Closed raihaan closed 9 years ago
What module do you load for N4BiasFieldCorrection
minc-toolkit
Perhaps this features is in minc-toolkit 1.9.2, this build is in progress.
Ok, I will give it a test when that is complete
What is your module configuration on scinet?
Turns out I was running N4BiasFieldCorrection on scinet off of Matt's own custom ants bin as opposed to one of our modules. Requires further investigation as to where it exactly came from.
For now, those running N4 correction can either do so on scinet, or locally using minc-toolkit/1.0.01 N4BiasFieldCorrection 3 -b [200] -c [100x100x100x100,0.0000000001] -i input.nii -o output.nii
Have you asked Matt where it came from?
Have you figured out where the "different" version from Matt came from?
Hi guys, I actually got this error, so it's good to know.
I'm using Matt's version for the N4 correction because it works best, but I will give a try the other one you mention here.
Thanks
Ed
By the way, this is Matt's version in case you don't have it:
usage: register input.mnc output.mnc
input=$1 output=$2
tmp=/tmp/N4minc_$$ mkdir $tmp
mnc2nii -signed -short $input $tmp/input.nii N4BiasFieldCorrection -d 3 -b [200] -c [100x100x100x100,0.0000000001] -i $tmp/input.nii -o $tmp/output$ nii2mnc $tmp/output.nii $output
rm -r $tmp
See minc-bpipe-toolkit for a implementation more similar to how the MNI runs N3.
I think I've figured out how to get bpipe working on scinet, implementation details as soon as I test it out.
Awesome, thanks.
bpipe is going to be sweet when it works.
Well..it does work. Just not on scinet yet. :-) On Apr 29, 2015 10:59 PM, "Eduardo Garza" notifications@github.com wrote:
Awesome, thanks.
bpipe is going to be sweet when it works.
— Reply to this email directly or view it on GitHub https://github.com/CobraLab/quarantine/issues/2#issuecomment-97644498.
I'm sure we will all be swimming in bpipe soon
El Wednesday, April 29, 2015, Gabriel A. Devenyi notifications@github.com escribió:
Well..it does work. Just not on scinet yet. :-) On Apr 29, 2015 10:59 PM, "Eduardo Garza" <notifications@github.com javascript:_e(%7B%7D,'cvml','notifications@github.com');> wrote:
Awesome, thanks.
bpipe is going to be sweet when it works.
— Reply to this email directly or view it on GitHub https://github.com/CobraLab/quarantine/issues/2#issuecomment-97644498.
— Reply to this email directly or view it on GitHub https://github.com/CobraLab/quarantine/issues/2#issuecomment-97659778.
Eduardo A. Garza Villarreal, M.D., Ph.D.
the command N4BiasFieldCorrection currently functions differently on scinet than it does locally.
On scinet (: N4BiasFieldCorrection -d 3 -b [200] -c [100x100x100x100,0.0000000001] -i $tmp/input.nii -o $tmp/output.nii
Locally: the script only functions without the "-d" option,
patrai@cicws25:/data/chamal/projects/raihaan/defaced$ N4BiasFieldCorrection -d 3 -b [200] -c [100x100x100x100,0.0000000001] -i test.nii -o n4test.nii Unsupported dimension
without -2, patrai@cicws25:/data/chamal/projects/raihaan/defaced$ N4BiasFieldCorrection 3 -b [200] -c [100x100x100x100,0.0000000001] -i test.nii -o n4test.nii Mask not read. Creating Otsu mask. Current level = 1 Iteration 1 (of 100). Current convergence value = 0.000867379 (threshold = 1e-10) ... .,.. running running
bit of googling suggests this may mean we have an old version of the N4BiasFieldCorrection script http://ehc.ac/p/advants/discussion/840261/thread/8145343e/