From f2b847de4796c13195b78a40f51796eb55dd99b3 Mon Sep 17 00:00:00 2001 From: David Meunier Date: Wed, 28 May 2025 16:41:34 +0200 Subject: [PATCH 01/15] -skull option --- docs/command.rst | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/docs/command.rst b/docs/command.rst index 8992554e..77af2a23 100644 --- a/docs/command.rst +++ b/docs/command.rst @@ -74,7 +74,8 @@ mandatory parameters * ``_4animal`` : will use bet4animal (FSL) for brain extraction, for faster computation (by default atlas_brex is used) * ``_quick`` : will use hd-bet (Deep Learning) for brain extraction, for faster computation (by default atlas_brex is used) - **NB: ** hd-bet requires a specific version of macapype/skullTo3d, not available by default + +**NB:** hd-bet requires a specific version of macapype/skullTo3d, not available by default This option should be used if the coregistration to template in preparation is not performed correctly: @@ -87,7 +88,11 @@ mandatory parameters * ``_noseg`` (at the end) will perform data preparation and brain extraction (no segmentation) **Some options are specific to skullTo3d:** - * ``_skull`` after SPM or ANTS if you want to process skull or angio *specific to skullTo3d*; otherwise the main pipelines of macapype will be launched (only brain segmentation will be performed) **NB : ** ``_skullnoisypetra`` instead of ``_skull`` available for macaque with issues on petra + * ``_skull`` after SPM or ANTS if you want to process skull or angio *specific to skullTo3d*; otherwise the main pipelines of macapype will be launched (only brain segmentation will be performed) + +**NB :** ``_skullnoisypetra`` instead of ``_skull`` available for macaque with issues on petra +**NB :** ``-soft skull`` without processing brain is possible, but is still experimental. It only works if ``-skull_dt CT petra`` and -deriv -padback are NOT defined + * ``_noskullmask`` (at the end) will perform realignement to stereo and headmask (only realignement for CT) * ``_noheadmask`` (at the end) will perform only realignement to stereo From 555cbe2217b8881adc0b4962d6beb5f346730edf Mon Sep 17 00:00:00 2001 From: David Meunier Date: Wed, 28 May 2025 16:46:52 +0200 Subject: [PATCH 02/15] NB --- docs/command.rst | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/docs/command.rst b/docs/command.rst index 77af2a23..db4820d2 100644 --- a/docs/command.rst +++ b/docs/command.rst @@ -75,7 +75,7 @@ mandatory parameters * ``_4animal`` : will use bet4animal (FSL) for brain extraction, for faster computation (by default atlas_brex is used) * ``_quick`` : will use hd-bet (Deep Learning) for brain extraction, for faster computation (by default atlas_brex is used) -**NB:** hd-bet requires a specific version of macapype/skullTo3d, not available by default + **NB:** hd-bet requires a specific version of macapype/skullTo3d, not available by default This option should be used if the coregistration to template in preparation is not performed correctly: @@ -88,10 +88,12 @@ mandatory parameters * ``_noseg`` (at the end) will perform data preparation and brain extraction (no segmentation) **Some options are specific to skullTo3d:** + * ``_skull`` after SPM or ANTS if you want to process skull or angio *specific to skullTo3d*; otherwise the main pipelines of macapype will be launched (only brain segmentation will be performed) -**NB :** ``_skullnoisypetra`` instead of ``_skull`` available for macaque with issues on petra -**NB :** ``-soft skull`` without processing brain is possible, but is still experimental. It only works if ``-skull_dt CT petra`` and -deriv -padback are NOT defined + **NB :** ``_skullnoisypetra`` instead of ``_skull`` available for macaque with issues on petra + + **NB :** ``-soft skull`` without processing brain is possible, but is still experimental. It only works if ``-skull_dt CT petra`` and -deriv -padback are NOT defined * ``_noskullmask`` (at the end) will perform realignement to stereo and headmask (only realignement for CT) * ``_noheadmask`` (at the end) will perform only realignement to stereo From cf0f16e150eb602f880544af63a610279be3c0af Mon Sep 17 00:00:00 2001 From: David Meunier Date: Wed, 28 May 2025 16:52:47 +0200 Subject: [PATCH 03/15] `` --- docs/command.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/command.rst b/docs/command.rst index db4820d2..4c8a472d 100644 --- a/docs/command.rst +++ b/docs/command.rst @@ -93,7 +93,7 @@ mandatory parameters **NB :** ``_skullnoisypetra`` instead of ``_skull`` available for macaque with issues on petra - **NB :** ``-soft skull`` without processing brain is possible, but is still experimental. It only works if ``-skull_dt CT petra`` and -deriv -padback are NOT defined + **NB :** ``-soft skull`` without processing brain is possible, but is still experimental. It only works if ``-skull_dt CT petra`` and ``-deriv`` and ``-padback`` are NOT defined * ``_noskullmask`` (at the end) will perform realignement to stereo and headmask (only realignement for CT) * ``_noheadmask`` (at the end) will perform only realignement to stereo From e5f807c71201300e9ed1d6d40ec3020b5f2131c3 Mon Sep 17 00:00:00 2001 From: David Meunier Date: Wed, 28 May 2025 17:13:33 +0200 Subject: [PATCH 04/15] | --- docs/command.rst | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/docs/command.rst b/docs/command.rst index 4c8a472d..2b12162b 100644 --- a/docs/command.rst +++ b/docs/command.rst @@ -77,16 +77,22 @@ mandatory parameters **NB:** hd-bet requires a specific version of macapype/skullTo3d, not available by default +| + This option should be used if the coregistration to template in preparation is not performed correctly: * ``_robustreg`` (at the end) to have a more robust registration (in two steps) +| + Finally, these option are available (to place after SPM or ANTS) and will modify the parameters but can be launched in sequence: * ``_test`` : (at the end) to check if the full pipeline is coherent (will only generate the graph.dot and graph.png) * ``_prep`` (at the end) will perform data preparation (no brain extraction and segmentation) * ``_noseg`` (at the end) will perform data preparation and brain extraction (no segmentation) +| + **Some options are specific to skullTo3d:** * ``_skull`` after SPM or ANTS if you want to process skull or angio *specific to skullTo3d*; otherwise the main pipelines of macapype will be launched (only brain segmentation will be performed) From 9524aa781cb3f8e033f76c432976e82d19bd3e89 Mon Sep 17 00:00:00 2001 From: David Meunier Date: Wed, 10 Dec 2025 10:30:08 +0100 Subject: [PATCH 05/15] Tips and tricks --- docs/index.rst | 3 +++ docs/tips_tricks.rst | 44 ++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 47 insertions(+) create mode 100644 docs/tips_tricks.rst diff --git a/docs/index.rst b/docs/index.rst index 7781d307..c6c22021 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -43,6 +43,8 @@ See :ref:`Commands ` for a description on the avalaible command paramet If ``-deriv``` is provided, see :ref:`Derivatives ` for a descrition of the outputs +Also, check `Tips and Tricks ` on how to format images to improve quality of registration between images and segmentation + Table of contents ****************** @@ -57,6 +59,7 @@ Table of contents derivatives params indiv_params + tips_tricks diff --git a/docs/tips_tricks.rst b/docs/tips_tricks.rst new file mode 100644 index 00000000..7d8fded8 --- /dev/null +++ b/docs/tips_tricks.rst @@ -0,0 +1,44 @@ +.. _tips_tricks: + +Tips and tricks +*************** + +CT images registration to MRI (be it T1w or T2w) can be somehow tricky. + +Here a few tricks: + +Reorientation can help +###################### + +The -orient LPS corresponds to the direction where the increasing numbers are pointing at (typically RAS in radiological convention) and take the opposite directions (special AFNI...). + +If you want to exchange to axis, change "target" letters accordingly +RPI -> RIP + +If you want to revert one dimension, be careful to modify another axis: +RPI -> RPS becomes LPS to exchange I by S, and good R-L dimension as well + +.. code:: bash + + $ 3drefit -orient LPS sub-Phoenix_ses-01_acq-CT_T2star.nii.gz + +Possibly followed by + +.. code:: bash + + $ fslreorient2std sub-Phoenix_ses-01_acq-CT_T2star.nii.gz sub-Phoenix_ses-01_acq-CT_T2star_reorient.nii.gz + + +Cropping (both T1w et T2w) can help +################################### + +Include the full head for the CT image + +Be careful with Left-Right orientation +###################################### + +Most of the images in our center are acquired in the right direction, but with an encoding matching inverse Left-Right Encoding to the one that is coming out of the MRI + +.. code:: bash + + $ 3drefit -orient LPI sub-Rusty/ses-01/anat/sub-Rusty_ses-01_acq-CT_run-02_T2star.nii.gz From 79b1a60c0efaae3907e2e12c61c48e5089f3cebd Mon Sep 17 00:00:00 2001 From: David Meunier Date: Wed, 10 Dec 2025 10:38:18 +0100 Subject: [PATCH 06/15] ref --- docs/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/index.rst b/docs/index.rst index c6c22021..006acdbb 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -43,7 +43,7 @@ See :ref:`Commands ` for a description on the avalaible command paramet If ``-deriv``` is provided, see :ref:`Derivatives ` for a descrition of the outputs -Also, check `Tips and Tricks ` on how to format images to improve quality of registration between images and segmentation +Also, check :ref:`Tips and Tricks ` on how to format images to improve quality of registration between images and segmentation Table of contents From 83889f09c53fd3b78871833240a1b6be7b7c68f5 Mon Sep 17 00:00:00 2001 From: David Meunier Date: Wed, 10 Dec 2025 10:41:19 +0100 Subject: [PATCH 07/15] ___ --- docs/.indiv_params.rst.kate-swp | Bin 0 -> 77 bytes docs/tips_tricks.rst | 4 +++- 2 files changed, 3 insertions(+), 1 deletion(-) create mode 100644 docs/.indiv_params.rst.kate-swp diff --git a/docs/.indiv_params.rst.kate-swp b/docs/.indiv_params.rst.kate-swp new file mode 100644 index 0000000000000000000000000000000000000000..0dfe6e8dc7a6d7dcefa5bdd06c0860a77c8895e0 GIT binary patch literal 77 zcmZQzU=Z?7EJ;-eE>A2_aLdd|RWQ;sU|?VniR3wVbB^Upt&q<%q~_nctg~9hVn%Qf TP=*;K3&f(X!JbH5#&}l%Jtq<= literal 0 HcmV?d00001 diff --git a/docs/tips_tricks.rst b/docs/tips_tricks.rst index 7d8fded8..a94c02d9 100644 --- a/docs/tips_tricks.rst +++ b/docs/tips_tricks.rst @@ -1,7 +1,9 @@ +:orphan: + .. _tips_tricks: Tips and tricks -*************** +_______________ CT images registration to MRI (be it T1w or T2w) can be somehow tricky. From 9823a9a03f1b5df4c8d64220599ba48e6f406b50 Mon Sep 17 00:00:00 2001 From: David Meunier Date: Wed, 10 Dec 2025 10:55:38 +0100 Subject: [PATCH 08/15] -skull option # Conflicts: # docs/command.rst --- docs/command.rst | 13 +++---------- 1 file changed, 3 insertions(+), 10 deletions(-) diff --git a/docs/command.rst b/docs/command.rst index 2b12162b..c30c3b65 100644 --- a/docs/command.rst +++ b/docs/command.rst @@ -75,9 +75,7 @@ mandatory parameters * ``_4animal`` : will use bet4animal (FSL) for brain extraction, for faster computation (by default atlas_brex is used) * ``_quick`` : will use hd-bet (Deep Learning) for brain extraction, for faster computation (by default atlas_brex is used) - **NB:** hd-bet requires a specific version of macapype/skullTo3d, not available by default - -| +**NB:** hd-bet requires a specific version of macapype/skullTo3d, not available by default This option should be used if the coregistration to template in preparation is not performed correctly: @@ -91,15 +89,10 @@ mandatory parameters * ``_prep`` (at the end) will perform data preparation (no brain extraction and segmentation) * ``_noseg`` (at the end) will perform data preparation and brain extraction (no segmentation) -| - - **Some options are specific to skullTo3d:** - * ``_skull`` after SPM or ANTS if you want to process skull or angio *specific to skullTo3d*; otherwise the main pipelines of macapype will be launched (only brain segmentation will be performed) - **NB :** ``_skullnoisypetra`` instead of ``_skull`` available for macaque with issues on petra - - **NB :** ``-soft skull`` without processing brain is possible, but is still experimental. It only works if ``-skull_dt CT petra`` and ``-deriv`` and ``-padback`` are NOT defined +**NB :** ``_skullnoisypetra`` instead of ``_skull`` available for macaque with issues on petra +**NB :** ``-soft skull`` without processing brain is possible, but is still experimental. It only works if ``-skull_dt CT petra`` and -deriv -padback are NOT defined * ``_noskullmask`` (at the end) will perform realignement to stereo and headmask (only realignement for CT) * ``_noheadmask`` (at the end) will perform only realignement to stereo From 4856a05f4efe46a7dcd78fc23340e67e8793088a Mon Sep 17 00:00:00 2001 From: David Meunier Date: Wed, 10 Dec 2025 11:02:27 +0100 Subject: [PATCH 09/15] indent NB --- docs/command.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/command.rst b/docs/command.rst index c30c3b65..a23574b5 100644 --- a/docs/command.rst +++ b/docs/command.rst @@ -75,7 +75,7 @@ mandatory parameters * ``_4animal`` : will use bet4animal (FSL) for brain extraction, for faster computation (by default atlas_brex is used) * ``_quick`` : will use hd-bet (Deep Learning) for brain extraction, for faster computation (by default atlas_brex is used) -**NB:** hd-bet requires a specific version of macapype/skullTo3d, not available by default + **NB:** hd-bet requires a specific version of macapype/skullTo3d, not available by default This option should be used if the coregistration to template in preparation is not performed correctly: From 1fa041ce03eb110c2fcb1314523e178252c3dd3e Mon Sep 17 00:00:00 2001 From: David Meunier Date: Wed, 10 Dec 2025 11:05:15 +0100 Subject: [PATCH 10/15] no indent --- docs/command.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/command.rst b/docs/command.rst index a23574b5..c30c3b65 100644 --- a/docs/command.rst +++ b/docs/command.rst @@ -75,7 +75,7 @@ mandatory parameters * ``_4animal`` : will use bet4animal (FSL) for brain extraction, for faster computation (by default atlas_brex is used) * ``_quick`` : will use hd-bet (Deep Learning) for brain extraction, for faster computation (by default atlas_brex is used) - **NB:** hd-bet requires a specific version of macapype/skullTo3d, not available by default +**NB:** hd-bet requires a specific version of macapype/skullTo3d, not available by default This option should be used if the coregistration to template in preparation is not performed correctly: From cb21cc064593fedb0566ac19c51d540ed0925d33 Mon Sep 17 00:00:00 2001 From: David Meunier Date: Wed, 10 Dec 2025 11:12:53 +0100 Subject: [PATCH 11/15] indent --- docs/command.rst | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/docs/command.rst b/docs/command.rst index c30c3b65..8d251382 100644 --- a/docs/command.rst +++ b/docs/command.rst @@ -88,11 +88,10 @@ mandatory parameters * ``_test`` : (at the end) to check if the full pipeline is coherent (will only generate the graph.dot and graph.png) * ``_prep`` (at the end) will perform data preparation (no brain extraction and segmentation) * ``_noseg`` (at the end) will perform data preparation and brain extraction (no segmentation) - * ``_skull`` after SPM or ANTS if you want to process skull or angio *specific to skullTo3d*; otherwise the main pipelines of macapype will be launched (only brain segmentation will be performed) -**NB :** ``_skullnoisypetra`` instead of ``_skull`` available for macaque with issues on petra -**NB :** ``-soft skull`` without processing brain is possible, but is still experimental. It only works if ``-skull_dt CT petra`` and -deriv -padback are NOT defined + **NB :** ``_skullnoisypetra`` instead of ``_skull`` available for macaque with issues on petra + **NB :** ``-soft skull`` without processing brain is possible, but is still experimental. It only works if ``-skull_dt CT petra`` and -deriv -padback are NOT defined * ``_noskullmask`` (at the end) will perform realignement to stereo and headmask (only realignement for CT) * ``_noheadmask`` (at the end) will perform only realignement to stereo From 737998aaa139d211b9e15d2e7e095753629c8616 Mon Sep 17 00:00:00 2001 From: David Meunier Date: Wed, 10 Dec 2025 11:16:41 +0100 Subject: [PATCH 12/15] simplified indent --- docs/command.rst | 18 +++--------------- 1 file changed, 3 insertions(+), 15 deletions(-) diff --git a/docs/command.rst b/docs/command.rst index 8d251382..ce12bc95 100644 --- a/docs/command.rst +++ b/docs/command.rst @@ -73,30 +73,18 @@ mandatory parameters For ``-soft`` value, it is possible to add some key words (e.g. ``-soft ANTS_robustreg_prep``) all these options are available (to place after SPM or ANTS, e.g) and will change the brain extraction: * ``_4animal`` : will use bet4animal (FSL) for brain extraction, for faster computation (by default atlas_brex is used) - * ``_quick`` : will use hd-bet (Deep Learning) for brain extraction, for faster computation (by default atlas_brex is used) - -**NB:** hd-bet requires a specific version of macapype/skullTo3d, not available by default - - This option should be used if the coregistration to template in preparation is not performed correctly: - - * ``_robustreg`` (at the end) to have a more robust registration (in two steps) - -| + * ``_quick`` : will use hd-bet (Deep Learning) for brain extraction, for faster computation (by default atlas_brex is used) **NB:** hd-bet requires a specific version of macapype/skullTo3d, not available by default + * ``_robustreg`` (at the end) to have a more robust registration (in two steps) . This option should be used if the coregistration to template in preparation is not performed correctly Finally, these option are available (to place after SPM or ANTS) and will modify the parameters but can be launched in sequence: * ``_test`` : (at the end) to check if the full pipeline is coherent (will only generate the graph.dot and graph.png) * ``_prep`` (at the end) will perform data preparation (no brain extraction and segmentation) * ``_noseg`` (at the end) will perform data preparation and brain extraction (no segmentation) - * ``_skull`` after SPM or ANTS if you want to process skull or angio *specific to skullTo3d*; otherwise the main pipelines of macapype will be launched (only brain segmentation will be performed) - - **NB :** ``_skullnoisypetra`` instead of ``_skull`` available for macaque with issues on petra - **NB :** ``-soft skull`` without processing brain is possible, but is still experimental. It only works if ``-skull_dt CT petra`` and -deriv -padback are NOT defined - + * ``_skull`` after SPM or ANTS if you want to process skull or angio *specific to skullTo3d*; otherwise the main pipelines of macapype will be launched (only brain segmentation will be performed) **NB :** ``_skullnoisypetra`` instead of ``_skull`` available for macaque with issues on petra **NB :** ``-soft skull`` without processing brain is possible, but is still experimental. It only works if ``-skull_dt CT petra`` and -deriv -padback are NOT defined * ``_noskullmask`` (at the end) will perform realignement to stereo and headmask (only realignement for CT) * ``_noheadmask`` (at the end) will perform only realignement to stereo - -------------------- exclusive parameters -------------------- From b86332c9f12c8f36052abef2acb01885acf164df Mon Sep 17 00:00:00 2001 From: David Meunier Date: Wed, 10 Dec 2025 11:21:54 +0100 Subject: [PATCH 13/15] all bold --- docs/command.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/command.rst b/docs/command.rst index ce12bc95..f0fc61de 100644 --- a/docs/command.rst +++ b/docs/command.rst @@ -73,7 +73,7 @@ mandatory parameters For ``-soft`` value, it is possible to add some key words (e.g. ``-soft ANTS_robustreg_prep``) all these options are available (to place after SPM or ANTS, e.g) and will change the brain extraction: * ``_4animal`` : will use bet4animal (FSL) for brain extraction, for faster computation (by default atlas_brex is used) - * ``_quick`` : will use hd-bet (Deep Learning) for brain extraction, for faster computation (by default atlas_brex is used) **NB:** hd-bet requires a specific version of macapype/skullTo3d, not available by default + * ``_quick`` : will use hd-bet (Deep Learning) for brain extraction, for faster computation (by default atlas_brex is used) **NB: hd-bet requires a specific version of macapype/skullTo3d, not available by default** * ``_robustreg`` (at the end) to have a more robust registration (in two steps) . This option should be used if the coregistration to template in preparation is not performed correctly Finally, these option are available (to place after SPM or ANTS) and will modify the parameters but can be launched in sequence: @@ -81,7 +81,7 @@ mandatory parameters * ``_test`` : (at the end) to check if the full pipeline is coherent (will only generate the graph.dot and graph.png) * ``_prep`` (at the end) will perform data preparation (no brain extraction and segmentation) * ``_noseg`` (at the end) will perform data preparation and brain extraction (no segmentation) - * ``_skull`` after SPM or ANTS if you want to process skull or angio *specific to skullTo3d*; otherwise the main pipelines of macapype will be launched (only brain segmentation will be performed) **NB :** ``_skullnoisypetra`` instead of ``_skull`` available for macaque with issues on petra **NB :** ``-soft skull`` without processing brain is possible, but is still experimental. It only works if ``-skull_dt CT petra`` and -deriv -padback are NOT defined + * ``_skull`` after SPM or ANTS if you want to process skull or angio *specific to skullTo3d*; otherwise the main pipelines of macapype will be launched (only brain segmentation will be performed) **NB: ``_skullnoisypetra`` instead of ``_skull`` available for macaque with issues on petra NB: ``-soft skull`` without processing brain is possible, but is still experimental. It only works if ``-skull_dt CT petra`` and -deriv -padback are NOT defined** * ``_noskullmask`` (at the end) will perform realignement to stereo and headmask (only realignement for CT) * ``_noheadmask`` (at the end) will perform only realignement to stereo @@ -93,8 +93,8 @@ exclusive parameters * ``-params`` : *(mandatory if -species is omitted)* a json file specifiying the global parameters of the analysis. See :ref:`Parameters ` for more details * ``-species`` : *(mandatory if -params is omitted)* followed the NHP species corresponding to the image, e.g. {macaque | marmo } -**NB** marmoT2 can be used for segmenting from the T2w image (by default, T1w is used for marmo) -**NB** macaque_0p5 is available to use downsampled template (faster results) +**NB:** marmoT2 can be used for segmenting from the T2w image (by default, T1w is used for marmo) +**NB:** macaque_0p5 is available to use downsampled template (faster results) ------------------- optional parameters From 0f56ac5b9a3c7c233a33755c1af3cd9baaf0bc3e Mon Sep 17 00:00:00 2001 From: David Meunier Date: Wed, 10 Dec 2025 11:24:21 +0100 Subject: [PATCH 14/15] NB --- docs/command.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/command.rst b/docs/command.rst index f0fc61de..3b654828 100644 --- a/docs/command.rst +++ b/docs/command.rst @@ -73,7 +73,7 @@ mandatory parameters For ``-soft`` value, it is possible to add some key words (e.g. ``-soft ANTS_robustreg_prep``) all these options are available (to place after SPM or ANTS, e.g) and will change the brain extraction: * ``_4animal`` : will use bet4animal (FSL) for brain extraction, for faster computation (by default atlas_brex is used) - * ``_quick`` : will use hd-bet (Deep Learning) for brain extraction, for faster computation (by default atlas_brex is used) **NB: hd-bet requires a specific version of macapype/skullTo3d, not available by default** + * ``_quick`` : will use hd-bet (Deep Learning) for brain extraction, for faster computation (by default atlas_brex is used) **NB:** hd-bet requires a specific version of macapype/skullTo3d, not available by default * ``_robustreg`` (at the end) to have a more robust registration (in two steps) . This option should be used if the coregistration to template in preparation is not performed correctly Finally, these option are available (to place after SPM or ANTS) and will modify the parameters but can be launched in sequence: @@ -81,7 +81,7 @@ mandatory parameters * ``_test`` : (at the end) to check if the full pipeline is coherent (will only generate the graph.dot and graph.png) * ``_prep`` (at the end) will perform data preparation (no brain extraction and segmentation) * ``_noseg`` (at the end) will perform data preparation and brain extraction (no segmentation) - * ``_skull`` after SPM or ANTS if you want to process skull or angio *specific to skullTo3d*; otherwise the main pipelines of macapype will be launched (only brain segmentation will be performed) **NB: ``_skullnoisypetra`` instead of ``_skull`` available for macaque with issues on petra NB: ``-soft skull`` without processing brain is possible, but is still experimental. It only works if ``-skull_dt CT petra`` and -deriv -padback are NOT defined** + * ``_skull`` after SPM or ANTS if you want to process skull or angio *specific to skullTo3d*; otherwise the main pipelines of macapype will be launched (only brain segmentation will be performed) **NB:** ``_skullnoisypetra`` instead of ``_skull`` available for macaque with issues on petra **NB:** ``-soft skull`` without processing brain is possible, but is still experimental. It only works if ``-skull_dt CT petra`` and -deriv -padback are NOT defined * ``_noskullmask`` (at the end) will perform realignement to stereo and headmask (only realignement for CT) * ``_noheadmask`` (at the end) will perform only realignement to stereo From 59cb168080eaedfed2d5f04fd1fedf49c794bb5a Mon Sep 17 00:00:00 2001 From: David Meunier Date: Wed, 10 Dec 2025 11:29:08 +0100 Subject: [PATCH 15/15] spaces --- docs/command.rst | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/docs/command.rst b/docs/command.rst index 3b654828..68f9649f 100644 --- a/docs/command.rst +++ b/docs/command.rst @@ -81,9 +81,12 @@ mandatory parameters * ``_test`` : (at the end) to check if the full pipeline is coherent (will only generate the graph.dot and graph.png) * ``_prep`` (at the end) will perform data preparation (no brain extraction and segmentation) * ``_noseg`` (at the end) will perform data preparation and brain extraction (no segmentation) + * ``_skull`` after SPM or ANTS if you want to process skull or angio *specific to skullTo3d*; otherwise the main pipelines of macapype will be launched (only brain segmentation will be performed) **NB:** ``_skullnoisypetra`` instead of ``_skull`` available for macaque with issues on petra **NB:** ``-soft skull`` without processing brain is possible, but is still experimental. It only works if ``-skull_dt CT petra`` and -deriv -padback are NOT defined - * ``_noskullmask`` (at the end) will perform realignement to stereo and headmask (only realignement for CT) + * ``_noheadmask`` (at the end) will perform only realignement to stereo + * ``_noskullmask`` (at the end) will perform realignement to stereo and compute headmask (only realignement for CT) + * ``_nofullskullmask`` (at the end) will not perform fullskullmask (only realignement for CT) -------------------- exclusive parameters