Il giorno lun 11 feb 2019 alle ore 18:59 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> ha scritto:

If mri_diff says that there is no difference, then there is something
wrong. Double check that your contrasts are correct.

On 2/10/19 9:47 AM, Francesca Strappini wrote:
>
> 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 <mailto: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>
> > <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>
> > <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>
> > <mailto:francesca.strappini@weizmann.ac.il
> <mailto:francesca.strappini@weizmann.ac.il>>
> >
> > _______________________________________________
> > Freesurfer mailing list
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>
>
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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
> <mailto:francesca.strappini@weizmann.ac.il>
>
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