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

[Andrew Janke]

Yes mat1dump will only parse older MATLAB .mat files. Someone else
wrote a another one for newer ones out there somewhere...  however I
see you are using octave which is a far better solution.


a


On 24 May 2016 at 22:10, Gabriel A. Devenyi <gdevenyi at gmail.com> wrote:
> 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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