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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
https://secure-web.cisco.com/17XF0ZnFdoeIqVKRGWwoBOtca4h4jeD6xXfzmAx0GK1TEHc6ku1GhIkdFBzbn36o1rcif4KRHO87IKXpdHGLZw1k-nZDyHz7Vu8uGwXT44KJEFVNXejSueSj1edsZc0D_huZabn0k0PREK7HsGlbw_JJp6YTehNNfStifBUn3N_zQAdgimUKnTIoZfx2y4VFLImcdmDMbUEFvkRKbMxPjcFDvSodvokrUNK-MvWRCpAyGS791OuFmDb1bKLcPrGDl5l1YMPd9-C_jIGJCHthGXRzd_AbIKNJbTeSISn5f_gtDVP5TOmez29S2bKF_QC1sWpcpYbHYx96jWplaNKSkjw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala
http://secure-web.cisco.com/1r9hdzClzfpb9wkcYJZzj-5x_1dXL8bvIXvPjcusisxNujtH5dYbdeMeOZI3hVO5OH-AJhxNvDP3jOSU2eMfIJ14UqSsl3htId6fnUaNMEe2yGFUve4qPdpc6cQuVpiRO5_VGD2WYb0-jKtf1iKI752MKosvbNWWL1SE0IZPABCzhKd-k-id0WN6O07i7BSy0JHF8Vx_-c7Te0SKbxEP9BS-KDDZ-7NcGDUVujRtWQwz0_-SoVaVmOAd1Y_rakZ2OvVahfuVFrZHYJxFBIPHnMaKRcfuNMwX_lZ7KxS5J1lGSkOcV92izLtUFFxpFgQCc2sEU3B_JvOCrMPFDXXLCNA/http%3A%2F%2Ffreesurfer.net%2Ffswiki%2FThalamicNuclei
https://secure-web.cisco.com/1zX2UZrV6ZpJQDeBcxFrsoi9bFd1JnN4YH4d0ttvaTwhHgn1HjqbunM0jDue4eUdn1YlXPQ361LMxCIeJFLbz0gcdJRYogkD_F3-br9S9jYnVdyU0zhc8tH0X4lshFbn84uCJmaueA-65PEIoEm-e1nTelyt7syg_uBH5_b_Rz_HUMLCmWL2_ztfk7YzttRGgwl4mC3P9s3VzNljVYi3tod5seYv4zQnko7SVgbfPMvSoVA1LjtqTLtsRzTUYZXxLpGzkiTmmf9-jD2NIFaHrGFTQJ7nDLBvCDsf83tLJiBOtPo0Lte-YHML38LRER7Ki8E1FaMa0mF2k-lKl5NObuA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBrainstemSubstructures";
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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