cheers Bruce
On Fri, 10 May 2013, Jonathan Holt wrote:
$ export SUBJECTS_DIR=/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer $
mris_make_surfaces -dura 001%d.mgz 4 s_MEMPRAGE lh
it's entirely possible I'm specifying the wrong mgz? After running recon-all on
the
RMS the usual directories were created, etc... including 001.mgz which is in
s_MEMPRAGE/mri/orig.
On Fri, May 10, 2013 at 12:39 PM, Jonathan Holt <whats...@umich.edu> wrote:
$ export SUBJECTS_DIR=/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer$
mris_make_surfaces -dura 001%d.mgz 4 s_MEMPRAGE lh
it's entirely possible I'm specifying the wrong mgz? After running recon-all on
the RMS the usual directories were created, etc... including 001.mgz which is
in s_MEMPRAGE/mri/orig.
On Fri, May 10, 2013 at 12:33 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
can you send details about the steps you carried out including full
command lines?
On Fri, 10 May 2013, Jonathan Holt wrote:
I've gotten as far as running the mris_make_surfaces on
the RMS, but after running for a bit it stopped with
this error
mghRead (file/path/s_MEMPRAGE/mri/0010.mgz -1): coult
not open file
mris_make_surfaces: could not read 0th echo for dura
localization from file/path/s_MEMPRAGE/mri/0010.mgz
for reference, the RMS file name is 001.mgz
jon
On May 9, 2013, at 8:44 PM, Douglas Greve wrote:
the dcmunpack command is right. You should
make sure to analyze only the
RMS in recon-all (ie , that is the only
volume that goes into mri/orig
doug
On 5/9/13 6:48 PM, Bruce Fischl wrote:
Hi Kayle
you would run recon-all on the
RMS, then run the dura stuff
posthoc.
cheers
Bruce
On Thu,
9 May 2013, Kayle Sawyer wrote:
Hi all,
Can the MEMPRAGE be
specified in
recon-all with the
-i flag? We have
been using the
MEMPRAGE RMS scans
and discarding the
multiecho scans. If
we instead specify
the multiecho scans
for recon-all, do
we need to give any
additional
parameters (e.g.
the number of
echoes) for it to
utilize the 4
echoes to detect
dura and refine
pial surfaces in
mris_make_surfaces,
as described below?
Or would we have to
run recon-all with
the RMS, then after
it finishes re-run
mris_make_surfaces
manually with the
-dura flag to
refine the pial
surface?
Also, I'd like to
make sure we are
using dcmunpack
properly. We take
the
scan.info file and parse it
like this: "-run
[MEMPRAGE_4e_p2_1mm_iso run
number] 3danat mgz 001.mgz" so
the multi echo scan gets put
into one mgz
file, and the RMS gets put into
a separate mgz file.
Thanks,
-Kayle
On May 9, 2013, at
12:00 PM,
freesurfer-requ...@nmr.mgh.harvard.edu
wrote:
Message:
35
Date:
Thu, 9
May
2013
10:44:23
-0400
(EDT)
From:
Bruce
Fischl
<fis...@nmr.mgh.harvard.edu>
Subject:
Re:
[Freesurfer]
Working
with
MEMPRAGE
To:
Jonathan
Holt
<whats...@umich.edu>
Cc:
freesurfer@nmr.mgh.harvard.edu
Message-ID:
<alpine.lrh.2.02.1305091043500.13...@gate.nmr.mgh.harvard.edu>
Content-Type:
TEXT/PLAIN;
format=flowed;
charset=US-ASCII
it
needs
to be:
mris_make_surfaces
-dura
memprage_echo%d.mgz
4
subjid
lh
note
the "4"
which
tells
it how
many
echoes
to read
On Thu,
9 May
2013,
Jonathan
Holt
wrote:
I
input:
mris_make_surfaces
-dura
memprage_echo%d.mgz
subjid
lh
it
returns:
detecting
dura
using
0
echos
from
memprage_echo%d.mgz
Should
I
execute
the
command
in
the
same
directory
as
the
mgz's?
Should
they
be
set
up
or
placed
in
a
specific
directory?
I
also,
as
with
recon-all,
exported
the
proper
subject
directory
beforehand.
On
May
9,
2013,
at
10:37
AM,
Bruce
Fischl
wrote:
can
you
send
me
the
full
command
line?
It
should
say
4
echoes,
not
0
On
Thu,
9
May
2013,
Jonathan
Holt
wrote:
Thanks
Bruce,
should
the
hemisphere's
be
processed
separately,
or
how
do
I
signify
lh
and
rh
simultaneously?
Also,
should
the
fact
that
after
running
mris_make_surfaces,
it
says
"detecting
dura
using
0
echos
from
memprage_echo%d.mgz"
be
worrisome?
I've
got
4
different
echos,
all
mgzs
in
the
directory.
I
have
a
feeling
I'm
doing
this
incorrectly.
jon
On
May
9,
2013,
at
8:50
AM,
Bruce
Fischl
wrote:
Hi
Jon
yes,
the
subject
and
hemi
need
to
be
defined
(they
are
required
parameters)
Bruce
On
Wed,
8
May
2013,
Jonathan
Holt
wrote:
Hi
all,
combed
through
the
mail
archives
to
figure
out
how
to
work
with
multi
echo
mprage,
found
what
I
need
but
I
wanted
to
confirm
which
of
these
two
commands
is
the
appropriate
mris_make_surfaces
-dura
memprage_echo%d.mgz
4
subjid
lh/rh
mris_make_surfaces
-dura
memprage_echo%d.mgz
do
the
subjid
and
hemispheres
need
to
be
specified
as
per
the
1st
line?
jon
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