On Fri, May 3, 2013 at 2:28 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

I can't remember why I excluded version 5. I put another version herethat will accept v5

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl

try it and let me know if it works

On 05/03/2013 02:13 PM, Corinna Bauer wrote:

/usr/local/freesurfer/subjects/symmetry/functional/antonio> epidewarp.fsl --debug --complex fieldmap/real_fmap2300.nii fieldmap/imag_fmap2300.nii fieldmap/real_fmap4600.nii fieldmap/imag_fmap4600.nii --tediff 2.3 --esp 0.59278 --vsm bold/b0dcmap.nii.gz | & tee dng.log
set echo = 1 ;
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 11 != 0 )

set flag = $argv[1] ; shift ;
set flag = --complex
shift

switch ( $flag )
switch ( --complex )
if ( $#argv < 4 ) goto arg4err ;
if ( 10 < 4 ) goto arg4err
set real1 = $argv[1] ; shift ;
set real1 = fieldmap/real_fmap2300.nii
shift
if ( ! -e $real1 ) then
if ( ! -e fieldmap/real_fmap2300.nii ) then
set imag1 = $argv[1] ; shift ;
set imag1 = fieldmap/imag_fmap2300.nii
shift
if ( ! -e $imag1 ) then
if ( ! -e fieldmap/imag_fmap2300.nii ) then
set real2 = $argv[1] ; shift ;
set real2 = fieldmap/real_fmap4600.nii
shift
if ( ! -e $real2 ) then
if ( ! -e fieldmap/real_fmap4600.nii ) then
set imag2 = $argv[1] ; shift ;
set imag2 = fieldmap/imag_fmap4600.nii
shift
if ( ! -e $imag2 ) then
if ( ! -e fieldmap/imag_fmap4600.nii ) then
set UseComplex = 1 ;
set UseComplex = 1
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 6 != 0 )

set flag = $argv[1] ; shift ;
set flag = --tediff
shift

switch ( $flag )
switch ( --tediff )
if ( $#argv == 0 ) goto arg1err ;
if ( 5 == 0 ) goto arg1err
set tediff = $argv[1] ; shift ;
set tediff = 2.3
shift
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 4 != 0 )

set flag = $argv[1] ; shift ;
set flag = --esp
shift

switch ( $flag )
switch ( --esp )
if ( $#argv == 0 ) goto arg1err ;
if ( 3 == 0 ) goto arg1err
set esp = $argv[1] ; shift ;
set esp = 0.59278
shift
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 2 != 0 )

set flag = $argv[1] ; shift ;
set flag = --vsm
shift

switch ( $flag )
switch ( --vsm )
if ( $#argv == 0 ) goto arg1err ;
if ( 1 == 0 ) goto arg1err
set vsm = $argv[1] ; shift ;
set vsm = bold/b0dcmap.nii.gz
shift
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 0 != 0 )

goto parse_args_return ;
goto parse_args_return

goto check_params ;
goto check_params

if ( ( $#mag || $#dph || $#ph ) && $UseComplex ) then
if ( ( 0 || 0 || 0 ) && 1 ) then

if ( $#ph && $#dph ) then
if ( 0 && 0 ) then

if ( ! $UseComplex ) then
if ( ! 1 ) then

if ( $#tediff == 0 ) then
if ( 1 == 0 ) then

if ( $#esp == 0 ) then
if ( 1 == 0 ) then

if ( $#epi == 0 && $exf == 0 ) then
if ( 0 == 0 && == 0 ) then

if ( $#vsm == 0 ) then
if ( 1 == 0 ) then

if ( $cleanup_forced ) set cleanup = 1 ;
if ( 0 ) set cleanup = 1

set outdir = `dirname $vsm` ;
set outdir = `dirname $vsm`
dirname bold/b0dcmap.nii.gz
mkdir -p $outdir
mkdir -p bold
if ( $status ) then
if ( 0 ) then

if ( $#tmpdir == 0 ) set tmpdir = $outdir/tmp-epidewarp.$$.fsl
if ( 0 == 0 ) set tmpdir = bold/tmp-epidewarp.18569.fsl
set tmpdir = bold/tmp-epidewarp.18569.fsl
mkdir -p $tmpdir
mkdir -p bold/tmp-epidewarp.18569.fsl
if ( $status ) then
if ( 0 ) then

if ( $#epidw != 0 ) then
if ( 0 != 0 ) then

if ( $#exfdw != 0 ) then
if ( 0 != 0 ) then

goto check_params_return ;
goto check_params_return

set FSLVersion = `cat $FSLDIR/etc/fslversion` ;
set FSLVersion = `cat $FSLDIR/etc/fslversion`
cat /usr/share/fsl/5.0/etc/fslversion
set FSLVerMaj = `echo $FSLVersion | cut -c 1`
set FSLVerMaj = `echo $FSLVersion | cut -c 1`
cut -c 1
echo 5.0.2
echo FSLVersion $FSLVersion
echo FSLVersion 5.0.2
FSLVersion 5.0.2
echo FSLVerMaj $FSLVerMaj
echo FSLVerMaj 5
FSLVerMaj 5
if ( $FSLVerMaj == 3 ) then
if ( 5 == 3 ) then
if ( $FSLVerMaj == 4 ) then
if ( 5 == 4 ) then

echo "FSL Version is $FSLVersion, must be 3.X or 4.X"
echo FSL Version is 5.0.2, must be 3.X or 4.X
FSL Version is 5.0.2, must be 3.X or 4.X
exit 1 ;
exit 1

On Fri, May 3, 2013 at 2:09 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

What is your cmd line? Can you run it with --debug as the first
arg, capture the output, and send it to me? eg,

dewarp.fsl --debug ... |& tee dng.log

On 05/03/2013 01:43 PM, Corinna Bauer wrote:

I get this:

FSLVersion 5.0.2
FSLVerMaj 5
FSL Version is 5.0.2, must be 3.X or 4.X

On Fri, May 3, 2013 at 1:42 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>

<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>> wrote:

What is going wrong when you run FSL 5?

On 05/03/2013 01:38 PM, Corinna Bauer wrote:

oh great. Is there a way to get this to work with FSL 5?

On Fri, May 3, 2013 at 1:11 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>> wrote:

It needs to be 0 to 4095, see below

--ph phasevolid

Phase volume from the B0 fieldmap (if the phases from
Echo1, Echo2 are
available instead of their difference). These are
assumed
to be scaled
between 0 to 4095 for -pi to pi. Eg, ph.ext, where
ext is
either nii,
nii.gz, or img. Not with --complex or with --dph.

This is made to work with the default Siemens
field map.
Note that
you can also use complex inputs instead of mag and
phase

doug

On 05/03/2013 01:05 PM, Corinna Bauer wrote:

Should the phase image be in rads? and does
the magnitude
image need to be skull-stripped first?

On Fri, May 3, 2013 at 12:30 PM, Corinna Bauer
<corinnab83@gmail.com
<mailto:corinnab83@gmail.com> <mailto:corinnab83@gmail.com
<mailto:corinnab83@gmail.com>>
<mailto:corinnab83@gmail.com
<mailto:corinnab83@gmail.com> <mailto:corinnab83@gmail.com
<mailto:corinnab83@gmail.com>>>
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<mailto:corinnab83@gmail.com>
<mailto:corinnab83@gmail.com
<mailto:corinnab83@gmail.com>> <mailto:corinnab83@gmail.com
<mailto:corinnab83@gmail.com>
<mailto:corinnab83@gmail.com
<mailto:corinnab83@gmail.com>>>>>

wrote:

thanks Doug, I will give that a try.

On Fri, May 3, 2013 at 12:27 PM, Douglas N
Greve
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>> wrote:

Create the B0 voxel shift map. Call it
b0dcmap.nii.gz
and put
it in
the bold folder, eg:

epidewarp.fsl \
--mag mag.nii.gz \
--dph dphase.nii.gz \
--tediff YOUR_TE_DIFF --esp YOUR_ESP \
--vsm bold/b0dcmap.nii.gz

When you run mkanalysis-sess and
preproc-sess, add
"-b0dc" to the
command lines.

doug

On 05/03/2013 12:16 PM, Corinna Bauer
wrote:

Yes, I am using FSFAST.

On Fri, May 3, 2013 at 12:08 PM,
Douglas N
Greve
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>

<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>>> wrote:

Hi Corinna, are you using
FSFAST? If
not, are you
still going to the
surface?
doug

On 05/03/2013 11:07 AM,
Corinna Bauer
wrote:
> Is there a way to correct
fmri data
for epi
distortions in
freesurfer?
> Or does the data need to be
first fun
through FSL's
B0 unwarping?
>
> Corinna
>
>
>
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>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
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<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
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<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
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<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>
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<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
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<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>

<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
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<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>>
Phone Number: 617-724-2358
<tel:617-724-2358>
<tel:617-724-2358 <tel:617-724-2358>>
<tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
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<tel:617-724-2358 <tel:617-724-2358>>>>
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<tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
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<tel:617-724-2358>
<tel:617-724-2358 <tel:617-724-2358>>>>>

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<tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422
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<tel:617-726-7422 <tel:617-726-7422>>>>
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<tel:617-726-7422 <tel:617-726-7422>
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<tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422
<tel:617-726-7422>>>>>

Bugs:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop:
https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
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<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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The information in this e-mail
is intended
only for
the person to
whom it is
addressed. If you believe this
e-mail
was sent
to you
in error and
the e-mail
contains patient information,
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-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
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<mailto:greve@nmr.mgh.harvard.edu
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Phone Number: 617-724-2358
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<tel:617-726-7422 <tel:617-726-7422>>
<tel:617-726-7422 <tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>>>>

Bugs:
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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop:
https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
Phone Number: 617-724-2358 <tel:617-724-2358>
<tel:617-724-2358 <tel:617-724-2358>>
<tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
<tel:617-724-2358>>>
Fax: 617-726-7422 <tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422
<tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>>>

Bugs:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
Phone Number: 617-724-2358 <tel:617-724-2358>
<tel:617-724-2358 <tel:617-724-2358>>
Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422
<tel:617-726-7422>>

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
Fax: 617-726-7422 <tel:617-726-7422>

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/