Try using this version
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl
On 7/22/15 4:03 AM, Bingjiang Lyu wrote:
Thanks a lot for your prompt reply, Doug and Bruce. I did collect
field maps and just tried epidewarp.fsl, but I met with the following
error "FSL Version is 5.0.6, must be 3.X or 4.X". I've searched the
email archives and found a message about epidewarp.fsl that works with
FSL 5 from Doug, however the link seems to be invalid now
(ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl).
Would you please update the link of this file? Thank you in advance.
Best regards,
Bingjiang
If you did collect field maps, you can use epidewarp.fsl to create a
voxel shift map (the only output of epidewarp.fsl that you need;
you'll
need to FSL to run that program), then use bbregister with the --vsm
option to register your func to the struct, then use mri_vol2vol with
the --vsm option to map your functional time courses to the anatomical
space, then use mri_segstats with the --avgwf (or --avgwfvol)
option to
get the average time courses for each ROI (or you can do this in
matlab
easily enough too)
doug
On 7/21/15 9:29 AM, Bruce Fischl wrote:
> Hi Bingjiang
>
> did you acquire any field maps? If so, you can them to undistort the EPIs
>
> cheers
> Bruce
>
>
> On Tue, 21 Jul 2015, Bingjiang Lyu wrote:
>
>> Dear all,
>> I've got the automaticlly parcellated 'aparc.a2009s+aseg.nii' file for
>> individual T1 image, and I want to calculate functional connectivity
between
>> each pair of the brain regions. I normalized both the T1 and EPI images
to
>> standard MNI space using SPM12, however, the normalized structural and
>> functional images didn't match very well due to the distortion of
>> susceptibility artifacts, especially for the inferior temporal and
orbital
>> frontal cortex (Please see the attached pictures). Could anyone give some
>> suggestions on better co-registration of the normalized structural and
>> functional images? Thanks a lot in advance.
>>
>> Best regards,
>> Bingjiang
>>
>> --
>> Bingjiang LyuPhD student
>> Center for MRI Research
>> Peking University
>> Beijing, China
>>
>>
>>
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>
>
--
Bingjiang Lyu
PhD student
Center for MRI Research
Peking University
Beijing, China
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