Hi Mark,
I forgot to mention that I do actually have a separate file which contains the magnitude volumes.
For the phase images (in the file I posted), I understand now that I will need to scale them (after fslsplit into 2 separate volumes) to [-pi, pi] but can you please elaborate on what you meant by "run unwrapping"? By the way, in the example from FSL course (http://fsl.fmrib.ox.ac.uk/fslcourse/lectures/practicals/reg/) the phase map was rescaled to [0, 2 *pi]. Do I need to do the same here too?
Finally, when looking at the report from FEAT GUI I noticed that the steps for fieldmap-based unwarping are somewhat different from the steps used in the script epi_reg (although I do realise that epi_reg can handle only one 3D volume at a time). Is there a "preferred" approach (the fieldmap-based unwarping in FEAT vs epi_reg) since I am also trying to come up with customised scripts for our data set? Or am I missing something here?
Thanks again for your advice.
Regards,
Louis.
On Wed, 2 Oct 2013 16:08:15 +0000, Mark Jenkinson <[log in to unmask]> wrote:
>Hi,
>
>From the images you uploaded it seems that you do have two phase images and no magnitude image.
>This is a problem in that you really do need a magnitude image. If you do not have one then a potential solution is to take a structural image from the same sequence (assuming there was no major movement in between) and resample this with (using your own filenames):
> flirt -in structural -ref fieldmap_phase -applyxfm -usesqform -out fmap_mag
>Check that the output (fmap_mag) looks well registered with the fieldmap_phase image (you'll have to do this by eye).
>
>For the phase images, you do have phase wraps in them, so you will need to scale each image to a range of -pi to +pi radians (divide by 4096 and multiply by 3.14159), then run unwrapping, then take the difference between the images. After this, just divide by the echo time difference of the fieldmap sequence (using units of seconds) and then you'll have a radians per second fieldmap image.
>
>Use this, in conjunction with the magnitude image above, and the brain extracted magnitude image, in the FEAT GUI as normal.
>
>All the best,
> Mark
>
>
>
>On 2 Oct 2013, at 14:21, "Harms, Michael" <[log in to unmask]> wrote:
>
>> Hi,
>> One of those volumes should be a magnitude image, and the other should be
>> a phase difference image.
>> Other than running BET on the magnitude image to create the necessary
>> Brain Extracted magnitude image input for fsl_prepare_fieldmap, so should
>> not need to do any other conversions. That is what fsl_prepare_fieldmap
>> is for.
>>
>> cheers,
>> -MH
>>
>> --
>> Michael Harms, Ph.D.
>>
>> -----------------------------------------------------------
>> Conte Center for the Neuroscience of Mental Disorders
>> Washington University School of Medicine
>> Department of Psychiatry, Box 8134
>> 660 South Euclid Ave. Tel: 314-747-6173
>> St. Louis, MO 63110 Email: [log in to unmask]
>>
>>
>>
>>
>> On 10/2/13 5:00 AM, "Louis Shue" <[log in to unmask]> wrote:
>>
>>> Dear FSL experts,
>>>
>>> We have received some new data (from a Siemens scanner) where the
>>> phasemap is of the following form (2 volumes, range is -4096 to +4092):
>>>
>>> https://dl.dropboxusercontent.com/u/8460189/HIN035_20130412_2819_027_fl2d_
>>> fieldmap.nii.gz
>>>
>>> May I know what are the steps needed to convert this to a format that can
>>> be used in fsl_prepare_fieldmap? It looks like I may need to use
>>> prelude??
>>>
>>> Thanks very much!
>>>
>>> Louis.
>>
>>
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