>Hi Mark, Many thanks.
Siewmin
Hi,
>
> 1 - Look in the unwarp directory - there you should be able to find
> the images that are used to generate the html page and should
> contain the skull. You should also turn the "BET brain extraction"
> button off in the pre-stats tab to avoid this happening.
>
> 2 - This is probably just a display issue. Load the image
> unwarp/ED_UD_fmap_sigloss into FSLView and see what
> the values are. They should hopefully all be around 1 and
> have no (or very few) voxels containing zero. If there are
> lots of voxels containing zero then there is a problem.
> As to whether there is an advantage to setting it to 0% or
> leaving it as 10%, I suspect it will not make a big difference.
> It only affects the registration parts and not the unwarping,
> so you will still get the unwarping in the inferior regions
> even when these are not included in this map. Hopefully these
> areas are unwarped successfully in the end.
>
> 3 - You can change the type with:
> fslmaths imagename imagename -odt short
> We choose to convert to 32 bit float as the interpolation which
> is done introduces non-integer values. However, if your dynamic
> range is large (so that the non-integer portion is negligible as a
> percentage of the main signal) then you can convert back to
> 16 bit integer without much loss in accuracy. There isn't any
> advantage to doing the conversion though, so unless you really
> need it for space reasons or for compatibility with other software
> then I would not convert it.
>
> All the best,
> Mark
>
>
> On 4 May 2009, at 05:39, Siew-Min Gan wrote:
>
>>> 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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