The --trgsurfval is just the output (ie, lh.atlas.nii.gz sampled onto the surface of the subject). Use nii.gz or mgz for the output (not img).

On 06/14/2018 01:46 PM, Ryan Flores wrote:

     External Email - Use Caution

Thank you for your response. Just to clarify, the first command should be mri_vol2surf, correct? It appears to have worked; however, I'm not sure what my --trgsurfval should be? I'm trying the following commands, where mni is the subject directory for the mni brain I recon-ed and sub01 is the subject I want to transfer the atlas to so that I can obtain the cortical thickness.

1. mri_vol2surf --mov atlas.nii.gz --regheader mni --hemi lh --projfrac-max 0 1 .1 --o lh.atlas.nii.gz
2. mri_surf2surf --srcsubject mni --srcsurfval lh.atlas.nii.gz --trgsubject sub01 --trgsurfval hammers-01-lh.img --mapmethod nnf

I tried running mri_surf2surf --help, but unfortunately the examples didn’t really apply to my case. I apologize for the potential trivial question in advance. Thanks again for your help.

Best,

Ryan

-- Ryan Flores Clinical Research Coordinator On 6/14/18, 8:33 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of dgreve@mgh.harvard.edu> wrote: You can always get info by running the command with --help. mri_vol2vol --mov atlas.nii.gz --regheader subject --hemi lh --projfrac-max 0 1 .1 --o lh.atlas.nii.gz This assumes that the atlas is in registration with the mni152 (you can test with tkregister --mov atlas.nii.gz --s subject --regheader --reg deleteme.dat, the two volumes should be in registration) You can take lh.atlas.nii.gz and use it as input to mri_surf2surf to transfer to an individual. Make sure to use --mapmethod nnf On 06/13/2018 06:59 PM, Ryan Flores wrote: > > External Email - Use Caution > > Hello all, > > I am hoping to obtain structural information (e.g., cortical > thickness, surface area, and volume) based on the n30r83 (aka > Hammersmith) atlas, which is in MNI space. The atlas differentiates > between the hemispheres by using odd/even numbers in the labels. > > After looking through the archives I found a potential solution, which > entails using the mri_vol2surf & mri_surf2surf commands. I’ve recon-ed > the MNI brain to obtain the proper space; however, I’m unsure of how > exactly to implement the commands and which flags are relevant. Any > advice would be greatly appreciated. > > Thank you for your time. I look forward to hearing from you. > > Best, > > Ryan > > -- > > Ryan Flores > > Clinical Research Coordinator > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

You can create an annotation with mris_seg2annot and then view it in freeview. Run it with --help to get docs

On 06/14/2018 02:18 PM, Ryan Flores wrote:

     External Email - Use Caution

Great. That seemed to have worked. Is there a way to inspect that the ROIs have been correctly placed? Perhaps by using freeview?

Best,

Ryan

- Ryan Flores Clinical Research Coordinator On 6/14/18, 11:02 AM,"freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of dgreve@mgh.harvard.edu> wrote:

The --trgsurfval is just the output (ie, lh.atlas.nii.gz sampled onto the surface of the subject). Use nii.gz or mgz for the output (not img).

On 06/14/2018 01:46 PM, Ryan Flores wrote: > External Email - Use Caution > > Thank you for your response. Just to clarify, the first command should be mri_vol2surf, correct? It appears to have worked; however, I'm not sure what my --trgsurfval should be? I'm trying the following commands, where mni is the subject directory for the mni brain I recon-ed and sub01 is the subject I want to transfer the atlas to so that I can obtain the cortical thickness. > > 1. mri_vol2surf --mov atlas.nii.gz --regheader mni --hemi lh --projfrac-max 0 1 .1 --o lh.atlas.nii.gz > 2. mri_surf2surf --srcsubject mni --srcsurfval lh.atlas.nii.gz --trgsubject sub01 --trgsurfval hammers-01-lh.img --mapmethod nnf > > I tried running mri_surf2surf --help, but unfortunately the examples didn’t really apply to my case. I apologize for the potential trivial question in advance. Thanks again for your help. > > Best, > > Ryan >

-- Ryan Flores Clinical Research Coordinator On 6/14/18, 8:33 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of dgreve@mgh.harvard.edu> wrote: You can always get info by running the command with --help. mri_vol2vol --mov atlas.nii.gz --regheader subject --hemi lh --projfrac-max 0 1 .1 --o lh.atlas.nii.gz This assumes that the atlas is in registration with the mni152 (you can test with tkregister --mov atlas.nii.gz --s subject --regheader --reg deleteme.dat, the two volumes should be in registration) You can take lh.atlas.nii.gz and use it as input to mri_surf2surf to transfer to an individual. Make sure to use --mapmethod nnf On 06/13/2018 06:59 PM, Ryan Flores wrote: > > External Email - Use Caution > > Hello all, > > I am hoping to obtain structural information (e.g., cortical > thickness, surface area, and volume) based on the n30r83 (aka > Hammersmith) atlas, which is in MNI space. The atlas differentiates > between the hemispheres by using odd/even numbers in the labels. > > After looking through the archives I found a potential solution, which > entails using the mri_vol2surf & mri_surf2surf commands. I’ve recon-ed > the MNI brain to obtain the proper space; however, I’m unsure of how > exactly to implement the commands and which flags are relevant. Any > advice would be greatly appreciated. > > Thank you for your time. I look forward to hearing from you. > > Best, > > Ryan > > -- > > Ryan Flores > > Clinical Research Coordinator > > > > _______________________________________________ > Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

There are files called lh.area and lh.volume that you can use instead of lh.thickness. Make sure to use the --jac flag when applying mri_surf2surf to area or volume (but not thickness). This applies jacobian correction to preserve the total area or volume. When you run mri_segstats, include the --accumulate flag so that it reports the total area or volume.

On 6/14/18 6:42 PM, Ryan Flores wrote:

     External Email - Use Caution

Hi again Doug,

Sorry for not realizing this earlier, but I actually found a workflow that you created, which outlines the steps really well. (https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness)

However, instead of 'fsaverage' I used the the MNI brain I had previously recon-ed to map the ROI to the surface. By using mri_surf2surf I mapped my subject's thickness data to the mni brain and optained the cortical thickness. My questions are the following: how do I obtain the surface area and volume for this ROI? Is there a way to also obtain non-segmented stats? Also, the reason I didn't map the ROI to fsaverage was because I didn’t have access...is there a way to change that?

Thank you for your time.

Best,

Ryan

-- Ryan Flores Clinical Research Coordinator On 6/14/18, 11:32 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of dgreve@mgh.harvard.edu> wrote: You can create an annotation with mris_seg2annot and then view it in freeview. Run it with --help to get docs On 06/14/2018 02:18 PM, Ryan Flores wrote: > External Email - Use Caution > > Great. That seemed to have worked. Is there a way to inspect that the ROIs have been correctly placed? Perhaps by using freeview? > > Best, > > Ryan > - Ryan Flores Clinical Research Coordinator On 6/14/18, 11:02 AM,"freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of dgreve@mgh.harvard.edu> wrote: The --trgsurfval is just the output (ie, lh.atlas.nii.gz sampled onto the surface of the subject). Use nii.gz or mgz for the output (not img). On 06/14/2018 01:46 PM, Ryan Flores wrote:

External Email - Use Caution > > Thank you for your response. Just to

clarify, the first command should be mri_vol2surf, correct? It appears to have worked; however, I'm not sure what my --trgsurfval should be? I'm trying the following commands, where mni is the subject directory for the mni brain I recon-ed and sub01 is the subject I want to transfer the atlas to so that I can obtain the cortical thickness. > > 1. mri_vol2surf --mov atlas.nii.gz --regheader mni --hemi lh --projfrac-max 0 1 .1 --o lh.atlas.nii.gz > 2. mri_surf2surf --srcsubject mni --srcsurfval lh.atlas.nii.gz --trgsubject sub01 --trgsurfval hammers-01-lh.img --mapmethod nnf > > I tried running mri_surf2surf --help, but unfortunately the examples didn’t really apply to my case. I apologize for the potential trivial question in advance. Thanks again for your help. > > Best, > > Ryan > -- Ryan Flores Clinical Research Coordinator On 6/14/18, 8:33 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of dgreve@mgh.harvard.edu> wrote: You can always get info by running the command with --help. mri_vol2vol --mov atlas.nii.gz --regheader subject --hemi lh --projfrac-max 0 1 .1 --o lh.atlas.nii.gz This assumes that the atlas is in registration with the mni152 (you can test with tkregister --mov atlas.nii.gz --s subject --regheader --reg deleteme.dat, the two volumes should be in registration) You can take lh.atlas.nii.gz and use it as input to mri_surf2surf to transfer to an individual. Make sure to use --mapmethod nnf On 06/13/2018 06:59 PM, Ryan Flores wrote: > > External Email - Use Caution > > Hello all, > > I am hoping to obtain structural information (e.g., cortical > thickness, surface area, and volume) based on the n30r83 (aka > Hammersmith) atlas, which is in MNI space. The atlas differentiates > between the hemispheres by using odd/even numbers in the labels. > > After looking through the archives I found a potential solution, which > entails using the mri_vol2surf & mri_surf2surf commands. I’ve recon-ed > the MNI brain to obtain the proper space; however, I’m unsure of how > exactly to implement the commands and which flags are relevant. Any > advice would be greatly appreciated. > > Thank you for your time. I look forward to hearing from you. > > Best, > > Ryan > > -- > > Ryan Flores > > Clinical Research Coordinator > > > > _______________________________________________ > Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer