Hi Kristen,

Yes, because of differences in "trackability" across subjects (there's
a very interesting thread on that), and because of differences in seed
masks size, you want to apply some kind of normalization to your tract
values before thresholding. That will ensure you threshold out the
same proportion of voxels in all your subjects.
Since you seem to be interested in FA and volume mostly, I don't think
it matters if you use waytotal, the max tract value, or the total
number of streamlines sent out, but there are differences there (see
previous threads).
waytotal = total number sent - excluded streamlines (i.e. waytotal =
number of streamlines that "made it")
streamlines are excluded if you have a waypoint (which you don't), or
exclusion criteria/masks.

You can calculate the total number sent by multiplying the number of
streamlines sent/voxel (from your probtrackX command) by the size of
your seed (fslstats <seed mask> -V).

Now to apply your normalization factor, you can use
fslmaths fdt_paths -div <waytotal> fdt_paths_norm
(or include this operation in the fslmaths command you already have).
Note that since your waytotal is different in all subjects (hence the
need to do this in the first place), you'll need to extract the
waytotal value for each and apply it separately.

Then you will look at your normalized paths and play around to find
the % threshold you want to use (now the same for all subjects). and
apply that.

Sorry if this reply jumps around a bit, I'm in a rush, and I probably
missed some of your questions, but hopefully it helps.

I just saw your last message. Using the total number of voxels in your
seeds is basically the same as using the total number sent out, since
hopefully you used the same number of streamlines sent out for
everything.

Best,
Cherif.


------------------------------------------------------------------------------------------
Cherif P. Sahyoun                                               HST-MEMP

Developmental Neuroimaging of Cognitive Functions

C: 617 688 8048
H: 617 424 6956
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"Live as if this were your last day. Learn as if you'll live forever"
Gandhi
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On Fri, Mar 27, 2009 at 8:44 AM, Lindgren, Kristen, Ann <[log in to unmask]> wrote:
> Whoops, so as followup to my question, I should note that I'm trying to figure out what was meant in the FSL list thread #017802 and its replies.  I've looked at the Rilling (2008) paper (trying to get a copy of Matt Glaser's 2008 paper) and read Matt's response:
>
> "I think two things are important: 1) That you use a consistent percentage of the total number of samples sent out for each tract across subjects (so that tracts created by larger ROIs, and thus have more total samples sent out, have higher thresholds) and 2) That in setting the percentage that you will use, you try a variety of values and see what seems to produce clean results showing the pathway of interest without many extraneous pathways not clearly connected to the ROI but at the same time does not remove large parts of the pathway of interest (because it is too high)."
>
> I used multiple masks for my probtrackx analyses (2 masks only, no waypoints), so would I still find the total number of samples sent out for each tract in the waytotal file?  If so, which number is that?  There are two numbers in mine.  Is the first number the number sent from ROI1 and the second is the number sent from ROI2, in which case I would just add them and make my threshold a consistent percentage of that number?
>
> I guess I'm just confused as to how to implement in my data what Matt recommended in the quote above.  It seems that Matt found thresholds of 2-6% of total samples sent out worked well for his dataset using structural space seeding points (similar to my study).  So if I'm understanding correctly, I would set the threshold for each subject for fdt_paths in fslmaths as a set percentage of the sum of the two values in waypoint.txt.  I'm still trying to get a hold of Matt's DTI tractography of language pathways paper to see what he used as a threshold, so any guidance on where to start would be great.
>
> Thanks so much!
>
> Kristen
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library on behalf of Lindgren, Kristen, Ann
> Sent: Thu 3/26/2009 10:56 PM
> To: [log in to unmask]
> Subject: [FSL] Post probtrackx analyses - thresholds for fdt_paths
>
> I was looking through some e-mails that I had saved about thresholding with probtrackx, but I'm still unsure if I'm thresholding my fdt_paths outputs properly so I wanted to double check one last time before committing to my analyses.  Any thoughts, concerns, or advice are greatly appreciated.
>
> Here's what I've done:
> 1) I used two freesurfer gray matter parcellation labels as seeding points in probtrackx for each subject.  There is a known connection between these two regions.
>
> 2) Now I'm pulling out the average FA and volume of the resulting fdt_paths using these formulas (thanks again to Steve for helping me figure out this one!)
>
> fslmaths fdt_paths -thr 50 -bin -mul dti_FA_str fdt_paths_values
> fslstats fdt_paths_values -M -V
>
> So here are my concerns:
>
> 1) I've been using 50 as my threshold for each subject (used the default value of 5000 samples for probtrackx).  Is this correct? Or should I be customizing this per subject since the volumes of the seeding points vary across subjects?  If I should be varying it, what should I be basing my thresholds on for each subject?  Any references in support of either method?
>
> 2) Should I only be including voxels that have an FA value above a certain threshold?  If so, anyone know of a paper that has looked at the normal range of FA values for white matter?
>
>
> Sorry for the ton of questions lately, I'm just in the last stretch of my dissertation analyses and I want to make sure I'm doing things correctly before moving forward.  Thanks so much for all of your help.  I really appreciate it!
>
> Kristen
>