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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
# 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 order/z.nii.gz --slabel AB lh /home/labs/malach/frastra/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg lh.V2dorsal_AB_order_avg --snr --sum lh.V2dorsal_AB_order_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 order/z.nii.gz # InVolFileTimeStamp 2018/12/08 20:12:49 # 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
Thanks a lot for the help Best Francesca