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| 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 eccentricity or polar angle stimulus and in what direction the stimulus was presented. |
For each session, create retinotopy paradigm files in each of the run directories: ||.../session/bold/001/rtopy.par || ||.../session/bold/002/rtopy.par (etc.) || 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 eccentricity or polar angle stimulus and in what direction the stimulus was presented. |
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||stimtype eccen || ||direction neg || |
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---- || stimtype eccen || || direction neg || ---- |
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---- || stimtype polar || || direction pos || ---- If needed, create a run-list file with the all retinotopy runs (regardless of whether it was eccen or polar). |
||stimtype polar || ||direction pos || |
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| '''2. Create the analysis:''' | |
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||[[mkanalysis-sess.new]] \ || || -a rtopy \ || || -TR 2 \ || || -designtype retinotopy \ || || -paradigm rtopy.par \ || || -funcstem fmcsm5 \ || || -ncycles 8 || |
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| '''3. Run the analysis:''' | If needed, create a run-list file with the all retinotopy runs (regardless of whether it was eccen or polar). |
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| [[sfa-sess]] -a rtopy -s sessid |
'''2. Run preprocessing''' ||preproc-sess -surface self lhrh -fwhm 5 || |
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||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 angle folder (with h volume) || |
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| '''4. View intermediate results''' | |
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| 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. | |
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The task-related activation for eccen can be viewed with: [[sliceview-sess]] -s sessid -a rtopy -c eccen -map h -slice mos The task-related activation for polar can be viewed with: [[sliceview-sess]] -s sessid -a rtopy -c polar -map h -slice mos |
'''3. Create the analysis''' |
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'''5. Cut the occipital patch''' || FreeSurferOccipitalFlattenedPatch || |
In the example below there is a 30 second period, and 'rtopy.par' is the name of the paradign file from above. ||[[mkanalysis-sess.new|mkanalysis-sess]]\ || ||-a rtopy.self.?h \ || ||-surface self ?h \|| ||-TR 2 \ || ||-retinotopy 30 \ || ||-paradigm rtopy.par \ || |
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| '''6. Run paint:''' | |
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| [[paint-sess]] -a rtopy -s sessid |
'''4. Run the analysis:''' ||selxavg3-sess -a rtopy.self.?h -sf ...|| ||fieldsign-sess -a rtopy.self.?h -occip -sf ...|| '''5. View intermediate results''' a. Significance maps: ||tksurfer-sess -a rtopy.self.?h -s sessid|| b. Display raw angle: ||tksurfer-sess -a rtopy.self.?h -s sessid -map angle|| c. Display angle masked by sig: ||tksurfer-sess -a rtopy.self.?h -s sessid -map angle.masked|| d. Display field sign: ||tksurfer-sess -a rtopy.self.?h -s sessid -fieldsign|| '''6. Cut the occipital patch''' ||FreeSurferOccipitalFlattenedPatch || '''7. Run paint:''' . [[paint-sess]] -a rtopy -s sessid |
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| '''7. View final results''' | '''8. View final results''' |
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| [[surf-sess]] -s sessid -a rtopy -retinotopy fieldsign -flat |
. [[surf-sess]] -s sessid -a rtopy -retinotopy fieldsign -flat |
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| [[surf-sess]] -s sessid -a rtopy -retinotopy eccen -flat |
. [[surf-sess]] -s sessid -a rtopy -retinotopy eccen -flat |
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| [[surf-sess]] -s sessid -a rtopy -retinotopy polar -flat |
. [[surf-sess]] -s sessid -a rtopy -retinotopy polar -flat |
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| [[surf-sess]] -s sessid -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:
.../session/bold/001/rtopy.par |
.../session/bold/002/rtopy.par (etc.) |
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 eccentricity or polar angle 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 is positive and what is 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. Run preprocessing
preproc-sess -surface self lhrh -fwhm 5 |
3. Create the analysis
In the example below there is a 30 second period, and 'rtopy.par' is the name of the paradign file from above.
-a rtopy.self.?h \ |
-surface self ?h \ |
-TR 2 \ |
-retinotopy 30 \ |
-paradigm rtopy.par \ |
4. Run the analysis:
selxavg3-sess -a rtopy.self.?h -sf ... |
fieldsign-sess -a rtopy.self.?h -occip -sf ... |
5. View intermediate results
a. Significance maps:
tksurfer-sess -a rtopy.self.?h -s sessid |
b. Display raw angle:
tksurfer-sess -a rtopy.self.?h -s sessid -map angle |
c. Display angle masked by sig:
tksurfer-sess -a rtopy.self.?h -s sessid -map angle.masked |
d. Display field sign:
tksurfer-sess -a rtopy.self.?h -s sessid -fieldsign |
6. Cut the occipital patch
7. Run paint:
paint-sess -a rtopy -s sessid
This will create map-imag-lh.w (the imaginary or sine part multiplied by the log10(sig)), map-real-lh.w (the real or cosine part multiplied 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.
8. View final results
To view the field-sign on the flattened patch (occip.patch.flat):
surf-sess -s sessid -a rtopy -retinotopy fieldsign -flat
To view the eccen on the flattened patch (occip.patch.flat):
surf-sess -s sessid -a rtopy -retinotopy eccen -flat
To view the polar on the flattened patch (occip.patch.flat):
surf-sess -s sessid -a rtopy -retinotopy polar -flat
To view the task-related polar activation on the flattened patch:
surf-sess -s sessid -a rtopy -c polar -flat