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Subject:

Re: tractography regarding cortical mask

From:

Matt Glasser <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Sat, 21 Jun 2008 16:29:06 -0500

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (144 lines)

I would agree that the second is probably better in your case.

Peace,

Matt.

-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Longchuan Li
Sent: Friday, June 20, 2008 2:02 PM
To: [log in to unmask]
Subject: Re: [FSL] tractography regarding cortical mask

Hi,
Thank your guys for the information.
The tracking from the deep white matter to cortical area may be a little 
different: when I track in this way: cortical mask (seed mask) -> internal 
capsule (waypoint mask) -> cerebral peduncle ( target mask), the tracts are 
very different compared to the case: cerebral peduncle (seed mask) -> 
internal capsule (waypoint mask) -> cortical mask (target mask). The former 
tracking method gives much weaker paths (this is reasonable as there is no 
strong coherent diffusion in the cortical area). My question is: is there 
fundamental difference between these two methods? Which way should be 
better?( I personally think the latter one).

Thanks

Longchuan


----- Original Message ----- 
From: "Ted Yanagihara" <[log in to unmask]>
To: <[log in to unmask]>
Sent: Friday, June 20, 2008 10:40 AM
Subject: Re: [FSL] tractography regarding cortical mask


> 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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