I recently moved form a relatively bog standard ~whole-brain EPI sequence with 3mm isotropic voxels to a 2x2x3mm sequence with axial slice acquisition, running parallel to the hippocampus on our Siemens Skyra scanner (as we only have 30 slices, we're getting somewhat restricted coverage of the brain).
Using data acquired under the old protocol, I had been able to run B0unwarping without error through the GUI. However, using the new protocol (holding everything else constant), I keep running into a non-terminal error when attempting B0unwarping. I've tweaked the field map parameters a few times, but that doesn't eliminate the appearance of the error messages. In all cases, the field map is acquired with the same slice prescription, FoV, thickness, skip, pixel resolution, and matrix size as the EPI. I've also tried running the unwarping procedure using FSL 5.
Specifically, the error ("WARNING:: Inconsistent orientations for individual images in pipeline! Will use voxel-based orientation which is probably incorrect - *PLEASE CHECK*!") crops up initially when making the FM_UD_fmap_mag_brain_mask and then reoccurs whenever the mask (or its progeny) is used in the unwarping process (see the snippet of the full log, below).
I looked at the header information for the images going into the first call to fslmaths that yielded the error (pasted below), but I didn't spot any obvious problems there, but perhaps I'm missing something.
Might you have any thoughts as to what might be going wrong/what I can do to check/fix the issue?
Greatly appreciated,
Justin Hulbert
FM_UD_fmap:
sizeof_hdr 348
data_type FLOAT32
dim0 3
dim1 128
dim2 116
dim3 30
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 16
nbyper 4
bitpix 32
pixdim0 0.0000000000
pixdim1 2.0000000000
pixdim2 2.0000000000
pixdim3 3.0000000000
pixdim4 1.0000000000
pixdim5 0.0000000000
pixdim6 0.0000000000
pixdim7 0.0000000000
vox_offset 352
cal_max 0.0000
cal_min 0.0000
scl_slope 1.000000
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
intent_p1 0.000000
intent_p2 0.000000
intent_p3 0.000000
qform_name Scanner Anat
qform_code 1
qto_xyz:1 -1.990752 -0.000000 0.288171 127.283028
qto_xyz:2 0.088222 1.776644 1.371294 -162.433670
qto_xyz:3 0.170659 -0.918443 2.652642 26.111223
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 -1.990752 0.000000 0.288169 127.283028
sto_xyz:2 0.088222 1.776644 1.371294 -162.433670
sto_xyz:3 0.170658 -0.918443 2.652642 26.111223
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 FSL4.1
aux_file 10-1-2.dcm
FM_UD_fmap_mag_brain_mask:
sizeof_hdr 348
data_type INT32
dim0 3
dim1 128
dim2 116
dim3 30
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 8
nbyper 4
bitpix 32
pixdim0 0.0000000000
pixdim1 2.0000000000
pixdim2 2.0000000000
pixdim3 3.0000000000
pixdim4 1.0000000000
pixdim5 0.0000000000
pixdim6 0.0000000000
pixdim7 0.0000000000
vox_offset 352
cal_max 0.0000
cal_min 0.0000
scl_slope 1.000000
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
intent_p1 0.000000
intent_p2 0.000000
intent_p3 0.000000
qform_name Scanner Anat
qform_code 1
qto_xyz:1 -1.990752 -0.000000 0.288171 127.283028
qto_xyz:2 0.088222 1.776644 1.371294 -162.433670
qto_xyz:3 0.170659 -0.918443 2.652642 26.111223
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 -1.990752 0.000000 0.288169 127.283028
sto_xyz:2 0.088222 1.776644 1.371294 -162.433670
sto_xyz:3 0.170658 -0.918443 2.652642 26.111223
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 FSL4.1
aux_file 10-1-2.dcm
FM_UD_fmap_mag_brain_mask_inv:
sizeof_hdr 348
data_type FLOAT32
dim0 3
dim1 128
dim2 116
dim3 30
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 16
nbyper 4
bitpix 32
pixdim0 0.0000000000
pixdim1 2.0000000000
pixdim2 2.0000000000
pixdim3 3.0000000000
pixdim4 1.0000000000
pixdim5 0.0000000000
pixdim6 0.0000000000
pixdim7 0.0000000000
vox_offset 352
cal_max 0.0000
cal_min 0.0000
scl_slope 1.000000
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
intent_p1 0.000000
intent_p2 0.000000
intent_p3 0.000000
qform_name Scanner Anat
qform_code 1
qto_xyz:1 -1.990752 -0.000000 0.288171 127.283028
qto_xyz:2 0.088222 1.776644 1.371294 -162.433670
qto_xyz:3 0.170659 -0.918443 2.652642 26.111223
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 -1.990752 0.000000 0.288169 127.283028
sto_xyz:2 0.088222 1.776644 1.371294 -162.433670
sto_xyz:3 0.170658 -0.918443 2.652642 26.111223
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 FSL4.1
aux_file 10-1-2.dcm
Progress Report / Log
Started at Fri Jan 18 16:01:59 EST 2013
Feat main script
/bin/cp /tmp/feat_9LLUoD.fsf design.fsf
/usr/local/fsl/bin/feat_model design
mkdir .files;cp /usr/local/fsl/doc/fsl.css .files;ln -s /usr/local/fsl/doc/images .files/images
/usr/local/fsl/bin/fsl_sub -T 94 -l logs -N feat2_pre -j featModelID /usr/local/fsl/bin/feat /mnt/cd/norman/hulbert/RIFdiff_ani2/fMRI_nii/13011701/RP1/RP1_5mm_NewFieldmap.feat/design.fsf -D /mnt/cd/norman/hulbert/RIFdiff_ani2/fMRI_nii/13011701/RP1/RP1_5mm_NewFieldmap.feat -I 1 -prestats
1990332
/usr/local/fsl/bin/fsl_sub -T 113 -l logs -N feat3_film -j 1990332 /usr/local/fsl/bin/feat /mnt/cd/norman/hulbert/RIFdiff_ani2/fMRI_nii/13011701/RP1/RP1_5mm_NewFieldmap.feat/design.fsf -D /mnt/cd/norman/hulbert/RIFdiff_ani2/fMRI_nii/13011701/RP1/RP1_5mm_NewFieldmap.feat -I 1 -film
1990333
/usr/local/fsl/bin/fsl_sub -T 3 -l logs -N feat4_post -j 1990333 /usr/local/fsl/bin/feat /mnt/cd/norman/hulbert/RIFdiff_ani2/fMRI_nii/13011701/RP1/RP1_5mm_NewFieldmap.feat/design.fsf -D /mnt/cd/norman/hulbert/RIFdiff_ani2/fMRI_nii/13011701/RP1/RP1_5mm_NewFieldmap.feat -poststats 0 0
1990334
/usr/local/fsl/bin/fsl_sub -T 30 -l logs -N feat5_reg -j 1990332 /usr/local/fsl/bin/feat /mnt/cd/norman/hulbert/RIFdiff_ani2/fMRI_nii/13011701/RP1/RP1_5mm_NewFieldmap.feat/design.fsf -D /mnt/cd/norman/hulbert/RIFdiff_ani2/fMRI_nii/13011701/RP1/RP1_5mm_NewFieldmap.feat -I 1 -reg
1990335
/usr/local/fsl/bin/fsl_sub -T 15 -l logs -N feat4_post -j 1990334,1990335 /usr/local/fsl/bin/feat /mnt/cd/norman/hulbert/RIFdiff_ani2/fMRI_nii/13011701/RP1/RP1_5mm_NewFieldmap.feat/design.fsf -D /mnt/cd/norman/hulbert/RIFdiff_ani2/fMRI_nii/13011701/RP1/RP1_5mm_NewFieldmap.feat -poststats 1 0
1990336
/usr/local/fsl/bin/fsl_sub -T 1 -l logs -N feat5_stop -j 1990332,1990333,1990336,1990335 /usr/local/fsl/bin/feat /mnt/cd/norman/hulbert/RIFdiff_ani2/fMRI_nii/13011701/RP1/RP1_5mm_NewFieldmap.feat/design.fsf -D /mnt/cd/norman/hulbert/RIFdiff_ani2/fMRI_nii/13011701/RP1/RP1_5mm_NewFieldmap.feat -stop
1990337
Prestats
/usr/local/fsl/bin/fslmaths /mnt/cd/norman/hulbert/RIFdiff_ani2/fMRI_nii/13011701/RP1/RP1 prefiltered_func_data -odt float
Total original volumes = 284
Deleting 5 volume(s) - BE WARNED for future analysis!
/usr/local/fsl/bin/fslroi prefiltered_func_data prefiltered_func_data 5 279
/usr/local/fsl/bin/fslroi prefiltered_func_data example_func 139 1
/usr/local/fsl/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -refvol 139 -rmsrel -rmsabs
refnum = 139
Original_refvol = 139
/bin/mkdir -p mc ; /bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc
/usr/local/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png
/usr/local/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png
/usr/local/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png
/bin/mkdir -p unwarp
/usr/local/fsl/bin/fslmaths ../example_func EF_D_example_func
/usr/local/fsl/bin/fslmaths /mnt/cd/norman/hulbert/RIFdiff_ani2/fMRI_nii/13011701/fieldmaps/fieldmap_phase_radsec01_brain FM_UD_fmap
/usr/local/fsl/bin/fslmaths /mnt/cd/norman/hulbert/RIFdiff_ani2/fMRI_nii/13011701/fieldmaps/fieldmap_magAVG_brain FM_UD_fmap_mag
/usr/local/fsl/bin/fslmaths FM_UD_fmap_mag FM_UD_fmap_mag_brain
/usr/local/fsl/bin/fslmaths FM_UD_fmap_mag -bin FM_UD_fmap_mag_brain_mask -odt short
/usr/local/fsl/bin/fslstats FM_UD_fmap_mag -V | awk '{ print }'
102817
/usr/local/fsl/bin/fslstats FM_UD_fmap_mag -v | awk '{ print }'
445440
/usr/local/fsl/bin/fslmaths FM_UD_fmap -abs -bin -mas FM_UD_fmap_mag_brain_mask -mul -1 -add 1 -bin FM_UD_fmap_mag_brain_mask_inv
WARNING:: Inconsistent orientations for individual images in pipeline!
Will use voxel-based orientation which is probably incorrect - *PLEASE CHECK*!
/usr/local/fsl/bin/cluster -i FM_UD_fmap_mag_brain_mask_inv -t 0.5 --no_table -o FM_UD_fmap_mag_brain_mask_idx
/usr/local/fsl/bin/fslstats FM_UD_fmap_mag_brain_mask_idx -R | awk '{ print }'
2.000000
/usr/local/fsl/bin/fslmaths FM_UD_fmap_mag_brain_mask_idx -thr 2.000000 -bin -mul -1 -add 1 -bin -mas FM_UD_fmap_mag_brain_mask FM_UD_fmap_mag_brain_mask
WARNING:: Inconsistent orientations for individual images in pipeline!
Will use voxel-based orientation which is probably incorrect - *PLEASE CHECK*!
/usr/local/fsl/bin/fslstats FM_UD_fmap -k FM_UD_fmap_mag_brain_mask -P 50
-142.227493
/usr/local/fsl/bin/fslmaths FM_UD_fmap -sub -142.227493 -mas FM_UD_fmap_mag_brain_mask FM_UD_fmap
/usr/local/fsl/bin/fslstats FM_UD_fmap_mag_brain -P 98
2034.000000
/usr/local/fsl/bin/fslmaths FM_UD_fmap_mag_brain -thr 1017.0 -bin FM_UD_fmap_mag_brain_mask50
/usr/local/fsl/bin/fslmaths FM_UD_fmap_mag_brain_mask -ero FM_UD_fmap_mag_brain_mask_ero
/usr/local/fsl/bin/fslmaths FM_UD_fmap_mag_brain_mask_ero -add FM_UD_fmap_mag_brain_mask50 -thr 0.5 -bin FM_UD_fmap_mag_brain_mask
WARNING:: Inconsistent orientations for individual images in pipeline!
Will use voxel-based orientation which is probably incorrect - *PLEASE CHECK*!
/usr/local/fsl/bin/fslmaths FM_UD_fmap -mas FM_UD_fmap_mag_brain_mask FM_UD_fmap
/usr/local/fsl/bin/fslmaths FM_UD_fmap_mag_brain_mask -ero FM_UD_fmap_mag_brain_mask_ero
/usr/local/fsl/bin/fugue --loadfmap=FM_UD_fmap --savefmap=FM_UD_fmap_tmp_fmapfilt -m FM_UD_fmap_mag_brain_mask --despike --despikethreshold=2.1
/usr/local/fsl/bin/fslmaths FM_UD_fmap_tmp_fmapfilt -sub FM_UD_fmap -mas FM_UD_fmap_mag_brain_mask_ero -add FM_UD_fmap FM_UD_fmap
/bin/rm -f FM_UD_fmap_tmp_fmapfilt* FM_UD_fmap_mag_brain_mask_ero* FM_UD_fmap_mag_brain_mask50* FM_UD_fmap_mag_brain_i*
/usr/local/fsl/bin/fslstats FM_UD_fmap -k FM_UD_fmap_mag_brain_mask -P 50
0.999084
/usr/local/fsl/bin/fslmaths FM_UD_fmap -sub 0.999084 -mas FM_UD_fmap_mag_brain_mask FM_UD_fmap
/usr/local/fsl/bin/fslstats FM_UD_fmap -R | awk '{ print }'
-456.358887
/usr/local/fsl/bin/fslmaths FM_UD_fmap -sub -456.358887 -add 10 -mas FM_UD_fmap_mag_brain_mask grot
/usr/local/fsl/bin/fslstats grot -l 1 -p 0.1 -p 95
219.432663 677.283447
/usr/local/fsl/bin/overlay 0 0 FM_UD_fmap_mag -a grot 219.432663 677.283447 grot
/usr/local/fsl/bin/slicer grot -s 3 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png fmap+mag.png
/usr/local/fsl/bin/sigloss -i FM_UD_fmap --te=0.03 -m FM_UD_fmap_mag_brain_mask -s FM_UD_fmap_sigloss
/usr/local/fsl/bin/fslmaths FM_UD_fmap_sigloss -mul FM_UD_fmap_mag_brain FM_UD_fmap_mag_brain_siglossed -odt float
WARNING:: Inconsistent orientations for individual images in pipeline!
Will use voxel-based orientation which is probably incorrect - *PLEASE CHECK*!
/usr/local/fsl/bin/fugue -i FM_UD_fmap_mag_brain_siglossed --loadfmap=FM_UD_fmap --mask=FM_UD_fmap_mag_brain_mask --dwell=0.00036 -w FM_D_fmap_mag_brain_siglossed --nokspace --unwarpdir=y-
/usr/local/fsl/bin/fugue -i FM_UD_fmap_sigloss --loadfmap=FM_UD_fmap --mask=FM_UD_fmap_mag_brain_mask --dwell=0.00036 -w FM_D_fmap_sigloss --nokspace --unwarpdir=y-
/usr/local/fsl/bin/fslmaths FM_D_fmap_sigloss -thr 0.9 FM_D_fmap_sigloss
The log then shows that the analysis continues without further error.
------------------
Here are the details of my EPI sequence:
Interleaved; Slices = 30; Dist. factor = 0; Orientation = T>C13.6 (axial); Phase enc. dir. = A >> P; AutoAlign = OFF; Phase oversampling = 0%; FoV read 256mm; FoV phase 90.6% (gives us a rectangular, rather than square FoV); Base Resolution = 128; Phase resolution = 100; Phase partial Fourier: Off; iPAT: GRAPPA, Accel. Factor PE: 2, Ref. lines PE: 58 Slice thickness = 3.0 mm; TR = 2000 ms; TE =30; FatSuppression = ON; Flip Angle = 71; Advanced Autoshim: ON; Bandwidth = 1562; EPI echo spacing = .72ms, but with iPAT acceleration factor = 2 I set the effective spacing for B0 unwarping to .72/2 = 0.36
And my field map:
TR = 1000ms; TE1 = 3.49; TE2 = 5.95; diff in TE = 2.46; Flip angle = 55; Bandwidth = 1502; Reconstruction: Magn/Phase (multiple series: Off); Fat suppression: OFF; Otherwise should be the same as the EPI, including slice prescription
What I did to prep the field map for unwarping:
#Average the two magnitude images (two are run for greater stability)
fslmaths $SUBJID/fieldmaps/fieldmap_magnitude01.nii.gz -add $SUBJID/fieldmaps/fieldmap_magnitude02.nii.gz -div 2 $SUBJID/fieldmaps/fieldmap_magnitudeAVG.nii.gz
#BET extraction, conversion to rad/sec and some smoothing for field map phase image (Skyra specific values):
# With phase values ranges (fslstats fieldmap_phase01 -R) are from -4096 to +4092, use this command to convert to rad/s to get it to a range of -1277 to +1277:
fslmaths $SUBJID/fieldmaps/fieldmap_phase01.nii.gz -mul 3.14159 -div 4096 -div 0.00246 $SUBJID/fieldmaps/fieldmap_phase_radsec01
fugue --loadfmap=$SUBJID/fieldmaps/fieldmap_phase_radsec01.nii.gz -s 2.0 --savefmap=$SUBJID/fieldmaps/fieldmap_phase_radsec_sm2
bet $SUBJID/fieldmaps/fieldmap_phase_radsec_sm2.nii.gz $SUBJID/fieldmaps/fieldmap_phase_radsec01_brain -Z
#BET extraction for field map magnitude image
bet $SUBJID/fieldmaps/fieldmap_magnitudeAVG.nii.gz $SUBJID/fieldmaps/fieldmap_magAVG_brain
Unwarp Direction: -y (for A>>P)
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