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vinod
Average Member
USA
68 Posts |
 Posted - Jul 23 2007 : 3:52:31 PM
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Are the default BIAC tools on golgi the same as the ones on gall? I am asking this question because I can open some of the FSL output files using readmr when I am running matlab locally but it doesnt work from golgi.
Vinod |
Vinod Venkatraman
IPCN Graduate Student
Huettel Lab
"UNIX is basically a simple operating system, but you have to be a genius to understand the simplicity." - Dennis Ritchie |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Jul 23 2007 : 4:00:18 PM
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| Please post more details about the problem. Do you get error messages? |
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vinod
Average Member
USA
68 Posts |
Posted - Jul 23 2007 : 4:18:45 PM
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Sorry, here it is.. And I run the exact same command in the same data directory from gall and it works fine.
>> data = readmr('cope1_std.nii.gz');
??? Error using ==> readmr
Can't figure out type for file "cope1_std.nii.gz"
>> which readmr
/usr/local/MATLAB/BIAC/mr/readmr.m
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Jul 23 2007 : 4:18:50 PM
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| I have just released a fix to showsrs2 that affected early versions of MATLAB (like the one installed on golgi). Let me know if that your problem. |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Jul 23 2007 : 4:24:22 PM
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Sorry, my bugfix release was to the "gall" copy. The version in /usr/local/MATLAB is older. You can use the latest "gall" version by executing the following:
export BIACMATLABROOT=${HOME}/net/gall/programs/MATLAB/BIAC
env MATLAB_JAVA=/usr/java14/jre matlab -jvm
I have been using this with success, and if this works for you and others we can make this the default on golgi. |
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vinod
Average Member
USA
68 Posts |
Posted - Jul 23 2007 : 4:32:55 PM
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The "gall" copy works fine for me.
On a similar note, is there a compilation/documentation of all the BIAC tools available? If not detailed help, atleast a list of names with a one-line description of what the function does? I have come across a lot of useful functions like readmr, showsrs2, overlay2 etc. by hearing it being mentioned by other people and I am sure there are other similar useful functions available that I am not even aware of! |
Edited by - vinod on Jul 23 2007 4:33:42 PM |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Jul 23 2007 : 4:41:12 PM
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| In the "general" and "mr" subdirectories of the tools are Contents.m files, which should have all the functions listed. I think these are supposed to interface with the MATLAB help system, but not sure how. |
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josh.bizzell
BIAC Staff
USA
118 Posts |
Posted - Jul 23 2007 : 5:44:15 PM
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If you use the help command at the Matlab command prompt, you'll get a description of all the tools in a particular folder (if there is a Contents.m file):
>> help \\Gall\Programs\MATLAB\BIAC\mr
-Josh |
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BIAC tools on golgi
