what do you mean when you say you "load it on FreeSurfer"? Do you mean FreeView? Please send command lines, and also please post to the list.

On 5/15/19 5:38 PM, Nillo, Ryan Michael R wrote:

External Email - Use Caution

When I run tkregisterfv --mov subject/surf/rh.custom.nii --reg subject/mri/transforms/talairach.lta --subject subject, the nii file does not seem to be in register with the orig.mgz. However, when I load it on FreeSurfer, they are in register. I am including a screenshot of what I see when I am running regular Freeview.

Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging

...

On May 15, 2019, at 1:46 PM, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:

You should check the registration with tkregisterfv, eg,

tkregisterfv --mov subject/mri/rh.custom.nii --regheader --reg deleteme.lta --s subject

On 5/15/19 4:28 PM, Nillo, Ryan Michael R wrote:

...

External Email - Use Caution

I reran the command with —regheader subjectname instead of —reg.  When I try to visualize the mgh file, I am still getting an overlay of zeros.

Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging

...

On May 15, 2019, at 11:41 AM, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote:

Is that registration accurate? That says that the rh.custom.nii is in "talaiarch" space. Actually, this it is its own space. I thought that your label was in the space of the orig.mgz. If so, then just use --regheader subjectname instead of --reg

On 5/15/19 2:12 PM, Nillo, Ryan Michael R wrote:

...

External Email - Use Caution

Hi Doug,

I ran this command:

mri_vol2surf --mov subject/mri/rh.custom.nii --reg subject/mri/transforms/talairach.lta --hemi rh --o subject/surf/rh.custom.mgh

However, when I try to visualize the resulting mgh file on the surface, I get a surface overlay of 0s, even though rh.custom.nii is a binary mask. Is this what is supposed to happen? I thought this would map the subcortical ROI to the nearest vertex?

Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging

...

On May 14, 2019, at 10:50 AM, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote:

Sorry, slipped through the cracks. That command will not generate a valid surface-based label. You should probably sample your volume-based mask (rh.custom.nii) to the surface with mri_vol2surf, then use mri_vol2label with the --surf option.

On 5/14/19 12:53 PM, Nillo, Ryan Michael R wrote: > >         External Email - Use Caution > > Hi Doug, > > I wanted to touch base with you on this. Is this the correct way to > project subcortical voxels to the nearest cortical vertex? We > want to > project subcortical ROI to the nearest cortical vertex. > Additionally, > is it possible to record which ROI in the Desikan atlas these > projected ROI fall under? > > Ryan Michael Nillo > Staff Research Associate I > University of California San Francisco > Department of Radiology and Biomedical Imaging > >> On Apr 24, 2019, at 10:50 AM, Nillo, Ryan Michael R >> <RyanMichael.Nillo@ucsf.edu mailto:RyanMichael.Nillo@ucsf.edu >> mailto:RyanMichael.Nillo@ucsf.edumailto:RyanMichael.Nillo@ucsf.edu >> mailto:RyanMichael.Nillo@ucsf.edu> wrote: >> >>         External Email - Use Caution >> >> >> Hi Doug, >> >> I used the command below to convert a volume to a label file. The >> volume is a binary mask highlighting a subcortical ROI that I am >> projecting to the closest vertex. I can visualize the label on the >> fsaverage lh.white surface. >> mri_vol2label --i >> /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/mri/rh.custom.nii >> >> --id 1 --l >> /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/label/rh.custom.label >> >> Ryan Michael Nillo >> Staff Research Associate I >> University of California San Francisco >> Department of Radiology and Biomedical Imaging >> >>> On Apr 24, 2019, at 9:48 AM, Greve, Douglas N.,Ph.D. >>> <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu> wrote: >>> >>> How did you create the label? Is it a surface-based label? Ie, >>> does >>> it have valid vertex indices as the first item in each label point >>> in the label file? >>> >>> On 4/24/2019 2:44 AM, Nillo, Ryan Michael R wrote: >>>> >>>>         External Email - Use Caution >>>> >>>> Hello Freesurfer developers, >>>> >>>> I am using the code below to generate the stats table for the >>>> ROI. >>>> mris_anatomical_stats -l >>>> /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/label/rh.custom.label >>>> >>>> -b subject rh white >>>> >>>> However, when I run this command, I get this output: >>>> >>>> limiting computations to label >>>> /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/label/rh.custom.label. >>>> >>>> >>>> reading volume >>>> /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/mri/wm.mgz... >>>> reading input surface >>>> /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/surf/rh.white... >>>> reading input pial surface >>>> /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/surf/rh.pial... >>>> reading input white surface >>>> /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/surf/rh.white... >>>> >>>> table columns are: >>>> number of vertices >>>> total surface area (mm^2) >>>> total gray matter volume (mm^3) >>>> average cortical thickness +- standard deviation (mm) >>>> integrated rectified mean curvature >>>> integrated rectified Gaussian curvature >>>> folding index >>>> intrinsic curvature index >>>> structure name >>>> >>>> I am getting no values for any of the metrics listed above. >>>> Is this >>>> a bug? >>>> >>>> Thanks in advance, >>>> >>>> Ryan Michael Nillo >>>> Staff Research Associate I >>>> University of California San Francisco >>>> Department of Radiology and Biomedical Imaging >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>> mailto:Freesurfer@nmr.mgh.harvard.edu >>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... >

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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . 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.

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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia.... 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.

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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia.... 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.