Re: [Freesurfer] Tracula Question-How the threshold in final merged tracts are defined?

2018-11-19 Thread Yendiki, Anastasia 
Hi June - Circling back to this to see if it was resolved. If you're just using 
the publicly available data, there should be 3x96 directions, with 3 different 
b-values. Which set of 96 are you using?


a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of June Kang 

Sent: Saturday, November 3, 2018 7:35:19 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula Question-How the threshold in final merged 
tracts are defined?


External Email - Use Caution

It’s just huge data collected from general population. Some data can have 
motion artifact, but I couldn’t find any special points in the protocol.

http://protocols.humanconnectome.org/HCP/3T/imaging-protocols.html

J.


On Nov 4, 2018, at 4:21 AM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi June - Not in principle, any number of directions > 30 should be compatible. 
Is there anything else that's different about this data, e.g., SNR, motion, 
population with more morphological variability, etc.?

a.y

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of June Kang mailto:cn...@korea.ac.kr>>
Sent: Saturday, November 3, 2018 12:24:54 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula Question-How the threshold in final merged 
tracts are defined?

External Email - Use Caution

Thanks, Professor Anastasia,

I am testing HCP data with 96 directions.
There are really frequent failure for right cingulum-angular bundle and right 
uncinate fasciculus (more than 25%), which not happened with my own 
64-direction data with Siemens Trio.

Is there any known issue or recommended modification of the pipeline for HCP 
data or data with more directions?

Bests,
J.


On Nov 2, 2018, at 10:44 AM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

They are not random, they are 20% of the maximum value. If you want to generate 
stats at a different threshold, you can find the dmri_pathstats command line in 
trac-all.log and add the --pthr option (the default 20% would be --pthr .2).

On Nov 1, 2018 9:01 PM, June Kang mailto:cn...@korea.ac.kr>> 
wrote:
External Email - Use Caution

In the visualization step of Tracula processing, freeview -tv 
merged_avg33_mni_bbr shows some tracts with very high threshold (i.e. 171), 
which make them look like the reconstruction-failed ones.
The tracts failed to reconstruction usually show threshold of 300 (not 
changeable) with tiny rounded cylinder shape.
In successfully reconstructed tracts with very high threshold, it looks ok, 
when I adjust threshold to the similar value from contralateral one.

Is there any reason for this extremely high threshold? or it’s just randomly 
set values?

Bests,
J.


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Re: [Freesurfer] Tracula Question-How the threshold in final merged tracts are defined?

2018-11-03 Thread June Kang 
External Email - Use Caution

It’s just huge data collected from general population. Some data can have 
motion artifact, but I couldn’t find any special points in the protocol.

http://protocols.humanconnectome.org/HCP/3T/imaging-protocols.html 
<http://protocols.humanconnectome.org/HCP/3T/imaging-protocols.html>

J.


> On Nov 4, 2018, at 4:21 AM, Yendiki, Anastasia  
> wrote:
> 
> Hi June - Not in principle, any number of directions > 30 should be 
> compatible. Is there anything else that's different about this data, e.g., 
> SNR, motion, population with more morphological variability, etc.?
> 
> a.y
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
>  <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of June Kang 
> mailto:cn...@korea.ac.kr>>
> Sent: Saturday, November 3, 2018 12:24:54 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Tracula Question-How the threshold in final merged 
> tracts are defined?
>  
> External Email - Use Caution
> Thanks, Professor Anastasia,
> 
> I am testing HCP data with 96 directions.
> There are really frequent failure for right cingulum-angular bundle and right 
> uncinate fasciculus (more than 25%), which not happened with my own 
> 64-direction data with Siemens Trio.
> 
> Is there any known issue or recommended modification of the pipeline for HCP 
> data or data with more directions?
> 
> Bests,
> J.
> 
> 
>> On Nov 2, 2018, at 10:44 AM, Yendiki, Anastasia > <mailto:ayend...@mgh.harvard.edu>> wrote:
>> 
>> They are not random, they are 20% of the maximum value. If you want to 
>> generate stats at a different threshold, you can find the dmri_pathstats 
>> command line in trac-all.log and add the --pthr option (the default 20% 
>> would be --pthr .2).
>> 
>> On Nov 1, 2018 9:01 PM, June Kang > <mailto:cn...@korea.ac.kr>> wrote:
>> External Email - Use Caution
>> 
>> In the visualization step of Tracula processing, freeview -tv 
>> merged_avg33_mni_bbr shows some tracts with very high threshold (i.e. 171), 
>> which make them look like the reconstruction-failed ones.
>> The tracts failed to reconstruction usually show threshold of 300 (not 
>> changeable) with tiny rounded cylinder shape.
>> In successfully reconstructed tracts with very high threshold, it looks ok, 
>> when I adjust threshold to the similar value from contralateral one.
>> 
>> Is there any reason for this extremely high threshold? or it’s just randomly 
>> set values?
>> 
>> Bests,
>> J.
>> 
>> 
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Re: [Freesurfer] Tracula Question-How the threshold in final merged tracts are defined?

2018-11-03 Thread Yendiki, Anastasia 
Hi June - Not in principle, any number of directions > 30 should be compatible. 
Is there anything else that's different about this data, e.g., SNR, motion, 
population with more morphological variability, etc.?


a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of June Kang 

Sent: Saturday, November 3, 2018 12:24:54 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula Question-How the threshold in final merged 
tracts are defined?


External Email - Use Caution

Thanks, Professor Anastasia,

I am testing HCP data with 96 directions.
There are really frequent failure for right cingulum-angular bundle and right 
uncinate fasciculus (more than 25%), which not happened with my own 
64-direction data with Siemens Trio.

Is there any known issue or recommended modification of the pipeline for HCP 
data or data with more directions?

Bests,
J.


On Nov 2, 2018, at 10:44 AM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

They are not random, they are 20% of the maximum value. If you want to generate 
stats at a different threshold, you can find the dmri_pathstats command line in 
trac-all.log and add the --pthr option (the default 20% would be --pthr .2).

On Nov 1, 2018 9:01 PM, June Kang mailto:cn...@korea.ac.kr>> 
wrote:
External Email - Use Caution

In the visualization step of Tracula processing, freeview -tv 
merged_avg33_mni_bbr shows some tracts with very high threshold (i.e. 171), 
which make them look like the reconstruction-failed ones.
The tracts failed to reconstruction usually show threshold of 300 (not 
changeable) with tiny rounded cylinder shape.
In successfully reconstructed tracts with very high threshold, it looks ok, 
when I adjust threshold to the similar value from contralateral one.

Is there any reason for this extremely high threshold? or it’s just randomly 
set values?

Bests,
J.


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Re: [Freesurfer] Tracula Question-How the threshold in final merged tracts are defined?

2018-11-03 Thread June Kang 
External Email - Use Caution

Thanks, Professor Anastasia,

I am testing HCP data with 96 directions.
There are really frequent failure for right cingulum-angular bundle and right 
uncinate fasciculus (more than 25%), which not happened with my own 
64-direction data with Siemens Trio.

Is there any known issue or recommended modification of the pipeline for HCP 
data or data with more directions?

Bests,
J.


> On Nov 2, 2018, at 10:44 AM, Yendiki, Anastasia  
> wrote:
> 
> They are not random, they are 20% of the maximum value. If you want to 
> generate stats at a different threshold, you can find the dmri_pathstats 
> command line in trac-all.log and add the --pthr option (the default 20% would 
> be --pthr .2).
> 
> On Nov 1, 2018 9:01 PM, June Kang  > wrote:
> External Email - Use Caution
> 
> In the visualization step of Tracula processing, freeview -tv 
> merged_avg33_mni_bbr shows some tracts with very high threshold (i.e. 171), 
> which make them look like the reconstruction-failed ones.
> The tracts failed to reconstruction usually show threshold of 300 (not 
> changeable) with tiny rounded cylinder shape.
> In successfully reconstructed tracts with very high threshold, it looks ok, 
> when I adjust threshold to the similar value from contralateral one.
> 
> Is there any reason for this extremely high threshold? or it’s just randomly 
> set values?
> 
> Bests,
> J.
> 
> 
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Re: [Freesurfer] Tracula Question-How the threshold in final merged tracts are defined?

2018-11-01 Thread Yendiki, Anastasia 
They are not random, they are 20% of the maximum value. If you want to generate 
stats at a different threshold, you can find the dmri_pathstats command line in 
trac-all.log and add the --pthr option (the default 20% would be --pthr .2).

On Nov 1, 2018 9:01 PM, June Kang  wrote:
External Email - Use Caution

In the visualization step of Tracula processing, freeview -tv 
merged_avg33_mni_bbr shows some tracts with very high threshold (i.e. 171), 
which make them look like the reconstruction-failed ones.
The tracts failed to reconstruction usually show threshold of 300 (not 
changeable) with tiny rounded cylinder shape.
In successfully reconstructed tracts with very high threshold, it looks ok, 
when I adjust threshold to the similar value from contralateral one.

Is there any reason for this extremely high threshold? or it’s just randomly 
set values?

Bests,
J.


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[Freesurfer] Tracula Question-How the threshold in final merged tracts are defined?

2018-11-01 Thread June Kang 
External Email - Use Caution

In the visualization step of Tracula processing, freeview -tv 
merged_avg33_mni_bbr shows some tracts with very high threshold (i.e. 171), 
which make them look like the reconstruction-failed ones.
The tracts failed to reconstruction usually show threshold of 300 (not 
changeable) with tiny rounded cylinder shape.
In successfully reconstructed tracts with very high threshold, it looks ok, 
when I adjust threshold to the similar value from contralateral one.

Is there any reason for this extremely high threshold? or it’s just randomly 
set values?

Bests,
J.


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