[MINC-users] Nu_correct error: mask volume and input volume different in size

[Hye Min Shin]

Hello,

I was wondering if someone can help me understand the issue I am running
into with nu_correct.

During the nu_correct stage while preprocessing MRI images through a
modified version of FreeSurfer and I ran into this error:

Iteration 1 2020. 09. 08. (화) 22:45:28 KST
nu_correct -clobber
/home/shinhm91/fastsurfer_analysis/005_S_0602/mri/tmp.mri_nu_correct.mni.9950/nu0.mnc
/home/shinhm91/fastsurfer_analysis/005_S_0602/mri/tmp.mri_nu_correct.mni.9950/nu1.mnc
-tmpdir
/home/shinhm91/fastsurfer_analysis/005_S_0602/mri/tmp.mri_nu_correct.mni.9950/0/
-iterations 1000 -distance 50 -mask
/home/shinhm91/fastsurfer_analysis/005_S_0602/mri/tmp.mri_nu_correct.mni.9950/mask.mnc
[shinhm91 at metamind-H270:/home/shinhm91/fastsurfer_analysis/005_S_0602/mri/]
[2020-09-08 22:45:28] running:
  /usr/local/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 -mask
/home/shinhm91/fastsurfer_analysis/005_S_0602/mri/tmp.mri_nu_correct.mni.9950/mask.mnc
-quiet -execute -clobber -nokeeptmp -tmpdir
/home/shinhm91/fastsurfer_analysis/005_S_0602/mri/tmp.mri_nu_correct.mni.9950/0/
/home/shinhm91/fastsurfer_analysis/005_S_0602/mri/tmp.mri_nu_correct.mni.9950/nu0.mnc
/home/shinhm91/fastsurfer_analysis/005_S_0602/mri/tmp.mri_nu_correct.mni.9950/nu1.imp

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Number of iterations: 56
CV of field change: 0.000980823
Mask volume and input volume must be the same size.
nu_evaluate: crashed while running evaluate_field (termination status=512)
nu_correct: crashed while running nu_evaluate (termination status=512)
ERROR: nu_correct
Command exited with non-zero status 1
@#@FSTIME  2020:09:08:22:45:23 mri_nu_correct.mni N 13 e 24.51 S 1.99 U
22.21 P 98% M 158792 F 108 R 587187 W 0 c 1830 w 5685 I 35488 O 1185720 L
3.65 2.13 1.79
@#@FSLOADPOST 2020:09:08:22:45:48 mri_nu_correct.mni N 13 3.24 2.15 1.81

So I was able to find from MINC wikibooks page (
https://en.wikibooks.org/wiki/MINC/Tools/N3) about possibly fixing this
issue with specified mask volume by running the code: mincmath -gt -const 0
mask.mnc new_mask.mnc but that still didn't solve the problem.

I tried checking file sizes for mask.mnc and nu0.mnc and the funny thing is
before running nu_correct both mask.mnc and nu0.mnc files are indeed same
in size:

211M . <---- parent directory size
65M ./nu0.mnc
65M ./new_mask.mnc
65M ./mask.mnc
19M ./0
140K ./mask.mgz
20K ./nu1.imp

but if you see the tmp file called 0 that is used to store files while
running nu_correct, mask.mnc and nu0.mnc files are different in size:

8.5M . <---- ./0 temp directory for running nu_correct
1.1M ./nu1_temp.mnc
1.1M ./nu1_residue.mnc
1.1M ./nu1_log.mnc
1.1M ./nu1_est.mnc.temp
1.1M ./nu1_est.mnc
1.1M ./nu1_corr.mnc
1.1M ./nu0.mnc
544K ./nu1_mask.mnc
276K ./new_mask.mnc
276K ./mask.mnc
8.0K ./nu1_est.sharp
8.0K ./nu1_est.hist

Does nu_correct re-process nu0.mnc and mask.mnc from original files? I just
want to understand how I got different file sizes in tmp directory.

Best,
Julia Shin