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Thank you for your prompt response!
On Tue, Nov 28, 2023 at 5:07 PM Douglas N. Greve <dgr...@mgh.harvard.edu>
wrote:
> You have to create your own registration. Eg, try bbregister
>
> On 11/28/2023 6:42 PM, Mirsol Choi wrote:
>
> External Email - Use Caution
>
> Hi there,
>
> I am currently trying to run vol2subfield command that allows us to get a
> registration between an input volume (ie. FA map) to a subfield volume
> (hippocampus segmentation).
>
> Upon tying vol2subfield --help, this was the message provided:
>
> "vol2subfield (run with --help to get more info)
>
> Required inputs
> --i input volume
> --sf subfield volume : full path or relative to subject/mri
> --reg reg.lta : registration that maps input volume to conformed
>
> Outputs
> --o output volume
> --outreg outreg.lta : registration between invol and subfield
> --stats stats.dat : run mri_segstats with --sum stats.dat output
> --avgwf avgwf.dat : run mri_segstats with --avgwf avgwf.dat output
> --avgwfvol avgwfvol : run mri_segstats with --avgwfvol avgwfvol output
>
> Other options
> --ctab ctab : color table to use with mri_segstats. Default is
> /home/masterslab/freesurfer/FreeSurferColorLUT.txt
> --nearest : use nearest neighbor interpolation (default)
> --trilin : use triliear interpolation
> --cubic : use cubic interpolation
> --tmp tmpdir : for debugging
>
> These are meant to make it easy to interface with the various subfield
> segs produced by FS
> --lh.hippoamyg : set subfield to lh.hippoAmygLabels-T1.v21.mgz
> --rh.hippoamyg : set subfield to rh.hippoAmygLabels-T1.v21.mgz
> --lh.hbt : set subfield to lh.hippoAmygLabels-T1.v21.HBT.mgz
> --rh.hbt : set subfield to rh.hippoAmygLabels-T1.v21.HBT.mgz
> --thalamus : set subfield to ThalamicNuclei.v10.T1.mgz
> --brainstem : set subfield to brainstemSsLabels.v12.mgz
>
> vol2subfield 7.4.1
>
> vol2subfield provides routines that make it easier to integrate
> arbitrary volumes with volumes that share a RAS space ("header
> registration") with the orig volume in the FreeSurfer mri folder.
> This script was written to manage "subfield" segmentations (eg,
> hippocampal, amygdalar, thalamic, and brainstem), but it can be used
> much more generally.
>
> The input registration is the LTA registration between the input
> volume and the orig.mgz (eg, computed with bbregister or
> mri_coreg). IF THIS REGISTRATION IS INACCURATE THEN THE OUTPUT OF THIS
> SCRIPT WILL BE WRONG!! To check the input registration run
> tkregisterfv --mov invol --reg reg.lta --surfs
>
> This script can have three types of outputs:
>
> 1. To get a registration between an input volume and a subfield volume
>
> vol2subfield --i fa.nii.gz --reg reg.lta --sf
> rh.hippoAmygLabels-T1.v21.HBT.mgz --outreg outreg.lta
>
> outreg.lta will map fa.nii.gz to
> rh.hippoAmygLabels-T1.v21.HBT.mgz. Note that the "subfield" volume can
> be anything that shares a RAS space with the orig.mgz (eg,
> orig/001.mgz). It does not need to be a segmentation volume.
>
> 2. To map the input volume into the subfield volume space
>
> vol2subfield --i fa.nii.gz --reg reg.lta --sf
> rh.hippoAmygLabels-T1.v21.HBT.mgz --o fa.rh.hbt.mgz
>
> fa.rh.hbt.mgz will be the fa.nii.gz sampled into the space of
> rh.hippoAmygLabels-T1.v21.HBT.mgz (ie, it will be in voxel-for-voxel
> registration). Again, the "subfield" volume can be anything that
> shares a RAS space with the orig.mgz (eg, orig/001.mgz). It does not
> need to be a segmentation volume. This volume is appropriate for running
> mri_segstats. Note that there is not an output registration, but, if you
> want to save it, just use --outreg as above.
>
> 3. To compute segmentation statistics of the input volume
>
> vol2subfield --i fa.nii.gz --reg reg.lta --sf
> rh.hippoAmygLabels-T1.v21.HBT.mgz \
> --o fa.rh.hbt.mgz --stats stats.dat --avgwf avgwf.dat --avgwfvol
> avgwfvol.mgz
>
> This will create three files (but you do not need to specify all of
> them) using mri_segstats (and excluding the 0 segmentation). See
> mri_segstats --help for what each of these outputs mean. Note that
> there is not an output registration, but, if you want to save it, just
> use --outreg as above.
>
>
> For information about the subfields created by FS, see
>
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> "
>
>
> In all 3 examples of codes provided here, they all require an input of
> "reg.lta." However upon searching all of my freesurfer folder or recon
> outputs, we do not see any file names "reg.lta."
> Is there a process I must take to create this file? If someone could
> answer this question for me, I will be eternally grateful.
>
> Best,
> M
>
>
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