[David Shattuck]

hi Wayne –

We list the requirements on the download page.

BrainSuite23a requires MATLAB 2023a or MATLAB Runtime 2023a. You don’t need other versions of the runtime if you are using BrainSuite23a.

Versions 19b through 21a required MATLAB (Runtime) 2019b
Versions 16a through 19a required MATLAB (Runtime) 2015a.

We’ll be moving to MATLAB 2024b for our next release (hopefully this month) because it provides improved support for Apple silicon and a number of other features we plan to use in the future.

The cortical extraction sequence doesn’t require the MATLAB libraries. If you are running the full anatomical pipeline, then the MATLAB dependencies begin with cortical thickness estimation. If the program is having trouble prior to this (e.g., if it isn’t generating the pial surface), then the problem isn’t MATLAB.

Can you provide more detail on how you are running the programs? Are you using the GUI or command line?

thanks,
David

[David Shattuck]

hi Wayne –

I think that could be it. Is 2523412.dwi.bfc.nii.gz a T1 and not a DWI image? The name suggests it was created from 2523412.dwi.nii.gz. I would check that first.

I would also just copy the files that worked as inputs on Windows over to your Linux machine and test those.

Thanks,
David

[David Shattuck]

hi –

It looks like you are running this on our sample data. We use those data routinely to test for cross-platform consistency, so we haven’t encountered this issue.

I do see some differences in the inputs between the two calls you make.

Your file on the linux line is named “/home/wayne/Desktop/mrtest2/2523412.dwi.bfc.nii.gz “, but the call in Windows uses 2523412.bfc.nii.gz. What is /home/wayne/Desktop/mrtest2/2523412.dwi.bfc.nii.gz? Is it the same as 2523412.bfc.nii.gz or did you apply bfc to the dwi data?

The other difference I see is 2523412.dwi.nii.gz vs 2523412.dwi.nii, but that shouldn’t affect anything unless the files don’t match.

thanks,
David

[David Shattuck]

hello –

I don’t use Alma, so I’m less familiar with the versions of the libraries it has available. It looks like Alma Linux 8 is somewhat out of date, with active support having just ended on 31 May 2024 (https://wiki.almalinux.org/release-notes/).

I took a look at Alma 8.10, and the latest versions it has are GLIBC_2.28 and GLIBCXX_3.4.25, both of which are one version too old.

Are you trying to run BrainSuite on the command line only, or are you trying to use the GUI?

thanks,
David

thanks,
David Shattuck

[David Shattuck]

Hello –

The mesh is relative to the voxel coordinates. We don’t have a file for the mesh transform, but its coordinates are all relative to the voxel grid of the input image.

The units for the surface are in mm, and we use voxel-centered coordinates.

How large of a shift are you seeing?

Anand is one of the developers of the software, as am I.

thanks,
David

[David Shattuck]

Sorry for the slow reply — the scripts that are in the bin folder (brainsuite_anatomical_pipeline.sh and brainsuite_anatomical_pipeline.bat) use the same settings as the GUI and should produce identical results.

thanks,
David Shattuck

[David Shattuck]

hello –

We don’t currently have a feature to load multiple sets of streamlines at the same time. I’m considering adding it for the next version.

thanks,
David Shattuck

[David Shattuck]

hi Huizhang –

All of the command-line programs in the BrainSuite bin dir that write surface files should save them as .stl files if you use the .stl extension for the output file. The caveat to this is that stl files don’t carry enough information for the BrainSuite pipelines to use them as inputs, so effectively you would need to run a step twice to get a .dfs version and a .stl version. We don’t have a file converter program included with the software, but I will probably add one for the next release.

You could try this with dfs if you have a mask file. Below is an example on my Mac. You can see it generates a .stl file.


shattuck:~>/Applications/BrainSuite21a/bin/dfs -i /Applications/BrainSuite21a/svreg/BCI-DNI_brain_atlas/BCI-DNI_brain.cortex.dewisp.mask.nii.gz -o brain.stl
wrote surface file brain.stl
shattuck:~>head brain.stl
solid brain.stl
facet normal 0 0 0
outer loop
vertex 46.5981 106.954 80.565
vertex 46.1262 106.945 80.6693
vertex 46.4666 106.725 80.639
endloop
endfacet
facet normal 0 0 0
outer loop


thanks,
David

[David Shattuck]

Hello — that is the only download link we have.

thanks,
David

[David Shattuck]

Hi Adrien –

It took a little longer than expected because we have been preparing a major release of BrainSuite (v23a, out now), as well as an updated BrainSuite BIDS App. We were making some improvements to the underlying methods, including some optimizations in how the streamline filtering is performed.

The new package includes a program call filterdft, which is in the bin directory. You can use it to perform all of the filtering options that are available in the GUI. These are performed (in order, but the order shouldn’t matter):

* remove streamlines shorter than the length threshold if specified (-l setting)
* remove streamlines that intersect labels in the exclude list (specified as –exclude # # #)
* remove streamlines based on spherical ROI filters if specified (uses an xml file)
* remove streamlines unless they intersect labels in the include list (specified as –include # # #)

By default, it will use an or operation for the final check, so if you wanted to include all streamlines that intersect the superior frontal gyri, you would run:

filterdft -i input.dft -o output.dft --include 120 121

You can use the –and flag if you want to have the streamlines go through *all* labels specified, e.g,. if you want to find streamlines that connect the brainstem (800) and cerebellum (900), you would use:

filterdft -i input.dft -o output.dft --include 800 900 --and

The full set of options is listed below.

Let me know if that provides the functionality that you need.

thanks,
David

usage: filterdft [settings]

required settings:
-i                       input file
-o                       output file
-l filename                    label volume (must be 16-bit)

optional settings:
--license                      show the license information
-g                             debug
-v                      verbosity [default: 0]
--length length                length threshold [default: 0]
--include           labelID1 ...  labelIDN (include these labels)
--exclude           labelID1 ...  labelIDN (exclude these labels)
--and                          tracks must pass through all labels in include list
--dont-merge                   don't merge cortical gm/wm labels
-s filename                    sphere ROI xml file

• This reply was modified 2 years, 3 months ago by David Shattuck.

[David Shattuck]

hi Adrien –

I’m working on it — still need to do some testing. Will follow up by email soon with a few questions.

thanks,
David

[David Shattuck]

I am not near a Windows machine at the moment, but I just tried this on Linux using the data from https://brainsuite.org/tutorials/dtiexercise/ and it started. I copied the arguments from your post.

I will try it on Windows later today and get back to you.

BrainSuiteTutorialDWI>/opt/BrainSuite21a/bdp/bdp.sh 2523412.bfc.nii.gz --tensor --nii 2523412.dwi.nii.gz -g 2523412.dwi.bvec -b 2523412.dwi.bval

BDP Version: 21a (build #0081), released 2021-05-05

================================================================================
                         Setting up dataset and inputs
================================================================================
Reading input flags...

Checking input files...

.mask.nii.gz file found: 2523412.mask.nii.gz
BDP will use this file as brain mask. You can specify a custom brain mask by
using flag --t1-mask . The custom mask must overlay correctly
with input BFC image in BrainSuite.

Processing data with fileprefix:
	2523412

================================================================================
                   Co-registration and Distortion Correction
================================================================================
Reading the input parameters for co-registration...
Total memory (physical+swap) found: 126.53GB

[David Shattuck]

If you enclose your text with pre tags, it should show it as you wrote it. [code] doesn’t work, unfortunately. pre uses angle brackets rather than square brackets.

• This reply was modified 2 years, 5 months ago by David Shattuck.

[David Shattuck]

If you install Matlab or the Matlab runtime library to the default location, the scripts should find it. If you installed it somewhere else, you can set an environment variable ‘BrainSuiteMCR’ on Linux or Mac before running the script. For Linux, the default for the Matlab runtime would be:

export BrainSuiteMCR="/usr/local/MATLAB/MATLAB_Runtime/v97"

or for the full Matlab install:

export BrainSuiteMCR="/usr/local/MATLAB/R2019b/runtime"

Note that this is different for Mac.

You can also edit the scripts in the BrainSuite svreg and bdp folders, but setting an environment variable will be easier.

You shouldn’t need to do this for Windows, because Windows stores the location in its registry.

-David

[David Shattuck]

hello –

Our forum software changes how hyphens appear, so it can be difficult to tell exactly what you wrote. I think you have two hyphens before g and b, but these should only have one. Try running this:

"C:\Program Files\BrainSuite21a\bdp\bdp.exe" 2523412.bfc.nii.gz --tensor –-nii 2523412.dwi.nii.gz -g 2523412.dwi.bvec -b 2523412.dwi.bval

and see if that fixes the problem.

thanks,
David

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