Hi,
On 26 Feb 2008, at 12:25, Lindgren, Kristen, Ann wrote:
> Thanks, Steve. You're right, I meant to write that I'd align to the
> nodif image. I will try the new fslmaths command and see if it
> works, but it looks like it should do the trick. I'll try again to
> add the structures in the JHU white matter atlas and see what
> happens. When I tried it, it showed the individual structures on
> the list, but then when I selected it, it brought up a mask with all
> labeled structures.
No - select the structure after pressing the 'structures' button not
the 'atlases' button.
Cheers.
> I tried saving that mask as a file, and the result was the same
> mask with all structures labeled except that the tract of interest
> was a different color. Maybe I'm using an older version of
> FSLview? I'm using FSL 4.0, but it may not be the newest version.
> Thanks again for all of your help... you're the best!
>
> Kristen
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library on behalf of Steve Smith
> Sent: Mon 2/25/2008 3:41 AM
> To: [log in to unmask]
> Subject: Re: [FSL] DTI-based White Matter Atlas
>
> Hi,
>
> On 23 Feb 2008, at 22:11, Lindgren, Kristen, Ann wrote:
>
>> Thanks for the info, Steve. Here's what I've done. Please let me
>> know if this sounds correct.
>>
>> 1) I've preprocessed all of the DTI data through FDT (eddycorrect,
>> dtifit, and bedpostx)
>>
>> 2) Using the FDT Registration GUI, I aligned dti_FA.nii.gz to both a
>> high-res anatomical image and the default standard brain.
>
> OK - though note that if you used the FDT GUI it is the b=0 ('nodif')
> image that is actually aligned to the hires image.
>
>> 3) Using ApplyXFM_gui, I selected diff2standard.mat as the transform
>> matrix, dti_FA.nii.gz as the input volume, and the MNI brain used in
>> the FDT registration as the reference volume and made a
>> dti_FA_alignstandard.nii.gz file.
>>
>> 4) I opened dti_FA_alignstandard.nii.gz in fslview and using the JHU
>> probabilistic atlas, I added the structure of interest then saved it
>> to file.
>>
>> 5) I used the following command to make a binary mask (What is the
>> rationale for using 25 as a threshold?)
>> fslmaths tract_mask -thr 25 -bin binary_tract_mask
>
> I assume 'tract_mask' is the atlas-derived mask that you saved out of
> FSLView? Yes, thresholding at a probability of 25% is just an
> arbitrary population-average level to threshold at, generally seems
> reasonable. You can obviously go lower or higher if you want to be
> more liberal or conservative, and that mostly depends on how confident
> you are in the registration between your data and standard space.
>
>> 6) Here's where I'm unsure of what to do. Before I had used the
>> following commands to get the average FA of a mask:
>> avwmaths_32R binary_tract_mask -mul dti_FA_alignstandard FA_tract
>> avwstats FA_tract -M
>> Now those commands don't exist, so I'm not sure how to use the
>> fslmaths command to get the same result. Any thoughts?
>
> Replace avwmaths_32R with fslmaths (and add '-odt float' to the end of
> the line to make sure it saves out in floating-point format - that's
> the equivalent of having the '_32R' in there before). Note that a
> danger with this approach is that the average that you get out doesn't
> just reflect the average FA within the tract, but also the quality of
> the alignment and intersection between your standard-space-derived
> mask and that tract in your subject - so unless you make the mask very
> conservative, may include lots of non-tract FA values in the
> averaging. For this you might consider either getting more
> sophisticated with the way you pull out information from the
> tractography, or use TBSS.
>
>> Also, is there any way to pull out the individual labels of the JHU
>> white matter label atlas? If I add one structure, it seems like it
>> adds the whole atlas.
>
> I'm confused - this works fine for individual structures for me using
> both JHU atlases.
>
> Cheers.
>
>
>>
>>
>> Thanks so much for your help!
>>
>> Kristen
>>
>>
>> -----Original Message-----
>> From: FSL - FMRIB's Software Library on behalf of Steve Smith
>> Sent: Sat 2/23/2008 2:12 AM
>> To: [log in to unmask]
>> Subject: Re: [FSL] DTI-based White Matter Atlas
>>
>> Hi,
>>
>> Yes, you can do this; it's particularly easy if you have run the
>> registration to highres and standard space in the FDT GUI.
>>
>> You can then go into FSLView, turn on atlas viewing, open
>> 'structures', select the atlas and the structure of interest, press
>> '+' to move that structure permanently into the image list, and then
>> save that image to file. In general this will be a probabilistic mask
>> so you may want to threshold it using fslmaths before using it as a
>> mask in tracking, e.g.
>>
>> fslmaths thalamus_mask -thr 25 -bin binary_thalamus_mask
>>
>> Cheers.
>>
>>
>> On 21 Feb 2008, at 12:34, Lindgren, Kristen, Ann wrote:
>>
>>> Thanks for the response, Steve. Really what I'd like to do is
>>> directly identify a particular tract on the FA maps as opposed to
>>> relying on tractography to identify it. Right now I'm getting
>>> results by identifying two seeds in anatomical space and connecting
>>> them, and I'm getting good results on some subjects but sometimes no
>>> track on others. I thought the atlas was something like the
>>> freesurfer atlas but for DTI data where I could create a label and
>>> use that as a mask to get an average FA. I will look more carefully
>>> at the atlas and see if it maybe would inform me of how to identify
>>> my seed points in my FA maps for tractography. Thanks!
>>>
>>> Kristen
>>>
>>>
>>> -----Original Message-----
>>> From: FSL - FMRIB's Software Library on behalf of Steve Smith
>>> Sent: Thu 2/21/2008 2:45 AM
>>> To: [log in to unmask]
>>> Subject: Re: [FSL] DTI-based White Matter Atlas
>>>
>>> Hi - the atlases are there as a guide for what structures are
>>> where -
>>> but they may not exactly related to a given new individual's scan.
>>> Using the masks directly in the context of TBSS results makes some
>>> sense, but for tractography, if you have already got your tracts,
>>> this
>>> implied that you chose your seed/target voxels/masks carefully and
>>> so
>>> presumably already have a strong idea of what tracts you are looking
>>> for? So I'm not quite sure how you are wanting to then use the
>>> atlases?
>>>
>>> Cheers.
>>>
>>>
>>> On 19 Feb 2008, at 21:18, Lindgren, Kristen, Ann wrote:
>>>
>>>> Hello. I am interested in using the JHU DTI-based white-matter
>>>> atlases
>>>> to obtain the average FA values of various tracts. I've created
>>>> masks
>>>> and gotten average FAs from our DTI using tractography, but I'm
>>>> wondering if there is documentation on how to use the available
>>>> atlases
>>>> to do this. Thanks and hopefully I explained that clearly!
>>>>
>>>> Kristen
>>>>
>>>
>>>
>>> ---------------------------------------------------------------------------
>>> 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
>>> ---------------------------------------------------------------------------
>>>
>>
>>
>> ---------------------------------------------------------------------------
>> 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
>> ---------------------------------------------------------------------------
>>
>
>
> ---------------------------------------------------------------------------
> 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
> ---------------------------------------------------------------------------
>
---------------------------------------------------------------------------
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
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