The rawavg.mgz is not empty. Many values are around 0 but there are also
values between 0.2 and 0.5 (and values between -0.4 and -0.5 in CSF).
It really seems like orig.mgz is all 0. How low do the values need to be for
the conversion to set them to 0?
Is there anything I can do to use recon-all on my data?
-----freesurfer-boun...@nmr.mgh.harvard.edu schrieb: -----An: Freesurfer
support list <freesurfer@nmr.mgh.harvard.edu>
Von: Bruce Fischl
Gesendet von: freesurfer-boun...@nmr.mgh.harvard.edu
Datum: 18.07.2017 16:11
Betreff: Re: [Freesurfer] t1 mri_convert fails
is the rawavg.mgz also empty? The TE=0 only means that nifti doesn't store
the MR parameters - it shouldn't change anything. If the rawavg.mgz is not
empty look at what the values are - maybe they (or the nifti) are too low
and the conversion to uchar sets them to 0?
On Tue, 18 Jul 2017,
clemens.schroe...@uzh.ch wrote:
> Hello Developers
>
> I am trying to run recon-all on a number of MP2RAGE T1 images but I fail.
>
> Using tkmedit, I noticed that orig/001.mgz looks fine but orig.mgz is
all-0.
> Also, mri_convert assumes TE=0, which is false.
>
> Do you have any advice for me?
>
> The recon-all.log is attached
>
> FreeSurfer freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
> My OS is OSX El Capitan 10.11.6
> uname -a: Darwin MAC15-0004.local 15.6.0 Darwin Kernel Version 15.6.0: Tue
> Apr 11 16:00:51 PDT 2017; root:xnu-3248.60.11.5.3~1/RELEASE_X86_64 x86_64
>
>
> Here is the print from the command:
>
> MAC15-0004:t1 clschr$ recon-all -s example -i example.nii -all
> -hippocampal-subfields-T1
> Subject Stamp:
> Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
> INFO: SUBJECTS_DIR is /Users/clschr/Desktop/7T/t1
> Actual FREESURFER_HOME /Applications/freesurfer
> Darwin vpn-89-206-117-41.uzh.ch 15.6.0 Darwin Kernel Version 15.6.0: Tue
Apr
> 11 16:00:51 PDT 2017; root:xnu-3248.60.11.5.3~1/RELEASE_X86_64 x86_64
> /Users/clschr/Desktop/7T/t1/example
> \n mri_convert /Users/clschr/Desktop/7T/t1/example.nii
> /Users/clschr/Desktop/7T/t1/example/mri/orig/001.mgz \n
> mri_convert.bin /Users/clschr/Desktop/7T/t1/example.nii
> /Users/clschr/Desktop/7T/t1/example/mri/orig/001.mgz
> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
> reading from /Users/clschr/Desktop/7T/t1/example.nii...
> niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-0.999967, 0.00331038, 0.00735774)
> j_ras = (0.00506133, 0.967573, 0.252542)
> k_ras = (0.00628314, -0.252571, 0.967558)
> writing to /Users/clschr/Desktop/7T/t1/example/mri/orig/001.mgz...
> #--------------------------------------------
> #@# MotionCor Tue Jul 18 09:20:32 CEST 2017
> Found 1 runs
> /Users/clschr/Desktop/7T/t1/example/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.
> \n cp /Users/clschr/Desktop/7T/t1/example/mri/orig/001.mgz
> /Users/clschr/Desktop/7T/t1/example/mri/rawavg.mgz \n
> /Users/clschr/Desktop/7T/t1/example
> \n mri_convert /Users/clschr/Desktop/7T/t1/example/mri/rawavg.mgz
> /Users/clschr/Desktop/7T/t1/example/mri/orig.mgz --conform \n
> mri_convert.bin /Users/clschr/Desktop/7T/t1/example/mri/rawavg.mgz
> /Users/clschr/Desktop/7T/t1/example/mri/orig.mgz --conform
> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
> reading from /Users/clschr/Desktop/7T/t1/example/mri/rawavg.mgz...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-0.999967, 0.00331038, 0.00735774)
> j_ras = (0.00506133, 0.967573, 0.252542)
> k_ras = (0.00628314, -0.252571, 0.967558)
> changing data type from float to uchar (noscale = 0)...
> MRIchangeType: Building histogram
> Reslicing using trilinear interpolation
> writing to /Users/clschr/Desktop/7T/t1/example/mri/orig.mgz...
> \n mri_add_xform_to_header -c
> /Users/clschr/Desktop/7T/t1/example/mri/transforms/talairach.xfm
> /Users/clschr/Desktop/7T/t1/example/mri/orig.mgz
> /Users/clschr/Desktop/7T/t1/example/mri/orig.mgz \n
> INFO: extension is mgz
> #--------------------------------------------
> #@# Talairach Tue Jul 18 09:20:41 CEST 2017
> /Users/clschr/Desktop/7T/t1/example/mri
> \n mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1
> --proto-iters 1000 --distance 50 \n
> /Users/clschr/Desktop/7T/t1/example/mri
> /Applications/freesurfer/bin/mri_nu_correct.mni
> --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000
> --distance 50
> nIters 1
> $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
> Darwin vpn-89-206-117-41.uzh.ch 15.6.0 Darwin Kernel Version 15.6.0: Tue
Apr
> 11 16:00:51 PDT 2017; root:xnu-3248.60.11.5.3~1/RELEASE_X86_64 x86_64
> Tue Jul 18 09:20:41 CEST 2017
> Program nu_correct, built from:
> Package MNI N3, version 1.12.0, compiled by ni...@gust.nmr.mgh.harvard.edu
> (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08
> /usr/bin/bc
> tmpdir is ./tmp.mri_nu_correct.mni.37996
> /Users/clschr/Desktop/7T/t1/example/mri
> mri_convert orig.mgz ./tmp.mri_nu_correct.mni.37996/nu0.mnc -odt float
> mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.37996/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, -5.82077e-10, -4.65661e-10)
> j_ras = (-4.65661e-10, 0, -1)
> k_ras = (3.49246e-10, 1, 1.49012e-08)
> changing data type from uchar to float (noscale = 0)...
> writing to ./tmp.mri_nu_correct.mni.37996/nu0.mnc...
>
> --------------------------------------------------------
> Iteration 1 Tue Jul 18 09:20:45 CEST 2017
> nu_correct -clobber ./tmp.mri_nu_correct.mni.37996/nu0.mnc
> ./tmp.mri_nu_correct.mni.37996/nu1.mnc -tmpdir
> ./tmp.mri_nu_correct.mni.37996/0/ -iterations 1000 -distance 50
> [cls...@vpn-89-206-117-41.uzh.ch:/Users/clschr/Desktop/7T/t1/example/mri/]
> [2017-07-18 09:20:45] 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.37996/0/
> ./tmp.mri_nu_correct.mni.37996/nu0.mnc
> ./tmp.mri_nu_correct.mni.37996/nu1.imp
>
> Error: Composite mask volume is empty. Check for one of the following:
> 1) the user supplied mask is empty (all zeros)
> 2) the values within the region of interest are entirely less than one
> 3) the user supplied background threshold is too high
> 4) the intersection of the various masking options yields an empty mask
> nu_correct: crashed while running nu_estimate_np_and_em (termination
> status=65280)
> ERROR: nu_correct
> Darwin vpn-89-206-117-41.uzh.ch 15.6.0 Darwin Kernel Version 15.6.0: Tue
Apr
> 11 16:00:51 PDT 2017; root:xnu-3248.60.11.5.3~1/RELEASE_X86_64 x86_64
>
>
> Here is the header information of the image:
>
> % vpn-89-206-116-146:t1 clschr$ fslhd example.nii
> filename example.nii
>
> sizeof_hdr 348
> data_type FLOAT32
> dim0 3
> dim1 180
> dim2 256
> dim3 256
> dim4 1
> dim5 1
> dim6 1
> dim7 1
> vox_units Unknown
> time_units Unknown
> datatype 16
> nbyper 4
> bitpix 32
> pixdim0 0.000000
> pixdim1 0.800000
> pixdim2 0.781000
> pixdim3 0.781000
> pixdim4 0.006900
> pixdim5 0.000000
> pixdim6 0.000000
> pixdim7 0.000000
> vox_offset 352
> cal_max 0.0000
> cal_min 0.0000
> scl_slope 0.000000
> scl_inter 0.000000
> phase_dim 0
> freq_dim 0
> slice_dim 0
> slice_name Unknown
> slice_code 0
> slice_start 0
> slice_end 0
> slice_duration 0.000000
> time_offset 0.000000
> intent Unknown
> intent_code 0
> intent_name T1TFE
> intent_p1 0.000000
> intent_p2 0.000000
> intent_p3 0.000000
> qform_name Scanner Anat
> qform_code 1
> qto_xyz:1 -0.799974 0.003954 0.004913 71.792442
> qto_xyz:2 0.002648 0.755674 -0.197258 -65.335892
> qto_xyz:3 0.005892 0.197235 0.755663 -137.084869
> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
> qform_xorient Right-to-Left
> qform_yorient Posterior-to-Anterior
> qform_zorient Inferior-to-Superior
> sform_name Scanner Anat
> sform_code 1
> sto_xyz:1 -0.799974 0.003953 0.004907 71.792442
> sto_xyz:2 0.002648 0.755674 -0.197258 -65.335892
> sto_xyz:3 0.005886 0.197235 0.755663 -137.084869
> sto_xyz:4 0.000000 0.000000 0.000000 1.000000
> sform_xorient Right-to-Left
> sform_yorient Posterior-to-Anterior
> sform_zorient Inferior-to-Superior
> file_type NIFTI-1+
> file_code 1
> descrip phase=-y;TE=2.5;time=20170201134952;
> aux_file ;Philips;WIP MP2RAGE 0p
>
>
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