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>> 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>> wrote:<mailto:greve@nmr.mgh.harvard.edu
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:Freesurfer@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
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu <tel:617-724-2358 <tel:617-724-2358>>
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422<mailto:Freesurfer@nmr.mgh.harvard.edu
<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/
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
<mailto: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 Centergreve@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/