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.
>
>
> On Sun, Mar 18, 2012 at 8:28 AM,
> <freesurfer-request@nmr.mgh.harvard.edu
> <mailto:freesurfer-request@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, "congel@gmail.com <mailto:congel@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-request@nmr.mgh.harvard.edu
>     <mailto:freesurfer-request@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-owner@nmr.mgh.harvard.edu
>     <mailto:freesurfer-owner@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
greve@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