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Recon

Your data should be in /mnt/mridata/[ProjectDir]

You want links to these data in /groups/Projects/[ProjectID]/data/

So...

cd into the place where you want to place the data. In this example, we will be reconning some retinotopy data for a project with ID 9999

So on the terminal, type....
 
cd /groups/Projects/P9999/data

If it doesn't already exist, make a subdirectory called 'RETINOTOPY'

mkdir RETINOTOPY


Change into the RETINOTOPY directory

cd RETINOTOPY


Make a data directory for the particular subject (in this case, we'll pretend we have a subject called R1111)

mkdir R1111

cd R1111

mkdir
20120523111836_P1194

cd 20120523111836_P1194

Next, start up matlab. You can use the most recent version if you're working with the modern release of VISTA. You will be in the directory you just made

matlab &

(Note - the trailing ampersand tells LINUX to start the process in the background. Basically you will still be able to type on the console later).

>>pwd


Now... we need to create the links between the actual data (on /mnt) and this directory where we can edit it.
This is a special matlab command called make_data_links. It needs two directory names. The subject R number and the long number telling you where the original data set is in the /mnt directory.

>>make_data_links('R1111','20120523111836_P1194')

This will go ahead and make a set of links ('symlinks'). You check that it's worked by typing ls -l

>>ls -l

... All the new linked directories should show up. Their permissions should be rwxrws---

Note the final 's'.

And note also: Don't >change< permissions without asking someone. YNIC has strange bit settings on their permissions and you will most likely break something.

Finally, we can run the recon script for YNiC data. This will bring up a GUI (a little set of menus) that ask you some questions about the data. Then the script turns the 'raw' scanner files into something that mrVista understands.

>>YNiC_prep('R1111','20120523111836_P1194')


Two GUIs will pop up, one after the other. In the first, you select the stages you want to run. Here, just >deselect' the DB query and the bottom two - I think these are to archive the data. Then a second GUI pops up so that we can enter scan-specific data.

You need to set the type of the different scans you ran. Specifically you should identify the inplane scan and set it to 'INPLANE' in the drop down. Then set all the functional scans to 'FUNCTIONAL'.

In the number columns, set the number skips to '0' (unless you know otherwise). And the number of cycles to whatever cycles you had in your retino scans. Typically 8

Then hit 'OK'. The recon should proceed.

At the end , you can type 'mlr' to look at your data.
>>mlr



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