[MINC-users] Nu_correct error: mask volume and input volume different in size
Hye Min Shin
shinhm91 at bu.edu
Mon Sep 14 11:21:58 EDT 2020
Hi Claude,
Thank you very much for your reply. Your suggestion to use mincresample
worked perfectly and I was able to run the freesurfer script
mri_nu_correct.mni successfully using the newly resampled mask.
For your information, from the freesurfer log file it looks like freesurfer
is using the following version of N3: Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks at terrier
(x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
Another interesting thing is that when I used mincinfo both on the volume
and the mask, it seems like both were in the same size and dimension order:
shinhm91 at metamind-H270:~$ mincinfo
/media/shinhm91/braindata/fastsurfer_analysis/005_S_0602/mri/tmp.mri_nu_correct.mni.19089/mask.mnc
file:
/media/shinhm91/braindata/fastsurfer_analysis/005_S_0602/mri/tmp.mri_nu_correct.mni.19089/mask.mnc
image: signed__ float 0 to 1
image dimensions: xspace yspace zspace
dimension name length step start
-------------- ------ ---- -----
xspace 256 1 -324.117
yspace 256 1 -670.137
zspace 256 1 165.341
shinhm91 at metamind-H270:~$ mincinfo
/media/shinhm91/braindata/fastsurfer_analysis/005_S_0602/mri/tmp.mri_nu_correct.mni.19089/nu0.mnc
file:
/media/shinhm91/braindata/fastsurfer_analysis/005_S_0602/mri/tmp.mri_nu_correct.mni.19089/nu0.mnc
image: signed__ float 0 to 255
image dimensions: xspace yspace zspace
dimension name length step start
-------------- ------ ---- -----
xspace 256 1 -324.117
yspace 256 1 -670.137
zspace 256 1 165.341
But I still used mincresample method as you mentioned anyway and I was able
to get past the error.
Best,
Julia Shin
On Mon, Sep 14, 2020 at 11:31 PM Claude LEPAGE <claude at bic.mni.mcgill.ca>
wrote:
> Hi,
>
> By same size, we mean the dimensions of the volume, not the file
> size on disk. Same number of voxels in x, y, z directions. You can
> use the command mincinfo on the volume and the mask.
>
> % mincinfo t1_final.mnc
>
> file: t1_final.mnc
> image: signed__ float 0 to 70760.0625
> image dimensions: zspace yspace xspace
> dimension name length step start
> -------------- ------ ---- -----
> zspace 255 0.25 -26.75
> yspace 430 0.25 -61.5
> xspace 421 0.25 -52.5
>
> The mask needs to be the same size with the same dimension order
> (here z, y, x).
>
> Use mincresample to resample the mask like the input volume.
>
> mincresample -clobber -like t1_image.mnc -nearest input_mask.mnc
> output_mask.mnc
>
> Note: -nearest is to have a binary mask 0,1.
>
> It would be interesting to know which version of N3 FreeSurfer is still
> using. Last I heard, it was an ancient version based on minc-1 format
> (uncompressed). But FreeSurfer does work without crashing at this stage,
> so maybe it's a problem introduced in your modified version.
>
> Claude
>
>
> >
> > 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
> >
> > Transforming
> >
> slices:.................................................................Done
> >
> Processing:.................................................................Done
> >
> Processing:.................................................................Done
> >
> Processing:.................................................................Done
> >
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> Processing:.................................................................Done
> > 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
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users
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