Hi Claire,
Registering a label image to a scan image is not recommended. For optimal alignment you would want the original image that the labels were generated from, and use that to generate the “parc2anat.mat” transform. Note that this assumes the original image was a structural image ( e.g. T1 scan ) if the original image was something like a grey-matter segmentation, ideally you would want to generate similar segmentations of your subject structural images and use those as the reference when generating parc2anat.mat. The Parcels_combo image would then only be used in your final command, when it is transformed to rest-space.
Hope this helps,
Kind Regards
Matthew
> On 17 Jul 2016, at 12:52, Claire O'Callaghan <[log in to unmask]> wrote:
>
> Hi Matthew,
>
> Thanks for your reply.
>
> The parcels combo is a labeled image with uniquely labeled parcels covering the whole brain (grey matter).. I've included below the output from running "fslhd Parcels_combo.nii", in case that helps with more information about it.
>
> The one "Parcels_combo" image is intended to be used across all subjects, so that time series from the same regions are extracted across all subjects.
>
> Best wishes,
> Claire
>
>
>
> filename Parcels_combo.nii
>
> sizeof_hdr 348
> data_type FLOAT64
> dim0 4
> dim1 91
> dim2 109
> dim3 91
> dim4 1
> dim5 1
> dim6 1
> dim7 1
> vox_units mm
> time_units ms
> datatype 64
> nbyper 8
> bitpix 64
> pixdim0 0.000000
> pixdim1 2.000000
> pixdim2 2.000000
> pixdim3 2.000000
> pixdim4 1000.000000
> pixdim5 0.000000
> pixdim6 0.000000
> pixdim7 0.000000
> vox_offset 352
> cal_max 375.0000
> cal_min 0.0000
> scl_slope 0.000000
> scl_inter 0.000000
> phase_dim 0
> freq_dim 0
> slice_dim 2
> 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 huh?
> intent_p1 0.000000
> intent_p2 0.000000
> intent_p3 0.000000
> qform_name Scanner Anat
> qform_code 1
> qto_xyz:1 2.000000 0.000000 0.000000 -90.000000
> qto_xyz:2 0.000000 2.000000 0.000000 -126.000000
> qto_xyz:3 0.000000 0.000000 2.000000 -72.000000
> 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 1
> sto_xyz:1 2.000000 0.000000 0.000000 -90.000000
> sto_xyz:2 0.000000 2.000000 0.000000 -126.000000
> sto_xyz:3 0.000000 0.000000 2.000000 -72.000000
> sto_xyz:4 0.000000 0.000000 0.000000 1.000000
> sform_xorient Left-to-Right
> sform_yorient Posterior-to-Anterior
> sform_zorient Inferior-to-Superior
> file_type NIFTI-1+
> file_code 1
> descrip FreeSurfer matlab
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