Further question...The file that I am looking at ('blockfh.nii') has some
things in it that I don't believe are possible to get out of AFNI.
Specifically,
the qform_code and sform_code are different, whereas the last line that
references either one of them in my output code is 'sform_code =
qform_code'.
Does SPM modify input files? Did you modify this one by hand?
rich
[log in to unmask] wrote:
> Dear Group,
>
> Following Richard Hammet's suggestion (below), I updated my afni
> version last
> night (It claims it is now AFNI_2005_07_28_1636) and regenerated the
> *.nii
> file. I updated spm5b with updates206. I tried realignment on the
> *.nii file
> and it had all the telltale signs of still having the problem: It took
> seconds
> to generate the mean image, no translation, rotation plots were
> generated, the
> rp*.txt file of translations rotations has only one row etc...do I
> correctly
> suspect that the *.nii file is being understood as a single volume
> instead of
> 125 volumes?
>
> So, I suppose I can use img/hdr pairs as we have in previous versions
> of spm.
> That seems to work fine.
>
> However, I'd like to see this single file *.nii work.
>
> Is there some other way to generate the *.nii file?
> Is there some way, in spm, to see whether spm understands the file to
> have
> multiple volumes? When I display my *.nii file, it claims the
> dimensions are
> 64x64x30...shouldn't it be telling me 64x64x30x125??
>
> Thankyou,
>
> Dianne
>
> Dianne K. Patterson Ph.D.
> Psychology, Room 217E
> (520) 626-4571
> Cognition and NeuroImaging Labs
> University of Arizona
> Tucson, AZ
>
>
> Quoting "Hammett, K. Richard (NIH/NIMH)" <[log in to unmask]>:
>
> > Please update your AFNI distribution. Several things have been
> > improved and errors fixed in the last week or so in the NIfTI
> > support.
> >
> > rich
> >
> >
> > -----Original Message-----
> > From: Dianne Patterson [mailto:[log in to unmask]]
> > Sent: Fri 7/29/2005 7:42 PM
> > To: [log in to unmask]
> > Subject: [SPM] spm5 and nifti format
> >
> > Dear Group,
> >
> > I have just run through a simple block dataset (preprocessing and
> analysis)
> > in
> > spm5 using img and hdr files written by afni's 3dAFNItoANALYZE.
> This worked
> > very easily.
> >
> > I also tried to run through using a *.nii file written by afni
> > 3dAFNItoNIFTI,
> > but this failed. I could view the *.nii file. It seemed that spm5 did
> > realignment, normalization and smoothing for me (it was EXTREMELY fast,
> > though...2 seconds for realignment for 125 volumes and didn't
> produce graphs
> > of
> > translation, rotation etc.) and when I tried to specify the design, my
> > matrix
> > was empty. I wasn't trying to do anything fancy, just a classic
> analysis.
> >
> > Is there a problem with handling the nifti format (or maybe a
> trick)? I can
> > scroll through all the timepoints in afni...so they seem to be there.
> >
> > Any suggestions would be appreciated.
> >
> > Thanks,
> >
> >
> > Dianne
> >
> > Dianne K. Patterson Ph.D.
> > Psychology, Room 217E
> > (520) 626-4571
> > Cognition and NeuroImaging Labs
> > University of Arizona
> > Tucson, AZ
>
--
\ Rich Hammett http://afni.nimh.nih.gov
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