Cherif and Matt, I'd love to know how you're integrating freesurfer into FSL. I don't know how to do Cherif's suggestion of projecting the mask ribbon onto the white matter before tracking. I'm guessing this would be something done within freesurfer. That sounds like it would get me to a point where I'd only be tracking from white matter like Matt suggested. How would I restrict tractography to be inside the freesurfer white matter surface, though? I'm thinking it would involve using a termination mask, but what would you use as a mask? For my current analyses, I'll have to just go forward with what I have, but for the future I'd love to refine my methods to be a little more kosher. Thanks for your input!
Kristen
-----Original Message-----
From: FSL - FMRIB's Software Library on behalf of Matt Glasser
Sent: Fri 3/27/2009 5:54 PM
To: [log in to unmask]
Subject: Re: [FSL] Post probtrackx analyses - thresholds for fdt_paths
I always track from white matter. If it is a cortical ROI I use the 1st
voxel of the white matter surface. Honestly, I have found that tracking
from/into cortical grey matter results in more error than useful information
(its easy to get pathways crossing sulci for example, if you combine partial
voluming with the fact that the principle diffusion direction in cortical
grey matter is oriented perpendicular to the cortical surface, and cortical
grey matter ROIs may be very close to brain rim voxels). Subcortical grey
matter is a different story, however, and I think probtrack does a good job
with that. I also restrict tractography to be inside the freesurfer white
matter surface, which is fine if you care about cortical-cortical
connections.
Sounds like you have a good plan for the normalization.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Cherif Sahyoun
Sent: Friday, March 27, 2009 4:06 PM
To: [log in to unmask]
Subject: Re: [FSL] Post probtrackx analyses - thresholds for fdt_paths
Hi Kristen,
You're very welcome. As a sidenote, I've used FS masks as well (from
"surface" fMRI activation), and what I found useful was to project the
mask ribbon into the white matter before tracking. You probably don't
need to, but my reasoning was that this avoided starting off tracking
from high uncertainty voxels. I've seen it done in deterministic
tractography papers, which would be more vulnerable to tracking from
gray matter.
Best,
Cherif
----------------------------------------------------------------------------
--------------
Cherif P. Sahyoun HST-MEMP
Developmental Neuroimaging of Cognitive Functions
C: 617 688 8048
H: 617 424 6956
[log in to unmask]
"Live as if this were your last day. Learn as if you'll live forever"
Gandhi
----------------------------------------------------------------------------
---------------
On Fri, Mar 27, 2009 at 4:29 PM, Lindgren, Kristen, Ann <[log in to unmask]> wrote:
> Ah, ok, it's all starting to make sense to me. Took me long enough :)
>
> Alright, so these are my two options for normalizing my data for
intersubject comparisons:
>
> Using waytotal values (this option will control for differences in
trackability and result in similar sized pathways across subjects, thus it
may remove potential interesting inter-group differences in the size of the
tracts):
> fslmaths fdt_paths -div Sumof2WaytotalValues -thr
ChosenPercentageSameAcrossSubjects -bin -mul dti_FA_str fdt_paths_norm -odt
float
>
> Using total ROI volumes (this option could result in over-thresholding if
there are a significant # of voxels in my ROI from which the pathway is not
tracked)
> fslmaths fdt_paths -div ((ROI1+ROI2)x5000) -thr
ChosenPercentageSameAcrossSubjects -bin -mul dti_FA_str fdt_paths_norm -odt
float
>
>
> I'm thinking I'll try running the analyses both ways. The first way, as I
mentioned, has the potential to make my group tract size analyses null and
void. The second way may be problematic since my two masks are mostly
composed of gray matter voxels, so it's likely that there are a good number
of voxels in my ROI from which the pathway won't track and I'll be
over-thresholding.
>
> Oh well, such is the world of imaging. There's always a drawback
depending on what method you do! Here's hoping this ends up working. I
seriously cannot thank all of you enough for all of your help. You guys are
godsends!
>
> Kristen
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library on behalf of Cherif Sahyoun
> Sent: Fri 3/27/2009 2:41 PM
> To: [log in to unmask]
> Subject: Re: [FSL] Post probtrackx analyses - thresholds for fdt_paths
>
> Hi Kristen,
>
> Since you're already normalizing in your fslmaths command, you
> probably don't need to use the ROI size in your thresholding. I'd go
> with a simple percentage.
> I haven't done multiple masks tracking, so i'm not sure, but I suspect
> that the different waytotals corespond to the diff masks. In that case
> yes, I'd add them.
> And yes, the -div is in the right spot.
>
> Best,
> Cherif.
>
----------------------------------------------------------------------------
--------------
> Cherif P. Sahyoun HST-MEMP
>
> Developmental Neuroimaging of Cognitive Functions
>
> C: 617 688 8048
> H: 617 424 6956
> [log in to unmask]
>
> "Live as if this were your last day. Learn as if you'll live forever"
> Gandhi
>
----------------------------------------------------------------------------
---------------
>
>
>
> On Fri, Mar 27, 2009 at 2:26 PM, Lindgren, Kristen, Ann <[log in to unmask]>
wrote:
>> Thanks, Matt. I actually just got the PDF of your paper along with
supplemental material, so I'm good to go on that.
>>
>> So, putting this all together, here's what I think I need to do
(questions marked with ***)
>>
>> 1) Threshold and normalize the results for intersubject analyses.
Threshold = ((ROI1 + ROI2) x 5000) x consistent percentage. 5000 = number
of samples per voxel in probtrackx command. I can divide in either of two
ways
>>
>> ***is -div in the correct place or should it be later in the list?***
>>
>> fslmaths fdt_paths -div WaytotalValue -thr valuefromabove -bin -mul
dti_FA_str fdt_paths_norm
>> -odt float
>>
>> or
>>
>> fslmaths fdt_paths -div TotalSamplesSentOut -thr valuefromabove -bin -mul
dti_FA_str fdt_paths_norm
>> -odt float
>>
>> I'm thinking since my masks are my ROIs from freesurfer and thus the
majority gray matter, it might make sense for me to divide by the waytotal
value instead of total samples.
>>
>> ***my waytotal file has two values in it - do I sum these?***
>>
>> 2) Then I can use fslstats to pull out mean FA and volume.
>>
>>
>> Do I finally have it? Here's hoping...
>>
>> Thanks again for all of your help!
>>
>> Kristen
>>
>>
>> -----Original Message-----
>> From: FSL - FMRIB's Software Library on behalf of Matt Glasser
>> Sent: Fri 3/27/2009 1:31 PM
>> To: [log in to unmask]
>> Subject: Re: [FSL] Post probtrackx analyses - thresholds for fdt_paths
>>
>> Hi Kristen,
>>
>> I'm happy to send you a copy of my 2008 Cerebral Cortex paper, but it
does
>> not have anything about probabilistic tractography thresholding in it,
just
>> let me know. What you say in your latest e-mail below is correct for
intra
>> subject comparisons. Keep in mind that that command only thresholds your
>> data, normalization would require you to divide the data by the total
number
>> of samples sent out or the waytotal (but this is not necessary in this
>> case).
>>
>> For intersubject comparisons, you may want to consider normalizing using
the
>> waytotal if you want to generate thresholded pathways of similar size
across
>> subjects. This is intended to remove differences related to
trackability,
>> but may also remove interesting inter-subject differences in pathway
size.
>> One way to get around this issue is to normalize based on a "control"
>> pathway, which you do not anticipate will vary across subjects in a
>> biologically meaningful way. Thus, you could theoretically remove global
>> trackability differences without affecting biological differences in the
>> pathway of interest. Assuming identical ROI size of the ROIs used to
track
>> the control tract, you could divide the tract of interest by the waytotal
of
>> the control tract to generate a normalized tract of interest (on the
>> assumption that differences in that waytotal are due entirely to
>> trackability differences). Keep in mind that I haven't actually done
this
>> and perhaps someone else can think of theoretical problems with this (not
to
>> mention practical ones). We did this in a qualitative sense in Rilling
et
>> al (2008), by showing that we were able to track robust CST and cingulate
>> pathways in all species, but not a robust arcuate. In terms of
>> thresholding, we only normalized for ROI size in Rilling et al (2008)
>> because waytotal had not been implemented yet.
>>
>> Regarding the exact percentage, it was not 2-6% but rather 2.0 X 10^-6%
>> (much lower). See also
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0811&L=FSL&P=R44426. A
>> word of caution with the total number of samples sent out approach: if
your
>> ROIs contain significant numbers of voxels from which the pathway is not
>> tracked, you will end up over thresholding your data.
>>
>> Regarding an FA threshold, I think it would be more appropriate to
segment
>> your structural images and find the FA values that lie both in the white
>> matter as defined by your structural and your thresholded pathway.
>>
>> Overall, what you suggest in your latest e-mail is probably fine, and we
>> have published using that method. I though I would make sure you are
aware
>> of its limitations and other potential options I can think of.
>>
>> Peace,
>>
>> Matt.
>>
>> -----Original Message-----
>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
Behalf
>> Of Lindgren, Kristen, Ann
>> Sent: Friday, March 27, 2009 11:21 AM
>> To: [log in to unmask]
>> Subject: Re: [FSL] Post probtrackx analyses - thresholds for fdt_paths
>>
>> Thanks, Cherif. I did see that thread about thresholding, and from what
>> parts I understood, it seemed like using the total number of streamlines
>> sent out may be the best method for my analyses (it sounds like Matt
Glasser
>> was doing something similar to mine, and he said that he found that
method
>> best for looking at for example asymmetries within subjects).
>>
>> So, putting all of this info together, this is what I'm planning on
doing.
>> Let me know if this sounds kosher.
>>
>> To calculate my threshold, I will add the # of voxels in both seeding
points
>> (# of voxels ROI1 + # of voxels ROI2), multiply that by the number of
>> streamlines per voxel (5000), and then multiply that result by the same
>> percentage for each subject.
>>
>> So my fslmaths command would like this:
>>
>> fslmaths fdt_paths -thr valuefromabove -bin -mul dti_FA_str
fdt_paths_norm
>> -odt float
>>
>> And just checking, because I'm using the percentage of total samples sent
>> out as my normalizing factor, I don't need to incorporate the waytotal
>> values into any of my equations.
>>
>> Phew! Here's hoping I finally got it...
>>
>> Kristen
>>
>> -----Original Message-----
>> From: FSL - FMRIB's Software Library on behalf of Cherif Sahyoun
>> Sent: Fri 3/27/2009 11:49 AM
>> To: [log in to unmask]
>> Subject: Re: [FSL] Post probtrackx analyses - thresholds for fdt_paths
>>
>> 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
>> [log in to unmask]
>>
>> "Live as if this were your last day. Learn as if you'll live forever"
>> Gandhi
>>
----------------------------------------------------------------------------
>> ---------------
>>
>>
>>
>> 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
>>>
>>
>
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