Re: [Freesurfer] Third party dependencies directory not found when building from source

[fsbuild]

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​Hello Christian,
When a test fails, it should leave behind a log in the subdir for the command, 
e.g., if the test for ./mri_aparc2aseg fails, then there should be a 
/mri_aparc2aseg fails,/test_mri_aparc2aseg.log to look at. But you will 
need a python3 with the modules from the scientific stack (scipy, numpy, etc.) 
installed for some tests to run. You can use python3 from the anaconda 
distribution, so you would end up with base path/anaconda3/bin in the 
head of your PATH, and you would also need to add at least base 
path/anaconda3/lib/python3.6/site-packages to PYTHONPATH
Please keep in mind that if you are building the latest freesurfer from the git 
dev branch, then it is not a release and has not been tested like a 
release. A more comprehensive test than "make test" is to run a recon-all 
command on the subject "bert" data. Please see Example 2 under the 
section "Testing your Freesurfer Installation" from the web page, 
https://surfer.nmr..mgh.harvard.edu/fswiki/DownloadAndInstall; (Setup your 
environment with the shell init files before running recon-all - see the 
section on the same page for "Setup  Configuration" using wherever you 
installed Freesurfer from your build).

On Nov 2, 2018, at 23:08, Christian Lee Mcdaniel clm...@uga.edu 
wrote:External Email - Use 
CautionThank you to all who are 
providing input for these issues. After ensuring the correct versions of gcc, 
g++, and gfortran were installed and being used, I am able to complete the 
`make` command. However, when I conduct `make test`, I receive the following 
output: ... output with errors not shown 

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

[June Kang]

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

[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?

[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] Stuck in "CORRECTING DEFECT"

[Saturne Fox]

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I don't want to be part of this mailing list.

Thanks in advance.
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[Freesurfer] Qdec table

[Miguel Ángel Rivas Fernández]

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Hi Freesurfer devs,

How can I create a qdec.table.dat file? I tried using a txt file but it
doesn´t works. I attached the qdec.table.dat file that I have created.

Sorry for this absurd question and thanks in advance.

Cheers,

-- 
*Miguel Ángel Rivas Fernández*


qdec.table.dat
Description: Binary data
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