hi Qingyang, you can simply copy and paste the command line into the shell.
cheers, satra On Mon, Mar 26, 2012 at 3:12 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > 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 >
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