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Thanks! There was a mistake in the contrasts indeed.
Best
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 CautionThanks 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 > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- 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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