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 https://secure-web.cisco.com/17XF0ZnFdoeIqVKRGWwoBOtca4h4jeD6xXfzmAx0GK1TEHc... http://secure-web.cisco.com/1r9hdzClzfpb9wkcYJZzj-5x_1dXL8bvIXvPjcusisxNujtH... https://secure-web.cisco.com/1zX2UZrV6ZpJQDeBcxFrsoi9bFd1JnN4YH4d0ttvaTwhHgn..."
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
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:
- 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.
- 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.
- 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmy... 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://freesurfer.net/fswiki/ThalamicNuclei 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thank you for your prompt response!
On Tue, Nov 28, 2023 at 5:07 PM Douglas N. Greve dgreve@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 CautionHi 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:
- 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.
- 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.
- 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
*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1Bcw_SYnH0V5_rsKV3Q9Pgyyj6vH2LSJ7eFqgpEQHoLHncV... 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1lcgEhLNwnh-majE0qTzqQL3F99RUI72XAsaqtvNfjVIAafS... 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1LVFJec76wYmbRfW-skb6mVrkh7pbduqG9EVI9rUf81z6nZ... 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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1U1WN-XYEomeLTnBWbpRtsRCRkyebG1E_n-455jmWNQmMiY... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1ieOB925PY8EN7q_ZTnsll6fr248EVYrcHmxfdBMwzsTJzJ... < https://secure-web.cisco.com/1ieOB925PY8EN7q_ZTnsll6fr248EVYrcHmxfdBMwzsTJzJ... . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Mirsol Choi