SVT_MNI9_5_3_MS_flt

purpose
usage
examples

Purpose:

This SVT command is used to statistically analyze the variations between groups of human brain functional volumes obtained under different stumulation paradigms.

You need to have all stereotactic data sets pre-processed according to the multi-subject part of the SVT manual. The output SVT volumes are 4 byte (floating point) per pixel stereotactic images of size 181x217y181z. The first image contains the positive and the second contains the negatively statistically significant voxels. Intensities of both SVT output images are in the range [0, infinity] and represent the exact Z-scores.

Usage:

SVT_MNI9_5_3_MS_flt FWHM Num_Files1grp A_1_Wp_2_T.img ... [[A_k_Wp_2_T.img]] R_1_Wp_2_T.img ... [[R_k_Wp_2_T.img]] SVT_MS_Pos.img SVT_MS_Neg.img

Usually we refer to the first paradigm as A (activation) and the second one as R (rest). Let A.img and R.img be the two volumes we are analyzing and let T.img be our anatomical reference (template, "avgedit.img"). We denote by A_2_R.img the warped-and-resliced (using any algorithm) A.img in R.img space. There are at least 3 different ways one can transform A.img and R.img in T.img space, see SVT manual.

In the above the following definitions are used:
FWHM The Full-Width-at-Half-Maximum (FWHM), e.g., 6.0, in the range [0.1;19.9] mm Num_Files1grp the number of volumes in one group (the two groups have an equal number of data sets A_1_Wp_2_T.img A(ctivation) paradigm data for subject 1, warped in T.img space A_k_Wp_2_T.img A(ctivation) paradigm data for subject k, warped in T.img space, 1<=k<=Num_Files1grp R_1_Wp_2_T.img R(est) paradigm data for subject 1, warped in T.img space R_k_Wp_2_T.img R(est) paradigm data for subject k, warped in T.img space, 1<=k<=Num_Files1grp Prob_Atlas.img The name of the file containing the probabilistic Atlas (lobes9_diff_intens.img) SVT_MS_Pos.img and SVT_MS_Neg.img The files where the (positive and negative) output of the multi-subject (MS) SVT statistical analysis will be saved

Examples:

./SVT_MNI9_5_3_MS_flt 6.0 Num_Files1grp ./A(1)Wp.img ... ./A(Num_Files1grp)Wp.img ./R(1)Wp.img ... ./R(Num_Files1grp)Wp.img ../lobes9_diff_intens.img ./A_R_SVT_MS_Pos.img ./A_R_SVT_MS_Neg.img

This command will use the post-processed groups of data (A's and R's are warped directly to the template, "avgedit.img", ICBM space) and the probabilistic partitioning information contained in "lobes9_diff_intens.img" to generate two multi-subject SVT output volumes (A_R_SVT_MS_Pos.img & A_R_SVT_MS_Neg.img) of the statistically significant differences between the two groups. Also look at the batch file "batch_SVT_MS". The FWHM is 6.0 mm. Note that the above example represents a single UNIX command-line.

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