devel-share dependency error

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Jonathan Peelle

Jan 15, 2014, 10:44:56 AM1/15/14
I updated to a current version of devel-share and am now getting the following error with aamod_coreg_noss:

Attempting to load stream from file /Users/peelle/experiments/MBSR/analysis02/aamod_coreg_noss_t1_00001/MBSR008_pre/stream_meanepi_outputfrom_aamod_coreg_noss_t1_00001.txt, but not found

Error using aas_log (line 58)
aa error

Error in aas_getfiles_bystream (line 20)
    aas_log(aap,true,sprintf('Attempting to load stream from file %s, but not found',inpstreamdesc));

Error in aamod_coreg_noss (line 43)
        meanepiImg = aas_getfiles_bystream(aap, subjInd, inStream);

The mean EPI image comes from aamod_realign_noreslice and is present in the aamod_coreg_noss module directory, so the files got copied correctly, but somehow the descriptive text files did not?

Any suggestions much appreciated. Thanks!


Conor Wild

Jan 15, 2014, 11:27:29 AM1/15/14
Hi Jonathan,

The problem is with aamod_realign_noreslice, not really with the dependencies.  aamod_realign_noreslice is very out of date, and describes the meanepi stream as a session level stream:

aap = aas_desc_outputs(aap,i,j,'meanepi',fn(1).name);

but meanepi is really a subject stream.  aamod_realign describes meanepi like this:

aap = aas_desc_outputs(aap,subj,'meanepi',fullfile(pth,fn(1).name));

You should probably use aamod_realign, and set the 'reslicewhich' option to 0.  

Maybe we should get rid of aamod_realign_noreslice.


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Conor Wild
Postdoctoral Fellow
Brain and Mind Institute
The University of Western Ontario
London, ON, N6A 5B7 

Jonathan Peelle

Jan 15, 2014, 4:18:32 PM1/15/14
Hi Conor,

Great, thanks! That fixed the problem.

In devel-share I have deleted aamod_realign_noreslice.m, but kept aamod_realign_noreslice.xml with mfile_alias='aamod_realign' (and appropriate changes in XML) so I don't think this will break anything.


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