Fixed broken links in documentation #3
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taha-abdullah
commented
Apr 5, 2024
taha-abdullah
commented
- Fixed typos in the examples links
- Added absolute links for links pointing to GH repo
- fixed broken links in the docmentation
dkuegler
added a commit
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Oct 9, 2024
run_fastsurfer.sh - 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
dkuegler
added a commit
that referenced
this pull request
Oct 9, 2024
run_fastsurfer.sh - 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
dkuegler
added a commit
that referenced
this pull request
Oct 10, 2024
run_fastsurfer.sh - 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
dkuegler
added a commit
that referenced
this pull request
Oct 10, 2024
run_fastsurfer.sh - 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
dkuegler
added a commit
that referenced
this pull request
Oct 11, 2024
- 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
dkuegler
added a commit
that referenced
this pull request
Oct 11, 2024
- 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
pushed a commit
that referenced
this pull request
Oct 12, 2024
- 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
dkuegler
added a commit
that referenced
this pull request
Nov 8, 2024
- 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
dkuegler
added a commit
that referenced
this pull request
Nov 11, 2024
- 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
dkuegler
added a commit
that referenced
this pull request
Nov 14, 2024
- 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
dkuegler
added a commit
that referenced
this pull request
Nov 19, 2024
- 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 asegdkt_segfile. 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
dkuegler
added a commit
that referenced
this pull request
Nov 20, 2024
- 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 asegdkt_segfile. 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
dkuegler
added a commit
that referenced
this pull request
Nov 20, 2024
- 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 asegdkt_segfile. 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
dkuegler
added a commit
that referenced
this pull request
Nov 20, 2024
- 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 asegdkt_segfile. 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
dkuegler
added a commit
that referenced
this pull request
Dec 12, 2024
- 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 asegdkt_segfile. 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
dkuegler
added a commit
that referenced
this pull request
Dec 19, 2024
- 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 asegdkt_segfile. 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
dkuegler
added a commit
that referenced
this pull request
Dec 19, 2024
- 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 asegdkt_segfile. 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
dkuegler
added a commit
that referenced
this pull request
Dec 19, 2024
- 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 asegdkt_segfile. 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
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