Differences between revisions 7 and 13 (spanning 6 versions)

Index

Contents

Name
Synopsis
Arguments
Outputs
Description
Examples
1. Example 1
2. Example 2
Bugs
See Also
Links
Methods Description
References
Reporting Bugs
Author/s

Name

mri_convert - converts MRI data format/file type

Synopsis

mri_convert [<options>] involume outvolume

Arguments

Positional Arguments

involume	input volume
outvolume	output volume

Required Flagged Arguments

None

Optional Flagged Arguments

-ro, --read_only
-nw, --no_write
-ii, --in_info
-oi, --out_info
-is, --in_stats
-os, --out_stats
-im, --in_matrix
-om, --out_matrix
-iis, --in_i_size <size>
-ijs, --in_j_size <size>
-iks, --in_k_size <size>
--force_ras_good	use default when orientation info absent
-iid, --in_i_direction <R direction> <A direction> <S direction>
-ijd, --in_j_direction <R direction> <A direction> <S direction>
-ikd, --in_k_direction <R direction> <A direction> <S direction>
-ic, --in_center <R coordinate> <A coordinate> <S coordinate>
-oni, -oic, --out_i_count <count>
-onj, -ojc, --out_j_count <count>
-onk, -okc, --out_k_count <count>
-ois, --out_i_size <size>
-ojs, --out_j_size <size>
-oks, --out_k_size <size>
--nskip n : skip the first n frames
-oid, --out_i_direction <R direction> <A direction> <S direction>
-ojd, --out_j_direction <R direction> <A direction> <S direction>
-okd, --out_k_direction <R direction> <A direction> <S direction>
-oc, --out_center <R coordinate> <A coordinate> <S coordinate>
-odt, --out_data_type <uchar\|short\|int\|float>		This may prompt rescale. To disable that, use no_scale option.
-rt, --resample_type <interpolate\|weighted\|nearest\|sinc\|cubic> (default is interpolate)
-ns, --no_scale <value>: 1 = dont rescale values for COR or MGH/MGZ output		example: --no_scale 1
-nc --nochange - don't change type of input to that of template
-tr TR : TR in seconds
--unwarp_gradient_nonlinearity	<sonata \| allegra \| GE>	<fullUnwarp \| through-plane> <JacobianCorrection \| noJacobianCorrection> <linear \| sinc> <sincInterpHW>
-r, --reorder olddim1 olddim2 olddim3	reorder dimensions	Reorders axes such that olddim1 is the new column dimension, olddim2 is the new row dimension, olddim3 is the new slice dimension. Example: 2 1 3 will swap rows and cols.
-invert_contrast threshold	applies threshold	all voxels in volume greater than threshold are replaced with 255-value. Only makes sense for 8 bit images. Only operates on the first frame.
-i, --input_volume
-o, --output_volume
-c, --conform	conform	conform to 1mm voxel size in coronal slice direction with 256^3 or more
-cm, --conform_min	conform to the src min direction size
-cs, --conform_size size	conform to the size given in mm
-po, --parse_only
-is, --in_stats
-os, --out_stats
-ro, --read_only
-nw, --no_write
-sn, --subject_name
-rl, --reslice_like
-tt, --template_type <type>
-f, --frame
-sc, --scale <scale factor>
-il, --in_like
-roi
-fp, --fill_parcellation
-sp, --smooth_parcellation
-zo, --zero_outlines
-cf, --color_file
-nt, --no_translate
--status	status file for DICOM conversion
--sdcmlist	list of DICOM files for conversion
-ti, --template_info	dump info about template
-gis <gdf image file stem>
-zgez, --zero_ge_z_offset		set c_s=0 (appropriate for dicom files from GE machines with isocenter scanning)

Applying Transforms

-T, -at, --apply_transform xfmfile	apply tranform given by xfm or m3z files
-ait, --apply_inverse_transform xfmfile	apply inverse of tranform given by xfm or m3z files
--devolvexfm subjectid
--like vol: output is embedded in a volume like vol

Outputs

outvolume

output volume

Description

mri_convert is a general purpose utility for convertin between different file formats. The file type can be specified in two ways. First, mri_convert will try to figure it out on its own from the format of the file name (eg, files thatend in .img are assumed to be in spm analyze format). Second, the user canexplicity set the type of file using --in_type and/or --out_type. Legal values for --in_type (-it) and --out_type (-ot) are:

cor	MGH-NMR COR format
minc	MNI's Medical Imaging NetCDF format (output may not work)
analyze	3D analyze (same as spm)
analyze4d	4D analyze
spm	SPM Analyze format (same as analyze and analyze3d)
ge	GE Genesis format (input only)
gelx	GE LX (input only)
lx	same as gelx
ximg	GE XIMG variant (input only)
siemens	Siemens IMA (input only)
dicom	generic DICOM Format (input only)
siemens_dicom	Siemens DICOM Format (input only)
afni	AFNI format
brik	same as afni
bshort	MGH-NMR bshort format
bfloat	MGH-NMR bfloat format
sdt	Varian (?)
outline	MGH-NMR Outline format
otl	same as outline
gdf	GDF volume (requires image stem for output; use -gis)

Notes:

If the user specifies any of the direction cosines, the ras_good_flag is set.

CONVERTING TO SPM-ANALYZE FORMAT

Converting to SPM-Analyze format can be done in two ways, depeding uponwhether a single frame or multiple frames are desired. For a single frame,simply specify the output file name with a .img extension, and mri_convert will save the first frame into the file. For multiple frames, specify the base as the output file name and add --out_type spm. This will save each frame as baseXXX.img where XXX is the three-digit, zero-padded frame number. Frame numbers begin at one. By default, the width the of zero padding is 3.This can be controlled with --in_nspmzeropad N where N is the new width.

Examples

Example 1

APPLYING TRANSFORMS (INCLUDING TALAIRACH)

The volume can be resampled into another space by supplying a transform using the --apply_transform flag. This reads the transform file and applies the transform (when --apply_inverse_transform is used, the transform is inverted and then applied). An example of a transform file is talairach.xfm as found in subjectid/mri/transforms. To convert a subject's orig volume to talairach space, execute the following lines:

cd subjectid/mri mkdir talairach mri_convert --apply_transform transforms/talariach.xfm --devolvexfm subjectid --ic 0 0 0 orig talairach

This properly accounts for the case where the input volume does not have it's coordinate center at 0.

To evaluate the result, run:

tkmedit -f $SUBJECTS_DIR/talairach/mri/orig -aux talairach

The main and aux volumes should overlap very closely. If they do not, use tkregister2 to fix it (run tkregister --help for docs).

Example 2

From the subject directory:

mri_convert -at mri/transforms/talairach_one.m3z mri/norm.mgz mri/norm_transformed_by_gca_one.mgz

Bugs

None

Links

FreeSurfer, FsFast

Methods Description

N/A

References

None

Reporting Bugs

Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>

Author/s

YasunariTosa, DougGreve, BruceFischl

-  ⇤ ← Revision 7 as of 2004-08-25 12:20:05 → 
  Size: 7310
  Editor: DavidTuch
  Comment: new page
+   ← Revision 13 as of 2008-04-29 11:45:05 → ⇥
  Size: 8139
  Editor: localhost
  Comment: converted to 1.6 markup
-Deletions are marked like this.
+Additions are marked like this.
 Line 9:
+<<Navigation(children)>>
'''Index'''
<<TableOfContents>>
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+Line 18:
-mri_convert [options] <in volume> <out volume>
+mri_convert [<options>] involume outvolume
-Line 17:
+Line 22:
-|| in volume || your input file name
+|| involume || input volume ||
|| outvolume || output volume ||
-Line 20:
+Line 26:
-None.
The file type can be specified in two ways. First, mri_convert will try
to figure it out on its own from the format of the file name (eg, files thatend in .img are assumed to be in spm analyze format). Second, the user canexplicity set the type of file using --in_type and/or --out_type. 
Legal values for --in_type (-it) and --out_type (-ot) are:
 
  cor           - MGH-NMR COR format

  minc          - MNI's Medical Imaging NetCDF format (output may not work)  analyze       - 3D analyze (same as spm)

  analyze4d     - 4D analyze

  spm           - SPM Analyze format (same as analyze and analyze3d)  ge            - GE Genesis format (input only)

  gelx          - GE LX (input only)

  lx            - same as gelx

  ximg          - GE XIMG variant (input only)

  siemens       - Siemens IMA (input only)

  dicom         - generic DICOM Format (input only)

  siemens_dicom - Siemens DICOM Format (input only)

  afni          - AFNI format

  brik          - same as afni

  bshort        - MGH-NMR bshort format

  bfloat        - MGH-NMR bfloat format

  sdt           - Varian (?)

  outline       - MGH-NMR Outline format

  otl           - same as outline

  gdf           - GDF volume (requires image stem for output; use -gis)
+None
-Line 64:
+Line 30:
-Options are
+|| -ro, --read_only || ||
|| -nw, --no_write  || ||
|| -ii, --in_info  || ||
|| -oi, --out_info || ||
|| -is, --in_stats || ||
|| -os, --out_stats || ||
|| -im, --in_matrix || ||
|| -om, --out_matrix|| ||
|| -iis, --in_i_size <size> || ||
|| -ijs, --in_j_size <size> || ||
|| -iks, --in_k_size <size> || ||
|| --force_ras_good || use default when orientation info absent||
|| -iid, --in_i_direction <R direction> <A direction> <S direction> || ||
|| -ijd, --in_j_direction <R direction> <A direction> <S direction> || ||
|| -ikd, --in_k_direction <R direction> <A direction> <S direction> || ||
|| -ic, --in_center <R coordinate> <A coordinate> <S coordinate> ||
|| -oni, -oic, --out_i_count <count>|| ||
|| -onj, -ojc, --out_j_count <count>|| ||
|| -onk, -okc, --out_k_count <count>|| ||
|| -ois, --out_i_size <size> || ||
|| -ojs, --out_j_size <size>|| ||
|| -oks, --out_k_size <size>|| ||
|| --nskip n : skip the first n frames|| ||
|| -oid, --out_i_direction <R direction> <A direction> <S direction>|| ||
|| -ojd, --out_j_direction <R direction> <A direction> <S direction>|| ||
|| -okd, --out_k_direction <R direction> <A direction> <S direction>|| ||
|| -oc, --out_center <R coordinate> <A coordinate> <S coordinate>|| ||
|| -odt, --out_data_type <uchar|short|int|float>|| || This may prompt rescale. To disable that, use no_scale option. ||
|| -rt, --resample_type <interpolate|weighted|nearest|sinc|cubic> (default is interpolate)|| ||
|| -ns, --no_scale <value>: 1 = dont rescale values for COR or MGH/MGZ output ||  || example: --no_scale 1 ||
|| -nc --nochange - don't change type of input to that of template|| ||
|| -tr TR : TR in seconds|| ||
|| --unwarp_gradient_nonlinearity|| <sonata | allegra | GE> || <fullUnwarp | through-plane> <JacobianCorrection | noJacobianCorrection> <linear | sinc> <sincInterpHW>||
|| -r, --reorder olddim1 olddim2 olddim3|| reorder dimensions || Reorders axes such that olddim1 is the new column dimension, olddim2 is the new row dimension, olddim3 is the new slice dimension. Example: 2 1 3 will swap rows and cols.||
|| -invert_contrast threshold || applies threshold || all voxels in volume greater than threshold are replaced with 255-value. Only makes sense for 8 bit images. Only operates on the first frame.||
|| -i, --input_volume|| ||
|| -o, --output_volume|| ||
|| -c, --conform|| conform ||conform to 1mm voxel size in coronal slice direction with 256^3 or more||
|| -cm, --conform_min || conform to the src min direction size|| ||
|| -cs, --conform_size size || conform to the size given in mm || ||
|| -po, --parse_only|| || ||
|| -is, --in_stats|| || ||
|| -os, --out_stats|| || ||
|| -ro, --read_only|| || ||
|| -nw, --no_write|| || ||
|| -sn, --subject_name|| || ||
|| -rl, --reslice_like|| || ||
|| -tt, --template_type <type> || || ||
|| -f,  --frame|| || ||
|| -sc, --scale <scale factor>|| || ||
|| -il, --in_like|| || ||
|| -roi|| || ||
|| -fp, --fill_parcellation|| || ||
|| -sp, --smooth_parcellation|| || ||
|| -zo, --zero_outlines|| || ||
|| -cf, --color_file|| || ||
|| -nt, --no_translate|| || ||
|| --status || status file for DICOM conversion|| ||
|| --sdcmlist || list of DICOM files for conversion|| ||
|| -ti, --template_info || dump info about template|| ||
|| -gis <gdf image file stem>|| || ||
|| -zgez, --zero_ge_z_offset || || set c_s=0 (appropriate for dicom files from GE machines with isocenter scanning)||
-Line 66:
+Line 93:
-  -ro, --read_only
+=== Applying Transforms ===
|| -T, -at, --apply_transform xfmfile || apply tranform given by xfm or m3z files || ||
|| -ait, --apply_inverse_transform xfmfile || apply inverse of tranform given by xfm or m3z files || ||
|| --devolvexfm subjectid || || ||
|| --like vol: output is embedded in a volume like vol|| || ||
-Line 68:
+Line 99:
-  -nw, --no_write
 
  -ii, --in_info

  -oi, --out_info

  -is, --in_stats

  -os, --out_stats

  -im, --in_matrix

  -om, --out_matrix
 
  -iis, --in_i_size <size>

  -ijs, --in_j_size <size>

  -iks, --in_k_size <size>

  --force_ras_good : use default when orientation info absent
 
  -iid, --in_i_direction <R direction> <A direction> <S direction>  -ijd, --in_j_direction <R direction> <A direction> <S direction>  -ikd, --in_k_direction <R direction> <A direction> <S direction> 

  -ic, --in_center <R coordinate> <A coordinate> <S coordinate> 

  -oni, -oic, --out_i_count <count>

  -onj, -ojc, --out_j_count <count>

  -onk, -okc, --out_k_count <count>
 
  -ois, --out_i_size <size>

  -ojs, --out_j_size <size>

  -oks, --out_k_size <size>

 --nskip n : skip the first n frames
 
  -oid, --out_i_direction <R direction> <A direction> <S direction>  -ojd, --out_j_direction <R direction> <A direction> <S direction>  -okd, --out_k_direction <R direction> <A direction> <S direction> 

  -oc, --out_center <R coordinate> <A coordinate> <S coordinate> 

  -odt, --out_data_type <uchar|short|int|float>

  -rt, --resample_type <interpolate|weighted|nearest|sinc|cubic> (default is interpolate)
 
  --no_scale flag <-ns>: 1 = dont rescale values for COR
 
  -nc --nochange - don't change type of input to that of template 
 
  -tr TR : TR in seconds
 
  --unwarp_gradient_nonlinearity
      <sonata | allegra | GE>
      <fullUnwarp | through-plane>
      <JacobianCorrection | noJacobianCorrection>
      <linear | sinc>
      <sincInterpHW>
-Line 131:
+Line 100:
-|| out volume || desired output filename.format ||
+|| outvolume || output volume ||
-Line 134:
+Line 103:
+mri_convert is a general purpose utility for convertin between different file formats. The file type can be specified in two ways. First, mri_convert will try to figure it out on its own from the format of the file name (eg, files thatend in .img are assumed to be in spm analyze format). Second, the user canexplicity set the type of file using --in_type and/or --out_type.
Legal values for --in_type (-it) and --out_type (-ot) are:
-Line 135:
+Line 106:
+||   cor           || MGH-NMR COR format ||
||   minc          || MNI's Medical Imaging NetCDF format (output may not work)  ||
||   analyze       || 3D analyze (same as spm)||
||   analyze4d     || 4D analyze||
||   spm           || SPM Analyze format (same as analyze and analyze3d)  ||
||   ge            || GE Genesis format (input only)||
||   gelx          || GE LX (input only)||
||   lx            || same as gelx||
||   ximg          || GE XIMG variant (input only)||
||   siemens       || Siemens IMA (input only)||
||   dicom         || generic DICOM Format (input only)||
||   siemens_dicom || Siemens DICOM Format (input only)||
||   afni          || AFNI format||
||   brik          || same as afni||
||   bshort        || MGH-NMR bshort format||
||   bfloat        || MGH-NMR bfloat format||
||   sdt           || Varian (?)||
||   outline       || MGH-NMR Outline format||
||   otl           || same as outline||
||   gdf           || GDF volume (requires image stem for output; use -gis)||

Notes:

If the user specifies any of the direction cosines, the ras_good_flag is set.

CONVERTING TO SPM-ANALYZE FORMAT

Converting to SPM-Analyze format can be done in two ways, depeding uponwhether a single frame or multiple frames are desired. For a single frame,simply specify the output file name with a .img extension, and mri_convert
will save the first frame into the file.  For multiple frames, specify the
base as the output file name and add --out_type spm. This will save each
frame as baseXXX.img where XXX is the three-digit, zero-padded frame number.
Frame numbers begin at one. By default, the width the of zero padding is 3.This can be controlled with --in_nspmzeropad N where N is the new width.
-Line 139:
+Line 142:
-    --apply_transform xfmfile (-T or -at)
  
  --apply_inverse_transform xfmfile (-ait)
  
  --devolvexfm subjectid :
  
  --like vol: output is embedded in a volume like vol
 
 The volume can be resampled into another space by supplying a transform using the --apply_transform flag. This reads the transform file and applies the transform (when --apply_inverse_transform is used, the transform is inverted and then applied). An example of a transform file is talairach.xfm as found in subjectid/mri/transforms. To convert a subject's orig volume to talairach space, execute the following lines:
+The volume can be resampled into another space by supplying a transform using the --apply_transform flag. This reads the transform file and applies the transform (when --apply_inverse_transform is used, the transform is inverted and then applied). An example of a transform file is talairach.xfm as found in subjectid/mri/transforms. To convert a subject's orig volume to talairach space, execute the following lines:
-Line 151:
+Line 147:
-Line 153:
+Line 149:
-  mri_convert --apply_transform transforms/talariach.xfm
     --devolvexfm subjectid --ic 0 0 0
     orig talairach
   This properly accounts for the case where the input volume does not have it's coordinate center at 0.
   To evaluate the result, run:
      tkmedit -f $SUBJECTS_DIR/talairach/mri/orig -aux talairach
   The main and aux volumes should overlap very closely. If they do not,
 use tkregister2 to fix it (run tkregister --help for docs).
+  mri_convert --apply_transform transforms/talariach.xfm --devolvexfm subjectid --ic 0 0 0 orig talairach

This properly accounts for the case where the input volume does not have it's coordinate center at 0.

To evaluate the result, run:

    [[tkmedit]] -f $SUBJECTS_DIR/talairach/mri/orig -aux talairach

The main and aux volumes should overlap very closely. If they do not, use [[tkregister2]] to fix it (run tkregister --help for docs).
-Line 168:
+Line 161:
-CONVERTING TO SPM-ANALYZE FORMAT
 
Converting to SPM-Analyze format can be done in two ways, depeding uponwhether a single frame or multiple frames are desired. For a single frame,simply specify the output file name with a .img extension, and mri_convert
will save the first frame into the file.  For multiple frames, specify the
base as the output file name and add --out_type spm. This will save each
frame as baseXXX.img where XXX is the three-digit, zero-padded frame number.
Frame numbers begin at one. By default, the width the of zero padding is 3.This can be controlled with --in_nspmzeropad N where N is the new width.
+From the subject directory:


mri_convert -at mri/transforms/talairach_one.m3z mri/norm.mgz mri/norm_transformed_by_gca_one.mgz
-Line 179:
+Line 169:
-= Other Available Options =
-r, --reorder olddim1 olddim2 olddim3
 
  Reorders axes such that olddim1 is the new column dimension,
  olddim2 is the new row dimension, olddim3 is the new slice
  dimension. Example: 2 1 3 will swap rows and cols.
 
  --invert_contrast threshold
 
  All voxels in volume greater than threshold are replaced
  with 255-value. Only makes sense for 8 bit images.
  Only operates on the first frame.
 

  -i, --input_volume

  -o, --output_volume

  -c, --conform
            conform to 1mm voxel size in coronal slice direction with 256^3 or more

  -cm, --conform_min
            conform to the src min direction size

  -cs, --conform_size size_in_mm
            conform to the size given in mm

  -po, --parse_only

  -is, --in_stats

  -os, --out_stats

  -ro, --read_only

  -nw, --no_write

  -sn, --subject_name

  -rl, --reslice_like

  -tt, --template_type <type> (see above)

  -f,  --frame

  -sc, --scale <scale factor>

  -il, --in_like

  -roi

  -fp, --fill_parcellation

  -sp, --smooth_parcellation

  -zo, --zero_outlines

  -cf, --color_file

  -nt, --no_translate

  --status (status file for DICOM conversion)

  --sdcmlist (list of DICOM files for conversion)

  -ti, --template_info : dump info about template

  -gis <gdf image file stem>

  -zgez, --zero_ge_z_offset

            set c_s=0 (appropriate for dicom files from GE machines with isocenter scanning)
 
Notes:
 
If the user specifies any of the direction cosines, the ras_good_flag is set.
-Line 258:
+Line 170:
+[[mris_convert]]
-Line 265:
+Line 177:
-description
description
+N/A
-Line 270:
+Line 181:
+None
-Line 276:
+Line 187:
-CherifSahyoun
+YasunariTosa, DougGreve, BruceFischl

Name

Synopsis

Arguments

Positional Arguments

Required Flagged Arguments

Optional Flagged Arguments

Applying Transforms

Outputs

Description

Examples

Example 1

Example 2

Bugs

See Also

Links

Methods Description

References

Reporting Bugs

Author/s