Dear Matt, Yes, I see the freesurfer pipeline fails, but i dont understand where exactly the problem occurs . In FS2CaretConvertRegisterNonlinear.sh , The problem occurs at the following lines of code.
#Find c_ras offset between FreeSurfer surface and volume and generate matrix to transform surfaces MatrixX=`mri_info "$FreeSurferFolder"/mri/brain.finalsurfs.mgz | grep "c_r" | cut -d "=" -f 5 | sed s/" "/""/g` MatrixY=`mri_info "$FreeSurferFolder"/mri/brain.finalsurfs.mgz | grep "c_a" | cut -d "=" -f 5 | sed s/" "/""/g` MatrixZ=`mri_info "$FreeSurferFolder"/mri/brain.finalsurfs.mgz | grep "c_s" | cut -d "=" -f 5 | sed s/" "/""/g` echo "1 0 0 ""$MatrixX" > "$FreeSurferFolder"/mri/c_ras.mat echo "0 1 0 ""$MatrixY" >> "$FreeSurferFolder"/mri/c_ras.mat echo "0 0 1 ""$MatrixZ" >> "$FreeSurferFolder"/mri/c_ras.mat echo "0 0 0 1" >> "$FreeSurferFolder"/mri/c_ras.mat Thanks Vasudev On 23 February 2017 at 22:16, Glasser, Matthew <[email protected]> wrote: > FreeSurfer failed to complete successfully. > > Peace, > > Matt. > > From: <[email protected]> on behalf of Dev vasu < > [email protected]> > Date: Thursday, February 23, 2017 at 3:14 PM > To: "<[email protected]>" <[email protected]>, " > [email protected]" <hcp-users-request@ > humanconnectome.org> > Subject: [HCP-Users] Freesurfer Non linear registration > > Dear all, > > When i tried to run Freesurfer Pipeline i am facing an error where the > pipeline could not generate brain.finalsurfs.mgz . Could you please let me > know the reason for this error?. > > > START: FS2CaretConvertRegisterNonlinear > FreeSurfer2CaretConvertAndRegisterNonLinear.sh: RegName: MSMSulc > mghRead(/media/vasudev/vkirsch4/Project_BLVP/HCP_ > Proj/KON2/T1w/KON2/mri/brain.finalsurfs.mgz, -1): could not open file > mghRead(/media/vasudev/vkirsch4/Project_BLVP/HCP_ > Proj/KON2/T1w/KON2/mri/brain.finalsurfs.mgz, -1): could not open file > mghRead(/media/vasudev/vkirsch4/Project_BLVP/HCP_ > Proj/KON2/T1w/KON2/mri/brain.finalsurfs.mgz, -1): could not open file > Cannot open volume > /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/wmparc_1mm > for reading! > > > Thanks > Vasudev > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > ------------------------------ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
