Hi Anastasia, stuff is running smoothly at last one quick question, is there
any 'disadvantage' in
using FSL to do the eddy correct and then feed
those images to trace-all ?
cheers
ds
http://www1.imperial.ac.uk/medicine/people/d.soto/
On 9 Aug 2013, at 15:33, David Soto <ds...@imperial.ac.uk>
wrote:
hi, for some reason FS does not like the
nii file from Mriconverter, ( I saw
a post about this
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19526.html
) but does like
the nii.gz outputs from FSL...
I'll try to debug the bepostx error
thanks!
ds
http://www1.imperial.ac.uk/medicine/people/d.soto/
On 09/08/13 14:26, Anastasia Yendiki wrote:
There is no reason to conevrt to .mnc. You should use your
original .nii, if that shows up correctly in freeview.
As for the bedpostx error, this is an Ubuntu issue that
has come to my attention very recently. In Ubuntu /bin/sh
is not a bash shell any more. To get around this, you'll
have to edit the first line of the scripts
$FREESURFER_HOME/bin/bedpostx_mgh and
$FREESURFER_HOME/bin/fsl_sub_mgh. You'll have to replace
"/bin/sh" with "/bin/bash" on the first line of those two
scripts.
On Fri, 9 Aug 2013, David Soto wrote:
hi- I tried to convert from nii to mnc becos
that is what i did when
I did recon-all
but I also tried with nii at the beggining and
got the same issues.
In fact in my last post (pasted below
again)the input was a nii file
could you please check the stuff below?
thanks! ds
Hi, further to my prior email
I made some progress. I noted that nii2mnc
does not seem to work on the diffusion
output.nii that I got from Mriconverter as the
output.mnc brain has parts chopped in
Freeview.
(I think there may be something funny about
this, as the recon-all does like the T1 output
form Mriconverter)
HENCE I tried use the output of eddycorrect
from FSL (which I already run for other thing)
Then I created a new folder where i placed the
output of FSL eddycorrect and in the
configuration file I did
(i) set dcmlist =
(fsleddycorrectoutput.nii.gz)
(ii) turned 'set doeddy = 0'
then run it
trac-all -c traculatest.txt -prep -log
trac_from_fsleddy
it seemed to complete without errors (log
attached)n and I checked the preprocessing
outputs in Freeview (FA, masks and
aparc+asegs) and all seemed
fine.
However when I attempt the next stage in
trac-all
i.e. trac-all -c traculatest.txt -bedp -log
trac_from_fsleddy_bedp
it fails saying the following
/usr/local/freesurfer/bin/bedpostx_mgh: 131:
/usr/local/freesurfer/bin/bedpostx_mgh: Syntax
error: "(" unexpected
the log is also attached.
any advise appreciated!
cheers
ds
http://www1.imperial.ac.uk/medicine/people/d.soto/
http://www1.imperial.ac.uk/medicine/people/d.soto/
On 09/08/13 14:02, Anastasia Yendiki wrote:
Why are you converting from .nii
to .mnc? Why are you not using the
.nii directly?
On Fri, 9 Aug 2013, David Soto
wrote:
hi - thanks for the
feedback
weirdly, the nii2mnc
transform of the
diffusion
data falters, I get a
part of the brain
chopped
have no idea why this
is the case, as it
worked fine
before for the T1 for
recon-all...I am using
Ubuntu 12.04
anyway am trying to
sort this out now, if
you have any
advise that would much
appreciated!!
cheers
ds
http://www1.imperial.ac.uk/medicine/people/d.soto/
On 08/08/13 17:03,
Anastasia Yendiki
wrote:
Hi David -
The fact
that it's
taking so
many tries
to
initialize
the left
ILF tells
me that
something
has gone
wrong with
the data,
either
with the
T1 to DWI
registration,
or with
the mask,
or
something
like that.
Have you
looked at
any of the
output
files of
the
pre-processing?
The FA
map, the
aparc+aseg,
etc?
a.y
On Wed, 7
Aug 2013,
Soto,
David
wrote:
Hi
Anastasia,
I
checked
the
becs
and
bvals
files,
there
was
a
bug
in
the
transposition
of
the
columns
into
3
rows
in
the
bvecs.
But
i
still
have
problems..
I
rerun
trac-all
-prep
and
seemed
fine
but
ended
with
a
Segmentation
fault
(core
dumped)
which
however
is
not
present
in
the
last
line
of
the
trac-all.log
(Attached).
Writing
output
files
to/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.ilf_AS_avg33_mn
i_bbr_*
Writing
spline
volume
to/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.ilf_AS_avg33_mn
i_bbr_cpts_5.nii.gz
Segmentation
fault
(core
dumped)
Just
in
case
I
tried
trac-all
-bedp
complains
like
these
below,
any
advise
appreciated,
cheers
-
ds
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/diffree/tracula02ST.txt
-bedp
INFO:
SUBJECTS_DIR
is
/home/dsoto/Documents/fmri/rsdtianawmgui
INFO:
Diffusion
root
is
/home/dsoto/Documents/fmri/rsdtianawmgui
Actual
FREESURFER_HOME
/usr/local/freesurfer
WARN:
Running
FSL's
bedbost
locally
-
this
might
take
a
while
WARN:
It
is
recommended
to
run
this
step
on
a
cluster
bedpostx_mgh
-n
2
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri
/usr/local/freesurfer/bin/bedpostx_mgh:
131:
/usr/local/freesurfer/bin/bedpostx_mgh:
Syntax
error:
"("
unexpected
http://www1.imperial.ac.uk/medicine/people/d.soto/
________________________________________
From:
Anastasia
Yendiki
[ayend...@nmr.mgh.harvard.edu]
Sent:
07
August
2013
17:22
To:
Soto,
David
Cc:
freesurfer@nmr.mgh.harvard.edu
Subject:
RE:
[Freesurfer]
trac-all
inquiry
Hi
David
-
Every
time
you
run
trac-all,
the
results
get
appended
to
this
file,
so
you
need
to
look
for
error
messages
only
in
the
more
recent
invocation
of
trac-all.
The
first
error
there
seems
to
be:
Error:
bvecs
and
bvals
don't
have
the
same
number
of
entries
Do
you
have
the
same
number
of
b-values
and
gradient
vectors
and
volumes
in
your
DWI
series?
a.y
On
Tue,
6
Aug
2013,
Soto,
David
wrote:
hi
I
upgraded
to
FS
5.3
but
still
encountering
issues
with
trac-all
prep.
The
log
is
attached,
things
I
noted
after
inspecting
it
1)
INFO:
FreeSurfer
build
stamps
do
not
match
Subject
Stamp:
freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Current
Stamp:
freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
2)
Error:
input
image
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb
not
valid
3)
Image
Exception
:
#22
::
ERROR:
Could
not
open
image
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb_brain
4)
Image
Exception
:
#22
::
ERROR:
Could
not
open
image
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/White-Matter++.
5)
ERROR:
Could
not
read
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dtifit_FA.nii.gz
but
despite
all
this
it
says:
trac-preproc
finished
without
error
at
Tue
Aug
6
21:27:30
BST
2013
thanks
for
your
help
cheers
ds
http://www1.imperial.ac.uk/medicine/people/d.soto/
________________________________________
From:
Anastasia
Yendiki
[ayend...@nmr.mgh.harvard.edu]
Sent:
06
August
2013
19:30
To:
Soto,
David
Cc:
freesurfer@nmr.mgh.harvard.edu
Subject:
RE:
[Freesurfer]
trac-all
inquiry
I
see,
you're
using
the
old
version
of
tracula
(from
freesurfer
5.1).
In
that
version,
you
had
to
define
the
number
of
low-b
images
in
the
configuration
file.
I
strongly
recommend
updating
to
freesurfer
5.3.
A
lot
of
things
have
improved
in
tracula
since
then.
Also,
in
the
future
please
attach
any
log
files
as
separate
attachments
instead
of
pasting
them
into
the
body
of
your
email
-
this
causes
the
body
of
the
email
to
exceed
the
limit
allowable
on
the
list.
Thanks,
a.y
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