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@@ -1,11 +1,11 @@
<!-- {{{ start -->
<HTML><HEAD>
-<TITLE>SIENA - Structural Brain Change Analysis</TITLE>
+<TITLE>SIENA - Analysis of Structural Brain MRI Data</TITLE>
</HEAD><BODY BACKGROUND="../images/fsl-bg.jpg">
<hr><TABLE BORDER=0 WIDTH="100%"><TR>
<TD ALIGN=CENTER><H1>SIENA Structural Brain Change Analysis</H1>
-SIENA - Structural Image Evaluation, using Normalisation, of Atrophy - Version 2.3<br><br>
+SIENA - Structural Image Evaluation, using Normalisation, of Atrophy - Version 2.4<br><br>
<a href="#intro">intro</a> - <a href="#tools">tools used</a> - <a href="#siena">SIENA</a> - <a
href="#sienax">SIENAX</a> - <a href="#sienar">voxelwise SIENA statistics</a>
@@ -21,34 +21,132 @@ href="#sienax">SIENAX</a> - <a href="#sienar">voxelwise SIENA statistics</a>
<p>SIENA is a package for both single-time-point ("cross-sectional")
and two-time-point ("longitudinal") analysis of brain change, in
particular, the estimation of atrophy (volumetric loss of brain
-tissue). SIENA has already been used in many clinical studies.
-
-<p><b>siena</b> estimates percentage brain
-volume change (PBVC) betweem two input images, taken of the same
-subject, at different points in time. It calls a series of image
-analysis programs (supplied with <a href="../index.html">FSL</a>) to
-strip the non-brain tissue from the two images, register the two
-brains (under the constraint that the skulls are used to hold the
-scaling constant during the registration) and analyse the brain change
-between the two time points.
-
-<p><b>sienax</b> estimages total brain tissue
-volume, from a single image, after registration to standard
-(Talairach) space. It calls a series of FSL programs: It first strips
-non-brain tissue, and then uses the brain and skull images to estimate
-the scaling between the subject's image and Talairach space. It then
-runs tissue segmentation to estimate the volume of brain tissue, and
-multiplies this by the estimated scaling factor, to reduce
-head-size-related variability between subjects.
-
-<p><b>Contributors</b>: There have been many contributions of various
-kinds from members of the FMRIB analysis group and collaborators
-mentioned on the <a href="../index.html">FSL page</a>.
-
-<p>For more detail on SIENA and updated journal references, see the <A
+tissue). SIENA has been used in many clinical studies.
+
+<p><b>siena</b> estimates percentage brain volume change (PBVC)
+betweem two input images, taken of the same subject, at different
+points in time. It calls a series of FSL programs to strip the
+non-brain tissue from the two images, register the two brains (under
+the constraint that the skulls are used to hold the scaling constant
+during the registration) and analyse the brain change between the two
+time points. It is also possible to project the voxelwise atrophy
+measures into standard space in a way that allows for multi-subject
+voxelwise statistical testing.
+
+<p><b>sienax</b> estimages total brain tissue volume, from a single
+image, normalised for skull size. It calls a series of FSL programs:
+It first strips non-brain tissue, and then uses the brain and skull
+images to estimate the scaling between the subject's image and
+Talairach space. It then runs tissue segmentation to estimate the
+volume of brain tissue, and multiplies this by the estimated scaling
+factor, to reduce head-size-related variability between subjects.
+
+<p>For more detail on SIENA and technical reports, see the <A
HREF="http://www.fmrib.ox.ac.uk/analysis/research/siena/">SIENA web
-page</A>. If you use SIENA in your research, please quote the journal
-references listed there.
+page</A>.
+
+<p>If you use SIENA in your research, please make sure that you
+reference the following articles. You may alternatively wish to use
+the brief descriptive methods text and expanded list of references
+given below.
+
+<!-- {{{ Referencing SIENA (minimal version) -->
+
+<hr><b>Referencing SIENA (minimal version)</b>
+
+<p>Two-timepoint percentage brain volume change was estimated with SIENA [Smith 2002], part of FSL [Smith 2004].
+<br> or
+<br>Brain tissue volume, normalised for subject head size, was estimated with SIENAX [Smith 2002], part of FSL [Smith 2004].
+
+<font size=-1><em>
+<p>[Smith 2002] S.M. Smith, Y. Zhang, M. Jenkinson, J. Chen, P.M. Matthews, A. Federico, and N. De Stefano.
+<BR> Accurate, robust and automated longitudinal and cross-sectional brain change analysis.
+<BR> NeuroImage, 17(1):479-489, 2002.
+
+<p>[Smith 2004] S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews.
+<BR> Advances in functional and structural MR image analysis and implementation as FSL.
+<BR> NeuroImage, 23(S1):208-219, 2004.
+</em></font>
+
+<!-- }}} -->
+<!-- {{{ Referencing SIENA (more detailed text and references) -->
+
+<hr><b>Referencing SIENA (more detailed text and references)</b>
+
+<p><b>SIENA</b>. Two-timepoint percentage brain volume change was
+estimated with SIENA [Smith 2001, Smith 2002], part of FSL [Smith
+2004]. SIENA starts by extracting brain and skull images from the
+two-timepoint whole-head input data [Smith 2002b]. The two brain
+images are then aligned to each other [Jenkinson 2001, Jenkinson 2002]
+(using the skull images to constrain the registration scaling); both
+brain images are resampled into the space halfway between the
+two. Next, tissue-type segmentation is carried out [Zhang 2001] in
+order to find brain/non-brain edge points, and then perpendicular edge
+displacement (between the two timepoints) is estimated at these edge
+points. Finally, the mean edge displacement is converted into a
+(global) estimate of percentage brain volume change between the two
+timepoints.
+
+<p><b>SIENAX</b>. Brain tissue volume, normalised for subject head
+size, was estimated with SIENAX [Smith 2001, Smith 2002], part of FSL
+[Smith 2004]. SIENAX starts by extracting brain and skull images from
+the single whole-head input data [Smith 2002b]. The brain image is
+then affine-registered to MNI152 space [Jenkinson 2001, Jenkinson
+2002] (using the skull image to determine the registration scaling);
+this is primarily in order to obtain the volumetric scaling factor, to
+be used as a normalisation for head size. Next, tissue-type
+segmentation with partial volume estimation is carried out [Zhang
+2001] in order to calculate total volume of brain tissue (including
+separate estimates of volumes of grey matter, white matter, peripheral
+grey matter and ventricular CSF).
+
+<p><b>Voxelwise multi-subject SIENA statistics</b>. First, SIENA was
+run separately for each subject. Next, for each subject, the edge
+displacement image (encoding, at brain/non-brain edge points, the
+outwards or inwards edge change between the two timepoints) was
+dilated, transformed into MNI152 space, and masked by a standard
+MNI152-space brain edge image. In this way the edge displacement
+values were warped onto the standard brain edge. Next, the resulting
+images from all subjects were fed into voxelwise statistical analysis
+to test for.....
+
+<font size=-1><em>
+<P>[Smith 2001] S.M. Smith, N. De Stefano, M. Jenkinson, and P.M. Matthews.
+<BR> Normalised accurate measurement of longitudinal brain change.
+<BR> Journal of Computer Assisted Tomography, 25(3):466-475, May/June 2001.
+
+<P>[Smith 2002] S.M. Smith, Y. Zhang, M. Jenkinson, J. Chen, P.M. Matthews, A. Federico, and N. De Stefano.
+<BR> Accurate, robust and automated longitudinal and cross-sectional brain change analysis.
+<BR> NeuroImage, 17(1):479-489, 2002.
+
+<P>[Smith 2004] S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews.
+<BR> Advances in functional and structural MR image analysis and
+ implementation as FSL.
+<BR> NeuroImage, 23(S1):208-219, 2004.
+
+<P>[Smith 2002b] S.M. Smith.
+<BR> Fast robust automated brain extraction.
+<BR> Human Brain Mapping, 17(3):143-155, November 2002.
+
+<P>[Jenkinson 2001] M. Jenkinson and S.M. Smith.
+<BR> A global optimisation method for robust affine registration of brain images.
+<BR> Medical Image Analysis, 5(2):143-156, June 2001.
+
+<P>[Jenkinson 2002] M. Jenkinson, P.R. Bannister, J.M. Brady, and S.M. Smith.
+<BR> Improved optimisation for the robust and accurate linear registration and motion correction of brain images.
+<BR> NeuroImage, 17(2):825-841, 2002.
+
+<P>[Zhang 2001] Y. Zhang, M. Brady, and S. Smith.
+<BR> Segmentation of brain MR images through a hidden Markov random field model and the expectation maximization algorithm.
+<BR> IEEE Trans. on Medical Imaging, 20(1):45-57, 2001.
+
+<P>[Bartsch 2004] A.J. Bartsch, N. Bendszus, N. De Stefano, G. Homola, and S. Smith.
+<BR> Extending SIENA for a multi-subject statistical analysis of sample-specific cerebral edge shifts: Substantiation of early brain regeneration through abstinence from alcoholism.
+<BR> In Tenth Int. Conf. on Functional Mapping of the Human Brain, 2004.
+
+</em></font>
+
+<!-- }}} -->
<!-- }}} -->
<!-- {{{ FSL Tools used -->
@@ -105,9 +203,10 @@ names - i.e. all must be done within a single directory.
<p><b>-d</b> : debug (don't delete intermediate files)
-<p><b>-f <BET threshold></b> : Threshold for BET brain
-extraction (default 0.5) - reduce this to make brain estimates larger
-and vice versa
+<p><b>-B "bet options"</b> : if you want to change the BET defaults,
+ put BET options inside double-quotes after using the -B flag. For
+ example, to increase the size of brain estimation, use: <code>-B "-f
+ 0.3"</code>
<p><b>-2</b> : two-class segmentation (don't segment grey and white
matter separately) - use this if there is poor grey/white contrast
@@ -126,6 +225,13 @@ subjects)
<p><b>-b <b></b>: ignore from b (mm) downwards in Talairach space; b should probably be -ve
+<p><b>-S "siena_diff options"</b> : if you want to send options to the
+ siena_diff program (that estimates change between two aligned
+ images), put these options in double-quotes after the -S flag. For
+ example, to tell siena_diff to run FAST segmentation with an
+ increased number of iterations, use <code>-S "-s -i 20"</code>
+
+
<h3>What the script does</h3>
@@ -203,22 +309,22 @@ images are called "A" and "B"):
<UL>
-<LI>A_to_B.siena the output information from the <b>siena</b> script.
+<LI><code>A_to_B.siena</code> the output information from the <b>siena</b> script.
-<LI>A_halfwayto_B_render a colour rendered image of edge motion
+<LI><code>A_halfwayto_B_render</code> a colour-rendered image of edge motion
superimposed on the halfway A image.
-<LI>B_regto_A.gif a gif image showing the results of the registration,
+<LI><code>B_regto_A.gif</code> a gif image showing the results of the registration,
using one transformed image as the background and the other as the
coloured edges foreground.
-<LI>A_to_B.mat the transformation taking A to B, using the brain and
+<LI><code>A_to_B.mat</code> the transformation taking A to B, using the brain and
skull images.
-<LI>B_to_A.mat the transformation taking B to A, using the brain and
+<LI><code>B_to_A.mat</code> the transformation taking B to A, using the brain and
skull images.
-<LI>A_halfwayto_B.mat and B_halfwayto_A.mat the transformations taking
+<LI><code>A_halfwayto_B.mat</code> and <code>B_halfwayto_A.mat</code> the transformations taking
the images to the halfway positions.
</UL>
@@ -244,9 +350,10 @@ names - i.e. all must be done within a single directory.
<p><b>-d</b> : debug (don't delete intermediate files)
-<p><b>-f <BET threshold></b> : Threshold for BET brain
-extraction (default 0.5) - reduce this to make brain estimates larger
-and vice versa
+<p><b>-B "bet options"</b> : if you want to change the BET defaults,
+ put BET options inside double-quotes after using the -B flag. For
+ example, to increase the size of brain estimation, use: <code>-B "-f
+ 0.3"</code>
<p><b>-2</b> : two-class segmentation (don't segment grey and white
matter separately) - use this if there is poor grey/white contrast
@@ -260,13 +367,19 @@ subjects)
<p><b>-b <b></b>: ignore from b (mm) downwards in Talairach space; b should probably be -ve
-<p><b>-r</b>: tell FAST to estimate "regional" volumes as well as
+<p><b>-r</b>: tell SIENAX to estimate "regional" volumes as well as
global; this produces peripheral cortex GM volume (3-class
segmentation only) and ventricular CSF volume
<p><b>-lm <mask></b>: use a lesion (or lesion+CSF) mask to
remove incorrectly labelled "grey matter" voxels
+<p><b>-S "FAST options"</b> : if you want to change the segmentation
+ defaults, put FAST options inside double-quotes after using the -S
+ flag. For example, to increase the number of segmentation
+ iterations use: <code>-S "-i 20"</code>
+
+
<h3>What the script does</h3>
@@ -322,14 +435,11 @@ image is called "A"):
<UL>
-<LI>A.sienax the output information from the <b>sienax</b> script.
+<LI><code>A.sienax</code> the output information from the <b>sienax</b> script.
-<LI>A_render a colour rendered image showing the segmentation
+<LI><code>A_render</code> a colour-rendered image showing the segmentation
output superimposed on top of the original image.
-<LI>A2tal.mat the transformation that takes the input image into
-standard space.
-
</UL>
<!-- }}} -->
@@ -337,14 +447,14 @@ standard space.
<a name="sienar"></a><p><hr><H2>Voxelwise SIENA Statistics</H2>
-<p>We have recently extended SIENA to allow the voxelwise statistical
-analysis of atrophy across subjects. This takes a SIENA-derived edge
-flow image for each subject, warps these to align with a
-standard-space edge image and then carries out voxelwise cross-subject
-statistical analysis to identify brain edge points which, for example,
-are signficantly atrophic for the group of subjects as a whole, or
-where atrophy correlates significantly with age or disease
-progression.
+<p>We have extended SIENA to allow the voxelwise statistical analysis
+of atrophy across subjects. This takes a SIENA-derived edge "flow
+image" (edge displacement between the timepoints) for each subject,
+warps these to align with a standard-space edge image and then carries
+out voxelwise cross-subject statistical analysis to identify brain
+edge points which, for example, are signficantly atrophic for the
+group of subjects as a whole, or where atrophy correlates
+significantly with age or disease progression.
<p>In order to carry out voxelwise SIENA statistics, do the following:
diff --git a/siena b/siena
index 25d813eeac04a03337633dc29aa7a2f607ecac66..a9fe9537a7b483b4f2b8fbc0b018ed30d0416e17 100755
--- a/siena
+++ b/siena
@@ -39,7 +39,7 @@ echo "-----------------------------------------------------------------------" >
echo "" >> ${A}_to_${B}.siena
echo " SIENA - Structural Image Evaluation, using Normalisation, of Atrophy" >> ${A}_to_${B}.siena
echo " part of FSL www.fmrib.ox.ac.uk/fsl" >> ${A}_to_${B}.siena
-echo " running longitudinal atrophy measurement: siena version 2.3" >> ${A}_to_${B}.siena
+echo " running longitudinal atrophy measurement: siena version 2.4" >> ${A}_to_${B}.siena
echo " siena $@" >> ${A}_to_${B}.siena
echo "" >> ${A}_to_${B}.siena
diff --git a/sienax b/sienax
index f581f448d3c581b83cd40b13e2d57a7b6e112d88..c913f0935f7a6a7ec8f79b04fa373591552dcc33 100755
--- a/sienax
+++ b/sienax
@@ -38,7 +38,7 @@ echo "-----------------------------------------------------------------------" >
echo "" >> ${I}.sienax
echo " SIENA - Structural Image Evaluation, using Normalisation, of Atrophy" >> ${I}.sienax
echo " part of FSL www.fmrib.ox.ac.uk/fsl" >> ${I}.sienax
-echo " running cross-sectional atrophy measurement: sienax version 2.3" >> ${I}.sienax
+echo " running cross-sectional atrophy measurement: sienax version 2.4" >> ${I}.sienax
echo " sienax $@" >> ${I}.sienax
echo "" >> ${I}.sienax