Hi Lino,
you can also try using epidewarp.fsl (distributed thru freesurfer). This
is a script that wraps prelude and fugue. I've used it successfully on
Siemens field mpas and epis.
doug
Mark Jenkinson wrote:
> Hi Lino,
>
> If your values are from -pi to pi then there are two problems:
> 1 - you haven't unwrapped your phase with prelude
> 2 - it isn't scaled to be in radians *per second*, but is just in radians
>
> Have a look at the page:
> http://www.fmrib.ox.ac.uk/fsl/fugue/feat_fieldmap.html
> which explains how to prepare phasemaps for input into FEAT.
> This has changed in the last release, and so maybe you haven't caught up
> with this before.
>
> All the best,
> Mark
>
>
>
> lino becerra wrote:
>
>> Hi Steve:
>> field map image is in rad/s (-pi to pi), since we only have the
>> phase difference image, we created the phase4d image with the first
>> image being just
>> ones and the second the field map one.
>> lino
>>
>>
>>
>> On Mar 12, 2007, at 8:14 AM, Steve Smith wrote:
>>
>>> Hi - the FEAT GUI requires that the fieldmap image should be a 3D
>>> image with units of rad/s - it sounds like maybe you haven't quite
>>> prepared it in this way?
>>>
>>> Cheers.
>>>
>>>
>>> On 9 Mar 2007, at 20:28, lino becerra wrote:
>>>
>>>> Hi:
>>>> We are having some trouble using fugue on our data.
>>>> It seems that only part of the epi image gets corrected and that
>>>> what seems unwarped is also displaced.
>>>> We have mag/phase images from a Siemens 3T, we prelude the phase
>>>> image and create a phase4d with the first image being 1's.
>>>> The phase image looks fine.
>>>> Any suggestions would be appreciate it.
>>>> Thanks !
>>>>
>>>> lino
>>>>
>>>>
>>>>
>>>>
>>>> Any information, including protected health information (PHI),
>>>> transmitted in
>>>> this email is intended only for the person or entity to which it
>>>> is addressed
>>>> and may contain information that is privileged, confidential and/
>>>> or exempt
>>>> from disclosure under applicable Federal or State law. Any review,
>>>> retransmission, dissemination or other use of or taking of any
>>>> action in reliance
>>>> upon, PHI by persons or entities other than the intended recipient
>>>> is prohibited. If you received this email in error, please contact
>>>> the sender
>>>> and delete the material from any computer.
>>>
>>>
>>>
>>>
>>> ----------------------------------------------------------------------
>>> -----
>>> Stephen M. Smith, Professor of Biomedical Engineering
>>> Associate Director, Oxford University FMRIB Centre
>>>
>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>>> +44 (0) 1865 222726 (fax 222717)
>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>>> ----------------------------------------------------------------------
>>> -----
>>>
>>
>>
>>
>> Any information, including protected health information (PHI),
>> transmitted in
>> this email is intended only for the person or entity to which it is
>> addressed
>> and may contain information that is privileged, confidential and/or
>> exempt
>> from disclosure under applicable Federal or State law. Any review,
>> retransmission, dissemination or other use of or taking of any action
>> in reliance
>> upon, PHI by persons or entities other than the intended recipient
>> is prohibited. If you received this email in error, please contact
>> the sender
>> and delete the material from any computer.
>
>
>
>
>
> If you look at the
>
> lino becerra wrote:
>
>> Hi Steve:
>> field map image is in rad/s (-pi to pi), since we only have the
>> phase difference image, we created the phase4d image with the first
>> image being just
>> ones and the second the field map one.
>> lino
>>
>>
>>
>> On Mar 12, 2007, at 8:14 AM, Steve Smith wrote:
>>
>>> Hi - the FEAT GUI requires that the fieldmap image should be a 3D
>>> image with units of rad/s - it sounds like maybe you haven't quite
>>> prepared it in this way?
>>>
>>> Cheers.
>>>
>>>
>>> On 9 Mar 2007, at 20:28, lino becerra wrote:
>>>
>>>> Hi:
>>>> We are having some trouble using fugue on our data.
>>>> It seems that only part of the epi image gets corrected and that
>>>> what seems unwarped is also displaced.
>>>> We have mag/phase images from a Siemens 3T, we prelude the phase
>>>> image and create a phase4d with the first image being 1's.
>>>> The phase image looks fine.
>>>> Any suggestions would be appreciate it.
>>>> Thanks !
>>>>
>>>> lino
>>>>
>>>>
>>>>
>>>>
>>>> Any information, including protected health information (PHI),
>>>> transmitted in
>>>> this email is intended only for the person or entity to which it
>>>> is addressed
>>>> and may contain information that is privileged, confidential and/
>>>> or exempt
>>>> from disclosure under applicable Federal or State law. Any review,
>>>> retransmission, dissemination or other use of or taking of any
>>>> action in reliance
>>>> upon, PHI by persons or entities other than the intended recipient
>>>> is prohibited. If you received this email in error, please contact
>>>> the sender
>>>> and delete the material from any computer.
>>>
>>>
>>>
>>>
>>> ----------------------------------------------------------------------
>>> -----
>>> Stephen M. Smith, Professor of Biomedical Engineering
>>> Associate Director, Oxford University FMRIB Centre
>>>
>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>>> +44 (0) 1865 222726 (fax 222717)
>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>>> ----------------------------------------------------------------------
>>> -----
>>>
>>
>>
>>
>> Any information, including protected health information (PHI),
>> transmitted in
>> this email is intended only for the person or entity to which it is
>> addressed
>> and may contain information that is privileged, confidential and/or
>> exempt
>> from disclosure under applicable Federal or State law. Any review,
>> retransmission, dissemination or other use of or taking of any action
>> in reliance
>> upon, PHI by persons or entities other than the intended recipient
>> is prohibited. If you received this email in error, please contact
>> the sender
>> and delete the material from any computer.
>
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[log in to unmask]
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
|