On 27 Sep 2018, at 10:17, Maedeh Khalilian <[log in to unmask]> wrote:
Dear fsl experts,Following the steps u said, i made a text file containing all my ROIs, using label2vol in Freesurfer, and what i type in terminal and the error i get is :probtrackx2 --network -x test1/seeds.txt -s test1/Maedeh.dti/dti/preprocessdata.bedpostX/merged -m test1/Maedeh.dti/dti/preprocessdata.bedpostX/nodif_brain_mask -l --usef --s2tastext --os2t --onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --xfm=test1/Maedeh.dti/dti/preprocessdata.bedpostX/xfms/str2diff.mat --invxfm=test1/Maedeh.dti/dti/preprocessdata.bedpostX/xfms/diff2str.mat --avoid=test1/anatomy/ventricles.nii.gz --seedref=test1/anatomy/fs.nii.gz --forcedir --opd -V 1 --dir=test1/result
Log directory is: test1/result
basename test1/Maedeh.dti/dti/preprocessdata.bedpostX/merged
maskfile test1/Maedeh.dti/dti/preprocessdata.bedpostX/nodif_brain_mask
seeds test1/seeds.txt
output fdt_paths
verbose 1
nparticles 5000
nsteps 2000
usef 1
rseed 12345
randfib 0
fibst 1
Running in network mode
load seeds
CSV::load_rois:Unknown file type: labeldti/lh.G_cingul_Post_dorsal.nii.gzi have no idea what the problem is from and why .nii.gz is unknown file type!!im quite sure that this is the recognizable format for fsl.i would be grateful if u could help me.cheers,Maedeh,
-----Original Message-----
From: Maedeh Khalilian <[log in to unmask]>
To: [log in to unmask]
Date: Tue, 25 Sep 2018 15:38:42 +0330
Subject: Re: [FSL] a problem using probtrackx
Dear Michiel Cottaar,Thank you very much for your great help.cheersMaedeh,-----Original Message-----
From: Michiel Cottaar <[log in to unmask]>
To: [log in to unmask]
Date: Sun, 23 Sep 2018 15:25:42 +0000
Subject: Re: [FSL] a problem using probtrackx
Dear Maedeh,All of the matrix options (matrix1, matrix2, and matrix3) will always give you a matrix of voxel/vertex by voxel/vertex and not ROIxROI. If you want to get the ROI by ROI connectivity (34x34 matrix in your case) you want the --network option. I don’t believe that this option is available from the GUI, so you will have to use the command line.So, your steps should be:1. Create 34 separate NIFTI files, one for each of your ROIs. Each NIFTI file should contain 1 for voxels in the ROI and 0 for all other voxels.2. Create a text file listing the filenames of all the 34 NIFTI files (1 line per file)3. Run probtrackx with the list of ROI filenames as seed and the --network option enabled. The simplest command line would be something like$ probtrackx2 -s <bedpostX directory>/merged -m nodif_brain_mask.nii.gz -x <text file listing ROIs> --networkNote that if your ROIs are still in structural rather than diffusion space, you will also have to include the transformation matrices and/or warp fields (using the --xfm and --invxfm option).Good luck,Michiel
On 22 Sep 2018, at 16:47, Maedeh Khalilian <[log in to unmask]> wrote:
Dear fsl experts,I have an anatomical MRI parcellation and i want to register it on its equivalent dMRI in order to compute its connectivity matrix using probtrackx in fsl.The parcellation is the output of Freesurfer "aparc+aseg.mgz" which is converted into .nii form, "aparc+aseg.nii". i have used it as a target mask and i have also used white.nii as a seed mask.( i have chosen "single mask" , "termination mask " in fsl Data part and i have also chosen matrix3 in fsl Options.the first question is that i didn't know what to import as row space and column space matrixes when choosing Matrix3 option, so i imported "aparc+aseg.nii" again.Actually my parcellation has 34 ROIs so i expected to have 34 elements with the number of fibres between each pair (at most 5000 )or sth like this, but when i read the "fdt_matrix3.dot" in MATLAB, i see 863808 elements !! and I'm completely confused.Now my questions are:1- Are the steps i have taken and my inputs correct?2- What should i have imported as my row space and column space matrixes?3- If the steps are right, why do i have such big number for the number of parcels?I would be grateful if you could help me,Best regards,Maedeh,
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