Hi Naveed,

How are you sourcing freesurfer? nu_correct is an mni tool that's shipped with FS in the 'mni' subdirectory. After sourcing FS, the command `which nu_correct` should produce a path that points to $FREESURFER_HOME/mni/bin/nu_correct. Is this the case for you?

best Andrew

________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Muhammad Naveed Iqbal Qureshi mniqureshi@hotmail.com Sent: Tuesday, November 19, 2019 4:35 PM To: Freesurfer maillist Subject: [Freesurfer] error in preprocessing

External Email - Use Caution

Hi please see the log below.

I do not understand the cause of the failure.

[nqureshi@qlogin1 ~]$ recon-all -s /hpf/projects/glongoni/ADHD-200/rest.nii -subject ADHD-1 -all -hippocampal-subfields-T1 -sd /hpf/projects/glongoni/ADHD-200/ -no-isrunning

Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

INFO: SUBJECTS_DIR is /hpf/projects/glongoni/ADHD-200

Actual FREESURFER_HOME /hpf/tools/centos6/freesurfer/6.0.0

-rw-rw-r-- 1 nqureshi glongoni 57759 Nov 19 16:32 /hpf/projects/glongoni/ADHD-200/ADHD-1/scripts/recon-all.log

Linux qlogin1.ccm.sickkids.ca 2.6.32-754.14.2.el6.x86_64 #1 SMP Tue May 14 19:35:42 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

nu_correct: Command not found.

`/hpf/tools/centos6/freesurfer/6.0.0/bin/recon-all' -> `/hpf/projects/glongoni/ADHD-200/ADHD-1/scripts/recon-all.local-copy'

#--------------------------------------------

#@# MotionCor Tue Nov 19 16:32:47 EST 2019

Found 1 runs

/hpf/projects/glongoni/ADHD-200/ADHD-1/mri/orig/001.mgz

Checking for (invalid) multi-frame inputs...

WARNING: only one run found. This is OK, but motion

correction cannot be performed on one run, so I'll

copy the run to rawavg and continue.

cp /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/orig/001.mgz /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/rawavg.mgz

/hpf/projects/glongoni/ADHD-200/ADHD-1

mri_convert /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/rawavg.mgz /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/orig.mgz --conform

mri_convert.bin /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/rawavg.mgz /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/orig.mgz --conform

$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $

reading from /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/rawavg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, -0, 0)

j_ras = (-0, 1, 0)

k_ras = (-0, -0, 1)

changing data type from short to uchar (noscale = 0)...

MRIchangeType: Building histogram

Reslicing using trilinear interpolation

writing to /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/orig.mgz...

mri_add_xform_to_header -c /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/transforms/talairach.xfm /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/orig.mgz /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/orig.mgz

INFO: extension is mgz

#--------------------------------------------

#@# Talairach Tue Nov 19 16:32:54 EST 2019

/hpf/projects/glongoni/ADHD-200/ADHD-1/mri

mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50

/hpf/projects/glongoni/ADHD-200/ADHD-1/mri

/hpf/tools/centos6/freesurfer/6.0.0/bin/mri_nu_correct.mni

--no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50

nIters 1

$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $

Linux qlogin1.ccm.sickkids.ca 2.6.32-754.14.2.el6.x86_64 #1 SMP Tue May 14 19:35:42 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

Tue Nov 19 16:32:54 EST 2019

nu_correct: Command not found.

/usr/bin/bc

tmpdir is ./tmp.mri_nu_correct.mni.50153

/hpf/projects/glongoni/ADHD-200/ADHD-1/mri

mri_convert orig.mgz ./tmp.mri_nu_correct.mni.50153/nu0.mnc -odt float

mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.50153/nu0.mnc -odt float

$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $

reading from orig.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

changing data type from uchar to float (noscale = 0)...

writing to ./tmp.mri_nu_correct.mni.50153/nu0.mnc...

--------------------------------------------------------

Iteration 1 Tue Nov 19 16:32:55 EST 2019

nu_correct -clobber ./tmp.mri_nu_correct.mni.50153/nu0.mnc ./tmp.mri_nu_correct.mni.50153/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.50153/0/ -iterations 1000 -distance 50

nu_correct: Command not found.

ERROR: nu_correct

Linux qlogin1.ccm.sickkids.ca 2.6.32-754.14.2.el6.x86_64 #1 SMP Tue May 14 19:35:42 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s ADHD-1 exited with ERRORS at Tue Nov 19 16:32:55 EST 2019

For more details, see the log file /hpf/projects/glongoni/ADHD-200/ADHD-1/scripts/recon-all.log

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

[nqureshi@qlogin1 ~]$

qsub: job 221779.qtorque2.ccm.sickkids.ca completed

Regards,

Naveed