final) >> Kernel info: Linux 2.6.32-431.11.2.e16.x86_64 x86_64 >> >> >> Is there a flag to push this subject through recon-all? >> >> Thanks in advance for your time. >> >> Best, >> Edgar Busovaca >> >> > _______________________________________________ > 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. 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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