Diff for "FsFastIndividualRetinotopyAnalysis"

Differences between revisions 2 and 11 (spanning 9 versions)

This page describes how to run the retinotopy analysis of the FreeSurfer Functional Analysis Stream (FS-FAST) version 5.X. You will need to know how to run FS-FAST for genernal task related studies. See http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt for more info.

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. THESE ARE SIMPLE TEXT FILES! DO NOT CREATE THEM WITH MS WORD!

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 (see 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 11 as of 2011-02-23 12:00:04 → ⇥
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  Editor: tanha
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
+This page describes how to run the retinotopy analysis of the FreeSurfer Functional Analysis Stream (FS-FAST) version 5.X. You will need to know how to run FS-FAST for genernal task related studies. See http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt for more info.
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+Line 6:
-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 10:
-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. THESE ARE SIMPLE TEXT FILES! DO NOT CREATE THEM WITH MS WORD!

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 18:
+||stimtype  eccen ||
||direction neg ||
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+Line 21:
-----
|| stimtype  eccen ||
|| direction neg ||
----
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+Line 25:
-----
|| 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 29:
-'''2. Create the analysis:'''
-Line 27:
+Line 30:
-||["mkanalysis-sess.new"] \ ||
|| -a rtopy   \ ||
|| -TR 2   \ ||
|| -designtype retinotopy  \ ||
|| -paradigm rtopy.par  \ ||
|| -funcstem fmcsm5  \ ||
|| -ncylcles 8 ||
-Line 35:
+Line 31:
-'''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 33:
-["sfa-sess"] -a rtopy -s sessid
+'''2. Run preprocessing'''
||preproc-sess -surface self lhrh -fwhm 5 ||
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+Line 36:
-||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) ||
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+Line 37:
-'''4. View intermediate results'''
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+Line 38:
-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 39:
- 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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+Line 41:
-'''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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+Line 49:
-'''6. Run paint:'''
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+Line 50:
-  ["paint-sess"] -a rtopy -s avdk
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+Line 51:
-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.
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+Line 52:
-'''7. View final results'''
+'''4. Run the analysis:'''
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+Line 54:
-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 56:
-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 57:
-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 59:
-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 
(see 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||