Hi Justin,
I haven't seen that before and can't see why it would happen.
You don't need to even match the EPI and fieldmap for resolution or FOV, so it is definitely not related to that.
Can you send us an example dataset (via our upload site, details on our Support page in the FSL website)?
We can then hopefully figure out if this is important or not (it may be the case that you can just ignore it).
All the best,
Mark
On 20 Jan 2013, at 18:35, Justin Hulbert <[log in to unmask]> wrote:
> 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)
|