BrainVISA

My turn to say sorry for the delay! I am now leaving this project (it was just a summer project for me), but want to say thanks a lot for all the support! Possibly new members on the project could post here in the future, seeking support. As to the problem: I didn't realize VBM was a separate toolbo...

Hello,

Can you please comment on this?

Thank you!

I open this process, select the subject from the BV database (already imported the .nii file for the subject), select the parameters, then click run. The window says the script finished running in about 14 seconds. In the BV database under the subject, the following new directories and files are cre...

Thanks for the reply Riviere. I think I understand now. I was able to select the [...] button in the Morphologist iterate menu for sulci recognition and add "true", which then automatically selected sulci recognition for each subject. But for Import T1 MRI iterate menu, I could never get D...

I've used the "iterate" functionality on two tools now, the Import T1 MRI and the Morphologist 2015 (non-UI) pipeline itself. They work great! These will be great for running 100+ scans automated. However, it would be nice if there was a way to set options globally for the whole set of ite...

Everything seemed to work, when I looked at the scans in the Anatomist viewers from BV "viewers" menu. I guess I will ignore the two issues I posted above, unless you have any suggestion. Now to figure out how to have the Morphologist pipeline run on 100 subjects automatically for 150hrs s...

Hello again, Morphologist pipeline worked using glibc 2.6 (Mandriva 2008) version on my computer running Ubuntu 16.04 . The process finished overall in about 1hour 20mins. Issues? 1) No MATLAB crash this time, but the same overall issue with normalization. Runs first time, skip unselected Reorient A...

Hi Everyone, The resident got me a 512x512x192 MRI scan (T1 MPRAGE). Now the Morphologist pipeline worked much better, but: 1. right at the start of "Trying 1st pass of normalization...", it crashed. Then "Killed", then RuntimeError: "in Anatomy Normalization (using SPM) 1 S...

Yann,

That's great! I will try that version on Wed and report back the results here.

Also, I will try to use an appropriate MRI scan by that time with correct 3D resolution! (this is in reference to the replies from Riviere on my other thread "Morphologist (pipline) fails")

Hello D.R., Thanks for the reply. By the way, I know you must be very busy! So it's really a great service when you have the time to help. **It could entirely be the case that I'm using an inappropriate MRI scan. It's a T1 Axial scan, so there are only 24 "slices" in that direction, with t...

I could not get the crash window to come back, even though I followed the steps for forcing Apport to work. I did try to comment out the two libraries suggested in post #4 by Riviere. The T1 Bias Correction process worked! Although there was an error reported: ------------------------------ !! VIP E...

Hi! Sorry I didn't see this thread before I posted my own thread "Morphologist (pipeline) fails". I have the exact same errors shown in my log file (Ctrl-L), as those shown in post #1 here. - AC/PC Or Normalization process succeeds - T1 Bias Correction process fails I'm also using Ubuntu 1...

Hello, Update: I was able to get both SPM8 and SPM12 standalone versions to work on my system. (aside: a required package 'libxp6' for Ubuntu is no longer available from version 15.10 onward. So, you can download the 15.04 .deb package here: http://www.ubuntuupdates.org/package/core/vivid/main/base/...

One last thing, I also downloaded the Matlab version of spm8. It gives the same result of spm12: failed at the T1 bias correction step of Morphologist (while image normalization works). In both cases, BrainVISA output to terminal says: " Exception in run_spm.runSpm8Standalone: SPM8 standalone i...

Hi riviere, I double checked again this morning in BrainVISA->Preferences->SPM: spm12_path = /home/[user]/spm12 spm8_path = /home/[user]/spm12 spm5_path = /home/[user]/spm12 If I delete all except spm12_path, then even the first task on non-UI Morphologist ('image nomalization') will fail! The termi...