Indeed - I guess no-one's using the 2-class-only option! (It was only
really needed for crappy old data with very poor grey-white
contrast.) This is a bug which we'll fix in the next release -
corrected script attached.
Cheers.
On 30 May 2007, at 23:26, Zografos Caramanos wrote:
> Hello!
>
> I think that I may have found a bug in SIENAX v-2.4 (FSL v-3.3.11).
>
> When I run a 3-mm, axial, T1-weighted scan with a 3-tissue
> segmentation,
> SIENAX v-2.4 gives you normalized GREY, WHITE, and BRAIN volumes:
>
> (SIENAX v-2.4, 3-tissue segmentation)
>
> ======================================================================
> ===
>
> Class: CSF tissue 1 tissue 2 brain %
> Volumes: 205237.1 566241.4 665635.7 0.857188
>
> ---------- convert brain volume into normalised volume
> --------------
>
> tissue volume unnormalised-volume
> GREY 760365.64 566240.07
> WHITE 893834.69 665633.72
> BRAIN 1654200.33 1231873.79
>
> ======================================================================
> ===
> (...excerpted from below)
>
>
> BUT, if I run the same scan with the -2 flag for a 2-tissue
> segmentation,
> SIENAX v-2.4 does not seem to properly calculate the normalized
> BRAIN volume:
>
> (SIENAX v-2.4, 2-tissue segmentation)
>
> ======================================================================
> ===
> Class: CSF tissue 1 brain percentage
> Volumes: 205237.1 1231946.5 0.857195
>
> ---------- convert brain volume into normalised volume
> --------------
> BRAIN 1 1
>
> ======================================================================
> ===
> (...excerpted from further below)
>
>
>
> Please note that this is not the case when I run the same scan using
> SIENAX v-2.3 (FSL v-3.2beta, FAST v-3.5), which gives slightly
> different
> values:
>
> (SIENAX v-2.3, 3-tissue segmentation)
>
> ======================================================================
> ===
> Class: CSF tissue 1 tissue 2 brain %
> Volumes: 195260.0 562279.6 662799.2 0.862526
>
> ---------- convert brain volume into normalised volume
> --------------
>
> GREY 757578.8396899881
> WHITE 893006.5301093496
>
> BRAIN 1650585.3697993377
>
> ======================================================================
> ===
> (...excerpted from further below)
>
>
> (SIENAX v-2.3, 2-tissue segmentation)
>
> ======================================================================
> ===
> Class: CSF tissue 1 brain percentage
> Volumes: 194299.3 1226099.5 0.863208
>
> ---------- convert brain volume into normalised volume
> --------------
>
> BRAIN 1651960.9049744302
>
> ======================================================================
> ===
> (...excerpted from further below)
>
>
> Please let me know if I am doing something wrong, or if there is
> some fix
> to this problem.
>
> Cheers!
> Aki
>
> Zografos Caramanos, M.A.
> Magnetic Resonance Studies Unit
> Montreal Neurological Institute, McGill University
> (e-mail) [log in to unmask]
>
> ======================================================================
> =
>
>
>
> +++++++++++++++++++++++++++++++++++++++++++++++
> SIENAX Version 2.4 with 3-tissue segmentation
> +++++++++++++++++++++++++++++++++++++++++++++++
>
> ----------------------------------------------------------------------
> -
>
> SIENA - Structural Image Evaluation, using Normalisation, of
> Atrophy
> part of FSL www.fmrib.ox.ac.uk/fsl
> running cross-sectional atrophy measurement: sienax version 2.4
> sienax mc_carz6809.2007-02-08.Scan_nt1p_none -d
>
> ---------- extract brain
> --------------------------------------------
>
> ---------- register to stdairach space using brain and skull
> --------
> (do not worry about histogram warnings)
> VSCALING 1.3428326384
>
> ---------- mask with std mask
> ---------------------------------------
>
> ---------- segment tissue into types
> --------------------------------
>
> FAST - FMRIB's Automated Segmentation Tool Version 3.53
>
> Image: /tmp/
> fsl_z5FSyo_mc_carz6809.2007-02-08.Scan_nt1p_none_stdmaskbrain
>
> T1-weighted image
> Imagesize : 192 x 256 x 60
> Pixelsize : 0.976562 x 0.976562 x 3
>
> Initial K-means segmentation...
> 8 main iterations ...
> Estimating PVE...
>
> Segmentation done successfully!
>
> Calculation time 234 seconds!
>
> Write segmentation image /tmp/fsl_z5FSyo.fastout/QQQQQ_seg.hdr
> Successfully!
> Write PVE image of tissue 0 Successfully!
> Write PVE image of tissue 1 Successfully!
> Write PVE image of tissue 2 Successfully!
>
> Class: CSF tissue 1 tissue 2 brain percentage
> Volumes: 205237.1 566241.4 665635.7 0.857188
>
> ---------- convert brain volume into normalised volume
> --------------
>
> tissue volume unnormalised-volume
> GREY 760365.64 566240.07
> WHITE 893834.69 665633.72
> BRAIN 1654200.33 1231873.79
>
>
>
>
> +++++++++++++++++++++++++++++++++++++++++++++++
> SIENAX Version 2.4 with 2-tissue segmentation
> +++++++++++++++++++++++++++++++++++++++++++++++
>
> ----------------------------------------------------------------------
> -
>
> SIENA - Structural Image Evaluation, using Normalisation, of
> Atrophy
> part of FSL www.fmrib.ox.ac.uk/fsl
> running cross-sectional atrophy measurement: sienax version 2.4
> sienax mc_carz6809.2007-02-08.Scan_nt1p_none -d -2
>
> ---------- extract brain
> --------------------------------------------
>
> ---------- register to stdairach space using brain and skull
> --------
> (do not worry about histogram warnings)
> VSCALING 1.3428326384
>
> ---------- mask with std mask
> ---------------------------------------
>
> ---------- segment tissue into types
> --------------------------------
>
> FAST - FMRIB's Automated Segmentation Tool Version 3.53
>
> Image: /tmp/
> fsl_69X29e_mc_carz6809.2007-02-08.Scan_nt1p_none_stdmaskbrain
>
> T1-weighted image
> Imagesize : 192 x 256 x 60
> Pixelsize : 0.976562 x 0.976562 x 3
>
> Initial K-means segmentation...
> 8 main iterations ...
> Estimating PVE...
>
> Segmentation done successfully!
>
> Calculation time 234 seconds!
>
> Write segmentation image /tmp/fsl_69X29e.fastout/QQQQQ_seg.hdr
> Successfully!
> Write PVE image of tissue 0 Successfully!
> Write PVE image of tissue 1 Successfully!
>
> Class: CSF tissue 1 brain percentage
> Volumes: 205237.1 1231946.5 0.857195
>
> ---------- convert brain volume into normalised volume
> --------------
> BRAIN 1 1
>
>
>
> +++++++++++++++++++++++++++++++++++++++++++++++
> SIENAX Version 2.3 with 3-tissue segmentation
> +++++++++++++++++++++++++++++++++++++++++++++++
>
> ----------------------------------------------------------------------
> -
>
> SIENA - Structural Image Evaluation, using Normalisation, of
> Atrophy
> part of FSL www.fmrib.ox.ac.uk/fsl
> running cross-sectional atrophy measurement: sienax version 2.3
> sienax mc_carz6809.2007-02-08.Scan_nt1p_none -d
>
> ---------- extract brain
> --------------------------------------------
>
> ---------- register to talairach space using brain and skull
> --------
> (do not worry about histogram warnings)
> WARNING: Both reference and input images have an sform matrix set
> The output image will use the sform from the reference image
> WARNING: Both reference and input images have an sform matrix set
> The output image will use the sform from the reference image
> WARNING: Both reference and input images have an sform matrix set
> The output image will use the sform from the reference image
> VSCALING 1.3473268622
>
> ---------- mask with talairach mask
> ---------------------------------
>
> ---------- segment tissue into types
> --------------------------------
>
> FAST - FMRIB's Automated Segmentation Tool Version 3.5
>
> Image: /tmp/
> fsl_mEUvrB_mc_carz6809.2007-02-08.Scan_nt1p_none_talmaskbrain
>
> T1-weighted image
> Imagesize : 192 x 256 x 60
> Pixelsize : 0.976562 x 0.976562 x 3
>
> Initial K-means segmentation...
> 8 main iterations ...
> Estimating PVE...
>
> Segmentation done successfully!
>
> Calculation time 234 seconds!
>
> Write segmentation image /tmp/fsl_mEUvrB.fastout/QQQQQ_seg.hdr
> Successfully!
> Write PVE image of tissue 0 Successfully!
> Write PVE image of tissue 1 Successfully!
> Write PVE image of tissue 2 Successfully!
>
> Class: CSF tissue 1 tissue 2 brain percentage
> Volumes: 195260.0 562279.6 662799.2 0.862526
>
> ---------- convert brain volume into normalised volume
> --------------
>
> GREY 757578.8396899881
> WHITE 893006.5301093496
>
> BRAIN 1650585.3697993377
>
>
> +++++++++++++++++++++++++++++++++++++++++++++++
> SIENAX Version 2.3 with 2-tissue segmentation
> +++++++++++++++++++++++++++++++++++++++++++++++
>
> ----------------------------------------------------------------------
> -
>
> SIENA - Structural Image Evaluation, using Normalisation, of
> Atrophy
> part of FSL www.fmrib.ox.ac.uk/fsl
> running cross-sectional atrophy measurement: sienax version 2.3
> sienax mc_carz6809.2007-02-08.Scan_nt1p_none -d -2
>
> ---------- extract brain
> --------------------------------------------
>
> ---------- register to talairach space using brain and skull
> --------
> (do not worry about histogram warnings)
> WARNING: Both reference and input images have an sform matrix set
> The output image will use the sform from the reference image
> WARNING: Both reference and input images have an sform matrix set
> The output image will use the sform from the reference image
> WARNING: Both reference and input images have an sform matrix set
> The output image will use the sform from the reference image
> VSCALING 1.3473268622
>
> ---------- mask with talairach mask
> ---------------------------------
>
> ---------- segment tissue into types
> --------------------------------
>
> FAST - FMRIB's Automated Segmentation Tool Version 3.5
>
> Image: /tmp/
> fsl_AlcxrX_mc_carz6809.2007-02-08.Scan_nt1p_none_talmaskbrain
>
> T1-weighted image
> Imagesize : 192 x 256 x 60
> Pixelsize : 0.976562 x 0.976562 x 3
>
> Initial K-means segmentation...
> 4 main iterations ...
> Estimating PVE...
>
> Segmentation done successfully!
>
> Calculation time 89 seconds!
>
> Write segmentation image /tmp/fsl_AlcxrX.fastout/QQQQQ_seg.hdr
> Successfully!
> Write PVE image of tissue 0 Successfully!
> Write PVE image of tissue 1 Successfully!
>
> Class: CSF tissue 1 brain percentage
> Volumes: 194299.3 1226099.5 0.863208
>
> ---------- convert brain volume into normalised volume
> --------------
>
> BRAIN 1651960.9049744302
------------------------------------------------------------------------
---
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
------------------------------------------------------------------------
---
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