Along with this issue of the cortical mask, another problem you may
have with a cortical seed is that fibers can often jump to adjacent
gyri and follow white matter there. This is especially bad in regions
where neighboring gyri have a lot of partial voluming of CSF and gray
matter between them. Symmetrical tracking will also take care of this
pretty well, but you can also use a CSF exclusion mask if you end up
wanting to see where a cortical seed tracks to.
ted
On Jun 20, 2008, at 10:15 AM, Matt Glasser wrote:
> Hi Longchuan,
>
> It would be sufficient to use the cortical mask as a target only,
> to get the
> result you desire.
>
> Tracts are not necessarily the same when tracked in the opposite
> direction.
> For one thing, your cortical mask is probably much larger than the
> cerebral
> peduncle mask, and thus many more samples will be sent out when you
> use it
> as the seed. Also, tracts may split off and depending on how you
> approach
> the split you might take one or both of the branches (approaching
> from a
> branch you might only continue into the portion before the branch,
> whereas
> if you approached from that side, you might take both branches). I
> typically use a symmetric method when tracking white matter
> pathways from
> white matter ROIs.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf
> Of Longchuan Li
> Sent: Wednesday, June 18, 2008 4:18 PM
> To: [log in to unmask]
> Subject: [FSL] tractography regarding cortical mask
>
> Hi, FSL users
>
> I drew a seed mask on the cerebral peduncle and a cortical mask on the
> precentral gyrus to see how the precentral pyramidal tracts go from
> brainstem to primary motor area. I want to show only the tracts
> that reach
> my cortical masks. Now I am using the cortical mask as the waypoint
> mask as
> well as target mask to show only those tracts that reach the
> cortical mask.
> My questions are:
> 1) Is this the correct way to do?
>
> 2) Is there any difference in interpreting the result as compared
> to the
> case when I use cortical mask as the seed mask and cerebral
> peduncle mask as
>
> the cortical mask?
>
> Thank you in advance
>
> Longchuan
>
> ----- Original Message -----
> From: "Christina Hugenschmidt" <[log in to unmask]>
> To: <[log in to unmask]>
> Sent: Wednesday, June 18, 2008 6:51 AM
> Subject: [FSL] TICA on resting state
>
>
>> Hi all (and Christian in particular),
>>
>> I am interested in running a TICA analysis comparing resting state
>> and
>> also video watching between two groups. From reading the posts and
>> information on the FSL website, I think I should be using the same
>> methodology described in the Damoiseaux 2007 Cerebral Cortex
>> paper, where
>> the data is fourier transformed prior to running the TICA
>> analysis. I was
>> wondering if you could tell me the process used to transform the data
>> prior to running the TICA?
>>
>> I would also like to be sure that I understand exactly what is being
>> compared between groups in this analysis. When the data is
>> transformed,
>> does this mean there is power spectrum information in each voxel? Are
>> networks then identified by shared power spectra? And when group
>> differences are evaluated in contrasts, a significant difference
>> means
>> that the spatial maps identified within the power spectrum for that
>> component are different between groups?
>>
>> Thanks for any insights you can offer,
>>
>> Christina
>>
>>
>>
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