Can you run it outside of the pipeline to assure that it is not a pipeline issue? doug
On 03/18/2012 08:54 AM, Qingyang Li wrote: > Hi all, > I am new to the freesurfer world. > I was running a pipeline where I met an error. Here is the command I > run and the error message: > > Command: > mri_vol2surf --hemi lh --noreshape --o > > /working_dir/SurfaceRegistration/_subject_id_sub/func_sampler_lh/mapflow/_func_sampler_lh4/lh.rest_mc.mgz > --reg > > /working_dir/SurfaceRegistration/_subject_id_sub/func_bbreg/mapflow/_func_bbreg4/rest_mc_bbreg_sub.dat > --projfrac 0.500 --mov > > /working_dir/SurfaceRegistration/_subject_id_sub/func_volreg/mapflow/_func_volreg4/rest_mc.nii.gz > Standard output: > srcvol = > > /working_dir/SurfaceRegistration/_subject_id_sub/func_volreg/mapflow/_func_volreg4/rest_mc.nii.gz > srcreg = > > /working_dir/SurfaceRegistration/_subject_id_sub/func_bbreg/mapflow/_func_bbreg4/rest_mc_bbreg_sub.dat > srcregold = 0 > srcwarp unspecified > surf = white > hemi = lh > ProjFrac = 0.5 > thickness = thickness > reshape = 0 > interp = nearest > float2int = round > GetProjMax = 0 > INFO: float2int code = 0 > INFO: changing type to float > Done loading volume > Reading surface /NKI_recon_subjects/sub/surf/lh.white > Done reading source surface > Reading thickness /NKI_recon_subjects/sub/surf/lh.thickness > Done > Mapping Source Volume onto Source Subject Surface > 1 0.5 0.5 0.5 > using old > Done mapping volume to surface > Standard error: > Segmentation fault > Return code: 139 > Interface SampleToSurface failed to run. > > > Thank you all in advance! > > Yang > > ------ > Qingyang Li > > Balance and focus. > > > On Sun, Mar 18, 2012 at 8:28 AM, > <freesurfer-requ...@nmr.mgh.harvard.edu > <mailto:freesurfer-requ...@nmr.mgh.harvard.edu>> wrote: > > Mailing list subscription confirmation notice for mailing list > Freesurfer > > We have received a request from 67.244.70.75 for subscription of your > email address, "con...@gmail.com <mailto:con...@gmail.com>", to the > freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> mailing list. To confirm > that you want > to be added to this mailing list, simply reply to this message, > keeping the Subject: header intact. Or visit this web page: > > > https://mail.nmr.mgh.harvard.edu/mailman/confirm/freesurfer/8f8fcc67483bbcee3ff0f76888c79e7704b4a03a > > > Or include the following line -- and only the following line -- in a > message to freesurfer-requ...@nmr.mgh.harvard.edu > <mailto:freesurfer-requ...@nmr.mgh.harvard.edu>: > > confirm 8f8fcc67483bbcee3ff0f76888c79e7704b4a03a > > Note that simply sending a `reply' to this message should work from > most mail readers, since that usually leaves the Subject: line in the > right form (additional "Re:" text in the Subject: is okay). > > If you do not wish to be subscribed to this list, please simply > disregard this message. If you think you are being maliciously > subscribed to the list, or have any other questions, send them to > freesurfer-ow...@nmr.mgh.harvard.edu > <mailto:freesurfer-ow...@nmr.mgh.harvard.edu>. > > > 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@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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
