Re: [Freesurfer] epi correction of fmri data

[Douglas N Greve]

If they don't match, then this is beyond the scope of the tools as they 
currently exist.

On 05/03/2013 04:40 PM, Corinna Bauer wrote:
> volume sizes don't match.
>
> INFO: could not find 
> fieldmap/20130409_153340FieldMappings011a001x1.mat file for direction 
> cosine info.
> INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped 
> (default).
> INFO: if not valid, please provide the information in 
> fieldmap/20130409_153340FieldMappings011a001x1.mat file
> -
>   analyzeRead() roi_scale   2.639800072
>   analyzeRead() changing type to float
>   analyzeRead() scaling by   2.639800072
> TR=20.00, TE=0.00, TI=0.00, flip angle=0.00
> volume sizes do not match
>
> fieldmap/20130409_153340FieldMappings011a001x1.img: (width, height, 
> depth, frames) = (256, 256, 52, 1)
>
> bold/005/f.nii: (width, height, depth, frames) = (64, 64, 36, 245)
>
>
>
> On Fri, May 3, 2013 at 4:36 PM, Corinna Bauer  > wrote:
>
> It did run all the way through using the .img files.
>
> Should I try that mri_convert on all 4 real/imaginary files?
>
>
> On Fri, May 3, 2013 at 4:30 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> It should actually run all the way through. If your field maps
> have the same geometry as your fmri volumes, and your fmri
> runs have correct geometry, then you can run
>
> mri_convert imag_fmap2300.nii imag_fmap2300.geo.nii --in_like
> fmri.nii
>
> Also note that you are just creating a voxel shift map with
> the epidewarp command, not applying it to the fmri. The
> application is done in a more complicated way during preproc-sess
>
> doug
>
>
>
> On 05/03/2013 04:10 PM, Corinna Bauer wrote:
>
> hmm. can anything be done to fix it?
>
> Work the preproc-sess and mkanalysis-sess steps work if I
> used B0 corrected images right from the get-go instead of
> raw fmri runs?
>
>
> On Fri, May 3, 2013 at 4:04 PM, Douglas N Greve
>  
>  >> wrote:
>
> yep, it is basically the same error
>
>
> On 05/03/2013 03:57 PM, Corinna Bauer wrote:
>
> I would imagine so. I tried it with the img files.
>
>
> /usr/local/freesurfer/subjects/symmetry/functional/antonio>
> epidewarp.fsl --complex
> fieldmap/20130409_153340FieldMappings011a001x1.img
> fieldmap/20130409_153340FieldMappings011a001x3.img
> fieldmap/20130409_153340FieldMappings011a001x2.img
> fieldmap/20130409_153340FieldMappings011a001x4.img
> --tediff
> 2.3 --esp 0.59278 --epi bold/005/f.nii --vsm
> bold/b0dcmap.nii.gz
> FSLVersion 5.0.2
> FSLVerMaj 5
> Logfile is bold/b0dcmap.nii.gz.log
> FSLOUTPUTTYPE NIFTI_GZ
> Extension is nii.gz
> nframes = 245, nmidframe = 122
> fslroi
>
> 
> /usr/local/freesurfer/subjects/symmetry/functional/antonio/bold/005/f.nii
> bold/tmp-epidewarp.19423.fsl/exf.nii.gz 122 1
> mri_convert
> fieldmap/20130409_153340FieldMappings011a001x1.img
> bold/tmp-epidewarp.19423.fsl/real1.nii
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16
> mreuter Exp $
> reading from
> fieldmap/20130409_153340FieldMappings011a001x1.img...
>
> -
> INFO: could not find
> fieldmap/20130409_153340FieldMappings011a001x1.mat
> file for
> direction cosine info.
> INFO: use Analyze 7.5 hdr->hist.orient value: 0,
> transverse
> unflipped (default).
> INFO: if not valid, please provide the information in
> fieldmap/20130409_153340FieldMappings011a001x1.mat
> file
>
> -
>   analyzeRead() roi_scale 2.639800072
>   analyzeRead() changing type to float
>   analyzeRead() scaling by 2.639800072
> TR=20.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, 1, 0)
> k_ras = (0, 0, 1)
> writi

Re: [Freesurfer] epi correction of fmri data

[Douglas N Greve]

It should actually run all the way through. If your field maps have the 
same geometry as your fmri volumes, and your fmri runs have correct 
geometry, then you can run

mri_convert imag_fmap2300.nii imag_fmap2300.geo.nii --in_like fmri.nii

Also note that you are just creating a voxel shift map with the 
epidewarp command, not applying it to the fmri. The application is done 
in a more complicated way during preproc-sess

doug


On 05/03/2013 04:10 PM, Corinna Bauer wrote:
> hmm. can anything be done to fix it?
>
> Work the preproc-sess and mkanalysis-sess steps work if I used B0 
> corrected images right from the get-go instead of raw fmri runs?
>
>
> On Fri, May 3, 2013 at 4:04 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> yep, it is basically the same error
>
>
> On 05/03/2013 03:57 PM, Corinna Bauer wrote:
>
> I would imagine so. I tried it with the img files.
>
> /usr/local/freesurfer/subjects/symmetry/functional/antonio>
> epidewarp.fsl --complex
> fieldmap/20130409_153340FieldMappings011a001x1.img
> fieldmap/20130409_153340FieldMappings011a001x3.img
> fieldmap/20130409_153340FieldMappings011a001x2.img
> fieldmap/20130409_153340FieldMappings011a001x4.img --tediff
> 2.3 --esp 0.59278 --epi bold/005/f.nii --vsm bold/b0dcmap.nii.gz
> FSLVersion 5.0.2
> FSLVerMaj 5
> Logfile is bold/b0dcmap.nii.gz.log
> FSLOUTPUTTYPE NIFTI_GZ
> Extension is nii.gz
> nframes = 245, nmidframe = 122
> fslroi
> 
> /usr/local/freesurfer/subjects/symmetry/functional/antonio/bold/005/f.nii
> bold/tmp-epidewarp.19423.fsl/exf.nii.gz 122 1
> mri_convert fieldmap/20130409_153340FieldMappings011a001x1.img
> bold/tmp-epidewarp.19423.fsl/real1.nii
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from fieldmap/20130409_153340FieldMappings011a001x1.img...
> -
> INFO: could not find
> fieldmap/20130409_153340FieldMappings011a001x1.mat file for
> direction cosine info.
> INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse
> unflipped (default).
> INFO: if not valid, please provide the information in
> fieldmap/20130409_153340FieldMappings011a001x1.mat file
> -
>   analyzeRead() roi_scale   2.639800072
>   analyzeRead() changing type to float
>   analyzeRead() scaling by   2.639800072
> TR=20.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, 1, 0)
> k_ras = (0, 0, 1)
> writing to bold/tmp-epidewarp.19423.fsl/real1.nii...
> mri_convert fieldmap/20130409_153340FieldMappings011a001x3.img
> bold/tmp-epidewarp.19423.fsl/imag1.nii
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from fieldmap/20130409_153340FieldMappings011a001x3.img...
> -
> INFO: could not find
> fieldmap/20130409_153340FieldMappings011a001x3.mat file for
> direction cosine info.
> INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse
> unflipped (default).
> INFO: if not valid, please provide the information in
> fieldmap/20130409_153340FieldMappings011a001x3.mat file
> -
>   analyzeRead() roi_scale   2.639800072
>   analyzeRead() changing type to float
>   analyzeRead() scaling by   2.639800072
> TR=20.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, 1, 0)
> k_ras = (0, 0, 1)
> writing to bold/tmp-epidewarp.19423.fsl/imag1.nii...
> mri_convert fieldmap/20130409_153340FieldMappings011a001x2.img
> bold/tmp-epidewarp.19423.fsl/real2.nii
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from fieldmap/20130409_153340FieldMappings011a001x2.img...
> -
> INFO: could not find
> fieldmap/20130409_153340FieldMappings011a001x2.mat file for
> direction cosine info.
> INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse
> unflipped (default).
> INFO: if not valid, please provide the information in
> fieldmap/20130409_153340FieldMappings011a001x2.mat file
> -
>   analyzeRead() roi_scale   2.639800072
>   analyzeRead() changing type to float
>   analyzeRead() scaling by   2.639800072
> TR=20.00, TE=0.00, TI=0.00, flip angle=0.00
>   

Re: [Freesurfer] epi correction of fmri data

[Douglas N Greve]

It might have something to do with the complex input. I don't have 
complex data handy. Can you upload yours to our filedrop?

On 05/03/2013 02:40 PM, Corinna Bauer wrote:
> I replaced the epidewarp.fsl file in the bin folder. Tried it again 
> and got this:
>
> /usr/local/freesurfer/subjects/symmetry/functional/antonio> 
> epidewarp.fsl --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
> FSLVersion 5.0.2
> FSLVerMaj 5
> Logfile is bold/b0dcmap.nii.gz.log
> FSLOUTPUTTYPE NIFTI_GZ
> Extension is nii.gz
> dirname: missing operand
> Try `dirname --help' for more information.
> (standard_in) 1: syntax error
> nframes = , nmidframe =
> fslroi bold/tmp-epidewarp.18792.fsl/exf.nii.gz 1
>
> Usage: fslroi
> 
>fslroi
>
>fslroi
>   
> Note: indexing (in both time and space) starts with 0 not 1! Inputting 
> -1 for a size will set it to the full image extent for that dimension.
> ERROR: cannot find bold/tmp-epidewarp.18792.fsl/exf.nii.gz
>
>
>
> On Fri, May 3, 2013 at 2:28 PM, Douglas N Greve 
> mailto:gr...@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

Re: [Freesurfer] epi correction of fmri data

[Douglas N Greve]

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 
> mailto:gr...@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
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
>
> What is going 

Re: [Freesurfer] epi correction of fmri data

[Douglas N Greve]

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 
> mailto:gr...@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
> mailto:gr...@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
> mailto:corinna...@gmail.com>
> >
>    
> wrote:
>
> thanks Doug, I will give that a try.
>
>
> On Fri, May 3, 2013 at 12:27 PM, Douglas N Greve
>  
>  >
>  
>  
> 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
>  
>  >
>  
>  >>
>  
>  >
>
>  
>   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
> >
> >
> >
> __

Re: [Freesurfer] epi correction of fmri data

[Douglas N Greve]

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 
> mailto:gr...@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
> mailto:corinna...@gmail.com>
> >>
> wrote:
>
> thanks Doug, I will give that a try.
>
>
> On Fri, May 3, 2013 at 12:27 PM, Douglas N Greve
>  
>  >> 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
>  
>  >
>  
>
>  
>
> 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
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
>  >
>  
>
>  >>
>
> >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@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/file

Re: [Freesurfer] epi correction of fmri data

[Corinna Bauer]

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
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 > corinna...@gmail.com>> wrote:
>>
>> thanks Doug, I will give that a try.
>>
>>
>> On Fri, May 3, 2013 at 12:27 PM, Douglas N Greve
>> > >
>> 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
>> > > >
>> >
>> >>
>> 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
>> >
>> >
>> > __**_
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> 
>> > >
>> 
>> >
>> 
>> > >>
>>
>> >
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**
>> freesurfer 
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> > >
>> >
>> > >>
>> Phone Number: 617-724-2358 
>> >
>> Fax: 617-726-7422  >
>> >
>>
>> Bugs: 
>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
>> 
>> 
>> >
>> > BugReporting >
>> FileDrop: 
>> https://gate.nmr.mgh.harvard.**edu/filedrop2
>> 
>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
>> > html >
>>> edu/facility/filedrop/index.**html
>> >
>>
>> Outgoing:
>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
>> greve/ 
>>
>> __**_
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> 
>> > >
>> 
>> >
>> 
>> > >>
>>
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**
>> freesurfer 
>>
>>
>>

Re: [Freesurfer] epi correction of fmri data

[Douglas N Greve]

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  > wrote:
>
> thanks Doug, I will give that a try.
>
>
> On Fri, May 3, 2013 at 12:27 PM, Douglas N Greve
> mailto:gr...@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
>  
>  >> 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
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
>  >
>
> >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@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/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> 
>  >
>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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, please contact the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was
> sent to
> you in error
> but does not contain patient information, please
> contact the
> sender and properly
> dispose of the e-mail.
>
>
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 

Re: [Freesurfer] epi correction of fmri data

[Corinna Bauer]

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  wrote:

> thanks Doug, I will give that a try.
>
>
> On Fri, May 3, 2013 at 12:27 PM, Douglas N Greve <
> gr...@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 <
>>> gr...@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
>>> >
>>> >
>>> > __**_
>>> > Freesurfer mailing list
>>> > Freesurfer@nmr.mgh.harvard.edu
>>> >> >
>>>
>>> > 
>>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer
>>>
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@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/
>>>
>>> __**_
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu >> harvard.edu >
>>>
>>> 
>>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer
>>>
>>>
>>> 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, please contact the Partners
>>> Compliance HelpLine at
>>> 
>>> http://www.partners.org/**complianceline.
>>>  If the e-mail was sent to
>>> you in error
>>> but does not contain patient information, please contact the
>>> sender and properly
>>> dispose of the e-mail.
>>>
>>>
>>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@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/ 
>>
>>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] epi correction of fmri data

[Corinna Bauer]

thanks Doug, I will give that a try.


On Fri, May 3, 2013 at 12:27 PM, Douglas N Greve
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 <
>> gr...@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
>> >
>> >
>> > __**_
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > >
>>
>> > 
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@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/
>>
>> __**_
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu > harvard.edu >
>>
>> 
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer
>>
>>
>> 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, please contact the Partners
>> Compliance HelpLine at
>> 
>> http://www.partners.org/**complianceline.
>>  If the e-mail was sent to
>> you in error
>> but does not contain patient information, please contact the
>> sender and properly
>> dispose of the e-mail.
>>
>>
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@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/ 
>
>
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] epi correction of fmri data

[Douglas N Greve]

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 
> mailto:gr...@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
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@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/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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, please contact the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to
> you in error
> but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] epi correction of fmri data

[Douglas N Greve]

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
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
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Re: [Freesurfer] epi correction of fmri data

[Bruce Fischl]

Hi Corinna

yes, we use the FSL tools for B0 correction.

cheers
Bruce
On Fri, 3 May 2013, 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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