I would ask on the FreeSurfer list, as that log doesn’t say what the error is and I believe there is some issue with FreeSurfer on Ubuntu 16.04.
Peace, Matt. From: Dev vasu <[email protected]<mailto:[email protected]>> Date: Friday, February 24, 2017 at 10:18 AM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "<[email protected]<mailto:[email protected]>>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Freesurfer Non linear registration Dear Matt, Yes, recon-all has failed, I am not sure why, I am annexing the recon-all.log file, I am using ubuntu 16.04, is it related to the default version of perl i.e 5.22.03 in my computer, i verified some freesurfer forums, but i did not get any answers, kindly review the log file. Thanks Vasudev On 23 February 2017 at 22:23, Glasser, Matthew <[email protected]<mailto:[email protected]>> wrote: You are showing errors from the PostFreeSurfer pipeline below. Peace, Matt. From: Dev vasu <[email protected]<mailto:[email protected]>> Date: Thursday, February 23, 2017 at 3:21 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "<[email protected]<mailto:[email protected]>>" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Freesurfer Non linear registration 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]<mailto:[email protected]>> wrote: FreeSurfer failed to complete successfully. Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of Dev vasu <[email protected]<mailto:[email protected]>> Date: Thursday, February 23, 2017 at 3:14 PM To: "<[email protected]<mailto:[email protected]>>" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> 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]<mailto:[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. 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