Dev #1
Closed
Dev #1
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
added 30 commits
August 12, 2016 14:17
/autofs/cluster/freesurfer/subjects/atlases/DKTatlas
to the atlas.acfb40.noaparc.i12.2016-08-02 tif used to
define fsaverage for V6. See reg-to-v6 in that folder
-greve
/autofs/cluster/freesurfer/subjects/atlases/christophe_atlas
to the atlas.acfb40.noaparc.i12.2016-08-02 tif used to
define fsaverage for V6. See reg-to-v6 in that folder
-greve
…generate
the ?h.aparc.annot. This atlas was generated using the registration to
folding.atlas.acfb40.noaparc.i12.2016-08-02.tif (which is what sphere.reg is
registered to in V6). This makes it consistent.
cd /autofs/cluster/freesurfer/subjects/atlases/aparc_atlas.V6
setenv SUBJECTS_DIR /autofs/cluster/freesurfer/subjects/atlases/aparc_atlas.V6
mris_ca_train -t
/average/colortable_desikan_killiany.txt
lh avgsubj.acfb40.noaparc.i12.sphere.reg aparc_edited 15_626 vc1265
vc604 16_vc660 19_vc681 20_vc700 21_vc716 vc722 23_vc740 vc747 vc764
31_vc783 18_vc792 vc799 32_vc809 33_vc876 35_vc891 vc922 34_vc1024
vc1172 vc1249 vc1289 vc1337 vc1379 24_vc1401 25_vc1420 vc1423
27_vc1425 vc1440 vc1456 vc1463 vc1465 vc1479 vc763 vc6126 vc1493 vc852
vc1474 vc803 lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs -greve
…009+aseg.mgz by adding --a2009s to the command line for this output.
…use aseg (allows backwards compatibility with 5.3 cross dirs). Added long-hippocampal-subfields help. -mreuter -zkaufman
… main subject. -eugenio
…otating volume. -rpwang
…bsequent commands were changed to access this file. The ?h.white surface is now the result of the second call to mris_make_surfaces. -greve
…aparc fix. -greve
…isting segmentation useing a mask. -fischl
…pful for tracking down the source of mislabelings. -fischl
…islabeled ventricles). -greve
… layer below after layer being deleted. color and size can be changed for cursor for inflated surface.
… layer below after layer being deleted. color and size can be changed for cursor for inflated surface.
Not sure what I'm doing here or if it is important.
Closed
htregidgo
added a commit
to htregidgo/freesurfer
that referenced
this pull request
Nov 30, 2021
htregidgo
added a commit
to htregidgo/freesurfer
that referenced
this pull request
Nov 30, 2021
Adds the flag --photo-seg to the run_samseg python script. The flag currently just disables the affine template registration as the photo volumes are missing the cerebelum and require separate registration. As the registration is disabled the photo-seg flag requires the filepath of a registered template as input. The plan is now to change the behaviour of the bias field correction when the photo-seg flag is active. This requires changing the bias field basis function generation and handling the downsampling so that there is no-downsampling in the z direction.
htregidgo
added a commit
to htregidgo/freesurfer
that referenced
this pull request
Nov 30, 2021
Adds brightness handling through bias field correction basis functions. The photo-seg flag now causes a change in the specification of the bias field basis functions so that the component vectors are full vectors of ones for the in plane directions and are vector elements of the identity in the out of plane direction. It remains to handle the downsampling so that the out of plane directions aren't adversely affected.
htregidgo
added a commit
to htregidgo/freesurfer
that referenced
this pull request
Nov 30, 2021
Modifies samsegment and estimateModelParameters to switch downsampling behaviour when photos have been specified as an input. This is achieved by skipping the out of plane resampling in estimateModelParameters and allows uniform in plane basis functions to be used.
htregidgo
added a commit
to htregidgo/freesurfer
that referenced
this pull request
Nov 30, 2021
Modifies the run_samseg script to add a flag that will bypass the affine template registration and use the one that has been provided as an accompanying input.
htregidgo
added a commit
to htregidgo/freesurfer
that referenced
this pull request
Nov 30, 2021
Modifies the samsegment file to generate bias field basis functions that are bilinear in plane and characteristic out of plane. current behaviour is to run this when the photoseg flag has been provided. redundant constant basis functions are still pressent within the code.
htregidgo
added a commit
to htregidgo/freesurfer
that referenced
this pull request
Nov 30, 2021
This commit adds a regularisation parameter for fitting the brightness bassis values when used on photos. At first a slight mistake meant that I specified too many linear basis funcions to be composed into the bilinear basis functions for the brightness field. Initially I didn't notice as I was getting quite good results, however eventually the fact that there was linear dependence between my basis functions meant that in some cases the system matrix would become singular and the segmentation would fail. The first solution we tried to this was to correctly specify the basis functions. However, this method was taking an excessive amount of time to converge. Eventually we decided to go back to the additional basis functions but add a regularisation penalty so that the system matrix didn't become singular.
yhuang43
pushed a commit
that referenced
this pull request
May 2, 2023
Update LUT with OB and hypothalamus labels
yhuang43
pushed a commit
that referenced
this pull request
May 2, 2023
OB and hypothalamus LUT updates
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.