#**********************************************************************
# AFNI_template_spaces.niml
# this file describes the kinds of spaces available to AFNI datasets,
# the transformation for switching among these spaces and locations
# of atlas datasets that are in a specified space
# new spaces should be added to this file or to a local directory version
# for subject-specific datasets
<TEMPLATE_SPACE
  space_name="TT_N27"
  generic_space="TLRC"
  comment="The TLRC templates made from MNI group templates were\n"
          "transformed using a 12 piece transformation\n"
></TEMPLATE_SPACE>

<TEMPLATE_SPACE
  space_name="TT_avg"
  generic_space="TLRC"
  comment="The TLRC templates made from MNI group templates were\n"
  "transformed using a 2 piece transformation for upper\n"
  "and lower transformations"
></TEMPLATE_SPACE>

<TEMPLATE_SPACE
  space_name="TLRC"
  generic_space="TLRC"
  comment="This is a generic TLRC space. Assuming transformation by 2-piece"
></TEMPLATE_SPACE>

<TEMPLATE_SPACE
  space_name="MNI_152"
  generic_space="MNI"
  comment="152-subject based space with templates available for T1,T2,EPI from MNI group"
></TEMPLATE_SPACE>

<TEMPLATE_SPACE
  space_name="MNI"
  generic_space="MNI"
  comment="The standard MNI space"
></TEMPLATE_SPACE>

<TEMPLATE_SPACE
  space_name="MNI_ANAT"
  generic_space="MNI_ANAT"
  comment="The standard MNI_ANAT space name - a shifted version of MNI space"
></TEMPLATE_SPACE>

<TEMPLATE_SPACE
  space_name="MNIa"
  generic_space="MNI_ANAT"
  comment="The MNI space shifted to have its origin at AC, the same location\n"
          "as the origin of the Talairach space"
></TEMPLATE_SPACE>

<TEMPLATE_SPACE
  space_name="MNI_SPM2"
  generic_space="MNI"
  comment="MNI Space used in SPM2 according to Lancaster, Fox\n"
          "They created a specific affine transform for this to and from TLRC"
></TEMPLATE_SPACE>

<TEMPLATE_SPACE
  space_name="MNI_FSL"
  generic_space="MNI"
  comment="MNI Space used in FSL according to Lancaster, Fox\n"
          "They created a specific affine transform for this to and from TLRC"
></TEMPLATE_SPACE>

<TEMPLATE_SPACE
  space_name="MNI_OTHER"
  generic_space="MNI"
  comment="MNI Space approximately between FSL,SPM2 according to Lancaster, Fox\n"
          "They created a specific affine transform for this to and from TLRC"
></TEMPLATE_SPACE>

<TEMPLATE_SPACE
  space_name="paxinos_rat_2007@Elsevier"
  generic_space="paxinos_rat_2007@Elsevier"
  comment="Elsevier Paxinos Rat 2007"
></TEMPLATE_SPACE>
 

#**********Atlas transformations****************
# *****tlrc type spaces to and from generic TLRC
# these share the same space but reflect a different
# history of transformations from MNI space.
# Here the transformations provide a way of transforming
# among the various spaces but no change to the x,y,z
# definition by using an identity transformation.
# The distance allows for a small cost to including
# the step in a chain/path/graph of transformations.
# These distances are used to find the shortest path
# required to go from one space to another (a la Dijkstra)
# The default distance for each transformation step is
# usually 1, but for transformations that are between
# specific and generic versions of the same space, 
# the distance is reduced to 0.1.

<XFORM
  ni_type="1*float"
  ni_dimen="1"
  xform_name="TT_N27::TLRC"
  source="TT_N27"
  dest="TLRC"
  distance="0.1"
  xform_type="Identity" >
  1
</XFORM>

<XFORM
  ni_type="1*float"
  ni_dimen="1"
  xform_name="TT_avg::TLRC"
  source="TT_avg"
  dest="TLRC"
  distance="0.1"
  xform_type="Identity" >
  1
</XFORM>

<XFORM
  ni_type="1*float"
  ni_dimen="1"
  xform_name="TLRC::TT_N27"
  source="TLRC"
  dest="TT_N27"
  distance="0.1"
  xform_type="Identity" >
  1
>
</XFORM>

<XFORM
  ni_type="1*float"
  ni_dimen="1"
  xform_name="TLRC::TT_avg"
  source="TLRC"
  dest="TT_avg"
  distance="0.1"
  xform_type="Identity" >
  1
>
</XFORM>


# *****tlrc type spaces to MNI

<XFORM
  ni_type="27*float"
  ni_dimen="1"
  xform_name="TT_avg::MNI"
  source="TT_avg"
  dest="MNI"
  xform_type="2-piece" >
   -9999.0 -9999.0  0.0
   1.0101  0        0         0
   0       1.02962 -0.05154   0
   0       0.05434  1.08554   0
   1       0        0         0
   0       1        0         0
   0       0        1.09523   0
>
</XFORM>

<XFORM
  ni_type="1*float"
  ni_dimen="1"
  xform_name="TLRC::MNI"
  source="TLRC"
  dest="MNI"
  distance="1.0"
  xform_type="brett_tt2mni"
  comment="Brett transform" >
  1
</XFORM>

# mni spaces to tlrc
<XFORM
  ni_type="12*float"
  ni_dimen="1"
  xform_name="MNI_SPM2::TLRC"
  source="MNI_SPM2"
  dest="TLRC"
  comment="Lancaster,Fox 2007"
  xform_type="Affine" >
  0.9254 0.0024 -0.0118 -1.0207
  -0.0048 0.9316 -0.0871 -1.7667
  0.0152 0.0883  0.8924  4.0926
>
</XFORM>

<XFORM
  ni_type="12*float"
  ni_dimen="1"
  xform_name="MNI_FSL::TLRC"
  source="MNI_FSL"
  dest="TLRC"
  comment="Lancaster,Fox 2007"
  xform_type="Affine" >
  0.9464 0.0034 -0.0026 -1.0680
  -0.0083 0.9479 -0.0580 -1.0239
  0.0053 0.0617  0.9010  3.1883
>
</XFORM>

<XFORM
  ni_type="12*float"
  ni_dimen="1"
  xform_name="MNI_OTHER::TLRC"
  source="MNI_OTHER"
  dest="TLRC"
  comment="Lancaster,Fox 2007"
  xform_type="Affine" >
  0.9357 0.0029 -0.0072 -1.0423
  -0.0065 0.9396 -0.0726 -1.3940
  0.0103 0.0752  0.8967  3.6475
>
</XFORM>

<XFORM
  ni_type="1*float"
  ni_dimen="1"
  xform_name="MNI::TLRC"
  source="MNI"
  dest="TLRC"
  distance="1.0"
  xform_type="brett_mni2tt"
  comment="Brett transform" >
  1
</XFORM>

<XFORM
  ni_type="360*float"
  ni_dimen="1"
  xform_name="MNI::TT_N27"
  source="MNI"
  dest="TT_N27"
  xform_type="12-piece" >
      0.9444444              0              0             0     0.9976303
     0.06880209              0    -0.05989829     0.8685252      1.058824
             -0              0             -0     0.9976304   -0.07902943
             -0      0.0688021       1.145927             0     -3.405704
      -4.103033             -0       3.073373      4.936095         -9999
          -9999              0              0             0        9999.9
      0.9315069              0              0             0     0.9976303
     0.06880209              0    -0.05989829     0.8685252      1.073529
             -0              0             -0     0.9976304   -0.07902943
             -0      0.0688021       1.145927             0     -3.405704
      -4.103033             -0       3.073373      4.936095             0
          -9999              0         9999.9             0        9999.9
      0.9444444              0              0             0     0.8154033
     0.05623471              0    -0.05989829     0.8685252      1.058824
             -0              0             -0      1.220581   -0.07902943
             -0     0.08417804       1.145927             0     -2.783618
      -4.103033             -0       3.073372      4.936095         -9999
              0              0              0            23        9999.9
      0.9315069              0              0             0     0.8154033
     0.05623471              0    -0.05989829     0.8685252      1.073529
             -0              0             -0      1.220582   -0.07902943
             -0     0.08417805       1.145927             0     -2.783618
      -4.103033             -0       3.073373      4.936095             0
              0              0         9999.9            23        9999.9
      0.9444444              0              0             0     0.9511568
     0.06559702              0    -0.05989829     0.8685252      1.058824
             -0              0             -0      1.046375   -0.07902944
             -0     0.07216377       1.145927             0     0.5821307
      -4.103033             -0     -0.9333872      4.659767         -9999
             23              0              0          9999        9999.9
      0.9315069              0              0             0     0.9511568
     0.06559702              0    -0.05989829     0.8685252      1.073529
             -0              0             -0      1.046375   -0.07902943
             -0     0.07216376       1.145927             0     0.5821307
      -4.103033             -0     -0.9333871      4.659767             0
             23              0         9999.9          9999        9999.9
      0.9444444              0              0             0     0.9976303
     0.06880209              0    -0.06148272     0.8914994      1.058824
             -0              0             -0     0.9976304   -0.07699282
             -0      0.0688021       1.116396             0     -3.405704
      -4.211566             -0       3.073373      4.936095         -9999
          -9999          -9999              0             0             0
      0.9315069              0              0             0     0.9976303
     0.06880209              0    -0.06148272     0.8914994      1.073529
             -0              0             -0     0.9976304   -0.07699282
             -0      0.0688021       1.116396             0     -3.405704
      -4.211566             -0       3.073373      4.936095             0
          -9999          -9999         9999.9             0             0
      0.9444444              0              0             0     0.8154033
     0.05623471              0    -0.06148272     0.8914994      1.058823
             -0              0             -0      1.220582   -0.07699282
             -0     0.08417804       1.116396             0     -2.783618
      -4.211566             -0       3.073373      4.936095         -9999
              0          -9999              0            23             0
      0.9315069              0              0             0     0.8154033
     0.05623471              0    -0.06148272     0.8914994      1.073529
             -0              0             -0      1.220582   -0.07699282
             -0     0.08417805       1.116396             0     -2.783618
      -4.211566             -0       3.073373      4.936095             0
              0          -9999         9999.9            23             0
      0.9444444              0              0             0     0.9511568
     0.06559702              0    -0.06148272     0.8914994      1.058824
             -0              0             -0      1.046375   -0.07699282
             -0     0.07216378       1.116396             0     0.5821307
      -4.211566             -0     -0.9333872      4.659767         -9999
             23          -9999              0          9999             0
      0.9315069              0              0             0     0.9511568
     0.06559702              0    -0.06148272     0.8914994      1.073529
             -0              0             -0      1.046375   -0.07699282
             -0     0.07216377       1.116396             0     0.5821307
      -4.211566             -0     -0.9333872      4.659767             0
             23          -9999         9999.9          9999             0
>
</XFORM>

# MNI_ANAT transformations
<XFORM
  ni_type="12*float"
  ni_dimen="1"
  xform_name="MNI_ANAT::MNI"
  source="MNI_ANAT"
  dest="MNI"
  comment="Eickhoff-Zilles"
  xform_type="Affine" >
  1 0 0 0
  0 1 0 -4
  0 0 1 -5
>
</XFORM>

<XFORM
  ni_type="12*float"
  ni_dimen="1"
  xform_name="MNI::MNI_ANAT"
  source="MNI"
  dest="MNI_ANAT"
  comment="Eickhoff-Zilles"
  xform_type="Affine" >
  1 0 0 0
  0 1 0 4
  0 0 1 5
>
</XFORM>

<XFORM
  ni_type="1*float"
  ni_dimen="1"
  xform_name="MNIa::MNI_ANAT"
  source="MNIa"
  dest="MNI_ANAT"
  distance="0.1"
  xform_type="Identity" >
  1
>
</XFORM>

#*******Atlas datasets ************************
# list of atlas datasets
# these are not templates. They contain segmentation
# that associates a position with an anatomical structure
##atlas_datasets

<ATLAS
   atlas_name="TT_Daemon"   
   dset_name="TTatlas+tlrc"
   template_space="TLRC"
   description="Talairach-Tournoux Atlas"
   comment="The standard talaraich atlas"
></ATLAS>

#Cytoarchitectonic atlases transformed to TT_N27 space with 12-piece transform
<ATLAS
   atlas_name="CA_N27_ML"   
   dset_name="TT_caez_ml_18+tlrc"
   template_space="TT_N27"
   description="Macro Labels (N27)"
   comment="Eickhoff-Zilles macro labels from N27 in Talairach TT_N27 space"
></ATLAS>

<ATLAS
   atlas_name="CA_N27_MPM"   
   dset_name="TT_caez_mpm_18+tlrc"
   template_space="TT_N27"
   description="Cytoarch. Max. Prob. Maps"
   comment="Eickhoff-Zilles maximum probability map on TT_N27 from post-mortem analysis"
></ATLAS>

<ATLAS
   atlas_name="CA_N27_PM"   
   dset_name="TT_caez_pmaps_18+tlrc"
   template_space="TT_N27"
   description="Cytoarch. Probabilistic Maps"
   comment="Eickhoff-Zilles probablity maps on TT_N27 from post-mortem analysis"
></ATLAS>

<ATLAS
   atlas_name="CA_N27_GW"   
   dset_name="TT_caez_gw_18+tlrc"
   template_space="TT_N27"
   description="Cytoarch. Prob. Maps for gray/white matter"
   comment="Eickhoff-Zilles probablity maps on MNI-152 from post-mortem analysis"
></ATLAS>

<ATLAS
   atlas_name="CA_N27_LR"
   dset_name="TT_caez_lr_18+tlrc"
   template_space="TT_N27"
   description="Left/Right (N27)"
   comment="Simple left, right hemisphere segmentation"
></ATLAS>

#Cytoarchitectonic atlases in original MNI_ANAT space
<ATLAS
   atlas_name="CA_ML_18_MNIA"   
   dset_name="MNIa_caez_ml_18+tlrc"
   template_space="MNI_ANAT"
   description="Macro Labels (N27)"
   comment="Eickhoff-Zilles macro labels from N27"
></ATLAS>

<ATLAS
   atlas_name="CA_MPM_18_MNIA"   
   dset_name="MNIa_caez_mpm_18+tlrc"
   template_space="MNI_ANAT"
   description="Cytoarch. Max. Prob. Maps"
   comment="Eickhoff-Zilles maximum probability map on MNI-152 from post-mortem analysis"
></ATLAS>

<ATLAS
   atlas_name="CA_PM_18_MNIA"   
   dset_name="MNIa_caez_pmaps_18+tlrc"
   template_space="MNI_ANAT"
   description="Cytoarch. Probabilistic Maps"
   comment="Eickhoff-Zilles probablity maps on MNI-152 from post-mortem analysis"
></ATLAS>

<ATLAS
   atlas_name="CA_GW_18_MNIA"   
   dset_name="MNIa_caez_gw_18+tlrc"
   template_space="MNI_ANAT"
   description="Cytoarch. Prob. Maps for gray/white matter"
   comment="Eickhoff-Zilles probablity maps on MNI-152 from post-mortem analysis"
></ATLAS>

<ATLAS
   atlas_name="CA_LR_18_MNIA"
   dset_name="MNIa_caez_lr_18+tlrc"
   template_space="MNI_ANAT"
   description="Left/Right (N27)"
   comment="Simple left, right hemisphere segmentation"
></ATLAS>

<ATLAS
   atlas_name="DKD_Desai_PM"
   dset_name="TT_desai_dkpmaps+tlrc"
   template_space="TT_N27"
   description="Probability maps of 35 cortical areas (gyri)"
   comment="Described in Desikan et al., Neuroimage 2006 (31) pp. 968-980."
></ATLAS>

<ATLAS
   atlas_name="DD_Desai_PM"
   dset_name="TT_desai_ddpmaps+tlrc"
   template_space="TT_N27"
   description="Probability maps of 75 cortical areas"
   comment=" For each hemisphere,including both gyri and sulci. Destrieux et al., Neuroimage 2010 (53) pp. 1-15."
></ATLAS>

<ATLAS
   atlas_name="FS_Desai_PM"
   dset_name="TT_desai_fspmaps+tlrc"
   template_space="TT_N27"
   description="Contains 40 subcortical areas"
   comment="15 in left & right hemispheres,10 midline structures parcellated by freesurfer"
></ATLAS>

<ATLAS
   atlas_name="DD_Desai_MPM"
   dset_name="TT_desai_dd_mpm+tlrc"
   template_space="TT_N27"
   description="Contains the maximum probability maps of Desai DD and FS maps"
   comment="Smoothed maximum maps masked by unsmoothed maximum map"
></ATLAS>

<ATLAS
   atlas_name="DKD_Desai_MPM"
   dset_name="TT_desai_dk_mpm+tlrc"
   template_space="TT_N27"
   description="Contains the maximum probability maps of Desai DKD and FS maps"
   comment="Smoothed maximum maps masked by unsmoothed maximum map"
></ATLAS>

<ATLAS
   atlas_name="Else_Rat_Tissue"
   dset_name="pax_rat_else_tissue+tlrc"
   template_space="paxinos_rat_2007@Elsevier"
   description="Contains the simplified tissue maps from Paxinos Rat 2007"
   comment="Elsevier provided for rough alignment"
></ATLAS>


#*******Template datasets ************************
# list of template datasets
# These are not atlases. They do not contain segmentation
# to associate a position with an anatomical structure.
# Multiple templates may share a common space. The template
# definition must contain the name of the file where the
# template dataset is located and the name of the space it
# is associated with. Dataset locations may be in the AFNI
# directory or specified explicitly here where the use of
# relative directories are allowed (".." and ".") with paths
# relative to the current working directory.
#

<TEMPLATE
   template_name="TT_N27+tlrc"
   template_space="TT_N27"
   comment="Colin brain. Single subject, 27 scan mean,manually transformed to Talairach" 
></TEMPLATE>

<TEMPLATE
   template_name="TT_avg152T1+tlrc"
   template_space="TT_avg"
   comment="152 subjects T1 scan aligned to Colin brain template.\n"
           "Brett transformed to TLRC"
></TEMPLATE>

<TEMPLATE
   template_name="TT_avg152T2+tlrc"
   template_space="TT_avg"
   comment="152 subjects T2 scan aligned to Colin brain template"
           "Brett transformed to TLRC"
></TEMPLATE>

<TEMPLATE
   template_name="TT_icbm452+tlrc"
   template_space="TT_avg"
   comment="452 subjects T1 scan aligned to Colin brain template\n"
           "This dataset was manually transformed to Talairach space from\n"
           "an Analyze format dataset from the ICBM/LONI site"
></TEMPLATE>

<TEMPLATE
   template_name="TT_EPI+tlrc"
   template_space="TT_avg"
   comment="EPI average template"
           "Brett transformed to TLRC"
></TEMPLATE>

<TEMPLATE
   template_name="MNI152.nii"
   template_space="MNI"
></TEMPLATE>

<TEMPLATE
   template_name="ICBM452.nii"
   template_space="MNI"
></TEMPLATE>

<TEMPLATE
   template_name="MNI_EPI.nii"
   template_space="MNI"
></TEMPLATE>

<TEMPLATE
   template_name="MNIa_caez_N27+tlrc"
   template_space="MNI_ANAT"
></TEMPLATE>

<TEMPLATE
   template_name="pax_rat_karolinska+tlrc"
   template_space="paxinos_rat_2007@Elsevier"
></TEMPLATE>


#**********************************************