Hi Freesurfer experts,
I am wondering if it is possible to remove the original labels after extending the parcellation by 2mm into the WM for tractography? I don't wish to have tractography run on both sets of labels considering the algorithm would take into account the streamlines terminating at nodes defined by the labels so it doesn't quite make sense to count streamlines terminating at both the original label separately from the new label extending into the WM.
I used the following command for growing the parcellation into WM:
mri_aparc2aseg --s subj --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o $SUBJECTS_DIR/$subj/mri/aparc+aseg+2mm.nii.gz
Would appreciate help and suggestions!
Thanks,
Michiko.
You mean you want to remove everything but the WM labels? You can do it in two steps:
1. Create a mask of the wm labels:
mri_binarize --i aparc+aseg+2mm.nii.gz --min 2999.5 --max 4035.5 --o wm.mask.nii.gz
2. Mask the wmparc:
mri_mask aparc+aseg+2mm.nii.gz wm.mask.nii.gz aparc+aseg+2mm.masked.nii.gz
On 2/4/18 5:28 PM, Michiko H. wrote:
Hi Freesurfer experts,
I am wondering if it is possible to remove the original labels after extending the parcellation by 2mm into the WM for tractography? I don't wish to have tractography run on both sets of labels considering the algorithm would take into account the streamlines terminating at nodes defined by the labels so it doesn't quite make sense to count streamlines terminating at both the original label separately from the new label extending into the WM.
I used the following command for growing the parcellation into WM:
mri_aparc2aseg --s subj --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o $SUBJECTS_DIR/$subj/mri/aparc+aseg+2mm.nii.gz
Would appreciate help and suggestions!
Thanks,
Michiko.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
That's very helpful, thank you! I have 2 follow-up questions though:
1. Is it possible to merge the cortical label (e.g. label 1001 ctx-lh-bankssts) with its corresponding label that extends into the WM (e.g. label 3001 wm-lh-bankssts)? I'm not completely sure but this may/may not give better results when tracking between labels as nodes.
2. Is it possible to include the subcortical structures in the final masked image?
Thank you so much! Michiko
On Mon, Feb 5, 2018 at 12:30 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
You mean you want to remove everything but the WM labels? You can do it in two steps:
- Create a mask of the wm labels:
mri_binarize --i aparc+aseg+2mm.nii.gz --min 2999.5 --max 4035.5 --o wm.mask.nii.gz
- Mask the wmparc:
mri_mask aparc+aseg+2mm.nii.gz wm.mask.nii.gz aparc+aseg+2mm.masked.nii.gz
On 2/4/18 5:28 PM, Michiko H. wrote:
Hi Freesurfer experts,
I am wondering if it is possible to remove the original labels after extending the parcellation by 2mm into the WM for tractography? I don't wish to have tractography run on both sets of labels considering the algorithm would take into account the streamlines terminating at nodes defined by the labels so it doesn't quite make sense to count streamlines terminating at both the original label separately from the new label extending into the WM.
I used the following command for growing the parcellation into WM:
mri_aparc2aseg --s subj --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o $SUBJECTS_DIR/$subj/mri/aparc+aseg+2mm.nii.gz
Would appreciate help and suggestions!
Thanks,
Michiko.
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
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.
On 2/6/18 5:26 PM, Michiko H. wrote:
Hi Doug,
That's very helpful, thank you! I have 2 follow-up questions though:
- Is it possible to merge the cortical label (e.g. label 1001
ctx-lh-bankssts) with its corresponding label that extends into the WM (e.g. label 3001 wm-lh-bankssts)? I'm not completely sure but this may/may not give better results when tracking between labels as nodes.
You can use something like mri_binarize --replaceonly 1001 3001 --i aparc+aseg+2mm.masked.nii.gz --o aparc+aseg+2mm.masked.merged.nii.gz
- Is it possible to include the subcortical structures in the final
masked image?
Yes, use mri_binarize --i aparc+aseg+2mm.nii.gz --match 10 11 12 ... --o aparc+aseg+2mm.subcort.nii.gz where 10 11 12 is a list of the ids of the subcortical structures you want Then fscalc aparc+aseg+2mm.subcort.nii.gz add aparc+aseg+2mm.masked.nii.gz -o both.nii.gz
Thank you so much! Michiko
On Mon, Feb 5, 2018 at 12:30 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
You mean you want to remove everything but the WM labels? You can do it in two steps: 1. Create a mask of the wm labels: mri_binarize --i aparc+aseg+2mm.nii.gz --min 2999.5 --max 4035.5 --o wm.mask.nii.gz 2. Mask the wmparc: mri_mask aparc+aseg+2mm.nii.gz wm.mask.nii.gz aparc+aseg+2mm.masked.nii.gz On 2/4/18 5:28 PM, Michiko H. wrote:Hi Freesurfer experts, I am wondering if it is possible to remove the original labels after extending the parcellation by 2mm into the WM for tractography? I don't wish to have tractography run on both sets of labels considering the algorithm would take into account the streamlines terminating at nodes defined by the labels so it doesn't quite make sense to count streamlines terminating at both the original label separately from the new label extending into the WM. I used the following command for growing the parcellation into WM: mri_aparc2aseg --s subj --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o $SUBJECTS_DIR/$subj/mri/aparc+aseg+2mm.nii.gz Would appreciate help and suggestions! Thanks, Michiko. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <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
Hi Doug,
Thanks - this is extremely helpful!
With regard to the first command: mri_binarize --replace 1001 3001 --i aparc+aseg+2mm.masked.nii.gz --o aparc+aseg+2mm.masked.merged.nii.gz Since I'd like to replace every cortical label with its corresponding WM label on both hemispheres, is there a more efficient way of doing this rather than having to manually write '--replace 10xx 30xx' repetitively?
Thanks very much again! M.
On Fri, Feb 9, 2018 at 12:53 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
On 2/6/18 5:26 PM, Michiko H. wrote:
Hi Doug,
That's very helpful, thank you! I have 2 follow-up questions though:
- Is it possible to merge the cortical label (e.g. label 1001
ctx-lh-bankssts) with its corresponding label that extends into the WM (e.g. label 3001 wm-lh-bankssts)? I'm not completely sure but this may/may not give better results when tracking between labels as nodes.
You can use something like mri_binarize --replaceonly 1001 3001 --i aparc+aseg+2mm.masked.nii.gz --o aparc+aseg+2mm.masked.merged.nii.gz
- Is it possible to include the subcortical structures in the final
masked image?
Yes, use mri_binarize --i aparc+aseg+2mm.nii.gz --match 10 11 12 ... --o aparc+aseg+2mm.subcort.nii.gz where 10 11 12 is a list of the ids of the subcortical structures you want Then fscalc aparc+aseg+2mm.subcort.nii.gz add aparc+aseg+2mm.masked.nii.gz -o both.nii.gz
Thank you so much! Michiko
On Mon, Feb 5, 2018 at 12:30 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
You mean you want to remove everything but the WM labels? You can do it in two steps:
- Create a mask of the wm labels:
mri_binarize --i aparc+aseg+2mm.nii.gz --min 2999.5 --max 4035.5 --o wm.mask.nii.gz
- Mask the wmparc:
mri_mask aparc+aseg+2mm.nii.gz wm.mask.nii.gz aparc+aseg+2mm.masked.nii.gz
On 2/4/18 5:28 PM, Michiko H. wrote:
Hi Freesurfer experts,
I am wondering if it is possible to remove the original labels after extending the parcellation by 2mm into the WM for tractography? I don't wish to have tractography run on both sets of labels considering the algorithm would take into account the streamlines terminating at nodes defined by the labels so it doesn't quite make sense to count streamlines terminating at both the original label separately from the new label extending into the WM.
I used the following command for growing the parcellation into WM:
mri_aparc2aseg --s subj --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o $SUBJECTS_DIR/$subj/mri/aparc+aseg+2mm.nii.gz
Would appreciate help and suggestions!
Thanks,
Michiko.
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
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 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
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.
No. I'd write a script to do it
On 02/12/2018 12:17 PM, Michiko H. wrote:
Hi Doug,
Thanks - this is extremely helpful!
With regard to the first command: mri_binarize --replace 1001 3001 --i aparc+aseg+2mm.masked.nii.gz --o aparc+aseg+2mm.masked.merged.nii.gz Since I'd like to replace every cortical label with its corresponding WM label on both hemispheres, is there a more efficient way of doing this rather than having to manually write '--replace 10xx 30xx' repetitively?
Thanks very much again! M.
On Fri, Feb 9, 2018 at 12:53 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
On 2/6/18 5:26 PM, Michiko H. wrote:Hi Doug, That's very helpful, thank you! I have 2 follow-up questions though: 1. Is it possible to merge the cortical label (e.g. label 1001 ctx-lh-bankssts) with its corresponding label that extends into the WM (e.g. label 3001 wm-lh-bankssts)? I'm not completely sure but this may/may not give better results when tracking between labels as nodes.You can use something like mri_binarize --replaceonly 1001 3001 --i aparc+aseg+2mm.masked.nii.gz --o aparc+aseg+2mm.masked.merged.nii.gz2. Is it possible to include the subcortical structures in the final masked image?Yes, use mri_binarize --i aparc+aseg+2mm.nii.gz --match 10 11 12 ... --o aparc+aseg+2mm.subcort.nii.gz where 10 11 12 is a list of the ids of the subcortical structures you want Then fscalc aparc+aseg+2mm.subcort.nii.gz add aparc+aseg+2mm.masked.nii.gz -o both.nii.gzThank you so much! Michiko On Mon, Feb 5, 2018 at 12:30 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: You mean you want to remove everything but the WM labels? You can do it in two steps: 1. Create a mask of the wm labels: mri_binarize --i aparc+aseg+2mm.nii.gz --min 2999.5 --max 4035.5 --o wm.mask.nii.gz 2. Mask the wmparc: mri_mask aparc+aseg+2mm.nii.gz wm.mask.nii.gz aparc+aseg+2mm.masked.nii.gz On 2/4/18 5:28 PM, Michiko H. wrote:Hi Freesurfer experts, I am wondering if it is possible to remove the original labels after extending the parcellation by 2mm into the WM for tractography? I don't wish to have tractography run on both sets of labels considering the algorithm would take into account the streamlines terminating at nodes defined by the labels so it doesn't quite make sense to count streamlines terminating at both the original label separately from the new label extending into the WM. I used the following command for growing the parcellation into WM: mri_aparc2aseg --s subj --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o $SUBJECTS_DIR/$subj/mri/aparc+aseg+2mm.nii.gz Would appreciate help and suggestions! Thanks, Michiko. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <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
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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Michiko H.