tcsh source your_freesurfer_dir/SetUpFreeSurfer.csh setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs cd $SUBJECTS_DIR
freeview -v \ good_output/mri/T1.mgz \ good_output/mri/wm.mgz \ good_output/mri/brainmask.mgz \ good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f good_output/surf/lh.white:edgecolor=blue \ good_output/surf/lh.pial:edgecolor=red \ good_output/surf/rh.white:edgecolor=blue \ good_output/surf/rh.pial:edgecolor=red
do those files exist in that path?
cheers
Bruce
On Sat, 2 Aug 2014, Isaiah C. Smith wrote:
Hello Bruce,_______________________________________________
I am trying to check the output of the mri data that I processed I start
using MNE. I placed the file in a folder called Practice in my documents,
and I am using the following command:
tcsh
source your_freesurfer_dir/SetUpFreeSurfer.csh
setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs
cd $SUBJECTS_DIR
and then
freeview -v \
good_output/mri/T1.mgz \
good_output/mri/wm.mgz \
good_output/mri/brainmask.mgz \
good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 \
-f good_output/surf/lh.white:edgecolor=blue \
good_output/surf/lh.pial:edgecolor=red \
good_output/surf/rh.white:edgecolor=blue \
good_output/surf/rh.pial:edgecolor=red
e
file
2014-08-01 19:53:06.207 Freeview[10239:303] modalSession has been exited
prematurely - check for a reentrant call to endModalSession:
MRISread(/Users/IsaiahSmith/Documents/LABData/Volume Conduction
Models/Practice/good_output/surf/rh.white): could not open file
No such file or directory
MRISread failed
MRISread(/Users/IsaiahSmith/Documents/LABData/Volume Conduction
Models/Practice/good_output/surf/rh.white): could not open file
e
file
2014-08-01 19:53:07.387 Freeview[10239:303] modalSession has been exited
prematurely - check for a reentrant call to endModalSession:
MRISread(/Users/IsaiahSmith/Documents/LABData/Volume Conduction
Models/Practice/good_output/surf/rh.pial): could not open file
No such file or directory
MRISread failed
MRISread(/Users/IsaiahSmith/Documents/LABData/Volume Conduction
Models/Practice/good_output/surf/rh.pial): could not open file
e
Do you know what is going on here?
On Jul 31, 2014, at 10:38 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
Hi Isaiah
you should go through the tutorials on our website - they detail
all this
information
cheers
Bruce
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
Yes, how do i view the files and where can I find
where every has been placed
On Jul 31, 2014, at 8:26 AM, "Bruce
Fischl" <fischl@nmr.mgh.harvard.edu>
wrote:
there are many, many files in many
different formats (e.g. volumes in
.mgz format, surfaces in our internal
format, labels, parcellations,
etc...)
On Thu, 31 Jul 2014, Isaiah
C. Smith wrote:
The files after recon-all
On Jul 31, 2014,
at 7:10 AM,
"Bruce Fischl"
<fischl@nmr.mgh.harvard.edu>
wrote:
the format of
what?
On
Thu,
31
Jul
2014,
Isaiah
C.
Smith
wrote:
Thank
you,
I
will
go
there
now.
But
regarding
the
output
of
freesurfer,
the
format
will
be
.ccd?
On
Jul
30,
2014,
at
7:23
PM,
Bruce
Fischl
<fischl@nmr.mgh.harvard.edu>
wrote:
Hi
Isaiah
you
might
check
out
MNE
from
Matti
Hamalainen
(ccd).
It
does
all
this
and
more
(using
FreeSurfer
surfaces
and
segmentations)
cheers
Bruce
On
Thu,
31
Jul
2014,
Isaiah
C.
Smith
wrote:
Thank
you
so
much,
Bruce.
I
think
that
I
got
it.
Overall,
I
am
trying
to
create
a
source
volume
conduction
model,
calculate
the
lead
field
matrix,
and
then
create
a
source
model.
My
instructor
said
that
it
might
be
possible
to
do
this
in
Freesurfer.
Sorry,
I
am
kind
of
new
to
using
the
terminal.
Could
you
tell
me
how
to
go
about
doing
that
in
this
program
or
direct
me
to
the
part
of
the
sit
where
I
can
start
working
on
next
steps?
Or
do
I
need
to
use
another
program
like
FieldTrip
for
the
model?
Also
what
will
the
format
of
the
file
be
after
the
command
is
finished?
Nine
parameter
search.
iteration
5
nscales
=
1
...
****************************************
Result
so
far:
scale
0.250:
max_log_p=-3.9,
old_max_log_p
=-3.9
(thresh=-3.9)
1.074
-0.133
0.048
-2.720;
0.105
1.397
-0.148
-56.728;
-0.031
0.191
1.157
-52.936;
0.000
0.000
0.000
1.000;
reducing
scale
to
0.0625
****************************************
Nine
parameter
search.
iteration
6
nscales
=
2
...
****************************************
Result
so
far:
scale
0.062:
max_log_p=-3.9,
old_max_log_p
=-3.9
(thresh=-3.9)
1.076
-0.124
0.028
-1.627;
0.096
1.401
-0.129
-58.732;
-0.015
0.165
1.156
-51.529;
0.000
0.000
0.000
1.000;
****************************************
Nine
parameter
search.
iteration
7
nscales
=
2
...
****************************************
On
Jul
29,
2014,
at
9:24
PM,
Isaiah
Smith
<Isaiah.C.Smith.17@dartmouth.edu>
wrote:
The
recon-all
option
is
no
longer
working
and
neither
is
the
other
one.
I
am
getting
an
error.
Isaiahs-MacBook-Pro:~
IsaiahSmith$
recon-all
help
ERROR:
Flag
help
unrecognized.
help
Darwin
Isaiahs-MacBook-Pro.local
13.3.0
Darwin
Kernel
Version
13.3.0:
Tue
Jun
3
21:27:35
PDT
2014;
root:xnu-2422.110.17~1/RELEASE_X86_64
x86_64
recon-all
-s
exited
with
ERRORS
at
Tue
Jul
29
21:23:06
PDT
2014
For
more
details,
see
the
log
file
To
report
a
problem,
see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Isaiahs-MacBook-Pro:~
IsaiahSmith$
On
Jul
22,
2014,
at
4:44
PM,
Bruce
Fischl
<fischl@nmr.mgh.harvard.edu>
wrote:
Hi
Isaiah
recon-all
-i
<input
file>
-s
<subject
identifier>
-sd
<dir
to
put
subject
in>
-all
should
do
the
trick.
<input
file>
should
be
a
*single*
file
in
the
right
dicom
series,
or
a
.nii
file.
Don't
use
analyze
Bruce
On
Tue,
22
Jul
2014,
Isaiah
C.
Smith
wrote:
Hello
Bruce,
Thanks
for
the
response;
I
tried
the
inputs
from
the
check
freesurfer
page.
I
just
tried
to
do
the
run
recon-all
and
got
the
list
of
possible
commands.
The
input
images
are
unix
executable
files
separately,
but
I
can
convert
them
to
.hdr/.img
or
.nii
using
mricron.
They
are
MRI
images.
How
do
I
direct
these
files
to
the
command?
And
this
is
the
command
to
do
the
things
I
previously
asked,
right?
Isaiah
Hi
Isaiah,
what
are
the
input
images
that
you
have?
What
format
and
what
imaging
sequence?
You
should
be
able
to
just
run
recon-all
on
them
(check
out
recon-all
-help)
cheers
Bruce
On
Tue,
22
Jul
2014,
Isaiah
C.
Smith
wrote:
Hello
All,
I
was
testing
to
see
if
the
freesurfer
program
works
and
it
does
seem
to
work
for
anything
besides
the
free
viewer
program.
I
do
not
know
what
is
wrong
with
the
others;
do
you
have
any
ideas?
Also
I
am
trying
to
use
the
inhomogeneity
correction,
convert
the
images
that
I
have
to
1x1x1
ratio,
arrange
the
directions
of
the
image,
and
save
the
program
in
analyze
format.
If
possible
could
you
outline
that
process
or
give
me
a
link
that
will
direct
me
on
the
process?
Thank
you.
Your
help
is
really
appreciated.
Isaiah
Smith
_______________________________________________
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list
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mailing
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The
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If
you
believe
this
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error
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the
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patient
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you
in
error
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does
not
contain
patient
information,
please
contact
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and
properly
dispose
of
the
e-mail.
_______________________________________________
Freesurfer
mailing
list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer
mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
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Freesurfer mailing list
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_______________________________________________
Freesurfer mailing list
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_______________________________________________
Freesurfer mailing list
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Freesurfer@nmr.mgh.harvard.edu
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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