Index TableOfContents

Name

roisummary-sess - outputs data from ["func2roi'] in ASCII format

Synopsis

roisummary-sess -sumfile (filename) -roidef (roidefname) -analysis (analysisname) -s (subjectname) or -sf (subjectfilename) -d (directory)

Arguments

Positional Arguments

none

Required Flagged Arguments

-sumfile filename

name of file in which to store the summary

-roidef name

name of ROI definition

-analysis name

source is averaged data from analysis

-sf sessidfile ...

-s sessid ...

-df srchdirfile ...

-d srchdir ...

Optional Flagged Arguments

-transpose

put sessid info on a row instead of a col

-excludesessid

do not include sess id in table

Description

Often, one wants to pool all the ROI averages across sessions into a single table so that they can be read into a statistics package for more elaborate analysis. The results from {\bf func2roi-sess} can be collected into such a table using {\bf roisummary-sess}, which has the following options:

Use -sumfile to specify the name of the file in which to store the ascii results. The ROI is specified with {\em -roidef}. Without any other options, roisummary-sess will get the ROI results from each session and store them into the summary file. Each session will have its own column, and each row represents a different measurement according to the following scheme as outlined in Outputs.

Outputs

1. session id - text identifier of the session

2. nlabel - number of functional voxels in the structural label regardless of whether they met the functional criteria.

3. nroi - number of functional voxels in the final mask (ie, ones that met the structural and functional criteria.

4. offset - mean functional baseline offset within the ROI (good for computing percent signal changes)

5. eresstd - standard deviation of the residual error. This is a measure of the variance left unexplained by the task.

6. DOF - degrees of freedom in $eresstd$. This can be used to asses whether there is a difference among the sessions in the DOF as could happen if some runs were excluded in some sessions and not in others.

7. TER - temporal resolution (in seconds) of the hemodynamic estimation. This is not a data value. This value is set at the time of mkanalysis-sess and is included here to facilitate plotting the results that follow. All sessions should have the same value.

8. tPreStim - time (in seconds) of the prestimulus baseline used in hemodynamic estimation. This is not a data value. This value is set at the time of {\bf mkanalysis-sess} and is included here to facilitate plotting the results that follow. All sessions should have the same value.

9. nconditions - number of conditions (excluding null condition). All sessions should have the same value.

10. nestspercond - number of estimates per conditions. For block analyses, this will have a value of 1. For event-related analyses, the value will equal to the number of points in the time window.

11. There will be nconditions times nestspercond numbers starting at this row. The first set of nestspercond numbers are the values for the first condition, the second set of nestspercond numbers are the values for the second condition, etc. Percent signal change can be obtained by dividing these numbers by offset and multiplying by 100.

The format of this table can be modified slightly with the -transpose and excludesessid flags. The -transpose flag creates the same table except that the data for the session is placed on a row instead of in a column. The -excludesessid flag will eliminate the session id row from the data. The -excludesessid is provided because some software does not allow data tables with text and numbers.

Examples

Example 1

roisummary-sess -sumfile fusi-avf-pos-2.dat -roidef fusi-avf-pos-2

This will create a file called fusi-avf-pos-2.dat in which you will find two columns. The contents will look something like the following (not including the text after the \#'s):

s1 s2 # session identifiers 480 467 # number of functional voxels in the fusiform 127 177 # number of active voxels 1117.06 1242.86 # average baseline activity 8.24 7.29 # std dev of residual error 574 574 # DOF 2.0 2.0 # TER = TR 4.0 4.0 # tPreStim 3 3 # number of conditions 9 9 # number of estimates per condition

-0.1867 -1.4410 # condition 1, 2 sec before stimulus onset

-0.2199 -0.2157 # condition 1, 2 sec after stimulus onset

-0.0956 1.1908 # condition 2, 4 sec before stimulus onset -0.8323 -1.2025 # condition 2, 2 sec before stimulus onset

-0.9678 0.0275 # condition 2, 2 sec after stimulus onset

-0.4462 -0.9337 # condition 2, 8 sec after stimulus onset

Example 2

command foo -i f -o out -f fvalue

description

Bugs

None

See Also

["func2roi-sess"]

Links

FreeSurfer, FsFast

Methods Description

description
description

References

["References/Lastname###"]

Reporting Bugs

Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>

Author/s

JaneSmith