Diff for "FsFastIndividualRetinotopyAnalysis"

Differences between revisions 2 and 9 (spanning 7 versions)

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.

mkanalysis-sess\

-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 ...

5. Create the field sign map:

fieldsign-sess -a rtopy.self.?h -occip -sf ...

This command assumes that you have created an occipital patch. If you have not, either do so

FreeSurferOccipitalFlattenedPatch

or run with -sphere instead of -occip.

6. View individual 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

-  ⇤ ← Revision 2 as of 2005-11-17 15:03:33 → 
  Size: 3263
  Editor: icebox
  Comment:
+   ← Revision 9 as of 2011-02-23 11:56:39 → ⇥
  Size: 2502
  Editor: tanha
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 3:
-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 each session, create retinotopy paradigm files in each of the run directories:
||.../session/bold/001/rtopy.par ||
||.../session/bold/002/rtopy.par (etc.) ||
-Line 5:
+Line 7:
-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.
+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.
-Line 8:
+Line 15:
+||stimtype  eccen ||
||direction neg ||
-Line 9:
+Line 18:
-----
|| stimtype  eccen ||
|| direction neg ||
----
-Line 15:
+Line 22:
-----
|| 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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+Line 26:
-'''2. Create the analysis:'''
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-||["mkanalysis-sess.new"] \ ||
|| -a rtopy   \ ||
|| -TR 2   \ ||
|| -designtype retinotopy  \ ||
|| -paradigm rtopy.par  \ ||
|| -funcstem fmcsm5  \ ||
|| -ncylcles 8 ||
-Line 35:
+Line 28:
-'''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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+Line 30:
-["sfa-sess"] -a rtopy -s sessid
+'''2. Run preprocessing'''
||preproc-sess -surface self lhrh -fwhm 5 ||
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+Line 33:
-||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) ||
-Line 44:
+Line 34:
-'''4. View intermediate results'''
-Line 46:
+Line 35:
-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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+Line 36:
- 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'''
-Line 53:
+Line 38:
-'''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  \ ||
-Line 56:
+Line 46:
-'''6. Run paint:'''
-Line 58:
+Line 47:
-  ["paint-sess"] -a rtopy -s avdk
-Line 60:
+Line 48:
-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.
-Line 63:
+Line 49:
-'''7. View final results'''
+'''4. Run the analysis:'''
-Line 65:
+Line 51:
-To view the field-sign on the flattend patch (occip.patch.flat): 
  ["surf-sess"] -s sessid  -a rtopy -retinotopy fieldsign -flat
+||selxavg3-sess -a rtopy.self.?h -sf ...||
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+Line 53:
-To view the eccen on the flattend patch (occip.patch.flat): 
  ["surf-sess"] -s sessid  -a rtopy -retinotopy eccen -flat
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+Line 54:
-To view the polar on the flattend patch (occip.patch.flat): 
  ["surf-sess"] -s sessid  -a rtopy -retinotopy polar -flat
+'''5. Create the field sign map:'''
-Line 74:
+Line 56:
-To view the task-related polar activation on the flattend patch 
  ["surf-sess"] -s sessid  -a rtopy -c polar -flat
+||fieldsign-sess -a rtopy.self.?h -occip -sf ...||
This command assumes that you have created an occipital patch. If you have not, either do so 
||FreeSurferOccipitalFlattenedPatch ||
or run with -sphere instead of -occip.

'''6. View individual 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||