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- trac-all . . . 5 matches
- ...)
'''Input image formats'''
* The input DWIs can be in any format recognized by [[mri_convert]]. If the format is DICOM, [[mri_convert]] will attempt to extract the b-values and...
- ReconAllDevTable . . . 5 matches
- ...' ||
||<style="text-align:left" |1>-i <invol1> ||invol1.dcm ''or .nii or .mgz'' ||[[mri_convert]] invol1.dcm orig/001.mgz ||orig/001.mgz ||
||<style="text-align:left" |1>-i <invol...
- mri_xvolavg . . . 3 matches
- ...ple volumes together (including 4D volumes). mri_xvolavg accepts all input types as mri_convert (see mri_convert --help for more information). There is another program called mri...
- mri_surf2surf . . . 3 matches
- ...r curvature file), paint or w (for FreeSurfer paint files), or anything accepted by mri_convert. If no type string is given, then the type is determined from the sourcefile (if p...
- mri_label2vol . . . 3 matches
- ... the registration. ||
= Outputs =
|| --o volid || Single frame output volume (any mri_convert format accepted) ||
|| volume2 || description ||
= Description =
Converts a label ...
- ReconAllTableStableV5.3 . . . 3 matches
- ...jid>''' ||
||<style="text-align: left;" |2>-i <invol1> -i <invol2> ||invol1.dcm ||[[mri_convert]] invol1.dcm orig/001.mgz ||orig/001.mgz ||
||invol2.dcm ||[[mri_convert]] invol2.d...
- ReconAllTableStableV5.1 . . . 3 matches
- ...jid>''' ||
||<style="text-align: left;" |2>-i <invol1> -i <invol2> ||invol1.dcm ||[[mri_convert]] invol1.dcm orig/001.mgz ||orig/001.mgz ||
||invol2.dcm ||[[mri_convert]] invol2.d...
- ReconAllTableStableV5 . . . 3 matches
- ...jid>''' ||
||<style="text-align: left;" |2>-i <invol1> -i <invol2> ||invol1.dcm ||[[mri_convert]] invol1.dcm orig/001.mgz ||orig/001.mgz ||
||invol2.dcm ||[[mri_convert]] invol2.d...
- ReconAllStableTablev4 . . . 3 matches
- ...FFFE0'>-i <invol1> -i <invol2>||<bgcolor='#E0E0FF'>invol1.dcm||<bgcolor='#E0E0FF'>[[mri_convert]] invol1.dcm orig/001.mgz||<bgcolor='#E0E0FF'>orig/001.mgz||
||<bgcolor='#E0E0FF'>i...
- FsTutorial/Tracula . . . 3 matches
- ... are in a format other than DICOM (e.g., NIfTI, or any format that can be read by [[mri_convert]]), you would still specify them here.
If your input DWIs are DICOM files, and the...
- FreeSurferTalairach . . . 3 matches
- ...matter set to have 110 only) and then "brain". Here are the steps you take:
||$ [[mri_convert]] T1 T1.mnc||
||$ mritotal -protocol icbm T1.mnc T1.xfm ||
Check the transform, us...
- mri_vol2vol . . . 2 matches
- ...specified implicitly (through the path name) or explicitly. All formats accepted by mri_convert can be used.
= Examples =
== Example 1 ==
If a functional volume is f.bhdr (or f....
- mri_surf2vol . . . 2 matches
- ...specified implicitly (through the path name)
or explicitly. All formats accepted by mri_convert can be used. In addition,
the surface value file can be paint format. If paint form...
- SPM . . . 2 matches
- ...= Topics on SPM and Freesurfer =
* [[mri_convert|mri_convert]] - converts SPM analyse formatted files to mgh format
* SpmPainting - Painting SPM data onto surfaces
* FsTutoria...
- FreeSurferCommandsVolumeConversion . . . 2 matches
- ... * [[mri_convert]]
* [[brik2bfloat]]
* [[minc_to_bshort]]
* [[mri_annotation2label]]
* [[mri_convert_mdh]]
* [[mri_vol2label]]
* [[mri_label2label]]
* [[mri_label2vol]]
* ...
- mris_convert . . . 1 match
- ...Examples =
== Example 1 ==
mris_convert
description
= Bugs =
None
= See Also =
[[mri_convert]]
= Links =
FreeSurfer
= Methods Description =
{{{
description
description
}}}
=...
- mri_ms_fitparms . . . 1 match
- ...sults on the same directory (subjectid/mri/flash).
= Bugs =
None
= See Also =
||[[mri_convert]] ||(to convert input volumes to mgh format) || ||
||[[mri_synthesize]] ||(to use t...
- mri_motion_correct2 . . . 1 match
- ...to ../orig.mgz
= Bugs =
None
= See Also =
[[mri_motion_correct]], [[mri_info]], [[mri_convert]], [[minctracc]], [[mincresample]], [[mincaverage]]
= Links =
FreeSurfer
= Method...
- mri_compute_overlap . . . 1 match
- ...e, that the label files (e.g. aseg.mgz) need to be in a common space. You can use [[mri_convert]] with -rt nearest and -at to apply a transform to the segmentations.
= Examples =...
- motioncor . . . 1 match
- ...is
then conformed to 255 cubed char images (1mm isotropic voxels) in
mri/orig.mgz.
=== Programs ===
* [[mri_robust_template]]
* [[mri_convert]]
* [[mri_add_xform_to_header]]...
- minc_to_bshort . . . 1 match
- ...amples =
== Example 1 ==
minc_to_bshort file.minc f
= Bugs =
none
= See Also =
[[mri_convert]]
= Links =
FreeSurfer
= Methods Description =
N/A
= References =
none
= Report...
- brik2bfloat . . . 1 match
- ...== Example 1 ==
brik2bfloat avgatt_fico+orig sigco 1
= Bugs =
none
= See Also =
[[mri_convert]]
= Links =
[[AFNI]]
= Methods Description =
{{{
N/A
}}}
= References =
none
= ...
- FreeSurferCommands . . . 1 match
- ...
== Recon-all ==
* [[recon-all]]
* Commands, in chronological order:
* [[mri_convert]]
* [[mri_robust_template]]
* [[mri_nu_correct.mni]]
* [[talairach]]
* [[mri_norm...