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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