External Email - Use Caution

Hi Andrew,

I am on a mac pro running Sierra 10.12.6

Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442@gmail.com ddcc2442@gmail.com* 443-254-6298

On Tue, Mar 19, 2019 at 2:40 PM Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:

Hi Daniel, I’ve never seen this error before. I assume you’re on a mac – what version are you using?

Andrew

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Daniel Callow ddcc2442@gmail.com *Reply-To: *FS Help freesurfer@nmr.mgh.harvard.edu *Date: *Tuesday, March 19, 2019 at 10:45 AM *To: *FS Help freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] recon-all error

•    External Email - Use Caution        *
  
  

Hello,

I am trying to run recon-all on a dataset and am running into errors with one of my subjects.

I get an error at the following point

---

Iteration 1 Tue Mar 19 10:11:08 EDT 2019

nu_correct -clobber ./tmp.mri_nu_correct.mni.40972/nu0.mnc ./tmp.mri_nu_correct.mni.40972/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.40972/0/ -iterations 1000 -distance 50

[administrator@hlhp-105.umd.edu:/Volumes/DANIEL/freesurfer/Ex.AES118/mri/] [2019-03-19 10:11:09] running:

/Applications/freesurfer//mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.40972/0/ ./tmp.mri_nu_correct.mni.40972/nu0.mnc ./tmp.mri_nu_correct.mni.40972/nu1.imp

Processing:.................................................................Done

Processing:.................................................................Done

Processing:.................................................................Done

Processing:.................................................................Done

Processing:.................................................................Done

Processing:.................................................................Done

Processing:.................................................................Done

Processing:.................................................................Done

Processing:.................................................................Done

Processing:.................................................................Done

ncvarget: ncid 4; varid 6: Argument list too long

miicv_get: MINC package entry point

nu_estimate_np_and_em: crashed while running mincmath (termination status=768)

nu_correct: crashed while running nu_estimate_np_and_em (termination status=768)

ERROR: nu_correct

Darwin hlhp-105.umd.edu 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018; root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64

recon-all -s Ex.AES118 exited with ERRORS at Tue Mar 19 10:11:18 EDT 2019

For more details, see the log file /Volumes/DANIEL/freesurfer/Ex.AES118/scripts/recon-all.log

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

Any help you can provide for troubleshooting would be greatly appreciated.

*Daniel Callow*

*PhD Student, Neuroscience and Cognitive Science*

Exercise for Brain Health Lab

University of Maryland, College Park

*ddcc2442@gmail.com ddcc2442@gmail.com*

443-254-6298 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Hello Andrew,

I tried deleting the files and running the recon-all script again and found I no longer got the nu_correct error. However, I am now getting the following error (which I have seen before).

#@# Make White Surf rh Thu Mar 21 13:52:31 EDT 2019

/Volumes/DANIEL/freesurfer/Rest.AES118/scripts

\n mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs Rest.AES118 rh \n

using white.preaparc as white matter name...

only generating white matter surface

using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline

not using aparc to prevent surfaces crossing the midline

INFO: assuming MGZ format for volumes.

using brain.finalsurfs as T1 volume...

$Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $

$Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $

reading volume /Volumes/DANIEL/freesurfer/Rest.AES118/mri/filled.mgz...

reading volume /Volumes/DANIEL/freesurfer/Rest.AES118/mri/brain.finalsurfs.mgz...

reading volume /Volumes/DANIEL/freesurfer/Rest.AES118/mri/../mri/aseg.presurf.mgz...

reading volume /Volumes/DANIEL/freesurfer/Rest.AES118/mri/wm.mgz...

25155 bright wm thresholded.

1843 bright non-wm voxels segmented.

reading original surface position from /Volumes/DANIEL/freesurfer/Rest.AES118/surf/rh.orig...

mris_make_surfaces: could not read surface file /Volumes/DANIEL/freesurfer/Rest.AES118/surf/rh.orig

ERROR: reading /Volumes/DANIEL/freesurfer/Rest.AES118/surf/rh.orig

Read 0 bytes, expected 1

Argument list too long

Darwin hlhp-105.umd.edu 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018; root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64

recon-all -s Rest.AES118 exited with ERRORS at Thu Mar 21 13:52:36 EDT 2019

For more details, see the log file /Volumes/DANIEL/freesurfer/Rest.AES118/scripts/recon-all.log

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

It seems that when I run this subject sometimes it runs no problem, but when I try again on the exact same subject Dicoms I may or may not get an error.

Any ideas what could be causing this/these errors?

Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442@gmail.com ddcc2442@gmail.com* 443-254-6298

On Tue, Mar 19, 2019 at 4:51 PM Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:

It’s only happening for one subject, right? nu_correct isn’t actually a freesurfer tool, it’s an mni tool. I would try to troubleshoot this by installing a newer version of minc for osx: http://packages.bic.mni.mcgill.ca/minc-toolkit/MacOSX/minc-toolkit-1.9.16-20...

Then, set the following BEFORE sourcing freesurfer and try rerunning the failed recon:

export MINC_BIN_DIR=/opt/minc/1.9.16/bin

export MINC_LIB_DIR=/opt/minc/1.9.16/lib

best

Andrew

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Daniel Callow ddcc2442@gmail.com *Reply-To: *FS Help freesurfer@nmr.mgh.harvard.edu *Date: *Tuesday, March 19, 2019 at 4:14 PM *To: *FS Help freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] recon-all error

•    External Email - Use Caution        *
  
  

Hi Andrew,

I am on a mac pro running Sierra 10.12.6

Best,

*Daniel Callow*

*PhD Student, Neuroscience and Cognitive Science*

Exercise for Brain Health Lab

University of Maryland, College Park

*ddcc2442@gmail.com ddcc2442@gmail.com*

443-254-6298

On Tue, Mar 19, 2019 at 2:40 PM Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:

Hi Daniel, I’ve never seen this error before. I assume you’re on a mac – what version are you using?

Andrew

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Daniel Callow ddcc2442@gmail.com *Reply-To: *FS Help freesurfer@nmr.mgh.harvard.edu *Date: *Tuesday, March 19, 2019 at 10:45 AM *To: *FS Help freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] recon-all error

•    External Email - Use Caution        *
  
  

Hello,

I am trying to run recon-all on a dataset and am running into errors with one of my subjects.

I get an error at the following point

---

Iteration 1 Tue Mar 19 10:11:08 EDT 2019

nu_correct -clobber ./tmp.mri_nu_correct.mni.40972/nu0.mnc ./tmp.mri_nu_correct.mni.40972/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.40972/0/ -iterations 1000 -distance 50

[administrator@hlhp-105.umd.edu:/Volumes/DANIEL/freesurfer/Ex.AES118/mri/] [2019-03-19 10:11:09] running:

/Applications/freesurfer//mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.40972/0/ ./tmp.mri_nu_correct.mni.40972/nu0.mnc ./tmp.mri_nu_correct.mni.40972/nu1.imp

Processing:.................................................................Done

Processing:.................................................................Done

Processing:.................................................................Done

Processing:.................................................................Done

Processing:.................................................................Done

Processing:.................................................................Done

Processing:.................................................................Done

Processing:.................................................................Done

Processing:.................................................................Done

Processing:.................................................................Done

ncvarget: ncid 4; varid 6: Argument list too long

miicv_get: MINC package entry point

nu_estimate_np_and_em: crashed while running mincmath (termination status=768)

nu_correct: crashed while running nu_estimate_np_and_em (termination status=768)

ERROR: nu_correct

Darwin hlhp-105.umd.edu 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018; root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64

recon-all -s Ex.AES118 exited with ERRORS at Tue Mar 19 10:11:18 EDT 2019

For more details, see the log file /Volumes/DANIEL/freesurfer/Ex.AES118/scripts/recon-all.log

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

Any help you can provide for troubleshooting would be greatly appreciated.

*Daniel Callow*

*PhD Student, Neuroscience and Cognitive Science*

Exercise for Brain Health Lab

University of Maryland, College Park

*ddcc2442@gmail.com ddcc2442@gmail.com*

443-254-6298

---

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