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
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