# 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 brain as delivered by freesurfer.

Most of those voxels are set to 0.
I presume that means that the probability that the tract passes through that
voxel is very near 0.0 .
For the forceps major, 7342 voxels have non-zero entries ranging from 1 to 255.
Most of them are pretty low numbers so the average value for the 7342 non-zero
For a voxel that has an entry of 1, I presume the probability that the tract
passes  through that voxel is near zero. For a voxel that has an entry of 127,
is the probability that the tract passes through it 0.5 ?
And if the entry is 255, is the probability 1.0?

It's that mapping of voxel value to probability that I'm trying to get at. Or
am I misunderstanding what the voxel value means?

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 12:46 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
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, "Krieger, Donald N."
<krieg...@upmc.edu<mailto:krieg...@upmc.edu>> wrote:
Thanks for getting back, Anastasia.

I'm not suggesting that it should be done differently than it is.

I'm just trying to understand how the voxel values map to probability. That's
why I described the wrong headed way I was thinking about it ... so you could
tell me where I'm going wrong.

From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto: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
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question

This wouldn't work because these 18 tracts do not include all tracts in the
brain.

On Apr 11, 2018 11:19 AM, "Krieger, Donald N."
<krieg...@upmc.edu<mailto:krieg...@upmc.edu>> wrote:
I was thinking that for a single voxel, the total of the values assigned to the
voxel over all the tracts would have a maximum of 255 and that 255 would
correspond to a probability of 1.0.
I can see is likely wrong but for sure it's too simple since each voxel could
contain crossing fibers from several tracts; hence the total probability
assigned to the voxel over all the tracts might be greater than 1.0.
??

Surely there is some normalization applied to the values assigned to the voxels
so they fall between 0 and 255.
Does that normalization vary from one subject to the next and perhaps even from
one tract to the next?
And how is the normalization mapped to probability?

Thanks - Don

From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.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
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
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:freesurfer-boun...@nmr.mgh.harvard.edu>

<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Krieger, Donald N. <krieg...@upmc.edu<mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 10:43:11 AM
To: Freesurfer 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 its probability, i.e. 0-255 -->
0.0 - 1.0

Thanks again - best - Don

From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto: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
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question

Hi Don - No, dlabel/ contains files that are used in the pathway
reconstruction, but the output of the reconstruction is saved in dpath/.
There's a subdirectory in there for each pathway, and it contains a volume
called path.pd.nii.gz. This is the probability that each voxel belongs to this
pathway, in the subject's native diffusion space. As TRACULA is a probabilistic
method, you get a probability associated with each voxel, rather than a set of
voxel coordinates.

https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputdirectoriesandfiles

Best,

a.y

________________________________

From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>

<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Krieger, Donald N. <krieg...@upmc.edu<mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 8:06:01 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question

Thanks for the additional information, Anastasia.

I will look for those files.

What I am after is a list of xyz coordinates for each of the 18 tracts. I see
masks in the trctrain/trc0xy/dlabel/mni directories which appear to be what I'm
looking for. They have names like

<roi>_AS_<str1>.<str2>.nii.gz

where str1 = bbr or flt and

str2 = roi1 or roi2

I can extract the lists of coordinates from them with mri_cor2label although I
haven't checked these lists to make sure they are actually what we need.

I haven't found documentation on these files nor do I see them in the tutorial
directories for the three elmo's.

I have bedbpostx running but do not expect it to produce them. I suppose it is
trac-all -path which will do so but I thought I would ask my questions anyway.

1.  Are these the files that I'm looking for?
2.  If so, where can I find documentation?
3.  What is the shortest path to generate them?

It strikes me that maybe it is the streamlines which best define the tracts
rather than these volumetric masks. I still do not thoroughly understand where
in the processing sequence the streamlines get assigned to specific tracts. ??

Thanks - Don

From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto: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
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question

Hi Don - If the output files described here show up in the end, all is well:

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#BEDPOSTX

Best,

a.y

________________________________

From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>

<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Krieger, Donald N. <krieg...@upmc.edu<mailto:krieg...@upmc.edu>>
Sent: Tuesday, April 10, 2018 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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Tuesday, April 10, 2018 4:24 PM
To: freesurfer
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
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:freesurfer-boun...@nmr.mgh.harvard.edu>

<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Krieger, Donald N. <krieg...@upmc.edu<mailto:krieg...@upmc.edu>>
Sent: Tuesday, April 10, 2018 1:15:05 PM
To: freesurfer
Subject: [Freesurfer] 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/kriegerd/Contrib/Freesurfer_6.0/subjects

Actual FREESURFER_HOME /media/portable/home/kriegerd/Contrib/Freesurfer_6.0

WARN: Running bedbostx locally - this might take a while

WARN: It is recommended to run this step on a cluster

bedpostx_mgh -n 2
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri

/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: 131:
/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected

I apologize for not finding the answer in the list archive.

It's probably there.

I'm running under ubuntu 14.04.

bedpostx_mgh is a shell script which calls for /bin/sh.

On my machine, that is a symlink to /bin/bash

If I change it to be explicitly /bin/bash, it runs a bit further.

Here is the full output:

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/subjects

Actual FREESURFER_HOME /media/portable/home/kriegerd/Contrib/Freesurfer_6.0

WARN: Running bedbostx locally - this might take a while

WARN: It is recommended to run this step on a cluster

bedpostx_mgh -n 2
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri

subjectdir is
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri

Making bedpostx directory structure

Queuing preprocessing stages

/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470:
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected
(expecting ";;")

Queuing parallel processing stage

0 slices processed

/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470:
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected
(expecting ";;")

Queuing post processing stage

/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470:
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected
(expecting ";;")

/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: line 439: 26461 Terminated
\${subjdir}.bedpostX/monitor

Thanks - Don

```
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