Re: fMRI analysis question

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Jonathan Peelle

May 21, 2013, 4:14:02 PM5/21/13
to Min Kim,
Dear Min Kim,

Great! Thanks for your interest. Probably the best way to ask for AA help is to try the email list,, which I've CC'd here—there is more of a chance that at least one person will be able to help.

For installing AA, you will need to:

1) Download the files (e.g., as a ZIP folder - there should be a link for this labeled "ZIP" on the automaticanalysis github page.)

2) Unzip the archive. It will probably be called "automaticanalysis-master" - it doesn't matter, but to keep things simple you may just want to rename it "automaticanalysis".

3) Add the automaticanalysis folder to your Matlab path. You can do this by changing your Matlab preferences, or by using the "addpath" function in Matlab: addpath('/path/to/automaticanalysis').

This is all that is required for installation. However, it does take some time to get used to, and by the end you will have to learn at least a basic level of Matlab scripting in order to have success. We are hoping that over the next 6-12 months there will be better documentation for all of this, which may also help you along the way.

Good luck!

Best regards,


PS As far as I know, most of the people using/developing AA are on Unix-related computer systems. It may be that there are some things that will require tweaking to work on Windows. Perhaps someone else can chime in and correct me if I am wrong?

> Hello. I'm a post-doc in the Herbew University. I've been using SPM8 and would like to run AA script for SPM. I've found the webpage that I can download the AA program ( and I also found your email address there. However, the instruction for the installation is not enough for non-computer expert like me. Could you briefly explain me how to install the program on the window 7? Is there a special way to install a program that runs on Matlab? Should I need to download all the files on the webpage?
> Thanks,
> Min Kim

Jonathan Peelle, PhD
Assistant Professor
Department of Otolaryngology
Washington University in St. Louis
Office: (314) 362-9044 ||

Jonathan Peelle

May 30, 2013, 10:30:30 AM5/30/13
to Min Kim,
hi Maria,

> I've an error on this line:
> ??? Undefined function or method 'aarecipe' for input arguments of type
> 'char'.
> aap=aarecipe('aap_parameters_defaults.xml','aap_tasklist_typical_fmri.xml')
> I've checked that the folder includes the two files. Can you think of any
> possible reasons why?

It is probably a path issue. Make sure the automaticanalysis folder is
in your matlab path - if you type

which aa_ver4_nocloud

it should tell you that it found the function. If not, you will need
to add that path.

This only adds the top level directory though - for the
subdirectories, these get added when you run aa_ver4_nocloud.

After running aa_ver4_nocloud without a problem, then if you type

which aarecipe

you should get an answer (meaning it's in your path - and thus that
your script should work).

Hope this helps!

Best regards,


Jonathan Peelle

Jul 15, 2013, 11:39:02 AM7/15/13
to Min Kim,
Dear Maria,

> Another question I have is how to setup the path
> for the raw data saved in F drive. I believe the default is C, so I wrote in
> the script that the data is in "F:/data/fmri", but I've got an error message
> saying that ":" is not allowded. Do you have any idea?
> Paths in aa can only contain the characters a-z, A-Z, 0-9, _, -, ., /
> Your path aap.directory_conventions.rawdatadir=':' does not satisfy this.
> for help, see the aa wiki

I am CC'ing the AA discussion list because I'm not entirely sure of
this. I am not sure how many other AA users are on windows platforms,
so some of the path-checking and so on my be problematic. Can anyone
else confirm?

It would be good to know whether it is reasonable to try running AA on
windows at this point, or if that is something that won't be well
supported until sometime in the future.


Conor Wild

Jul 15, 2013, 11:49:22 AM7/15/13
to, Min Kim
Hi Jonathan and Maria (and everyone else!)

AA has been developed in Linux (and OSX), so you are definitely going to run into problems in Windows.  Paths are probably the first barrier, which you seem to have encountered, but there will likely be some other issues related to system commands (like rsync, mkdir, cp, etc.)  I can't say exactly how much work it will be to update AA to run in windows, but it will likely be a significant amount.

Unfortunately, I think the easiest solution is to use the UBUNTU windows installer (WUBI) to set up a UBUNTU partition.  

Sorry I can't offer more help at the moment.


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

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