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| Registration in this context is the processes of computing a linear (affine) transformation matrix to map between the individual's functional data and his/her FreeSurfer structural/anatomical data (namely, the orig.mgz volume in the FreeSurfer mri directory). Before computing the registration, FS-FAST needs to know what the name of the subject is in the $SUBJECTS_DIR. You do this by creating a file in the functional directory called "subjectname". Eg: | |
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| Registration in this context is the processes of computing a linear (affine) transformation matrix to map between the individual's functional data and his/her FreeSurfer structural/anatomical data (namely, the orig.mgz volume in the FreeSurfer mri directory). Before computing the registration, FS-FAST needs to know what the name of the subject is in the $SUBJECTS_DIR. You do this by creating a file in the functional directory called "subjectname". Eg:[br] |
cd bert-functional [[br]] echo "bert" > subjectname [[br]] |
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cd bert-functional [br] echo "bert" > subjectname[br] Then there must be FreeSurfer data for bert under $SUBJECTS_DIR/bert. FS-FAST will then get the name of the subject from this file and automatically know where to find the anatomicals.[br] |
Then there must be FreeSurfer data for bert under $SUBJECTS_DIR/bert. FS-FAST will then get the name of the subject from this file and automatically know where to find the anatomicals. This registration is used both for mapping to the standard volume space (talairach) and the standard surface space (fsaverage). When mapping to talairach space, the mri/transforms/talairach.xfm is used. Note that the raw functional data is not mapped. Rather, the GLM analysis is done in native space, and the regression coefficients are mapped to the higher level. |
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| There are 2 options for registering to the structural: | There are 2 options for automatically registering to the structural: |
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2. ["autoreg-sess"] Regardless of which method you use, you should manually inspect/tune the registration with ["tkregister-sess"]. |
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| or | With either method, a registration file will be created in bold/register.dat. This is a simple text file with the name of the subject, some parameters, and the registration matrix. |
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| 1. ["autoreg-sess"] | spmregister-sess uses the registration program in SPM (http://www.fil.ion.ucl.ac.uk/spm). It registers directly from the functional to the anatomical (so you do not need to collect an anatomical during your functional session if you don't want to). spmregister-sess also uses matlab "under-the-hood", but that's only important if you don't have matlab. Finally, there have been some troubles as of spring 2006 in running this on 64-bit machines. |
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| 1. followed by manual registration with ["tkregister-sess"] |
|
Registration in this context is the processes of computing a linear (affine) transformation matrix to map between the individual's functional data and his/her FreeSurfer structural/anatomical data (namely, the orig.mgz volume in the FreeSurfer mri directory). Before computing the registration, FS-FAST needs to know what the name of the subject is in the $SUBJECTS_DIR. You do this by creating a file in the functional directory called "subjectname". Eg:
cd bert-functional br echo "bert" > subjectname br
Then there must be FreeSurfer data for bert under $SUBJECTS_DIR/bert. FS-FAST will then get the name of the subject from this file and automatically know where to find the anatomicals. This registration is used both for mapping to the standard volume space (talairach) and the standard surface space (fsaverage). When mapping to talairach space, the mri/transforms/talairach.xfm is used. Note that the raw functional data is not mapped. Rather, the GLM analysis is done in native space, and the regression coefficients are mapped to the higher level.
By default, FS-FAST will use the first-volume of the first run as the functional template for registration. It is important that this template be the same one used for motion correction (which will be done by default).
There are 2 options for automatically registering to the structural:
["spmregister-sess"] -s <subject> -df sesspar
- ["autoreg-sess"]
Regardless of which method you use, you should manually inspect/tune the registration with ["tkregister-sess"].
With either method, a registration file will be created in bold/register.dat. This is a simple text file with the name of the subject, some parameters, and the registration matrix.
spmregister-sess uses the registration program in SPM (http://www.fil.ion.ucl.ac.uk/spm). It registers directly from the functional to the anatomical (so you do not need to collect an anatomical during your functional session if you don't want to). spmregister-sess also uses matlab "under-the-hood", but that's only important if you don't have matlab. Finally, there have been some troubles as of spring 2006 in running this on 64-bit machines.