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 satra@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 < greve@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.
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