Thanks Rich,

Sounds like the problem is on the spm5b side...and I am forwarding this to the
spm listserv.   SPM5 is still under development...my understanding is that it
is supposed to be happy with the nifti format...but it sure seems to dislike
the single big nii file...I hope someone gets an opportunity to look into
it...and I certainly appreciate your work and patience on the issue.

-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]>:

> Okay, that makes me feel better.
>
> The file Virgin.nii is in good shape.  the file in the
> higher directory, blockfh.nii, has been modified by
> something besides AFNI to be somewhat incompatible.  Programs
> that modify input files make me uncomfortable.
>
> I don't think this is the source of your problems,
> though it might be related.  Unfortunately, this is
> going to have to go back to the SPM list.  Feel free
> to forward this message to the list, I can't post
> to the list from home.
>
> I can try to help you with the SPM side of things, but
> you'll have to walk me through the commands step by
> step.  It would go much faster if one of the SPM
> development team would look at it with you!
>
> rich
>
>
> -----Original Message-----
> From: [log in to unmask] [mailto:[log in to unmask]]
> Sent: Mon 8/1/2005 5:02 PM
> To: [log in to unmask]
> Subject: Re: [SPM] spm5 and nifti format
>
> I think I brought the wrong distribution from home and installed it. I'm
> mortified.
> At any rate, I have reinstalled afni and triple checked.  Just to assure
> you,
> here's what it said at the command line when I ran 3dAFNItoNIFTI:
>
> [dpat@charlie Test]> 3dAFNItoNIFTI blockfh+orig.
> ++ Program 3dAFNItoNIFTI: AFNI version=AFNI_2005_07_28_1636
>
> =============================================
> Here is what I'm uploading for you:
>
> DiannePatterson3:
> Afni  blockfh.nii  meanblockfh.nii  rp_blockfh.txt
>
> DiannePatterson3/Afni:
> blockfh+orig.BRIK  blockfh+orig.HEAD  Virgin.nii
>
> The stuff in the Afni subdirectory is untouched.  The stuff in the main
> directory has been subjected to realignment in spm5b. The problem remains.
>
> -Dianne
>
> Dianne K. Patterson Ph.D.
> Psychology, Room 217E
> (520) 626-4571
> Cognition and NeuroImaging Labs
> University of Arizona
> Tucson, AZ
>
>
> Quoting Rich Hammett <[log in to unmask]>:
>
>> That could cause certain errors, possibly even the problems you are
>> seeing in trying to use it with SPM.  I had a pretty serious flaw in
>> locating the origin in space before last week.
>>
>> However, this new problem I'm seeing in this file...I can't think of a way
>> that it could happen.
>>
>> Test it carefully with the new AFNI distro when you get a chance,
>> and send me one of those files you generate that you are absolutely
>> sure which version generated it, and no use with SPM, etc, just to
>> try to rule out other longshot errors.
>>
>> Thanks!  Hope we can fix this quickly.  If you happen to get
>> the files done in the evening, I tend to check my e-mail around
>> the clock, so I might be able to get to it even outside of
>> business hours.
>>
>> rich
>>
>> [log in to unmask] wrote:
>>
>>> Uh oh...I just rechecked and it looks like somehow my new afni install
> isn't
>>> here at work...not sure how I could have done this...but I'll figure it
>>> out and
>>> make it right...very sorry. Given how it worked at home, the results
>>> should be
>>> the same...but I'll fix it here and repost files for you.
>>>
>>> -Dianne
>>>
>>> Dianne K. Patterson Ph.D.
>>> Psychology, Room 217E
>>> (520) 626-4571
>>> Cognition and NeuroImaging Labs
>>> University of Arizona
>>> Tucson, AZ
>>>
>>>
>>> Quoting Rich Hammett <[log in to unmask]>:
>>>
>>> > Thanks.  This is kind of bizarre.  This particular thing shouldn't
>>> > affect the results, but it's
>>> > weird.
>>> >
>>> > Make sure you're using all of the latest version of AFNI that you just
>>> > downloaded to
>>> > generate these files with!
>>> >
>>> > rich
>>> >
>>> > [log in to unmask] wrote:
>>> >
>>> >> I certainly didn't modify them by hand as I don't even know what
>>> they are.
>>> >> I don't know whether spm modifies them.  How about if I generate a
>>> >> fresh one and
>>> >> upload it without touching it with spm?
>>> >>
>>> >> It should be there in a few minutes...let's say I'll call it
>>> >> DiannePatterson2.tgz.
>>> >>
>>> >> -Dianne
>>> >>
>>> >> Dianne K. Patterson Ph.D.
>>> >> Psychology, Room 217E
>>> >> (520) 626-4571
>>> >> Cognition and NeuroImaging Labs
>>> >> University of Arizona
>>> >> Tucson, AZ
>>> >>
>>> >>
>>> >> Quoting Rich Hammett <[log in to unmask]>:
>>> >>
>>> >> > 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
>>> >> > /  [log in to unmask]          sun dogs fire on the horizon
>>> >> > \                      meteor rain stars across the night
>>> >> > /                                this moment may be brief
>>> >> > \                                 but it can be so bright
>>> >>
>>> >
>>> >
>>> > --
>>> > \  Rich Hammett       http://afni.nimh.nih.gov
>>> > /  [log in to unmask]          sun dogs fire on the horizon
>>> > \                      meteor rain stars across the night
>>> > /                                this moment may be brief
>>> > \                                 but it can be so bright
>>>
>>
>>
>> --
>> \  Rich Hammett       http://afni.nimh.nih.gov
>> /  [log in to unmask]          sun dogs fire on the horizon
>> \                      meteor rain stars across the night
>> /                                this moment may be brief
>> \                                 but it can be so bright