Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP

We’re showing branches in this repository, but you can also compare across forks.

base fork: Garyfallidis/didaktoriko
base: 254aaf68ef
...
head fork: Garyfallidis/didaktoriko
compare: fbac0ac5e1
  • 3 commits
  • 4 files changed
  • 0 commit comments
  • 1 contributor
36 Chapter_1.lyx
View
@@ -3380,7 +3380,7 @@ status open
<column alignment="center" valignment="top" width="0">
<column alignment="center" valignment="top" width="0">
<row>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" bottomline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
@@ -3389,7 +3389,7 @@ status open
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" bottomline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
@@ -3400,7 +3400,7 @@ Deterministic
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" bottomline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
@@ -3413,7 +3413,7 @@ Probabilistic
</cell>
</row>
<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
@@ -3424,7 +3424,7 @@ Voxel Noise Resistance
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
@@ -3435,7 +3435,7 @@ Less
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
@@ -3448,7 +3448,7 @@ More
</cell>
</row>
<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
@@ -3459,7 +3459,7 @@ Non-existing Tracts
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
@@ -3470,7 +3470,7 @@ Yes
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
@@ -3483,7 +3483,7 @@ Yes
</cell>
</row>
<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
@@ -3494,7 +3494,7 @@ Execution Time
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
@@ -3505,7 +3505,7 @@ Fast
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
@@ -3518,7 +3518,7 @@ Slow
</cell>
</row>
<row>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
@@ -3529,7 +3529,7 @@ Memory Size
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
@@ -3540,7 +3540,7 @@ Less
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
@@ -3553,7 +3553,7 @@ More
</cell>
</row>
<row>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" bottomline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
@@ -3564,7 +3564,7 @@ Biased on Tract Length
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" bottomline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
@@ -3575,7 +3575,7 @@ Yes
\end_inset
</cell>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" bottomline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
173 Chapter_3.lyx
View
@@ -5206,8 +5206,9 @@ reference "Flo:eudx_fromABCD"
\end_layout
\begin_layout Standard
-Independently from the deterministic tractography described above we also
- generated probabilistic tracks using the Camino Diffusion MRI Toolkit
+Independently from the deterministic tractography described previously we
+ repeated the same experiments with probabilistic tracks generated from
+ the Camino Diffusion MRI Toolkit
\begin_inset Foot
status open
@@ -5225,19 +5226,27 @@ cmic.cs.ucl.ac.uk/camino
For the fitting method we used the standard non-linear fit provided in
Camino with positivity constraints.
For this purpose we used the command
-\emph on
-modelfit -model cylcyl nldt_pos
-\emph default
+\begin_inset Formula $\text{modelfit -model cylcyl nldt\_pos}$
+\end_inset
+
.
The probabilistic tractography was generated using Pico PDFs sampled from
a Watson distribution (
\emph on
-picopdfs -pdf watson
+
+\begin_inset Formula $\texttt{picopdfs -pdf watson}$
+\end_inset
+
+
\emph default
).
In order to generate the streamlines we used the Camino command
\emph on
-track
+
+\begin_inset Formula $\texttt{track}$
+\end_inset
+
+
\emph default
which took as input the PDFs from before and a seed file with the mask.
@@ -5246,7 +5255,7 @@ track
\begin_layout Standard
As previously we performed two experiments; one where the seeds could be
anywhere in the simulated bundles and a second where the seeds were constrained
- in the pre-specified ROIs A,B,C or D (see Fig.
+ in the pre-specified ROIs A, B, C or D (see Fig.
\begin_inset space ~
\end_inset
@@ -5262,14 +5271,14 @@ reference "Flo:eudx_fromABCD"
\begin_inset space ~
\end_inset
-
+
\begin_inset CommandInset ref
LatexCommand ref
reference "Flo:PMT_phantom"
\end_inset
-
+.
\end_layout
\begin_layout Standard
@@ -5294,7 +5303,7 @@ status open
\begin_inset Caption
\begin_layout Plain Layout
-Here we presenting the probabilistic tractography performed on the digital
+Here we present the probabilistic tractography performed on the digital
phantom shown in Fig.
\begin_inset CommandInset ref
@@ -5304,7 +5313,7 @@ reference "Flo:crossing_eudx_sims"
\end_inset
.
- We use here Pico and a Two Tensor model (PMT) to generate the tracks.
+ We use Pico and a Two Tensor model (PMT) to generate the tracks.
In (i) we see the result with
\begin_inset Formula $1$
\end_inset
@@ -5315,11 +5324,11 @@ reference "Flo:crossing_eudx_sims"
tracks).
In (ii) we see a detail of the left bundle.
- We can see that some of the tracks are diverting on zig-zag fashion althought
+ We can see that some of the tracks are diverting on a zig-zag fashion althought
the phantom at these voxels has only one main direction.
In (iii) we concentrate to the crossing region of the phantom where we
- observer that many of the PMT tracks are able to propagate towarch both
- pathways.
+ observe that many of the PMT tracks are successfuly propagating towards
+ both pathways.
\end_layout
\end_inset
@@ -5343,7 +5352,58 @@ name "Flo:PMT_phantom"
\end_layout
\begin_layout Standard
-asdfasfasf
+For illustration purposes we see in Fig.
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "Flo:PMT_phantom"
+
+\end_inset
+
+(i) the result with
+\begin_inset Formula $321$
+\end_inset
+
+ of
+\begin_inset Formula $1$
+\end_inset
+
+ iteration of the Camino
+\begin_inset Formula $\texttt{track}$
+\end_inset
+
+.
+ In Fig.
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "Flo:PMT_phantom"
+
+\end_inset
+
+(ii) we see a detail of the left bundle.
+ We can see that some of the tracks are diverting vigourosly on a zig-zag
+ fashion althought the phantom at these voxels has only one main direction.
+ In Fig.
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "Flo:PMT_phantom"
+
+\end_inset
+
+(iii) we zoom in the crossing region of the phantom where we observe that
+ many of the PMT tracks are successfuly propagating towards both pathways
+ through the crossing region.
\end_layout
\begin_layout Standard
@@ -5360,7 +5420,7 @@ status open
\backslash
-small
+footnotesize
\backslash
addtolength{
\backslash
@@ -6144,6 +6204,75 @@ name "Flo:PMT_table"
\end_layout
+\begin_layout Standard
+The results from the second experiment where the seeding takes place only
+ in specific regions of the phantom are summarized in Tab.
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "Flo:PMT_table"
+
+\end_inset
+
+.
+ The distinction between PMT100 and PMT500 is in the number of iterations
+ run from Camino
+\begin_inset Formula $\texttt{track}$
+\end_inset
+
+ command.
+ The default value recommended is
+\begin_inset Formula $5000$
+\end_inset
+
+ however for this experiment we do not see a significant difference between
+
+\begin_inset Formula $100$
+\end_inset
+
+ and
+\begin_inset Formula $5000$
+\end_inset
+
+ iterations.
+ In comparison with Tab.
+\begin_inset space ~
+\end_inset
+
+
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "Tab:EuDX_AtoB"
+
+\end_inset
+
+ we observe that PMT performed worse that EuDX with DSI, GQI or EIT.
+ This becomes obvious when observing the
+\begin_inset Formula $\emptyset$
+\end_inset
+
+ columns of the corresponding tables where we can see that EuDX had a lower
+ percentage of tracks that did not reach any of the other end-points.
+ This an exciting outcome because usually probabilistic approaches are supposed
+ to perform better than deterministic
+\begin_inset CommandInset citation
+LatexCommand cite
+key "Behrens2007NeuroImage"
+
+\end_inset
+
+,
+\begin_inset CommandInset citation
+LatexCommand cite
+key "Parker2003"
+
+\end_inset
+
+.
+ In this study we have not investigated if PMT performs poorly because of
+ the Two Tensor fit or because of the orientation sampling.
+ However, we plan to investigate this further in the future.
+\end_layout
+
\begin_layout Subsection
Results with humans
\end_layout
@@ -6230,7 +6359,9 @@ status open
\begin_layout Plain Layout
-fos.me
+$
+\backslash
+texttt{fos.me}$
\end_layout
\end_inset
@@ -6245,7 +6376,11 @@ fos.me
more BOIs interactively and hide the other parts of the tractography which
are not interesting to their investigations.
This application will not be the topic of this chapter but it is further
- explained in Chapter 5.
+ explained in Chapter
+\begin_inset space ~
+\end_inset
+
+5.
\begin_inset Note Note
status collapsed
15 Chapter_4.lyx
View
@@ -5561,21 +5561,6 @@ key "Smith2006NeuroImage"
\end_inset
-\change_deleted 1 1319032671
-
-\begin_inset ERT
-status open
-
-\begin_layout Plain Layout
-
-
-\backslash
-texttt{flirt}
-\end_layout
-
-\end_inset
-
-
\change_unchanged
,
\begin_inset Formula $\texttt{invwarp}$
BIN  QB/Fig_9_QB_registration2_only.png
View
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.

No commit comments for this range

Something went wrong with that request. Please try again.