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

$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://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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: 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

$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

$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://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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
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