External Email - Use Caution        

Thanks a lot for the reply!
If I run mri_diff order/z.nii.gz disorder/z.nii.gz I indeed get zero.
However, if I perform the contrast "order minus disorder" I get 0.1, so I should see some difference although very small, right? 
These are the outputs:

francesca@francesca-desktop:/opt/freesurfer/fsfast/OrderDisorder/AB/bold/AB_OrderDisorder_lh$ mri_segstats --i order/z.nii.gz --slabel AB lh /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg lh.V2dorsal_AB_order_avg --snr --sum lh.V2dorsal_AB_order_sum

$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd 
cmdline mri_segstats --i order/z.nii.gz --slabel AB lh /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg lh.V2dorsal_AB_order_avg --snr --sum lh.V2dorsal_AB_order_sum 
sysname  Linux
hostname francesca-desktop
machine  x86_64
user     francesca
UseRobust  0
Constructing seg from label
Loading order/z.nii.gz
Vertex Area is 0.65781 mm^3
Generating list of segmentation ids
Found   2 segmentations
Computing statistics for each segmentation

Reporting on   2 segmentations
Using PrintSegStat
Computing spatial average of each frame
  0  1
Writing to lh.V2dorsal_AB_order_avg
0 -0.950279
1 1.31525
mri_segstats done

francesca@francesca-desktop:/opt/freesurfer/fsfast/OrderDisorder/AB/bold/AB_OrderDisorder_lh$ mri_segstats --i disorder/z.nii.gz --slabel AB lh /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg lh.V2dorsal_AB_disorder_avg --snr --sum lh.V2dorsal_AB_disorder_sum

$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd 
cmdline mri_segstats --i disorder/z.nii.gz --slabel AB lh /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg lh.V2dorsal_AB_disorder_avg --snr --sum lh.V2dorsal_AB_disorder_sum 
sysname  Linux
hostname francesca-desktop
machine  x86_64
user     francesca
UseRobust  0
Constructing seg from label
Loading disorder/z.nii.gz
Vertex Area is 0.65781 mm^3
Generating list of segmentation ids
Found   2 segmentations
Computing statistics for each segmentation

Reporting on   2 segmentations
Using PrintSegStat
Computing spatial average of each frame
  0  1
Writing to lh.V2dorsal_AB_disorder_avg
0 -0.950279
1 1.31525
mri_segstats done

mri_segstats --i order-vs-disorder/z.nii.gz --slabel AB lh /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg lh.V2dorsal_AB_orderVsdisorder_avg --snr --sum lh.V2dorsal_AB_orderVsdisorder_sum

$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd 
cmdline mri_segstats --i order-vs-disorder/z.nii.gz --slabel AB lh /opt/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg lh.V2dorsal_AB_orderVsdisorder_avg --snr --sum lh.V2dorsal_AB_orderVsdisorder_sum 
sysname  Linux
hostname francesca-desktop
machine  x86_64
user     francesca
UseRobust  0
Constructing seg from label
Loading order-vs-disorder/z.nii.gz
Vertex Area is 0.65781 mm^3
Generating list of segmentation ids
Found   2 segmentations
Computing statistics for each segmentation

Reporting on   2 segmentations
Using PrintSegStat
Computing spatial average of each frame
  0  1
Writing to lh.V2dorsal_AB_orderVsdisorder_avg
0 0.119339
1 -1.93788
mri_segstats done

Thanks again for the help!
Best
Francesca



Il giorno mar 22 gen 2019 alle ore 20:55 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> ha scritto:
I don't know what is happening. If the two z-maps are really different,
then it should have given different values. Run this
mri_diff order/z.nii.gz disorder/z.nii.gz
Does it indicate that there is a difference? If so, can you run your two
mri_segment commands and send me the terminal output of each?
As for the two mean intensity values, one (Seg0001) is from inside your
ROI and the other (Seg0000) is outside. You can have it exclude Seg0000
with --excludeid 0


On 1/20/19 10:00 AM, Francesca Strappini wrote:
>
>         External Email - Use Caution
>
> 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
> <http://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
> <http://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
> --
> Francesca Strappini, Ph.D.
> Neurobiology Department
> Weizmann Institute of Science
> 234 Herzl Street, Rehovot 7610001 Israel
> Tel.: +972 58 444 2584
> E-mail: francesca.strappini@weizmann.ac.il
> <mailto:francesca.strappini@weizmann.ac.il>
>
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--
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strappini@weizmann.ac.il