External Email - Use Caution Thank you. How do I generate this image? It wasn't generated using recon-all.
On Thu, Jul 23, 2020 at 10:55 AM Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > aparc+aseg does not have the thalamic nuclei. You need to run it on > ThalamicNuclei.v10.T1.FSvoxelSpace.mgz > > On 7/22/2020 6:26 PM, Al Qadi, Ameen wrote: > > External Email - Use Caution > > Hi Douglas, > > > mri_segstats wouldn't generate binary ROI masks, so I tried using > *mri_binarize* and *mri_extract_label* to produce masks for thalamic > nuclei, but I run into the same problem of generating empty masks (these > commands worked for other ROIs): > > > > - $: mri_extract_label aparc+aseg.nii 8005 thalamus_vent_lat.nii > > > > reading volume from aparc+aseg.nii... > > extracting label 8005 () > > writing output to thalamus_vent_lat.nii. > > > > - $: mri_binarize --i aparc+aseg.nii --o thalamus_vent_lat.nii --match > 8005 > > 7.1.0 > > cwd /data/freesurfer/subjects/S12452/mri > > cmdline mri_binarize --i aparc+aseg.nii --o thalamus_vent_lat.nii --match > 8005 > > sysname ##### > > hostname ##### > > machine ##### > > user ###### > > > input aparc+aseg.nii > > frame 0 > > nErode3d 0 > > nErode2d 0 > > output thalamus_vent_lat.nii > > Binarizing based on matching values > > nMatch 1 > > 0 8005 > > binval 1 > > binvalnot 0 > > fstart = 0, fend = 0, nframes = 1 > > Found 0 values in range > > Counting number of voxels in first frame > > Found -1 voxels in final mask > > Count: -1 -0.343000 32768000 -0.000003 > > mri_binarize done > > > I'd appreciate any feedback you may have. > > > > Best, > > Ameen > > > On Tue, Jul 21, 2020 at 10:34 AM Douglas N. Greve <dgr...@mgh.harvard.edu> > wrote: > >> I don't know. I'm not that familiar with FSL programs. If you want our >> help, try using mri_segstats. If something goes wrong send the command line >> >> On 7/21/2020 10:26 AM, Al Qadi, Ameen wrote: >> >> External Email - Use Caution >> Hi Douglas, >> >> I see the CLUT file, it's the same one I've been using. I have been using >> FSL (fslmaths) to extract anatomical ROIs from the aparc+aseg using the >> CLUT indices as thresholds. This normally works, but results in empty ROIs >> for thalamic nuclei (but not for whole thalamus). What do you think could >> be the problem? >> >> Best, >> Ameen >> >> On Fri, Jul 17, 2020 at 10:33 AM Douglas N. Greve <dgr...@mgh.harvard.edu> >> wrote: >> >>> >>> >>> On 7/17/2020 10:25 AM, Al Qadi, Ameen wrote: >>> >>> External Email - Use Caution >>> >>> Dear Freesurfer Developers, >>> >>> >>> I hope this email finds you all safe and well. I have two questions >>> regarding the new version of freesurfer: >>> >>> - Is there a new CLUT associated with FS7? I tried to use the CLUT >>> labels to extract thalamic subnuclei ROIs, but got empty ROI files. >>> >>> They should be in $FREESURFER/FreeSurferColorLUT.txt >>> How are you extracting? >>> >>> >>> - Given that Freesurfer version 7 contains segmentations not >>> previously generated in recon-all (i.e. hippocampal subfields), is it >>> possible to extract these ROIs using aparc+aseg images generated using >>> previous versions of Freesurfer? Or do we need to repeat the cortical >>> parcellations (i.e. rerun recon-all) using FS7? >>> >>> You can run the hippocamal and thalamic segs on FS version 6 subjects. >>> >>> I’d highly appreciate your time and feedback on this matter. Thank you. >>> >>> >>> Best, >>> >>> Ameen >>> -- >>> Ameen Al Qadi >>> MSBS Candidate >>> Icahn School Of Medicine at Mount Sinai '20 >>> +1-646-500-1521 >>> ameen.alq...@icahn.mssm.edu >>> >>> _______________________________________________ >>> Freesurfer mailing >>> listfreesur...@nmr.mgh.harvard.eduhttps://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 >> >> >> >> -- >> Ameen Al Qadi >> MSBS Candidate >> Icahn School Of Medicine at Mount Sinai '20 >> +1-646-500-1521 >> ameen.alq...@icahn.mssm.edu >> -- >> Ameen Al Qadi >> MSBS Candidate >> Icahn School Of Medicine at Mount Sinai '20 >> +1-646-500-1521 >> ameen.alq...@icahn.mssm.edu >> >> >> 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. >> > > > -- > Ameen Al Qadi > MSBS Candidate > Icahn School Of Medicine at Mount Sinai '20 > +1-646-500-1521 > ameen.alq...@icahn.mssm.edu > > > -- Ameen Al Qadi MSBS Candidate Icahn School Of Medicine at Mount Sinai '20 +1-646-500-1521 ameen.alq...@icahn.mssm.edu
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