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Hi Vasudev,

No - your functional and structural data should be in the resolution they were acquired in respectively, and should match the resolution of the images you used in the registration process. The dimensions you have quoted look like reasonable values for T1/functional EPI data.
To solve your problem, you need to identify the specific point of failure, and focus on fixing that. Refer to the list of steps in my previous email.
In your other email thread, it looked to me like the non-linear registration was not ideal - this could be caused by a poor brain extraction, or an atypical brain. In your most recent screenshot it looks like something more fundamental has gone wrong - I would hazard a guess that one of the files you have used is incorrect.
Paul
On Feb 20 2020, at 9:43 am, Dev vasu <[log in to unmask]> wrote:
> Dear Sir,
>
> - that all of the input files have the correct dimensions , is it necessary that dimensions of all functional and structural files should be same ?
>
> The Dimensions of all structural files is
> sizeof_hdr 348
> data_type FLOAT32
> dim0 3
> dim1 160
> dim2 256
> dim3 256
> dim4 1
> dim5 1
> dim6 1
> dim7 1
> vox_units mm
> time_units s
> datatype 16
> nbyper 4
> bitpix 32
> pixdim0 0.000000
> pixdim1 1.000000
> pixdim2 1.000000
> pixdim3 1.000000
> pixdim4 1.000000
> pixdim5 0.000000
> pixdim6 0.000000
> pixdim7 0.000000
> vox_offset 352
>
> Dimensions of all Functional files
>
> sizeof_hdr 348
> data_type INT16
> dim0 4
> dim1 64
> dim2 64
> dim3 46
> dim4 300
> dim5 1
> dim6 1
> dim7 1
> vox_units mm
> time_units s
> datatype 4
> nbyper 2
> bitpix 16
> pixdim0 0.000000
> pixdim1 3.000000
> pixdim2 3.000000
> pixdim3 3.000000
> pixdim4 2.500000
> pixdim5 1.000000
> pixdim6 0.253332
> pixdim7 47455.246094
> 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 3
> slice_name alternating_increasing_2
> slice_code 5
> slice_start 0
> slice_end 45
> 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
>
>
>
>
>
>
> On Thu, Feb 20, 2020 at 10:26 AM paul mccarthy <[log in to unmask] (mailto:[log in to unmask])> wrote:
> > Hi Vasudev,
> >
> > As I said in your other thread, this is due to a poor registration. Double check the following:
> > - that all of the input files have the correct dimensions
> > - The structural brain extraction is good
> > - The func-struc registration is good
> > - The struc-standard registration is good
> > - The process you used to generate highres2standard_warp_inv is valid
> >
> > Paul
> >
> > On Feb 19 2020, at 8:09 pm, Dev vasu <[log in to unmask] (mailto:[log in to unmask])> wrote:
> > > Dear all,
> > >
> > > I have done functional preprocessing using FEAT and i would like to perform seed based correlation for visual cortex seed regions, my seed is defined in MNI152 space.
> > >
> > > The seed and example_func.nii.gz are completely mismatched ( see picture ) , I have used Visual_thr_mask.nii.gz as seed ( see attachment) and tried to transform by doing
> > >
> > > applywarp -i Visual_thr_mask.nii.gz -r reg/example_func.nii.gz -o Visual_func
> > >
> > > --postmat=reg/highres2example_func.mat -w reg/highres2standard_warp_inv
> > >
> > > I dont understand what is the problem with my approach-could you please provide
> > >
> > > me some input.
> > >
> > >
> > >
> > >
> > >
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> > >
> > >
> >
> >
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>
>
>
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