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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.
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 cnsla@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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 AYENDIKI@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 <cnsla@korea.ac.kr mailto:cnsla@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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of June Kang cnsla@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 <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@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 <cnsla@korea.ac.krmailto:cnsla@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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 AYENDIKI@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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of June Kang <cnsla@korea.ac.kr mailto:cnsla@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 CautionThanks, 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 <AYENDIKI@mgh.harvard.edu mailto:AYENDIKI@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 <cnsla@korea.ac.kr mailto:cnsla@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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of June Kang cnsla@korea.ac.kr 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 <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of June Kang <cnsla@korea.ac.krmailto:cnsla@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 <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@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 <cnsla@korea.ac.krmailto:cnsla@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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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June Kang -
Yendiki, Anastasia