Thank you Doug and Satra, I ran the same pipeline on another machine after I post the question and it went through with no problem...
On the machine which the pipeline failed, I have freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0. And on the machine that the pipeline went through, I have freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 on. This might be a version issue? To rule out this possibility, we are testing the ver 5.0.0 of Freesurfer on the machine that failed this step... Will keep you posted when we finish testing ... Also, we did tried to run the script outside the pipeline and received the same error... Yang ------ Qingyang Li Balance and focus. On Mon, Mar 26, 2012 at 3:36 PM, Satrajit Ghosh <sa...@mit.edu> wrote: > 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. 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