Dear Jessica,
Thanks, this is useful. The error message seems to indicate that the
images are realigned and resliced within sessions but not across
sessions. When using Realign:Est&Reslice or Realign&Unwarp, do you all
the images in multiple sessions within the same module or did you
specify one module per session? The latter would explain the current
situation and a fix would be to implement the former.
Best regards,
Guillaume.
On 25/05/2021 09:32, Jessica Emily wrote:
> Dear Guillaume,
>
> this is the error message I received while trying to create the GLM with
> realigned and resliced (*uf / *rf) images:
>
> [-2.99755 0.0146489 0.132234 96.5791; 0.0212308 2.99542 0.18082
> -91.6535; 0.119227 -0.165099 3.29239 -63.2758]
> ...\fMRI_analysis\rawdata\subject1\session_1\cmrr_mb3ip2_Precon_FOV210_45slc_tr900_3x3x310gap_0013\uf2019-12-02_14-22-150800-00294-00294-1.nii
> [-2.99755 0.0146489 0.132234 96.5791; 0.0212308 2.99542 0.18082
> -91.6535; 0.119227 -0.165099 3.29239 -63.2758]
> ...\fMRI_analysis\rawdata\subject1\session_1\cmrr_mb3ip2_Precon_FOV210_45slc_tr900_3x3x310gap_0013\uf2019-12-02_14-22-150801-00295-00295-1.nii
> [-2.99755 0.0146489 0.132234 96.5791; 0.0212308 2.99542 0.18082
> -91.6535; 0.119227 -0.165099 3.29239 -63.2758]
> ...\fMRI_analysis\rawdata\subject1\session_1\cmrr_mb3ip2_Precon_FOV210_45slc_tr900_3x3x310gap_0013\uf2019-12-02_14-22-150802-00296-00296-1.nii
> .
> .
> .
> [-2.99131 0.0543026 0.243838 97.0224; 0.0492209 2.99877 -0.0774424
> -85.5381; 0.222855 0.0665612 3.29007 -74.1587]
> ...\fMRI_analysis\rawdata\subject1\session_2\cmrr_mb3ip2_Postcon_FOV210_45slc_tr900_3x3x310gap_0021\uf2019-12-09_15-13-170241-00784-00784-1.nii
> [-2.99131 0.0543026 0.243838 97.0224; 0.0492209 2.99877 -0.0774424
> -85.5381; 0.222855 0.0665612 3.29007 -74.1587]
> ...\fMRI_analysis\rawdata\subject1\session_2\cmrr_mb3ip2_Postcon_FOV210_45slc_tr900_3x3x310gap_0021\uf2019-12-09_15-13-170242-00785-00785-1.nii
> [-2.99131 0.0543026 0.243838 97.0224; 0.0492209 2.99877 -0.0774424
> -85.5381; 0.222855 0.0665612 3.29007 -74.1587]
> ...\fMRI_analysis\rawdata\subject1\session_2\cmrr_mb3ip2_Postcon_FOV210_45slc_tr900_3x3x310gap_0021\uf2019-12-09_15-13-170242-00786-00786-1.nii
>
> 25-May-2021 10:24:48 - Failed 'fMRI model specification'
> Error using spm_check_orientations (line 65)
> The orientations etc must be identical for this procedure.
> In file "...\fMRI_analysis\toolbox\spm12\spm_check_orientations.m"
> (v6894), function "spm_check_orientations" at line 65.
> In file "...\fMRI_analysis\toolbox\spm12\spm_fmri_spm_ui.m" (v7018),
> function "spm_fmri_spm_ui" at line 293.
> In file "...\fMRI_analysis\toolbox\spm12\config\spm_run_fmri_spec.m"
> (v6562), function "spm_run_fmri_spec" at line 386.
>
> No executable modules, but still unresolved dependencies or incomplete
> module inputs.
> The following modules did not run:
> Failed: fMRI model specification
> Skipped: Model estimation
>
> I hope it is fine that I cut the lines in between, because the list
> contained thousands of functional images.
>
> Thank you again!
>
> Best,
> Jessica
>
> On Mon, May 24, 2021 at 2:28 PM Guillaume Flandin <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Dear Jessica,
>
> SPM should display a list of all images and their orientation: could you
> share this with us in the hope it will gives us a hint of what your
> issue is?
>
> Best regards,
> Guillaume.
>
>
> On 20/05/2021 15:04, Jessica Emily wrote:
> > Dear Dr. Glauche,
> >
> >
> > thank you for the suggestion! In my pre-processing steps, I did
> try with
> > realign -> estimate and reslice, where I got *rf images and also with
> > realign & unwarp, where I got *uf images instead. Indeed, the
> > interpolation is also set with b-spline for both cases. However, I
> still
> > encountered the same error when I retrieved either *rf or *uf images,
> > but it was fine with normalized (*w) images.
> >
> > I was under the impression that aligning the orientations are
> completed
> > in realignment procedure and not in normalization. Maybe I have a
> false
> > understanding here?
> >
> > To update a bit, I got a suggestion from my supervisor to provide the
> > inverse segmented image (*iy_s) as the input in the normalization
> > routine in order to warp the voxels to its own T1 image, and not
> to MNI
> > space. Then again, the same question still holds, whether it is
> > justified to normalize again to the MNI space on contrast images from
> > MVPA analysis?
> >
> >
> > Thank you again!
> >
> >
> > Best,
> >
> > Jessica Emily Antono
> >
> >
> > On Thu, May 20, 2021 at 12:57 PM Volkmar Glauche
> > <[log in to unmask]
> <mailto:[log in to unmask]>
> > <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>> wrote:
> >
> > Dear Jessica,
> > you don't need to run a dummy normalisation step to reslice the
> > images. You may instead run Realign->Estimate&Reslice instead of
> > just Realign->Estimate. In order to minimise motion induced
> rounding
> > errors you should set the reslice interpolation option to b-spline
> > instead of trilinear.
> > Hope this helps,
> > Volkmar
> >
>
> --
> Guillaume Flandin, PhD
> Wellcome Centre for Human Neuroimaging
> UCL Queen Square Institute of Neurology
> London WC1N 3BG
>
--
Guillaume Flandin, PhD
Wellcome Centre for Human Neuroimaging
UCL Queen Square Institute of Neurology
London WC1N 3BG
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