Hi Gari - The authors of probtrackx would be able to give you more
information on how to normalize probtrackx outputs, but I'd suggest taking
a look at the methods section of this paper as an example:
S. B. Eickhoff, S. Jbabdi, S. Caspers, A. R. Laird, P. T. Fox, K.
Zilles, and T. E. J. Behrens, “Anatomical and Functional Connectivity of
Cytoarchitectonic Areas within the Human Parietal Operculum,” J Neurosci,
vol. 30, no. 18, pp. 6409–6421, May 2010.
Hope this helps,
a.y
On Mon, 24 Feb 2014, Garikoitz Lerma-Usabiaga wrote:
Thanks Anastasia!
On Thu, Feb 6, 2014 at 1:11 AM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
Hi Gari - You're talking about thresholding the probtrackx maps, right?
Yes
If so the 20% at which the tracula maps are thresholded by default is
probably too high for
probtrackx, I'd try something like 2%. (Tracula is global and probtrackx
is local tractography, so
their outputs are different beasts.)
OK, thanks! The problem is that at 2% I think the tracts I obtain are too big.
I attached a subject example
(S_02) with thresholds at 2%, 5%, 20% and 30% in order to have an idea of what
do you think it would be normal.
The file is called tracts.png.
Inline image 2
Are the waytotal values very different among subjects?
I think there is quite high variability, but I don't know what's normal. In the
next figure, values.png, you can
find the values:
- Waytotal values for the two new tracts
- Max values in the tracts after normalizing
- Seed mask size
Inline image 1
Are the anatomical seed mask sizes very different?
I don't think so. They are in values.png as well if you want to take a look.
Did you take that into account? Probtrackx will generate X sample paths
for each voxel in the seed
mask.
I didn't take either the waytotal or seed mask or waypoint mask sizes into
account when thresholding. How would
you recommend doing that?
Did you threshold the tracula tracts before using them as waymasks?
Yes, using fslmath I used -thrp 20 first to threshold them and after that I
binarize it to create the waypoint.
Thank you very much for your help again,
Gari
a.y
On Tue, 14 Jan 2014, Garikoitz Lerma-Usabiaga wrote:
Hi Anastasia, it worked perfectly and I could run probtrack between
my anatomical seed
and using waypoints from Tracula tracts.
I have another doubt right now. The probabilities in each new tract
are very different.
I divided every value with waytotal using fslmaths -div in order to
normalize them, and
obtained something like this:
subject: S_20, Max Value after normalizing with waytotal: 0.75533
subject: S_23, Max Value after normalizing with waytotal: 0.27883
subject: S_25, Max Value after normalizing with waytotal: 0.60251
subject: S_27, Max Value after normalizing with waytotal: 0.32355
Should I consider the same absolute value for all tracts in order
to threshold them or
should I threshold all tracts independently with the 20%?
I want to check visually the existence of the tract between the
anatomical and the
tract, with the same probability across subjects, and afterwards
obtain the FA values
in order to correlate with behavior.
Thanks again!
Gari
On Mon, Jan 13, 2014 at 7:55 PM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu>
wrote:
Hi Gari - Yes, fslmaths should be able to do it, with -thrp
20.
a.y
On Mon, 13 Jan 2014, Garikoitz Lerma-Usabiaga wrote:
Thanks Anastasia, I finally got it, I had to do
mri_vol2vol
twice to have it
in the diffusion space.
I have an additional question:
I want to create waypoint masks for probtracx from
Tracula
tracts (for
example, uncinate).
Should I use mri_binarize on path.pd.nii to create the
mask?
Should I use 20% of the maximum value as the threshold
in order
to do so? (a
little help with the command line will be greatly
appreciated)
thanks again!
Gari
On Sun, Jan 12, 2014 at 3:08 AM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
Has mri/hippo_subfield_in_diffusion_space.nii been
actually
transformed to diffusion space by applying the
anatorig2diff
transformation? I'm assuming that your diffusion
data is
not
0.5mm resolution? You can search for the name of
the
transformation in trac-all.log to see examples of
how it
is
applied to volumes.
On Sat, 11 Jan 2014, Garikoitz Lerma-Usabiaga
wrote:
Hi Anastasia,the problem is
with
mri/hippo_subfield_in_diffusion_space.nii,
which originally is mri/hippo_subfield.mgz,
the
output of running recon-all
-hippo-subfields. So as far as I understand
it is
not in anatomical space,
according to MRI info, it is (one example):
- LIA
- 85x97x141
- 0.5x0.5x0.5
So, how could I convert it to the
diffussion space
in FSL format in order to
be able to use it in probtrackx?
Should I do 2 steps or 3 steps?
1.- mri_convert to anatorig space
(brainmask.mgz
space, LIA, 256x256x256)
2.- anatorig2diff in order to change to FSL
format
and to diffusion space?
(3.- would be the previous one in two
steps, first
from anatorig to anat and
then from anat to diff)
Any indication of the best programs to do
all the
change will be appreciated
(I've seen in trac-all.log that mostly fsl
programs
are being used to do the
flips, and then tkregister2 and bbregister
for the
registrations)
Thanks for the help!
Gari
On Sat, Jan 11, 2014 at 1:31 AM, Anastasia
Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
Hi Gari - So if I understand
correctly, your
inputs to
probtrackx are:
mri/hippo_subfield_in_diffusion_space.nii
dmri.bedpostX/merged
dmri.bedpostX/nodif_brain_mask
If these all come from the output of
tracula,
aren't these all
in LAS orientation?
a.y
On Thu, 9 Jan 2014, Garikoitz
Lerma-Usabiaga
wrote:
Hi Anastasia,I want to use a
hippocampal
subfield as
a seed in FSL. I am having
problems
understanding
how
to change spaces around...
1.- Is this command ok?
mri_vol2vol --mov
dmri/dtifit_FA.nii.gz
--targ
mri/hippo_subfield_in_anatomical_space.mgz
--inv
--interp
nearest --o
mri/hippo_subfield_in_diffusion_space.nii
--reg
dmri/xfms/anatorig2diff.bbr.dat
--no-save-reg
2.- I would like to visualize
it in
freeview in
anatomical space to check if it
is ok,
if I load
nu.mgz and
hippo_subfield_in_anatomical_space.mgz
and then load
hippo_subfield_in_diffusion_space.nii
with the
registration file
dmri/xfms/anatorig2diff.bbr.dat,
should I visualize it ok?
If I don't register it, they
show to be
displaced
(more than expected).
3.- Afterwards I want to run
probtracx
with the
following command (my doubt is
mainly
about the
files to
use, since FSL files are RAS,
freesurfer
anatomical
are LIA and freesurfer
diffusion are
LIA, are all
the
files in the same format and
FSL is ok
with it?):
/usr/local/fsl/bin/probtrackx
--mode=seedmask
-x
mri/hippo_subfield_in_diffusion_space.nii -s
dmri.bedpostX/merged -m
dmri.bedpostX/nodif_brain_mask
-o
fdt_paths_hippo_subfields
--dir=FSL_ConnResults_Hipp -c
0.2 -S
2000
--steplength=0.5 -P 5000 --opd
many thanks!
Gari
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