Hi Jack,
Did you make symbolic links or use the Finder's own Mac alias mechanism?
If it was the latter then it creates rather strange files that normal
unix commands
can't cope with. If you try using symbolic links instead (using "ln
-s") then
everything should work fine. I suspect that it is this if you are only
having the
problem on a Mac.
Glad to hear that the other problem is resolved (or non-existent!)
:)
All the best,
Mark
Jack Grinband wrote:
>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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