Support for edits #591
Support for edits #591
Conversation
|
Hi, thanks for the pr. It would be great to fix the spelling errors and also add a readme for edits, which can be pretty short in the first iteration, with a 1-2 sentence description of each possible edit. |
|
Spelling should be fixed, documentation will need to be a future thing for now. |
run_fastsurfer.sh
Outdated
| @@ -220,6 +227,9 @@ SURFACE PIPELINE: | |||
| to exist already in this case. | |||
| --3T Use the 3T atlas for talairach registration (gives better | |||
| etiv estimates for 3T MR images, default: 1.5T atlas). | |||
| --edits Disable the check for existing recon-surf.sh run and enables | |||
| edits of mri/wm.mgz and brain.finalsurfs.mgz by manedit | |||
| files as well as FreeSurfer-style WM control points. | |||
There was a problem hiding this comment.
I think it is strange to have the flag --edits in the help text at multiple places. I think it should be a single help block explaining all of its effects in one location.
There was a problem hiding this comment.
I guess consolidating this into the first text makes more sense. On hindsight, I agree. I think --no_biasfield also has multiple mentions, so that should also be changed.
dkuegler
force-pushed
the
feature/edits
branch
from
ad7ed78
to
b24182b
Compare
|
This branch is currently a mess of fixes and features for 6 different things. Those need to be separated into individual branches and PRs. At a minimum, this version seems to work for longitudinal processing (still unclear for edits). |
dkuegler
force-pushed
the
feature/edits
branch
2 times, most recently
from
21f9e19
to
82cd0aa
Compare
- Adds the --edits flag - Add additional log messages for edits - Support for manedit files for asegdkt_segfile. - Also propagate asegdkt_segfile into aseg_segfile and mask_name recon_surf/recon-surf.sh - Adds the --edits flag - Add additional log messages for edits - Change check for existing run into a message instead a fail criteria in edits mode - Do not delete logfile in edits mode - Make mask and aseg_noCC required for edits mode (otherwise it might get unclear what should or was already done between run_fastsurfer and recon-surf) - Add manedit "search" for mask and aseg_nocc (the latter is recon_surf/talairach-reg.sh - Add an extra argument (new argument #3 to indicate whether talairach.reg should support edits) - Support for edits: some messages and if in edit mode, only run talairach registration if mri/transforms/talairach.xfm and mri/transforms/talairach.auto.xfm are the same (so there are no edits) -- thus edits in talairach.xfm superceed automatic results - talairch-reg.sh will now fail if mri/transforms/talairach.xfm exists, but the script is not running in edits mode (independent if talairach.auto.xfm is the same or not). recon_surf/functions.sh - add the add_file_suffix function, which adds a file suffix (for example manedits) to a file name
m-reuter
force-pushed
the
feature/edits
branch
from
82cd0aa
to
8bccee7
Compare
|
I rebased this to current dev which disentangles the edits from the other changes. Please check :
Also update your local with a hard reset. |
This PR adds support for edits in FastSurfer.
Edits are enabled by the
--editsflag forrun_fastsurfer.sh.Edits supported:
<asegdkt_segfile> via <asegdkt_segfile-w/o-ext>.manedit.
white matter segmentation (wm.mgz) via wm.manedit.mgz
white matter control points (via the standard FreeSurfer control points file)
talairach registration via mri/mri/transforms/talairach.xfm (overwriting talairach registration via mri/mri/transforms/talairach.xfm)
brain.finalsurfs.mgz via brain.finalsurfs.manedit.mgz
This PR also move the allow_root check into functions.sh and introduces run_it and run_it_cmdf function variants that are more clear wrt. argument splitting (see SC2206, SC2207 and similar).