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Re: 3dMVM error - 5 months ago
In the meantime, I've been using 3dLME (with my old AFNI binaries folder) for the analysis I would eventually like to run in 3dMVM. It is quite a large dataset - 1 between subject variable (3 groups, n = 16, 16, 28), and 3 within-subject task variables (each with two levels). I've been getting the following error message when I try to run an omnibus analysis with 3dLME: R(19088,0xac6e5a28) malby Liesel-Ann Meusel - AFNI Message Board
Re: 3dMVM error - 5 months ago
Hi Rick, I tried that but I get the same error message.by Liesel-Ann Meusel - AFNI Message Board
Re: 3dMVM error - 5 months ago
Thanks. Just to note, when I try to run 3dLME with the updated AFNI binaries, I get the same message (missing R_is.so). Everything works fine when I use my old binaries folder.by Liesel-Ann Meusel - AFNI Message Board
3dMVM error - 5 months ago
Hi AFNI people, I'm getting the following error while trying to run 3dMVM. I'm on a Mac OS 10.8.2, R version 2.15.2, and I just updated AFNI yesterday (downloaded the precompiled binaries ). ***Error: Missing R_io.so Error in if (an$type == "BRIK" && !is.na(an$view)) { : missing value where TRUE/FALSE needed Calls: process.MVM.opts -> exists.AFNI.name -> fby Liesel-Ann Meusel - AFNI Message Board
Re: ANALYZE object maps to AFNI - 10 months ago
Awesome, worked like a charm! Thanks so much, Lby Liesel-Ann Meusel - AFNI Message Board
Re: ANALYZE object maps to AFNI - 10 months ago
Thanks for the quick response. I've played around with the 3drefit command, and it definitely seems to be what I'm looking for; however, no matter what I try, I can't seem to make the orientation of the datasets line up. The original anatomical dataset that I reconstruct from DICOM to AFNI is in RSA orientation. When I transform the anatomical dataset from AFNI to ANALYZE, I use the -orientby Liesel-Ann Meusel - AFNI Message Board
ANALYZE object maps to AFNI - 10 months ago
Hello again AFNI people, I have been tasked with figuring out a way to import ROI tracings from ANALYZE into AFNI so that we can overlay them onto 3D+time datasets and extract functional information. After scanning, all of our data was reconstructed from DICOM to AFNI format. Then, for tracing, the anatomical dataset was put into ANALYZE format using 3dAFNItoANALYZE -orient LPI. In ANALYZEby Liesel-Ann Meusel - AFNI Message Board
Re: ICV and website issues - 10 months ago
No worries, thanks for looking into it, I really appreciate it! With respect to the website, I've managed to find what I needed, so not an issue anymore. Take care, Lieselby Liesel-Ann Meusel - AFNI Message Board
Re: ICV and website issues - 10 months ago
Hi Ziad, Thanks for your help. I've come across the following references that may be helpful? The first describes an automatic algorithm for segmentation of the brain and total intracranial CSF (called Exbrain v.2), whereas the second and third compare various methods of estimating ICV. The third article article also describes a method for estimating ICV with reverse MNI brain masking. 1.by Liesel-Ann Meusel - AFNI Message Board
Re: ICV and website issues - 11 months ago
Hi Ziad, Thanks for your help. I've come across the following references that may be helpful? The first describes an automatic algorithm for segmentation of the brain and total intracranial CSF (called Exbrain v.2), whereas the second and third compare various methods of estimating ICV. The third article article also describes a method for estimating ICV with reverse MNI brain masking. 1.by Liesel-Ann Meusel - AFNI Message Board
Re: ICV and website issues - 11 months ago
Great, I'll definitely play around with 3dseg. Will Ziad weigh in on this thread or should I send him something directly? Thanks again! Lieselby Liesel-Ann Meusel - AFNI Message Board
Re: ICV and website issues - 11 months ago
Hi Rick, Thanks for your reply. Yes, I'm basically looking for everything within the skull (i.e., brain volume+CSF). We are studying an older population and we want to control for premorbid brain size (i.e., before atrophy), and intra-cranial capacity seems to be the ideal way to do this. I've done some research, and it seems like many of the programs out there (i.e., Freesurfer, etc..) cby Liesel-Ann Meusel - AFNI Message Board
ICV and website issues - 11 months ago
Hello AFNI people! Two questions: First, is there a method in AFNI for calculating intracranial volume/capacity? (NOT brain volume) Also, I'm having issues accessing materials on the AFNI website (for example, any of the educational materials). It has been like this for weeks now. I'm getting the following message: Forbidden You don't have permission to access /pub/dist/edu/latest/afby Liesel-Ann Meusel - AFNI Message Board
