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- PreviousReleaseNotes . . . 103 matches
- ...a 18, Ubuntu 13, and Gentoo 64 glibc crashes (seg-faults on any binary).
* fix for recon-all tal-check failure-threshold sensitivity.
=== Known Issues ===
* On Mac OSX platfor...
- FsTutorial/MorphAndRecon . . . 42 matches
- ... Reconstruction (90 minutes of exercises)'''+~
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<<TableOfContents>>
=== 1.0 The recon-all command and alternatives ===
The [[recon-all]] script is used to process raw scan da...
- OtherUsefulFlags . . . 13 matches
- ...
== FreeSurfer Tutorial: Useful recon-all flags. ==
This page extends ReconAllDevTable.
The following flags can be used in conjunction with individual steps or the entire proce...
- ReconAllDevTable . . . 8 matches
- ...
== FreeSurfer Tutorial: Process Flow ==
This table shows the recon-all steps for the current '''dev''' version of FreeSurfer [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfe...
- ReconAllTableStableV5.3 . . . 6 matches
- ...
== FreeSurfer Tutorial: Process Flow ==
This table shows the recon-all steps for stable version 5.3 of FreeSurfer.
See also the OtherUsefulFlags for other recon-all options.
|...
- ReconAllTableStableV5.1 . . . 6 matches
- ...
== FreeSurfer Tutorial: Process Flow ==
This table shows the recon-all steps for stable version 5.1 of FreeSurfer.
See also the OtherUsefulFlags for other recon-all options.
||'...
- ReconAllTableStableV5 . . . 6 matches
- ...
== FreeSurfer Tutorial: Process Flow ==
This table shows the recon-all steps for version 5.0 of FreeSurfer. See ReconAllDevTable for the most current development-code process flo...
- ReconAllStableTablev4 . . . 6 matches
- ...
== FreeSurfer Tutorial: Process Flow ==
This table shows the recon-all steps for the latest '''stable''' version of FreeSurfer, '''v4.0.2'''. See ReconAllDevTable for the dev ve...
- FreeSurferFill . . . 3 matches
- ...chment:CCsag.jpg}}
1. Copy the MNI coordinates to the command line for either
[[recon-all]] -cc-xyz ....
or in
[[mri_fill]] -C ....
Alternatively seed point can be giv...
- mri_strip_skull . . . 2 matches
- ...iption =
= Examples =
== Example 2 ==
description
= Bugs =
None
= See Also =
[[recon-all-nmr]], [[recon-all]]
= Links =
FreeSurfer, FsFast
= Methods Description =
= Refe...
- dmri_bids_config . . . 2 matches
- ...bject names in your '''SUBJECTS_DIR''' (i.e., the names that you used when you ran [[recon-all]] on the structural images).
* If this is a longitudinal study, then the '''subjlis...
- FreeSurferCommands . . . 2 matches
- ...
== Recon-all ==
* [[recon-all]]
* Commands, in chronological order:
* [[mri_convert]]
* [[mri_robust_template]]
* [[mri_nu_correct.mni]]
* [[talairach]]
* [[mri_norm...
- trac-all . . . 1 match
- ...see 1.3 below). The default is to use the whole-brain anatomical segmentation from [[recon-all]] as the mask in all subsequent steps.
1.2 '''Image quality assessment'''
. Thi...
- make_average_volume . . . 1 match
- ....mgz, brain.mgz, and T1.mgz which will be averages of subjects 1-4.
= See Also =
[[recon-all]], [[make_final_surfaces]], [[morph_subject]]
= Reporting Bugs =
Report bugs to fre...
- make_average_subject . . . 1 match
- ...e will be blurry.
= See Also =
[[make_average_volume]], [[make_average_surface]], [[recon-all]], [[make_final_surfaces]], [[morph_subject]]
= Reporting Bugs =
Report bugs to fre...
- Tracula . . . 1 match
- ...fusion MRI data with TRACULA, you will have to analyze your subjects' T1 data with [[recon-all]] and make sure that they have a good-quality '''mri/aparc+aseg.mgz'''. In addition ...
- FreeSurferTalairach . . . 1 match
- ...from one person to the next.
The first step is to look at the result of mritotal ([[recon-all]] leaves a '''mritotal.log''' in $subjid/scripts directory).
At the end of this log,...