Hi Gari - You're talking about thresholding the probtrackx maps, right? 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.)
Are the waytotal values very different among subjects? Are the anatomical
seed mask sizes very different? Did you take that into account? Probtrackx
will generate X sample paths for each voxel in the seed mask. Did you
threshold the tracula tracts before using them as waymasks?
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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