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Currently, we don’t have a children-specific atlas, however, the results generated by the default atlases should be reasonable for 4yr+ children.
Hi, The labeled volume should be automatically stored in the same directory as the MRI scan. They have filenames <subjectid>.svreg.label.nii.gz
Are you able to find that file?
Here is the list of output files
http://brainsuite.org/processing/svreg/output/Please let me know if you find these files generated in your mri directory.
Hi Tod,
SVReg definitely makes use of available cores. So for surface registration, it processes 2 cortical hemispheres on 2 separate threads. During volume registration, whenever possible, it processes 3 coordinates on 3 threads.
Moreover, each of the separate threads use multiple CPUs during various operations such as conjugate gradient minimization and interpolations.So yes, the more cores, the better it is for SVReg processing.
Additionally, you can also process multiple subjects simultaneously if you have computing power.
The system you mention is definitely great (both).
Can you just type path in the matlab command window?
How are you running the svreg execuable from witin matlab? Are you using !svreg.exe …. ?
Can you send me steps to reproduce the issue?
It might be that it is trying to use a different runtime version when called from matlab.
Note that the environment variables and the path is different in dos and in matlab.
check environment variables in matlab by typing env. Make sure that the correct MCR is first on the path.Thank you for using BrainSuite and reporting this issue.
You can run the svreg on the command line in a single threaded mode using -U flag.One of the unique features of BrainSuite is that the volumetric registration used is ‘surface constrained volumetric registration’. This means that during the registration process, cortical surface and subcortical structures are aligned simultaneously leading to a consistent registration.
Another unique feature is that the cortical thickness analysis used in BrainSuite uses computation of cortical thickness using partial tissue fraction information.
For the subcortex, the total volumes of various structures, as well as gray matter and white matters, are reported in detail by BrainSuite. I am not aware of any other functionality that other software has and is missing in BrainSuite for structural analysis.Hi Fatima,
Please take a look at BrainSuite diffusion pipeline:
http://brainsuite.org/processing/diffusion/Here is a step by step tutorial on how to use it.
http://brainsuite.org/quickstart/dti/Hi Leon, Thank you for using BrainSuite and I am glad that your study was positively received.
I would answer by saying that BrainSuite release is relatively frequent (approximately every 6 months). The latest release has been Feb 19, this year. I think this is more frequent than other competing software. I doubt it can be called outdated due to that reason. Additionally, the interactive GUI and fast processing speed allow rapid experimentation and visualization.
Unless there is some feature that is needed for the study, that is not in BrainSuite, it is unclear why a switch is needed, especially since the results of the analysis seem to be not as expected. But the reviewers seem to like them.Usually, most researchers and different labs have their favorite software and pipelines. The user base of BrainSuite is quite large and is growing.
Additionally, we as developers and maintainers of the software are ready to support and enhance the software.
SVReg is a bit memory intensive, so if you running multiple subjects simultaneously, then it might fail due to memory issue. Also please make sure that most all the other program windows are closed.
Please make sure that you are using the latest version (19a). I can’t think of any other reason.You get subject.roiwise.stats.txt after running svreg.
This has a detailed report of volumes of different tissues.Discussed this by email with you but posting here so that it is useful to others.
Yes, the program expects .gz extension. So if you compress it back the program should work.Thank you for using BrainSuite and very happy to hear that you like it.
The SVReg module computes thickness only for the cortical surface using inner and pial cortical surface representations.
Since the hippocampus and amygdala are subcortical structures, their volumes are not computed, but gray and white matter volumes are reported. The ‘thickness’ computation for hippocampus will involve generating surfaces only for that structure and not the entire brain. We don’t have that functionality implemented.
