Dear Jessica,
Not sure what the best answer is here but, yes, I would use both
sessions in the same Realign&Unwarp module. That would be enough to
estimate a GLM in subject space. What do you need the T1 for? If it's
just for visualisation (underlay) then you could coregister one T1 (or
the other one, or their average) to the mean functional scan.
Best regards,
Guillaume.
On 25/05/2021 10:14, Jessica Emily wrote:
> Dear Guillaume,
>
> thank you for the quick response!
> Yes, indeed, I did the Realign&Unwarp separately for each session.
> Could I ask for some further guidance: the session term in my case means
> two different days of scanning (i.e. two different T1 images).
> Is the solution still hold to run the module on both sessions?
> Because afterwards I coregistered the realigned images of each
> corresponding session to their own T1 images.
>
> Best regard,
> Jessica
>
> On Tue, May 25, 2021 at 10:53 AM Guillaume Flandin <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> 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]>
> > <mailto:[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]>>
> > > <mailto:[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
>
--
Guillaume Flandin, PhD
Wellcome Centre for Human Neuroimaging
UCL Queen Square Institute of Neurology
London WC1N 3BG
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