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: 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
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: 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
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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you need to scale them. WHy do you have negative values? I would scale them so that the min is 0 and the mean is around 100 or so. In matlab it would be something like:
first copy 001.mgz to 001.orig.mgz
thne in matlab do: [v,M,mr] = load_mgh('001.orig.mgz') ; v = (v - min(v(:))) * 100; save_mgh(v, '001.mgz', M,mr);
I'm guessing about the 100. You could use hist to check where the peak of the distribution is and be more accurate if you want
cheers Bruce
On Tue, 18 Jul 2017, clemens.schroeder@uzh.ch wrote:
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: 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline%C2%A0. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
clemens.schroeder＠uzh.ch