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.
- 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?
I’d highly appreciate your time and feedback on this matter. Thank you.
Best,
Ameen
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.alqadi@icahn.mssm.edu mailto:ameen.alqadi@icahn.mssm.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 dgreve@mgh.harvard.edu wrote:
On 7/17/2020 10:25 AM, Al Qadi, Ameen wrote:
External Email - Use CautionDear 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.alqadi@icahn.mssm.edu
Freesurfer mailing listFreesurfer@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
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 dgreve@mgh.harvard.edu wrote:
On 7/17/2020 10:25 AM, Al Qadi, Ameen wrote:
External Email - Use CautionDear 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.alqadi@icahn.mssm.edu
Freesurfer mailing listFreesurfer@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
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 <dgreve@mgh.harvard.edu mailto:dgreve@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.alqadi@icahn.mssm.edu <mailto:ameen.alqadi@icahn.mssm.edu> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.alqadi@icahn.mssm.edu mailto:ameen.alqadi@icahn.mssm.edu -- Ameen Al Qadi MSBS Candidate Icahn School Of Medicine at Mount Sinai '20 +1-646-500-1521 ameen.alqadi@icahn.mssm.edu mailto:ameen.alqadi@icahn.mssm.edu
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 dgreve@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 CautionHi 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 dgreve@mgh.harvard.edu wrote:
On 7/17/2020 10:25 AM, Al Qadi, Ameen wrote:
External Email - Use CautionDear 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.alqadi@icahn.mssm.edu
Freesurfer mailing listFreesurfer@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.alqadi@icahn.mssm.edu -- Ameen Al Qadi MSBS Candidate Icahn School Of Medicine at Mount Sinai '20 +1-646-500-1521 ameen.alqadi@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.
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 ######
inputaparc+aseg.nii
frame0
nErode3d 0
nErode2d 0
output thalamus_vent_lat.nii
Binarizing based on matching values
nMatch 1
08005
binval1
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 <dgreve@mgh.harvard.edu mailto:dgreve@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 <dgreve@mgh.harvard.edu <mailto:dgreve@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.alqadi@icahn.mssm.edu <mailto:ameen.alqadi@icahn.mssm.edu> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.alqadi@icahn.mssm.edu <mailto:ameen.alqadi@icahn.mssm.edu> -- Ameen Al Qadi MSBS Candidate Icahn School Of Medicine at Mount Sinai '20 +1-646-500-1521 ameen.alqadi@icahn.mssm.edu <mailto:ameen.alqadi@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.alqadi@icahn.mssm.edu mailto:ameen.alqadi@icahn.mssm.edu
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 dgreve@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 CautionHi 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 dgreve@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 CautionHi 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 dgreve@mgh.harvard.edu wrote:
On 7/17/2020 10:25 AM, Al Qadi, Ameen wrote:
External Email - Use CautionDear 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.alqadi@icahn.mssm.edu
Freesurfer mailing listFreesurfer@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.alqadi@icahn.mssm.edu -- Ameen Al Qadi MSBS Candidate Icahn School Of Medicine at Mount Sinai '20 +1-646-500-1521 ameen.alqadi@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.alqadi@icahn.mssm.edu
http://freesurfer.net/fswiki/ThalamicNuclei
On 7/23/2020 11:04 AM, Al Qadi, Ameen wrote:
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 <dgreve@mgh.harvard.edu mailto:dgreve@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 ###### inputaparc+aseg.nii frame0 nErode3d 0 nErode2d 0 output thalamus_vent_lat.nii Binarizing based on matching values nMatch 1 08005 binval1 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 <dgreve@mgh.harvard.edu <mailto:dgreve@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 <dgreve@mgh.harvard.edu <mailto:dgreve@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.alqadi@icahn.mssm.edu <mailto:ameen.alqadi@icahn.mssm.edu> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.alqadi@icahn.mssm.edu <mailto:ameen.alqadi@icahn.mssm.edu> -- Ameen Al Qadi MSBS Candidate Icahn School Of Medicine at Mount Sinai '20 +1-646-500-1521 ameen.alqadi@icahn.mssm.edu <mailto:ameen.alqadi@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.alqadi@icahn.mssm.edu <mailto:ameen.alqadi@icahn.mssm.edu>-- Ameen Al Qadi MSBS Candidate Icahn School Of Medicine at Mount Sinai '20 +1-646-500-1521 ameen.alqadi@icahn.mssm.edu mailto:ameen.alqadi@icahn.mssm.edu
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Al Qadi, Ameen -
Douglas N. Greve