[MINC-users] Handling conversion from SPM "analyze" format?

[Gabriel A. Devenyi]

Thanks Andrew,

It looks like mat1dump doesn’t support the .mat format these files are in.

$ spm2xfm 1001794_wba_001.mat /tmp/test.xfm
Use of uninitialized value $P in hash element at
/opt/quarantine/minc-toolkit-extras/1.0/build/mat1dump line 61.
Use of uninitialized value in multiplication (*) at
/opt/quarantine/minc-toolkit-extras/1.0/build/mat1dump line 61.
Use of uninitialized value $P in hash element at
/opt/quarantine/minc-toolkit-extras/1.0/build/mat1dump line 62.
Use of uninitialized value in concatenation (.) or string at
/opt/quarantine/minc-toolkit-extras/1.0/build/mat1dump line 62.
Invalid type '1' in unpack at
/opt/quarantine/minc-toolkit-extras/1.0/build/mat1dump line 70.
Use of uninitialized value $dump[1] in substitution (s///) at
/opt/quarantine/minc-toolkit-extras/1.0/build/spm2xfm line 228.
Use of uninitialized value $dump[2] in substitution (s///) at
/opt/quarantine/minc-toolkit-extras/1.0/build/spm2xfm line 228.
Use of uninitialized value $dump[3] in substitution (s///) at
/opt/quarantine/minc-toolkit-extras/1.0/build/spm2xfm line 228.
Use of uninitialized value $dump[3] in substitution (s///) at
/opt/quarantine/minc-toolkit-extras/1.0/build/spm2xfm line 230.
Use of uninitialized value $dump[1] in join or string at
/opt/quarantine/minc-toolkit-extras/1.0/build/spm2xfm line 235.
Use of uninitialized value $dump[2] in join or string at
/opt/quarantine/minc-toolkit-extras/1.0/build/spm2xfm line 235.
Use of uninitialized value $dump[3] in join or string at
/opt/quarantine/minc-toolkit-extras/1.0/build/spm2xfm line 235.

Do you think octave may be able to parse out the matrix?
​

--
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
Affiliate, Department of Psychiatry
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

On Tue, May 17, 2016 at 4:53 PM, Andrew Janke <a.janke at gmail.com> wrote:

> Hi Gabriel,
>
> If you call ana2mnc as spm2mnc (make a symlink) it will attempt to
> make a MINC file with the correct orientation. There is also a spm2xfm
> that will convert the .mat to a .xfm file. It uses mat1dump (something
> I wrote in Perl many years ago).
>
>
> a
>
> On 18 May 2016 at 06:24, Gabriel A. Devenyi <gdevenyi at gmail.com> wrote:
> > Hi minc-users,
> >
> > I've inherited some data I think was touched by SPM at some point, as I
> > have a hdr/img/mat for each.
> >
> > Upon conversion (with ana2mnc) they're not oriented properly. I suspect I
> > can rectify this with information in the .mat file?
> >
> > Does anyone know how I can do this with the minc tools? Or will I have to
> > figure out something with SPM?
> >
> > --
> > Gabriel A. Devenyi B.Eng. Ph.D.
> > Research Computing Associate
> > Computational Brain Anatomy Laboratory
> > Cerebral Imaging Center
> > Douglas Mental Health University Institute
> > Affiliate, Department of Psychiatry
> > McGill University
> > t: 514.761.6131x4781
> > e: gdevenyi at gmail.com
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
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>