Hi, I have been trying but I only get errors,
something I’m missing or maybe I’m distracted.
Currently, I’m in Ubuntu Maverick, I have converted my 120 axial T1w MR
DICOM images into NIFTI and then into MNC
with nii2mnc. I have checked the
following componentes in Ubuntu: libminc-dev, libminc2-1, libmni-perllib-perl
I have been trying to run T1 demos without
success and then
I have tried with niak_brick_nu_correct (because I have seen in
niak_brick_t1_preprocess.m that is the first of the 10 scrips for he flowchart
of the brick). Do I have to follow the 10 steps for segmenting the brain or
is there a fast way?
I attach a document with my errors, please
could you help me
to solve them?
Thanks very much
Sorry for the late reply. You certainly made the right move by going for an Ubuntu virtual machine. Looking at the error message you get, it seems like the system cannot find the nu_correct command. There may be two reasons for that. The most likely is that you installed only the "minctools" package. I realized that the installation section of the wiki was not explicit enough regarding the list of required minc packages, which goes beyond the core minc tools. I updated this section, you can have a look here :
If it is available for your version of ubuntu, just install the mincbundle package that includes every single minc package. The tutorial can be found here :
The other possibility is that you installed all of the tools, but somehow there are not found by default of your system. That happens sometimes, even thought the mincbundle package would be supposed to take care of that for you. Here is a tutorial on how to change your .bashrc file to add the minc tools :
When you're done with that, just go in the folder where you have a MINC volume and try in a bash :
nu_correct -distance 200 my_vol.mnc my_vol_nu.mnc
This should run a non-uniformity correction on my_vol.mnc and generate the results in my_vol_nu.mnc. If not then there is something wrong with the installation. In this case please post more details regarding the installation steps you followed.
Good luck with getting the software to work. The MINC community is currently putting efforts into simplifying the installation documentation and procedure, but there is still much room for imporvement. Your feedback is very much appreciated.
Hi, thank you for
previous message, it solved my problems. I
installed mincbundle, then I had to modify the paths and I had
problems with the files' permissions too but now it works. I have tried
only with niak_brick_nu_correct and then with
niak_brick_mask_brain_t1, with the default parameters, but my results
I attach a screenshot
of some slices (the
important ones for me are the axial ones).One question: for a not
very accurate (but better than current segmentation) can I just use
nu_correct and mask_brain_t1 and forget the stereotactic
coregistration etc? In this case, do you think I only have to modify
the parameters in opt for mask_brain_t1?
Thank you very
>> [hdr,vol] = niak_read_vol('file_anat.mnc');
>> vol(vol>1000) = 1000;
>> hdr.file_name = 'file_anat_clipped.mnc';
where the value 1000 is an example and needs to be determined based on the histogram. The changes I mentioned above will involve some automated clipping. If you would be willing to share one problematic brain, please email me and I'll have a look. I am very interested in collecting those "hard" brains to test further updates of the brain segmentation/coregistration tools.
Best regards and thank you for your help,