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-bounces@nmr.mgh.harvard.edu schrieb: ----- An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Von: Bruce Fischl Gesendet von: freesurfer-bounces@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.schroeder@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 nicks@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 [clschr@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:
- the user supplied mask is empty (all zeros)
- the values within the region of interest are entirely less than one
- the user supplied background threshold is too high
- 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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