Hi Samantha
I suspect this has to do with the sform being non-invertible (maybe Matt Webster can chime in as I don’t know why invalid sform would be problematic?).
One thing you can try is to use fslcpgeom to correct the ROI header using a T1. Another thing you can try is to use MNI space ROIs directly. Remember that in probtrackx2, ROIs can be defined in any space you like provided that you give the transformations to diffusion space.
Cheers
Saad
> On 2 Apr 2019, at 09:57, Samantha Baldi <[log in to unmask]> wrote:
>
> Dear Saad,
>
> Thanks a lot for your answer. I took my ROIs from different atlases (Harvard-Oxford, STN atlas and BNST mask from https://afni.nimh.nih.gov/BNSTM_Atlas), I thresholded them at different values using fslmaths, and I then registered them to T1 space using ANTs.
> I copy here the header information of the thresholded ROIs and the warped ROIs:
>
> ROI in MNI SPACE:
> size of header 348
> data_type FLOAT32
> dim0 3
> dim1 364
> dim2 436
> dim3 364
> dim4 1
> dim5 1
> dim6 1
> dim7 1
> vox_units mm
> time_units s
> datatype 16
> nbyper 4
> bitpix 32
> pixdim0 -1.000000
> pixdim1 0.500000
> pixdim2 0.500000
> pixdim3 0.500000
> pixdim4 1.000000
> pixdim5 1.000000
> pixdim6 1.000000
> pixdim7 1.000000
> vox_offset 352
> cal_max 0.000000
> cal_min 0.000000
> 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
> toffset 0.000000
> intent Unknown
> intent_code 0
> intent_name
> intent_p1 0.000000
> intent_p2 0.000000
> intent_p3 0.000000
> qform_name MNI_152
> qform_code 4
> qto_xyz:1 -0.500000 0.000000 -0.000000 90.000000
> qto_xyz:2 0.000000 0.500000 -0.000000 -126.000000
> qto_xyz:3 0.000000 0.000000 0.500000 -72.000000
> 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 MNI_152
> sform_code 4
> sto_xyz:1 -0.500000 0.000000 0.000000 90.000000
> sto_xyz:2 0.000000 0.500000 0.000000 -126.000000
> sto_xyz:3 0.000000 0.000000 0.500000 -72.000000
> 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 6.0.0
> aux_file
>
> ROI in T1 SPACE:
> size of header 348
> data_type FLOAT64
> dim0 4
> dim1 153
> dim2 191
> dim3 178
> dim4 1
> dim5 1
> dim6 1
> dim7 1
> vox_units mm
> time_units Unknown
> datatype 64
> nbyper 8
> bitpix 64
> pixdim0 1.000000
> pixdim1 1.000000
> pixdim2 0.976600
> pixdim3 0.976600
> pixdim4 1.000000
> pixdim5 0.000000
> pixdim6 0.000000
> pixdim7 0.000000
> vox_offset 352
> cal_max 0.000000
> cal_min 0.000000
> 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
> toffset 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 1.000000 0.000000 0.000000 -76.000000
> qto_xyz:2 0.000000 0.976600 0.000000 -92.776993
> qto_xyz:3 0.000000 0.000000 0.976600 -86.429100
> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
> qform_xorient Left-to-Right
> qform_yorient Posterior-to-Anterior
> qform_zorient Inferior-to-Superior
> sform_name Scanner Anat
> sform_code 0
> sto_xyz:1 0.000000 0.000000 0.000000 0.000000
> sto_xyz:2 0.000000 0.000000 0.000000 0.000000
> sto_xyz:3 0.000000 0.000000 0.000000 0.000000
> sto_xyz:4 0.000000 0.000000 0.000000 1.000000
> sform_xorient Unknown
> sform_yorient Unknown
> sform_zorient Unknown
> file_type NIFTI-1+
> file_code 1
> descrip
> aux_file
>
> Do you think that there is a problem there then? Is what you see here consistent with what you thought about a wrong qform? (or sform?)
>
> Best,
> Sam
>
> ########################################################################
>
> To unsubscribe from the FSL list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
########################################################################
To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
|