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
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