-cw256 flag - Freesurfer

16 Feb 2022


      External Email - Use Caution
Hi, sorry, this just bounced back due to an issue with my subscription which is now fixed. Please see below
From: Harriet Dempsey-Jones h.dempseyjones@uq.edu.au
Date: Thursday, 17 February 2022 at 11:56 am
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] -cw256 flag
Hi there,
Thanks for getting back to me
I tried using the -cw256 flag and I still got an error (and freesurfer stopped recon-all). The error was asking me to use the flag, though I had already put the flag in.
Could you look at my code (below) to see if I have implemented it incorrectly?
Thank you,
Harriet
----------------------------
MY CODE
#!bin/tcsh
# Freesurfer start-up
module load freesurfer
# Set up vars
set subj = P00_FG
set recon_use = (-all)
set anat = /scratch/inode/uqhdemp1/Fingertip_maps/{$subj}/{$subj}.results/{$subj_init}_uniden_avg_wholebrain_unpad_warped_3dQ.nii
set base_dir = /scratch/inode/uqhdemp1
set expert_file = 1b_FS_expertfile
## 1. Freesurfer recon all
recon-all {$recon_use} -cw256 -s {$subj}_3dD_cw_try2 -hires -i $anat -sd $base_dir/Surfaces -openmp 12 -expert $base_dir/Parent_scripts/Surfaces/$expert_file
SAMPLE OF ERROR IN COMMAND WINDOW
#--------------------------------------------
#@# MotionCor Thu Feb 17 11:44:30 AEST 2022
Found 1 runs
/scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
Only one run found so motion
correction will not be performed. I'll
copy the run to rawavg and continue.
cp /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/orig/001.mgz /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/rawavg.mgz
/scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2
mri_convert /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/rawavg.mgz /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/orig.mgz --conform_min
mri_convert /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/rawavg.mgz /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/orig.mgz --conform_min
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0, -1, 0)
j_ras = (-0, -0, -1)
k_ras = (1, -0, 0)
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 0 4078 1000, flo=0, fhi=0.999, dest_type=0
Reslicing using trilinear interpolation
writing to /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/orig.mgz...
****************************************
ERROR! FOV=273.000 > 256
Include the flag -cw256 with recon-all!
Inspect orig.mgz to ensure the head is fully visible.
****************************************
Linux inode2.hpc.dc.uq.edu.au 3.10.0-1160.36.2.el7.x86_64 #1 SMP Wed Jul 21 11:57:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s P00_FG_3dD_cw_try2 exited with ERRORS at Thu Feb 17 11:45:38 AEST 2022
For more details, see the log file /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/scripts/recon-all.log
To report a problem, see http://secure-web.cisco.com/1EazoIQDEQ5C0xk6kgC_HrVs1qLbDRhir6_Z00m8PdXgaaA6...
Recon-all-status.log
status file for recon-all
Thu Feb 17 11:44:10 AEST 2022
#@# MotionCor Thu Feb 17 11:44:30 AEST 2022
Linux inode2.hpc.dc.uq.edu.au 3.10.0-1160.36.2.el7.x86_64 #1 SMP Wed Jul 21 11:57:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s P00_FG_3dD_cw_try2 exited with ERRORS at Thu Feb 17 11:45:38 AEST 2022
Recon-all.error
------------------------------
SUBJECT P00_FG_3dD_cw_try2
DATE Thu Feb 17 11:45:38 AEST 2022
USER uqhdemp1
HOST inode2.hpc.dc.uq.edu.au
PROCESSOR x86_64
OS Linux
Linux inode2.hpc.dc.uq.edu.au 3.10.0-1160.36.2.el7.x86_64 #1 SMP Wed Jul 21 11:57:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
$Id: recon-all,v 1.601 2017/02/08 21:17:33 greve Exp $
/opt/ohpc/pub/apps/freesurfer/bin/recon-all
PWD /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2
CMD mri_convert /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/rawavg.mgz /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/orig.mgz --conform_min
Recon-all.log
Thu Feb 17 11:44:09 AEST 2022
/scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2
/opt/ohpc/pub/apps/freesurfer/bin/recon-all
-all -cw256 -s P00_FG_3dD_cw_try2 -hires -i /scratch/inode/uqhdemp1/Fingertip_maps/P00_FG/P00_FG.results/FG_uniden_avg_wholebrain_unpad_warped_3dQ.nii -sd /scratch/inode/uqhdemp1/Surfaces -openmp 12 -expert /scratch/inode/uqhdemp1/Parent_scripts/Surfaces/1b_FS_expertfile
subjid P00_FG_3dD_cw_try2
setenv SUBJECTS_DIR /scratch/inode/uqhdemp1/Surfaces
FREESURFER_HOME /opt/ohpc/pub/apps/freesurfer
Actual FREESURFER_HOME /opt/ohpc/pub/apps/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-dev-20181029-665a1b6
Linux inode2.hpc.dc.uq.edu.au 3.10.0-1160.36.2.el7.x86_64 #1 SMP Wed Jul 21 11:57:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    8192 kbytes
coredumpsize 0 kbytes
memoryuse    unlimited
vmemoryuse   unlimited
descriptors  1024
memorylocked 64 kbytes
maxproc      4096
maxlocks     unlimited
maxsignal    2059413
maxmessage   819200
maxnice      0
maxrtprio    0
maxrttime    unlimited
total        used        free      shared  buff/cache   available
Mem:      527413880   142260852   261204056     4462024   123948972   379278760
Swap:       4192252     2147228     2045024
########################################
program versions used
$Id: recon-all,v 1.601 2017/02/08 21:17:33 greve Exp $
$Id: lta_convert.cpp,v 1.10 2016/08/09 02:11:11 zkaufman Exp $
ProgramName: lta_convert  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: lta_convert.cpp,v 1.10 2016/08/09 02:11:11 zkaufman Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_and  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_annotation2label  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_annotation2label.c,v 1.32 2016/08/02 21:20:27 nicks Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_aparc2aseg  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_aparc2aseg.c,v 1.54 2016/12/26 15:29:30 fischl Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_aparc2wmseg  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_aparc2wmseg.c,v 1.6 2011/03/02 00:04:13 nicks Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_binarize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_ca_label.c,v 1.115 2016/10/22 17:31:36 fischl Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_ca_normalize.c,v 1.69 2016/10/22 17:30:57 fischl Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_ca_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_ca_register.c,v 1.99 2016/10/22 17:31:24 fischl Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_cc  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_cc.c,v 1.39 2015/12/04 13:59:56 fischl Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_compute_overlap  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_compute_overlap.c,v 1.19 2015/10/20 20:07:19 fischl Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_compute_seg_overlap  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_compute_seg_overlap.c,v 1.18 2015/08/28 18:05:30 greve Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_concat  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_concat.c,v 1.67 2017/02/16 19:49:35 greve Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_concatenate_lta  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
mri_convert -all-info
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_diff  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_diff.c,v 1.37 2017/01/11 18:15:33 greve Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_edit_wm_with_aseg.c,v 1.25 2012/03/29 13:17:38 fischl Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_em_register.c,v 1.106 2016/10/22 17:31:12 fischl Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_fill  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_fuse_segmentations  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_fuse_segmentations.cpp,v 1.8 2011/03/02 00:04:15 nicks Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_fwhm  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_fwhm.c,v 1.35 2016/11/01 20:25:24 greve Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_info  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_info.c,v 1.87 2014/11/20 23:46:54 greve Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_label2label  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_label2label.c,v 1.50 2016/12/10 22:57:43 fischl Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_label2vol  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_log_likelihood  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_log_likelihood.c,v 1.4 2011/03/02 00:04:22 nicks Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_mask  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_mask.c,v 1.24 2016/11/28 20:30:57 fischl Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_matrix_multiply  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_matrix_multiply.c,v 1.13 2011/03/02 00:04:23 nicks Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_normalize.c,v 1.92 2017/01/27 22:31:34 ah221 Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_normalize_tp2  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_or  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_relabel_hypointensities  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_relabel_nonwm_hypos.c,v 1.2 2014/04/17 18:03:22 greve Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_remove_neck  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_remove_neck.c,v 1.10 2011/03/02 00:04:24 nicks Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
$Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $
ProgramName: mri_robust_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
$Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $
ProgramName: mri_robust_template  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mris_anatomical_stats  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mris_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mris_calc  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mris_calc.c,v 1.55 2016/09/27 18:50:16 greve Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mris_convert  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id$  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mris_curvature  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mris_curvature_stats  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mris_diff  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mris_diff.c,v 1.20 2014/03/21 23:57:48 greve Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mris_divide_parcellation  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mris_divide_parcellation.c,v 1.12 2012/10/24 19:50:06 maritza Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_segment.c,v 1.44 2016/10/22 17:29:37 fischl Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_segstats  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_segstats.c,v 1.122 2017/01/23 18:23:14 greve Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mris_euler_number  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mris_fix_topology  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mris_fix_topology.c,v 1.51 2016/10/27 19:43:58 fischl Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mris_topo_fixer  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mris_jacobian  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mris_jacobian.c,v 1.11 2015/02/05 23:34:40 zkaufman Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mris_label2annot  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mris_left_right_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mris_left_right_register.c,v 1.2 2011/12/16 20:49:37 greve Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mris_make_surfaces  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mris_make_surfaces.c,v 1.172 2017/02/16 19:42:36 fischl Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mrisp_paint  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mris_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mris_register.c,v 1.64 2017/02/07 19:04:44 fischl Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mris_smooth  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mris_sphere  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mris_sphere.c,v 1.62 2017/02/07 19:04:37 fischl Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mris_surface_stats  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mris_surface_stats.c,v 1.10 2011/03/02 00:04:34 nicks Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_stats2seg  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_stats2seg.c,v 1.9 2011/03/02 00:04:24 nicks Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mris_thickness  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mris_thickness.c,v 1.28 2012/11/27 17:41:26 fischl Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mris_thickness_diff  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mris_thickness_diff.c,v 1.16 2011/03/02 00:04:34 nicks Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mris_topo_fixer  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_surf2surf  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_surf2vol  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_surf2vol.c,v 1.28 2014/12/08 19:49:02 greve Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_surfcluster  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_surfcluster.c,v 1.60 2016/11/01 19:49:22 greve Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mris_volmask  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mris_volmask.cpp,v 1.28 2016/11/18 19:19:29 fischl Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_tessellate  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_tessellate.c,v 1.39 2016/07/20 21:05:04 zkaufman Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_vol2surf  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_vol2surf.c,v 1.68 2014/05/30 20:58:47 greve Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_vol2vol  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_vol2vol.c,v 1.89 2016/06/22 22:33:40 fischl Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_voldiff  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_voldiff.c,v 1.6 2011/03/02 00:04:25 nicks Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
ProgramName: tkregister2_cmdl  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:09-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: tkregister2.c,v 1.133 2016/08/02 21:17:11 greve Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert -all-info
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2022/02/17-01:44:10-GMT  BuildTimeStamp: Oct 29 2018 00:06:18  Id: $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $  User: uqhdemp1  Machine: inode2.hpc.dc.uq.edu.au  Platform: Linux  PlatformVersion: 3.10.0-1160.36.2.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800
FLIRT version 6.0
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /opt/ohpc/pub/apps/freesurfer/average
GCA RB_all_2016-05-10.vc700.gca
GCASkull RB_all_withskull_2016-05-10.vc700.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /opt/ohpc/pub/apps/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################
-cw256 option is now persistent (remove with -clean-cw256)
/scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2
mri_convert /scratch/inode/uqhdemp1/Fingertip_maps/P00_FG/P00_FG.results/FG_uniden_avg_wholebrain_unpad_warped_3dQ.nii /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/orig/001.mgz
mri_convert /scratch/inode/uqhdemp1/Fingertip_maps/P00_FG/P00_FG.results/FG_uniden_avg_wholebrain_unpad_warped_3dQ.nii /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/orig/001.mgz
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from /scratch/inode/uqhdemp1/Fingertip_maps/P00_FG/P00_FG.results/FG_uniden_avg_wholebrain_unpad_warped_3dQ.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0, -1, 0)
j_ras = (-0, -0, -1)
k_ras = (1, -0, 0)
writing to /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Thu Feb 17 11:44:30 AEST 2022
Found 1 runs
/scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
Only one run found so motion
correction will not be performed. I'll
copy the run to rawavg and continue.
cp /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/orig/001.mgz /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/rawavg.mgz
/scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2
mri_convert /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/rawavg.mgz /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/orig.mgz --conform_min
mri_convert /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/rawavg.mgz /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/orig.mgz --conform_min
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0, -1, 0)
j_ras = (-0, -0, -1)
k_ras = (1, -0, 0)
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 0 4078 1000, flo=0, fhi=0.999, dest_type=0
Reslicing using trilinear interpolation
writing to /scratch/inode/uqhdemp1/Surfaces/P00_FG_3dD_cw_try2/mri/orig.mgz...
****************************************
ERROR! FOV=273.000 > 256
Include the flag -cw256 with recon-all!
Inspect orig.mgz to ensure the head is fully visible.
****************************************
Linux inode2.hpc.dc.uq.edu.au 3.10.0-1160.36.2.el7.x86_64 #1 SMP Wed Jul 21 11:57:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s P00_FG_3dD_cw_try2 exited with ERRORS at Thu Feb 17 11:45:38 AEST 2022
To report a problem, see http://secure-web.cisco.com/1EazoIQDEQ5C0xk6kgC_HrVs1qLbDRhir6_Z00m8PdXgaaA6...
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU
Date: Monday, 14 February 2022 at 8:35 am
To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] -cw256 flag
Yes, this is ok. This was a bit of a hack that someone introduced into recon-all a number of years ago, and we have not gotten around to fixing it.
On 2/8/2022 7:25 PM, Harriet Dempsey-Jones wrote:
External Email - Use Caution
Hi there,
I am using AFNI to process some epi data. As part of this analysis, I am creating anatomical surfaces on which to project my data using recon-all in Freesurfer.
My pre-processing in AFNI indicated that best alignment of my epi to anatomical image is achieved using a combination of affine and non-linear warping (3dQwarp in AFNI). So I was hoping to use this warped anatomical image from my experimental data to create a surface from with recon-all.
I just tried to set this to run, and it errored and failed (see bottom of email)
The gist appears to be that when it was completing the mri_convert stage it errored because the anatomical nifti image I had fed it, was not 256 FOV. It appears to be larger because I had to add some space to the image to rotate it during alignment.
The error suggests using the flag -cw256 with recon-all, but I cannot find any documentation about how this works or what it does. I searched the forum archives as well, which came up with 60k hits, but none of them seemed to contain -cw256 when I control+f looking for it.
Could someone let me know a bit more about this flag and whether it is ok to use for my purposes?
I have included my recon-all code too for reference purposes. Please also let me know if there is anything glaringly wrong there, I am very new to fMRI analysis.
Thank you for any help you might be able to give me!
ERROR
--------------------
mri_convert /scratch/inode/uqhdemp1/Surfaces/P00_FG/mri/rawavg.mgz /scratch/inode/uqhdemp1/Surfaces/P00_FG/mri/orig.mgz --conform_min
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from /scratch/inode/uqhdemp1/Surfaces/P00_FG/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0, -1, 0)
j_ras = (-0, -0, -1)
k_ras = (1, -0, 0)
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 0 4078 1000, flo=0, fhi=0.999, dest_type=0
Reslicing using trilinear interpolation
writing to /scratch/inode/uqhdemp1/Surfaces/P00_FG/mri/orig.mgz...
****************************************
ERROR! FOV=273.000 > 256
Include the flag -cw256 with recon-all!
Inspect orig.mgz to ensure the head is fully visible.
****************************************
Linux inode2.hpc.dc.uq.edu.au 3.10.0-1160.36.2.el7.x86_64 #1 SMP Wed Jul 21 11:57:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s P00_FG exited with ERRORS at Tue Feb  8 22:13:53 AEST 2022
MY CODE
--------------------------
#!bin/tcsh
# Freesurfer start-up
module load freesurfer
# Set up vars
set subj_init = FG
set subj_num = P00
set subj = {$subj_num}_{$subj_init}
set recon_use = (-all)
# set recon_use = (-autorecon1)
set anat = /scratch/inode/uqhdemp1/Fingertip_maps/{$subj}/{$subj}.results/{$subj_init}_uniden_avg_wholebrain_unpad_warped_3dQ.nii
set base_dir = /scratch/inode/
set subj = {$subj_num}_{$subj_init}
set expert_file = 1b_FS_expertfile
## 1. Freesurfer recon all
recon-all $recon_use -s $subj -hires -i $anat -sd $base_dir/Surfaces -openmp 12 -expert $base_dir/Parent_scripts/Surfaces/$expert_file
[cid:part1.ftNxeNKN.hsfFhubR@mgh.harvard.edu]
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