[RTM] RF: Use N4BiasFieldCorrection(copy_header=True) #542
Conversation
| @@ -75,7 +75,7 @@ def _pick1st(inlist): | |||
| magmrg = pe.Node(IntraModalMerge(), name='magmrg') | |||
|
|
|||
| # de-gradient the fields ("bias/illumination artifact") | |||
| n4 = pe.Node(ants.N4BiasFieldCorrection(dimension=3), name='n4') | |||
| n4 = pe.Node(ants.N4BiasFieldCorrection(dimension=3, copy_header=True), name='n4') | |||
There was a problem hiding this comment.
Note that this wasn't using init_n4bias_wf already. If there's a good reason for not copying the header, let me know and I'll revert this.
|
This is failing a 4GB memory limit. (Memory usage) I'm not sure why this would newly be an issue. Could be the type of the bias-corrected image (which is now restored to that of the input T1w image). Should I re-run, or is there something obvious to fix up? |
|
This is very weird. Additionally, the process crashing is antsRegistration, not the bias correction. |
|
Let's try running first.
…On May 30, 2017 11:55 AM, "Chris Markiewicz" ***@***.***> wrote:
This is failing a 4GB memory limit. (Memory usage
<https://457-78558509-gh.circle-artifacts.com/0/tmp/memory-usage.txt>)
I'm not sure why this would newly be an issue. Could be the type of the
bias-corrected image (which is now restored to that of the input T1w
image). Should I re-run, or is there something obvious to fix up?
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
<#542 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AAOkp6livY4wdpT7lfAKxTN9fFhLORe9ks5r_GYlgaJpZM4NqgCb>
.
|
effigies
changed the title
|
Rerunning. Also, there's a workflow in niworkflows that should be updated along with this batch. Blocking merge for nipreps/niworkflows#173. |
|
That one worked. Updating pins and rebasing for a final test. |
effigies
force-pushed
the
rf/n4bias_interface
branch
from
820a079 to
05c1798
Compare
effigies
changed the title
| @@ -81,7 +81,7 @@ def init_anat_preproc_wf(skull_strip_ants, output_spaces, template, debug, frees | |||
| RobustMNINormalizationRPT( | |||
| generate_report=True, | |||
| num_threads=omp_nthreads, | |||
| testing=debug, | |||
| flavor='testing' if debug else 'precise', | |||
There was a problem hiding this comment.
@oesteban I believe this is the 0.0.7+ equivalent?
Taking advantage of nipy/nipype#2034 to simplify workflows slightly.