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Regarding execstack – We have not encountered this error before. So you will have to try and see if that command has to be executed each time. If so, it should be possible for you to add it to bdp.sh. Please do give us an update on that so we can add it to our FAQ.
Regarding mask – Can you check your T1 mask as well.
And share all the logs that BDP spits out on the terminal. That will help narrow down which masking step is failing.Both BrainSuite 16a1 and 17a use the same MCR – I doubt changing the executable will help.
Can you check if your MCR folder needs have executable permissions ?
I noticed that the error you shared has “/my/path/” printed in the path – Did you type this for the forum or is the actual path that got printed in the error ?
Please check if all your paths are correct and accessible to bdp.sh.You will have to edit bdp.sh and change the path of the matlab compile runtime there.
Remove # from
#BrainSuiteMCR=”/path/to/your/MCR”;and add your path.
Hi Rob,
Did you get this error while running BDP or has BDP code been modified for some other purpose ?
Bvalue (.bval) and Bvector (.bvec) files are sampling protocol information of your dwi file. This should be provided as input to run BDP – It should have been published along with your diffusion data.
Hi Saske,
Here are the steps:
1. Create the first ROI (plus symbol in Track filtering) – you should see a sphere in the surface view and circles in the volume view.
2. Go to the volume view, press ctrl (command for mac) and move the circl to desired location.
3. Add another ROI – you should see sphere of different color. Select it by clicking on the ROI description in the track filtering menu. This means you have selected the desired ROI.
4. Go to volume view and move it around. You should see tracks that pass through both spheres.Here is a ppt from an earlier training event that explains how to create spherical ROIs in section 3.3.
Link – http://brainsuite.org/wp-content/uploads/2015/10/Part3b_Bhushan_BDP_workshop_hands_on.pdfHi Nicolò,
Sorry for the late response.
This looks like a mask issue, even though your mask inputs are reasonable there could be processing steps changing the mask.
Here are a few things I can think of
1. Can you check if your t1.mask.nii.gz looks reasonable ?
2. Since the program crashed, can you check if BDP created a temporary mask file called epi_mask.nii.gz. BDP deletes these files but may be in this case it stopped before deleting. If you do find such a file, how does it look?
4. Run BDP to save intermediate png files using the flag –png-out or –p. This will save snapshots of the masks prior to this failure. Can you check the output <name>.approx_align.png. I have to warn you that this is a very memory intensive process.Hi Luca,
BrainSuite16a now supports multiple ODF estimation methods and we plan to add more in the upcoming releases. In this release we support FRT, FRACT and 3DSHORE based ODF estimation.
3D SHORE Analytical ODF estimation method implemented is as described in
[1] Merlet S. et. al, “Continuous diffusion signal, EAP and ODF estimation via Compressive Sensing in diffusion MRI”, Medical Image Analysis, 2013.
[2] Cheng J. et. al, “Theoretical Analysis and Pratical Insights on EAP Estimation via Unified HARDI Framework”, MICCAI workshop on Computational Diffusion MRI, 2011.In order to use these methods you need to choose them using –frt,–fract or –3dshore flags. All information on flags supported can be accessed using –help command or by accessing ReadMe.html provided with the release. The website will also be updated soon.
Hi Luca,
You need to run both these tools separately on Matlab. The download links are at http://brainsuite.org/processing/additional-tools/.Order of usage : You should run the joint denoising prior to running BDP. Then run BDP and use BDP results to calculate tracts on BrainSuite. And finally use the Tract Connect software (that uses multiple BrainSuite outputs including tractography results) to analyze white matter.
