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
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