December 5, 2018 at 3:35 pm #1564
I have a modified atlas made out of the default BrainSuiteAtlas1 using the Label editor gui. The label description is modified accordingly. Modifications just amount to making subparcels from large gyri, and merging smaller ones, to create parcels of overall similar sizes.
I would like to use the default svreg results to warp the modified atlas onto a subject brain. My notion is that the same warp transformation resulting from the original BrainSuiteAtlas1 running svreg should be applicable to the modified Atlas derived from it.
I would prefer not to create a completely new Atlas and install it in BrainSuite for many reasons, especially since I have been tweaking the modifications very frequently. Many troubles when I tried to do that and it takes too long to rerun the whole process every time I modify the Atlas. It should be simple enough to run the default svreg sequence with a subject brain, then apply the default Atlas’ transformation using the modified Atlas, no?
I won’t go through all of the things I have tried unsuccessfully. I hope you have a simple way to do this.
I am using the command line tools, Windows10, BrainSutie18a, Matlab. This is part of a processing pipeline that has been really really helpful.
I hope the question is clear and you are able to help. Thank you very very much.
PS- your email support link ‘email@example.com’ is undeliverable
December 6, 2018 at 4:57 am #1565
FYI, I sent email to your response but got this:
” —– The following addresses had permanent fatal errors —– <firstname.lastname@example.org>
(reason: 550-5.2.1 The email account that you tried to reach is disabled. Learn more at)”
Thank you for your prompt response! Difficult to troubleshoot, but I get this error:
C:\Program Files\BrainSuite18a\svreg\bin>svreg_labelwith_atlas.exe C:\Users\lolson\Desktop\JJnew\IA\bfc\nrT1 C:\Users\lolson\Desktop\BrainSuiteAtlas1\mri mod
Error using copyfile
No matching files were found.
Error in svreg_labelwith_atlas (line 77)
Not sure which files are missing?
December 6, 2018 at 12:37 pm #1568
Yes, this file exists: C:\Users\lolson\Desktop\JJnew\IA\bfc\nrT.svreg.init.label.nii.gz as C:\Users\lolson\Desktop\JJnew\IA\bfc\nrT1.svreg.init.label.nii but has been converted to uncompressed nifty for compatibility with Matlab SPM tools.
Is that really a problem?
April 11, 2019 at 4:37 pm #1805
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.
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