Dear Freesurfer's experts,

I'm trying to run a ROIs mean intensity analysis using mri_segstat.
I'm using as an input contrast maps created with mkcontrast-sess and selxavg3-sess (block-design experiment) and as masks, some labels created on the surface with a retinotopic analysis.

I noticed that all my outputs with the same label have the same values, regardless of the contrast map that I'm giving as an input. However, if I plot the contrast maps on the surface I can clearly see that there are differences, so also the mean signal should be different.

Maybe I'm not running the command correctly:

mri_segstats --i z.nii.gz --slabel sub1 lh lh.V2dorsal_sub1.label --sfavg lh.V2dorsal_sub1_condition1_avg --snr --sum lh.V2dorsal_sub1_condition1_sum

These are two outputs from the same regions but with two different z maps as inputs.

I can also see that are indicated two different values as mean intensity, -0.95028 and 1.31525, what's the difference between them?

# Title Segmentation Statistics

# generating_program mri_segstats

# cvs_version $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $

# cmdline mri_segstats --i disorder/z.nii.gz --slabel AB lh /home/labs/malach/frastra/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg lh.V2dorsal_AB_disorder_avg --snr --sum lh.V2dorsal_AB_disorder_sum

# sysname Linux

# hostname access4.wexac.weizmann.ac.il

# machine x86_64

# user frastra

# anatomy_type surface

# SUBJECTS_DIR /home/labs/malach/frastra/freesurfer/subjects

# subjectname AB

# Label AB lh /home/labs/malach/frastra/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label

# InVolFile disorder/z.nii.gz

# InVolFileTimeStamp 2018/12/08 20:12:18

# InVolFrame 0

# ExcludeSegId

# Only reporting non-empty segmentations

# VertexArea_mm2 0.657815

# TableCol 1 ColHeader Index

# TableCol 1 FieldName Index

# TableCol 1 Units NA

# TableCol 2 ColHeader SegId

# TableCol 2 FieldName Segmentation Id

# TableCol 2 Units NA

# TableCol 3 ColHeader NVertices

# TableCol 3 FieldName Number of Vertices

# TableCol 3 Units unitless

# TableCol 4 ColHeader Area_mm2

# TableCol 4 FieldName Area

# TableCol 4 Units mm^2

# TableCol 5 ColHeader Mean

# TableCol 5 FieldName Intensity Mean

# TableCol 5 Units unknown

# TableCol 6 ColHeader StdDev

# TableCol 6 FieldName Itensity StdDev

# TableCol 6 Units unknown

# TableCol 7 ColHeader Min

# TableCol 7 FieldName Intensity Min

# TableCol 7 Units unknown

# TableCol 8 ColHeader Max

# TableCol 8 FieldName Intensity Max

# TableCol 8 Units unknown

# TableCol 9 ColHeader Range

# TableCol 9 FieldName Intensity Range

# TableCol 9 Units unknown

# NRows 2

# NTableCols 9

# ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range SNR

1 0 161272 106116.2 Seg0000 -0.9503 2.4005 -13.2314 11.4302 24.6617 -0.3959

2 1 1369 871.1 Seg0001 1.3153 3.8989 -8.2296 10.3666 18.5962 0.3373