:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 2:10:50 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question
Ok - I have that sum.
For the forceps major, it's
0:50 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question
Ok – I have that sum.
For the forceps major, it’s 111,685.
If I normalize by that, i.e. divide each voxel value by that, then I certainly
get something that looks like a probability distribution since the
d.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 1:55 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question
Hi Don - You would normalize these numbers by their sum, not by their maximum
(i.e., not by 255).
: Re: [Freesurfer] newbie trac-all -bedp question
Hi, Anastasia.
Yes, that makes it simpler.
I can see that each of the path.pd.nii.gz has a voxel entry for the same number
of voxels. I’m looking at elmo.2008 for which that number is 1,294,336 which I
presume is the volume of this person’s
: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question
The probability maps are independent for each tract. Each one just tells you
how likely this one tract is to go through any given voxel, but it tells you
nothing about other tracts. Does this make sense?
On A
t
Subject: Re: [Freesurfer] newbie trac-all -bedp question
The probability maps are independent for each tract. Each one just tells you
how likely this one tract is to go through any given voxel, but it tells you
nothing about other tracts. Does this make sense?
On Apr 11, 2018 12:00 PM, "
urfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 11:54 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question
This wouldn't work because these 18 tracts do not include all tracts in
I'm going wrong.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 11:54 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question
This wouldn't work b
mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:48 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question
The volume would have to be normalized to a total sum of 1 for the voxel values
list
Subject: Re: [Freesurfer] newbie trac-all -bedp question
The volume would have to be normalized to a total sum of 1 for the voxel values
to represent an actual distribution.
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesur
support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question
Great – thanks – that’s what I need.
I can use the probability for each pixel as a weight for the neuroelectric
current count for that pixel to quantify the activity for the tract.
I assume that each voxel value maps directly to
n - best - Don
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:26 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question
Hi Don - No, dlabel/ contains fi
i/trac-all#Outputdirectoriesandfiles
Best,
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Krieger, Donald N.
Sent: Wednesday, April 11, 2018 8:06:01 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question
Thanks for the
n
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Tuesday, April 10, 2018 9:23 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question
Hi Don - If the output files described here show up in the e
4:52:57 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question
Great – thanks.
It’s running.
I see several warnings which I presume can be ignored:
hostname: Name or service not known
Best - Don
From: freesurfer-boun...@nmr.mgh.harvard.edu
24 PM
To: freesurfer
Subject: Re: [Freesurfer] newbie trac-all -bedp question
Hi Don - See:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html
Best,
a.y
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesur
] newbie trac-all -bedp question
I am getting the following output with error on this command:
trac-all -bedp -s HDFT1001 -i ep2d_diff_SliceAcc_b1k_64_768x768.23
INFO: SUBJECTS_DIR is
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
INFO: Diffusion root is
/media/portable/home
I am getting the following output with error on this command:
trac-all -bedp -s HDFT1001 -i ep2d_diff_SliceAcc_b1k_64_768x768.23
INFO: SUBJECTS_DIR is
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
INFO: Diffusion root is
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/sub
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