Hi Dianne,I've updated the wiki doc on matrix options. (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#Options_Tab)Hopefully, the doc should answer some of your questions. Let me know if something is still not clear.Cheers,SaadOn 18 Jun 2013, at 18:39, Matt Glasser <[log in to unmask]> wrote:Unfortunately I'm not too familiar with the probtrackx GUI.The .dot file is a sparse representation of the matrix, which you can make full in matlab with this kind of command:dot = load(inputdot);X = spconvert(dot);mat = single(full(X+X'));As for displaying all this stuff easily, that is coming but not yet ready yet.Peace,Matt.From: Dianne Patterson <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Tuesday, June 18, 2013 10:18 AM
To: <[log in to unmask]>
Subject: Re: [FSL] probtrackx2 with matrix3 options
Hi Matt,Thanks again for your answer!As for my 2nd question:-I used the probtrack gui to set up this test of matrix3.-In the data panel of that gui I have to select what I want probtrack to do (e.g., single voxel tracking, single mask, multiple mask etc).-In the options panel I select matrix 3 and a column and row mask.I was trying to ask this question: Are the choices I make in the options panel dependent upon the choices I make in the data panel?====================================Is there anywhere I can read about the output files created by running probtrackx2 with matrix3? I have gotten out some results, but I'm not sure exactly what they are telling me (i.e., what are the values in the fdt_matrix3.dot file and the fdt_paths.nii.gz?)Thankyou,DianneOn Mon, Jun 17, 2013 at 7:38 PM, Matt Glasser <[log in to unmask]> wrote:
Overkill on the run time. As for the best way to measure whole brain connectivity, we don't yet know if matrix1 or matrix3 is better. That is an active research question.I don't understand your other question.Peace,Matt.From: Dianne Patterson <[log in to unmask]>Date: Monday, June 17, 2013 7:13 PM
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
To: <[log in to unmask]>
Subject: Re: [FSL] probtrackx2 with matrix3 options
Dear Matt,I suppose I'm not just interested in making it run fast...I'd like to get a good measure of whole brain connectivity....Are you suggesting that 5000 samples is overkill for matrix3...or just overkill if I want it to run in a reasonable amount of time?I'm really just guessing at how to use the tool. For example, do I need to track between the same 2 masks that I use for matrix3?Thankyou for your help,DianneOn Mon, Jun 17, 2013 at 5:53 PM, Matt Glasser <[log in to unmask]> wrote:
I don't know that matrix3 meets the criteria of "most efficient (fastest). You would not want to use nearly as many samples in matrix3 as matrix1. A quick calculation showed that 100 samples in matrix3 was roughly equivalent to 5000 samples in matrix1 when trying to match how long it would take to compute.Peace,Matt.From: Dianne Patterson <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Monday, June 17, 2013 5:27 PM
To: <[log in to unmask]>
Subject: [FSL] probtrackx2 with matrix3 options
Dear Group,I am exploring the new "matrix3" option in probtrackx2. I am looking for the most efficient (fastest)way to generate the whole brain connectivity matrix.Currently, the command I'm running looks like this. Is this the optimal choice?probtrackx2 --network -x Matrix/masks.txt -l --onewaycondition --omatrix3 --target3=sub001_nodif_mask.nii.gz--lrtarget3=sub001_nodif_mask.nii.gz -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0--sampvox=0.0 --forcedir --opd -s Bed.bedpostX/merged -m Bed.bedpostX/nodif_brain_mask --dir=MatrixThankyou very much for your time and the cool new tools! The FSL course was fantastic.Dianne--Dianne Patterson, Ph.D.or[log in to unmask]
University of Arizona
Speech and Hearing Science 3141131 E 2nd Street, Building #71
(Just East of Harvill)621-9877=============="If you have an apple and I have an apple and we exchange these apples then you and I will still each have one apple. But if you have an idea and I have an idea and we exchange these ideas, then each of us will have two ideas." - George Bernard Shaw==============--Dianne Patterson, Ph.D.or[log in to unmask]
University of Arizona
Speech and Hearing Science 3141131 E 2nd Street, Building #71
(Just East of Harvill)
621-9877=============="If you have an apple and I have an apple and we exchange these apples then you and I will still each have one apple. But if you have an idea and I have an idea and we exchange these ideas, then each of us will have two ideas." - George Bernard Shaw==============--Dianne Patterson, Ph.D.or[log in to unmask]
University of Arizona
Speech and Hearing Science 3141131 E 2nd Street, Building #71
(Just East of Harvill)
621-9877=============="If you have an apple and I have an apple and we exchange these apples then you and I will still each have one apple. But if you have an idea and I have an idea and we exchange these ideas, then each of us will have two ideas." - George Bernard Shaw==============--Saad JbabdiUniversity of Oxford, FMRIB CentreJR Hospital, Headington, OX3 9DU, UK(+44)1865-222466 (fax 717)