>Hi Mark, thanks for your replies. With the GUI output, I have a few
queries, in particular with coversion of the datatype in the undistorted
file.
1.The undistorted images all have skull removed (example_ func and
filtered_func_data). The images of the undistorted 4D dti data on the feat
report prestats_html page don't have skull removed. How can I get an
undistorted 4D data with skull, or is the default output all skullless?
2. When I select % signal loss threshold as 10, the red region in the
brain in row 2 of the html page( also described as the region that will be
ignored during registration), are mainly in the temporal and inferior
frontal lobes. This is also the region where most of the distortion and B0
inhomogeniety occurs in the fieldmap. If this is the case, would it be
better to select the % signal threshold as 10, so these regions with
signal loss and that also tends to be distorted, would be ignored in the
registration, or it doesn't matter as you have mentioned in the previous
email. Next, when I select the % signal loss threshold to 0, the threshold
signal loss weighting image becomes mainly all red. In the practical
notes, it mentioned that the red regions will be ignored during
registration. Is it just a colour display issue as I thought all the brain
regions in the 2nd row would be yellow instead of red, because if I
select 0, then none of the regions would not ignored during
registration. I tried to attached a screenshot but the emails bounced back.
3. The result of my undistorted 4D data is of format datatype float 32. I
would like to convert it to an integer 16 datatype to how the 4D data
originally was? Is there an fsl command that can do that or how would you
suggest I do that? If I did convert it like this, would there be some data
loss during the conversion from float to integer?
Thanks
Siewmin
Hi,
>
> I'm glad it is working now.
>
> The answer to which way you need to calculate the fieldmap
> is the first way. The reason is that prelude is a tool for
> unwrapping *phase* only, so it requires its input to be in radians,
> in the range -pi to pi (or 0 to 2*pi). The second method you list
> divides by the TE *before* running prelude, which will stop prelude
> working correctly, and so it will not unwrap the phase.
>
> There should be no problems with running things using the
> first method of preparing your fieldmap.
>
> All the best,
> Mark
>
>
> On 3 May 2009, at 02:07, Siew-Min Gan wrote:
>
>>> Hi,thanks, I tried again and it worked fine. The unwarp directory and
>> GUI are both looking good. I think it's because the intensity of my
>> prepared fieldmap is not right the first time. I have input a fieldmap
>> intensty of -pi to pi then and it didn't work.
>>
>> I have rechecked that my fieldmap would be similiar to the
>> phase-difference map in the fsl practical. It worked after I have
>> prepared
>> it as in the instructions on the practical. However, i noticed I get
>> different results if I prepare it slightly differently from the
>> suggestions on the email list.
>>
>> I have posted a question about which way and order to best calculate
>> and
>> prepare the fieldmap in another email i posted today "Order of
>> preparing
>> Phase_Difference Map to rad/secs". Can I ask you this question on this
>> email regarding this?
>>
>> I get these 2 fieldmaps which are similiar in calculations but of
>> different order of calculation and unwarping, and hence different
>> intensities.
>>
>> The first way has a phasedif map of 0 to 4094 intensity range). It is
>> rescaled to -pi to pi, then unwarped in prelude, then changed to rad/
>> sec
>> by div on the TE dif (0.00246). The resulting fieldmap has an
>> intensity
>> range of -3165.861328 to 2801.69702.
>> The second way has a phasedifmap of -4096 to 4092 intensity. It is
>> rescaled by dv 4096, -mul by 3.14 then div 0.00246, followed by
>> prelude.
>> The resultant fieldmap has intensity -2801.073486 to 2790.472900.
>>
>> I'm not sure which one would be the more correct way, or if it doesn't
>> matter? The undistorted dti using 1st way of preparation from the fsl
>> practical instructions is a bit more undistorted than the results of
>> the
>> 2nd one in the -y direction ( unwarped direction). Why that would be
>> the
>> case?
>>
>> Thanks
>>
>> Siewmin
>>>
>>> It sounds like it hasn't worked unfortunately.
>>> The errors in fslview are simply because the images are in an
>>> incomplete
>> feat directory. If you change the name of the directory (so it
>>> doesn't end in
>>> .feat) or move the files outside of the feat directory. However, the
>> static
>>> movies and lack of difference between distorted and undistorted is
>>> a much
>>> worse problem.
>>>
>>> What files are in your unwarp directory (within the feat
>>> directory)? And
>> what images are you passing into the FEAT GUI?
>>>
>>> As for the rescaling - that is simply something that FEAT does
>>> automatically (and unfortunately can't be turned off) but it won't
>> affect any processing, as the diffusion fitting process will remove
>> any
>> global scaling.
>>>
>>> Let me know about the unwarp directory and GUI setup and
>>> hopefully we can sort out the problem.
>>>
>>> All the best,
>>> Mark
>>>
>>>
>>>
>>>
>>> On 1 May 2009, at 19:55, Siewmin Gan wrote:
>>>
>>>> Hi,
>>>> I have a couple of questions regarding the output data when I
>>>> used the FEAT Gui to do
>>>> distortion correction of DTI data. The movie section comparing
>>>> distorted and undistorted
>>>> example_func data (third last rows) showed a stationary row of
>>>> images ( i.e there is no
>>>> flipping between one image to another). When I tried to fslview the
>> example_func.nii.gz,
>>>> filtered_func_data.nii.gz or the
>>>> example_func_orig_distorted.nii.gz, i
>> could only view the
>>>> first two and not able to view the last image. Also in all cases,
>>>> there
>> would be error
>>>> messages as below for all three:
>>>> ERROR (nifti_image_read): failed to find header file for
>>>> '/Users/siewmingan/Desktop/DATASET/patient_1/tryfieldmap_y.feat/
>> stats/pe1'
>>>> ** ERROR:
>>>> nifti_image_open(/Users/siewmingan/Desktop/DATASET/patient_1/
>>>> tryfieldmap_y.feat/stat
>>>> s/pe1): bad header info
>>>> Error: failed to open file
>>>> /Users/siewmingan/Desktop/DATASET/patient_1/tryfieldmap_y.feat/
>>>> stats/ pe1.
>>>> Why does the error message occurs and how I can resolve it?
>>>> Because the movie section did not display the contrast between the
>> distorted and
>>>> undistorted images, and the 4th row displaying the original
>>>> distorted images looks
>>>> similiar to the 5th row displaying the undistorted images , and I
>> couldn't view the
>>>> example_func.nii with the example_func_orig_distorted.nii.gz, I then
>> tried to compare the
>>>> example_func.nii.gz with my original 4D data file. I noticed the
>> intensity in the
>>>> example_func.nii.gz file is around 2-3 times lower than the
>>>> original 4D
>> data. May I ask
>>>> why that would be so and would that be a problem? Also, if both the
>> example_func.nii.gz
>>>> file and the filtered_func_data.nii.gz are both the undistorted 4D
>>>> DTI
>> data from running
>>>> FEAT, why do they have different intensity with the former in 100s
>>>> and
>> the latter in
>>>> 10000s?
>>>> Apart from the difference in the intensity in the original 4D data
>>>> and the
>>>> example_func.nii.gz, it was quite hard to detect differences due
>>>> to the
>> different intensity
>>>> of the brain on display ( I've tried both distortion correction with
>> the "y" and "-y" option.)
>>>> Is there any way to resolve the previous error messages so I can
>> directly compare the
>>>> distorted and undistorted images with the same intensity, and
>>>> check if
>> I have done the
>>>> distortion correction step correctly?
>>>> Many Thanks
>>>> Siewmin
>>>
>>
>
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