BrainVISA

Hi When processing the anatomical pipeline, we have the following problem with the Split Brain step: in Vip Split Brain 1 RuntimeError: System command exited with non null value : 111 In the log, we found the following information: erosion of size 4.000000 mm dist: 4.0 cc(16928) highest point: x:83,...

Thanks anyway...

Hi,

Which options should I use in VipHistoAnalysis in order to obtain the mean and standard-deviation of CSF, in addition to those of GM and WM?

Many thanks,
Olivier

PS: I put this question in this forum even though it is not a Aims command. Please let me know if I should post it elsewhere.

Thanks a lot.

Hi,

Is there a process or command-line in BV that computes the intracranial volume?

There is a "Brainvolume" process but the CSF segmentation does not seem to include all of the outer CSF (which I guess is not distinguishable from skull based on T1 only)

Thanks
Olivier

Thanks a lot!

I will delete the .minf files before calling NmrSNR.
Just out of curiosity, is there a tool that would automatically convert an AIMS-readable ".minf" to a NMR-readable one?

Olivier

You can use AimsLinearComb (with -a 1 -c -1).

Yes, NmrSNR is in my package and this is exactly what I need. Thanks! Just two last questions/remarks: 1) When giving the ROI as a mask, I guess that the mean of the signal is computed on the mask and the SD of the noise is computed on the complementary of the mask. Is it possible to compute the sig...

Hi, I am having difficulties using AimsSNR command line. As far as I understand, I guess that one has to provide a ROI in which the standard deviation of the noise will be estimated. It seems that this ROI can be provided either as a sphere (coordinates x,y,z and radius) or as a binary volume. But I...

Hi, Just to mention that I also have a problem when importing under Windows. However the error message is a bit different: ncopen: filename "D:UsersColliotTransferttrashBERg_tal.mnc": No such file or directory miopen: MINC package entry point DcmElement: Unknown Tag & Data(0000,0a00) l...

Hi,

I may be wrong, but I think in some anatomist version, if the "save" panel window is over the image, some part of the output JPEG will be missing.
Have you tried dragging the "save" window so that it does not overlap with the "image" window ?

Olivier

I downloaded the new source of cartodata.

Everything now seems to work fine.

Thanks a lot !
Olivier

Concerning the missing libaimsminc.so (with the previous development version, not the one you uploaded yesterday) I think I found the problem. In this previous version, there was no directory bundle_aimsminc under aimsdata/src So I just copied this directory from the new version of the package and ...

Concerning the cartobase package: Thanks a lot uploading the new version. The link that previously failed now succeeds. However, there is another problem further in the compilation, in cartodata: c++ -c -g -Wall -W -D_REENTRANT -dynamic -DCARTO_DEBUGMODE=\"debug\" -DCARTO_DEBUG=1 -I/Appli...

Thanks a lot Denis. It helps. I decided to conform to the binary distrib and it seems to work, except that it still does not find the minc plugin (even though it finds the jpeg plugin). I have the impression that it is related to a .so vs .dylib issue. It seems that I have a .dylib library for each ...