| Deletions are marked like this. | Additions are marked like this. |
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| ["sfa-sess"] -s avdk -a rtopy | ["sfa-sess"] -a rtopy -s sessid |
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| ||This will create avdk/bold/rtopy in which will be: || | ||This will create sessid/bold/rtopy in which will be: || |
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| ["sliceview-sess"] -s avdk -a rtopy -c eccen -map h -slice mos | ["sliceview-sess"] -s sessid -a rtopy -c eccen -map h -slice mos |
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| ["sliceview-sess"] -s avdk -a rtopy -c polar -map h -slice mos | ["sliceview-sess"] -s sessid -a rtopy -c polar -map h -slice mos |
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| ["surf-sess"] -s avdk -a rtopy -retinotopy fieldsign -flat | ["surf-sess"] -s sessid -a rtopy -retinotopy fieldsign -flat |
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| ["surf-sess"] -s avdk -a rtopy -retinotopy eccen -flat | ["surf-sess"] -s sessid -a rtopy -retinotopy eccen -flat |
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| ["surf-sess"] -s avdk -a rtopy -retinotopy polar -flat | ["surf-sess"] -s sessid -a rtopy -retinotopy polar -flat |
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| ["surf-sess"] -s avdk -a rtopy -c polar -flat | ["surf-sess"] -s sessid -a rtopy -c polar -flat |
1. Create Paradigm Files
For each session, create retinotopy paradigm files in each of the run directories. These paradigm files are different than an event-related or block paradigm (which list which stimulus was presented when). A retinotopy paradigm file has information about whether the run was an eccentricy or polar stimulus and in what direction the stimulus was presented.
For polar, the direction is indicates whether the spoke was traveling clockwise or counter-clockwise. For eccen, the direction is indicates whether the ring was expanding or contracting. The definition of what's positive and what's negative is arbitrary, though it must be consistent. If you don't have both directions, just use positive.
For example, if there were four runs (001, 002, 003, 004), two eccen and two polar, both in the positive and negative directions. Create a file (eg, rtopy.par) in each run. Assuming run 001 was eccen in the negative direction, then the rtopy.par for run 001 would look like:
stimtype eccen |
direction neg |
The polar type in the positive direction would look like this:
stimtype polar |
direction pos |
If needed, create a run-list file with the all retinotopy runs (regardless of whether it was eccen or polar).
2. Create the analysis:
["mkanalysis-sess.new"] \ |
-a rtopy \ |
-TR 2 \ |
-designtype retinotopy \ |
-paradigm rtopy.par \ |
-funcstem fmcsm5 \ |
-ncylcles 8 |
3. Run the analysis:
["sfa-sess"] -a rtopy -s sessid
||This will create sessid/bold/rtopy in which will be: ||
1. volume h-offset (the mean function intensity) |
2. eccen - eccentricity folder (with h volume) |
3. polar - polar folder (with h volume) |
4. View intermediate results
The task-related activation can be viewed as with any other contrast in a non-retinotopy application. Just use eccen or polar as the contrast and specify h as the map.
- The task-related activation for eccen can be viewed with:
- ["sliceview-sess"] -s sessid -a rtopy -c eccen -map h -slice mos
- ["sliceview-sess"] -s sessid -a rtopy -c polar -map h -slice mos
5. Cut the occipital patch
6. Run paint:
- ["paint-sess"] -a rtopy -s avdk
This will create map-imag-lh.w (the imaginary or sine part muliplied by the log10(sig)), map-real-lh.w (the real or cosine part muliplied both the polar and eccen. It will also create a directory called fieldsign in bold/rtopy in which fieldsign-lh (or -rh) along with fieldsignmask-lh will be found.
7. View final results
To view the field-sign on the flattend patch (occip.patch.flat):
- ["surf-sess"] -s sessid -a rtopy -retinotopy fieldsign -flat
To view the eccen on the flattend patch (occip.patch.flat):
- ["surf-sess"] -s sessid -a rtopy -retinotopy eccen -flat
To view the polar on the flattend patch (occip.patch.flat):
- ["surf-sess"] -s sessid -a rtopy -retinotopy polar -flat
To view the task-related polar activation on the flattend patch
- ["surf-sess"] -s sessid -a rtopy -c polar -flat