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
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
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
thanks Doug, I will give that a try.
On Fri, May 3, 2013 at 12:27 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
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
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
gr...@nmr.mgh.harvard.edu
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
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
gr...@nmr.mgh.harvard.eduwrote:
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
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
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
It needs to be 0 to 4095,
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
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:
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:
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
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
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