Dear Takuya,

You are right that for accelerated sequences it is usually
correct to use the echo spacing divided by the acceleration
factor.  We are planning to write some more complete documentation
on this shortly.  However, I believe that Valentin's problem
did not involve accelerated scans - just a comparison problem
of comparing the right images in the right space.

All the best,
	Mark



On 5 Feb 2007, at 02:21, Takuya Hayashi wrote:

> Dear Valentin and Mark,
> If it is already fixed, please dicard this.
>
> I'm just wondering whether or not Valentin's fMRI data was obtained by
> accelerated mode (ASSET in GE scanner). We also use the same scanner,
> and get perfect unwarping by using the ESP time as that appears CV
> window by entering "esp", divided by the ASSET factor (usually 2.0),
> although I don't know if ESP time in the CV is same as that you see in
> dicom because we cannot find it in dicom.
>
> With best,
>
> Takuya
>
> Mark Jenkinson <[log in to unmask]> :
>> Dear Valentin,
>>
>> I have just managed to get around to re-running feat-fugue on your
> data.
>> It actually appears to me that in fact 552us is giving the best
> results.
>> Certainly the brain stem ends up much more symmetrical and not  
>> shifted
> to
>> one side when using 552 versus the smaller values.
>>
>> I noticed that you only sent me the following files:
>>   EF_UD_example_func (at various dwell times)
>>   EF_D_example_func
>>   fieldmap_*
>>   FM_D_fmap_mag_brain (at various dwell times)
>>
>> However, when comparing the outputs you want to look at the
>> unwarped, and registered, example_func versus the fieldmap
>> *in the same space*.  Note that the start of the filename represents
>> the space that the image is in.  Hence EF_UD_fmap_mag_brain
>> is the sensible image to compare to EF_UD_example_func as both
>> are in example func (EF), undistorted (UD) space.  These are the
>> images that are included on the unwarping report page generated
>> by FEAT.
>>
>> So maybe it is just that you have not been comparing the right  
>> images.
>> Have a look at EF_UD_fmap_mag_brain vs EF_UD_example_func
>> and see if you agree that the correct dwell time (552) gives the best
>> result.
>>
>> All the best,
>>     Mark
>>
>>
>> Valentin Piech wrote:
>>
>>> Dear Mark,
>>>
>>> Thank you very much for your reply.
>>>
>>> I've talked to our physicist, and he says the value for the dwell
> time in
>>> the DICOM field should be the correct one. I've also found a program
> at
>>> UCSD's fmri center to unwarp EPI volumes called "ppge2", and this
> programs
>>> searches for the same DICOM header field to get the dwell time.
> Moreover,
>>> according to their website, they are also using a GE Excite 3.0T
> scanner,
>>> and thus presumably the same software.
>>>
>>> I am judging that the unwarping is to strong by looking, for  
>>> example,
> at the
>>> curvature of midline of the brain in an axial view in the volumes
> that have
>>> the phase direction from left to right because the field is changing
>>> relatively slowly in the center of the brain. Another place where it
> becomes
>>> obvious is by looking at the position of the cerebellum in the
> saggital view
>>> of the volumes where the phase directions is anterior-posterior, but
> there
>>> are many places it can be seen, particularly in the moving GIFs from
> the
>>> html report. I don't pay too much attention to the regions with  
>>> drop-
> out, as
>>> they can't be really restored anyhow.
>>>
>>> The actual dwell time is 552 microseconds, and I've tried 552, 460,
> 368, 276
>>> and 184 microseconds, both with and without using BET, and for
> volumes with
>>> the phase directions being AP or LR. I've uploaded the EPI distorted
> and
>>> undistorted EPI volumes, the fieldmap and its magnitude, the  
>>> fieldmap
>>> magnitude maps being forward warped according to the field, and a
>>> high-resolution MPRAGE of the subject. The six-digit reference  
>>> number
> for
>>> this upload session is 177941.
>>>
>>> By the way, the field map used for unwarping the EPI volumes with
> phase
>>> direction AP was aquired with the phase direction LR, but I have a
> different
>>> data set where the phase direction for the fieldmap was also AP, and
> the
>>> effect is the same (and the field maps are very similar).
>>>
>>> I think that the best match can be found with half of the dwell time
> (276
>>> microseconds), or perhaps 2/3 (368 us) of the actual dwell time.
>>>
>>> I don't have any further details on the ramp sampling, but if you
> agree that
>>> the unwarping effect is to strong, and there isn't a mistake on my
> part in
>>> the way I am running FUGUE, the fMRI center will contact GE to  
>>> double
> check
>>> on the field values, and we'll run a test session with and without
> ramp
>>> sampling, see if the DICOM field changes, and whether the geometric
>>> distortion depends on the ramp sampling.
>>>
>>> Thank you very much for your help.
>>>
>>> Have a great weekend,
>>>
>>> Valentin
>>>
>>>
>>>
>>