Hi Mark,
I think I found the problem!
When I ran flirt from the command line, I got the same error message. When I ran FEAT (reg only)
I got the following message when loading the highres file:
Warning: standard image not valid
I only get this message on the Mac, not on the Sun. I tried loading several different feat
directories using several different "Main structural images" and it resulted in the same error every
time. I did not get any errors when I loaded different "Standard space" images.
WRT the previous reg problem, I couldn't replicate it. So... problem solved.
cheers,
jack
On Thu, 11 Mar 2004 11:38:52 +0000, Mark Jenkinson <[log in to unmask]> wrote:
>Hi Jack,
>
>Sounds like you are doing the right things.
>The .xfm files are for MEDx and are just included for historical
>reasons - you can ignore them.
>
>As for the standard - I'm not sure what is wrong. The error
>message is definitely what I'd expect if the standard was wrong
>or missing. What happens if you run the offending flirt command
>on its own at the command line? And did you create the appropriate
>directories and files in C1-ISI-C2+.feat or just C1-ISI-C2.feat ?
>
>If this doesn't help, then send us a full directory listing (ls -l) of
>your feat and feat/reg directories, together with the avwhd output
>for the standard and example_func images.
>
>All the best,
> Mark
>
>P.S. Did you have any luck with your other registration problem?
>
>
>
>Jack Grinband wrote:
>
>>Hi All,
>>I'm having some trouble registering my feat directories. I used FEAT to run a bunch of first
level
>>analyses without doing registration. In a separate step I ran FLIRT and created an
>>example_func2highres and an example_func2standard. I then created a reg directory inside
.feat/
>>and placed the example_func2standard.mat and aliases to example_func.hdr/.img,
highres.hdr/
>>.img, and standard.hdr/.img. I got the following error when doing the higher level analysis:
>>
>>---------------------------------
>>Started higher-level FEAT at Wed Mar 10 23:47:00 EST 2004 on sunbolt
>>
>>/bin/cp /tmp/feat_p9a4a2.fsf design.fsf
>>
>>/export/apps/fsl_3.1/bin/feat_model design
>>
>>/export/apps/fsl_3.1/bin/featregapply /home/jgrinband/data/decide/jg/decide6/r1/C1-ISI-
>>C2+.feat
>>
>>/export/apps/fsl_3.1/bin/flirt -ref reg/standard -in example_func.hdr -out reg_standard/
>>example_func.hdr -applyxfm -init reg/example_func2standard.mat -interp sinc -datatype
float
>>AvwOpen: Error while reading header!: Error 0
>>ERROR: Could not open image reg/standard
>>Image Exception : #8 :: Attempted to use affine transform with no voxels in vout
>>Abort - core dumped
>>---------------------------------
>>
>>I am able to open standard.img in the FSLviewer without a problem and it's in a directory that I
>>have read permissions for. I've deleted and created the aliases to standard.img/hdr several
times.
>>
>>Any ideas what could be going wrong?
>>
>>Also, which files need to be in the reg directory for creating reg_standard? For example, I don't
>>have highres2standard.xfm and I'm not sure how to create it (or what it's used for).
>>thanks a lot,
>>
>>jack
>>
>>
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