Respected Sir,
I meant to ask that if i want to separate for example hippocampus and view as a separate volume what code should i implement?
On Mon, Oct 2, 2017 at 6:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
what do you mean by separate? Extract into a separate volume? If so, you can use mri_extract_labels or mri_binarize with the --match flag.
cheers Bruce On Mon, 2 Oct 2017, Vidhu Agrawal wrote:
how to separate any sub cortical region in freesurfer ?
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Hi Vidhu, You could use mri_vol2label or mri_binarize ( check freesurfer site or help in terminal for details ) Cheers On Tue, Oct 3, 2017 at 11:05 AM Vidhu Agrawal mail2vidhu.alld@gmail.com wrote:
Respected Sir,
I meant to ask that if i want to separate for example hippocampus and view as a separate volume what code should i implement?
On Mon, Oct 2, 2017 at 6:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
what do you mean by separate? Extract into a separate volume? If so, you can use mri_extract_labels or mri_binarize with the --match flag.
cheers Bruce On Mon, 2 Oct 2017, Vidhu Agrawal wrote:
how to separate any sub cortical region in freesurfer ?
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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.
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Respected sir,
I have run the code:
mri_label2vol --label lh-avg_central_sulcus.label --temp 1.nii --reg register.dat --fillthresh .5 --o cent-lh.nii.gz
it is giving error:
Loading registration from register.dat regio_read_register(): No such file or directory Could not open register.dat
*There is no such directory formed after recon-all.*
On Tue, Oct 3, 2017 at 1:08 PM, Fereshte fereshte.ramezani@gmail.com wrote:
Hi Vidhu, You could use mri_vol2label or mri_binarize ( check freesurfer site or help in terminal for details ) Cheers
On Tue, Oct 3, 2017 at 11:05 AM Vidhu Agrawal mail2vidhu.alld@gmail.com wrote:
Respected Sir,
I meant to ask that if i want to separate for example hippocampus and view as a separate volume what code should i implement?
On Mon, Oct 2, 2017 at 6:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
what do you mean by separate? Extract into a separate volume? If so, you can use mri_extract_labels or mri_binarize with the --match flag.
cheers Bruce On Mon, 2 Oct 2017, Vidhu Agrawal wrote:
how to separate any sub cortical region in 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 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 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.
Respected Sir,
A segment.dat file is formed and when i am running:
mri_label2vol --label lh-avg_central_sulcus.label --temp 1.nii --reg segment.dat --fillthresh .5 --o cent-lh.nii.gz
Then error is coming:
Error reading betplaneres from segment.dat
On Tue, Oct 3, 2017 at 4:13 PM, Vidhu Agrawal mail2vidhu.alld@gmail.com wrote:
Respected sir,
I have run the code:
mri_label2vol --label lh-avg_central_sulcus.label --temp 1.nii --reg register.dat --fillthresh .5 --o cent-lh.nii.gz
it is giving error:
Loading registration from register.dat regio_read_register(): No such file or directory Could not open register.dat
*There is no such directory formed after recon-all.*
On Tue, Oct 3, 2017 at 1:08 PM, Fereshte fereshte.ramezani@gmail.com wrote:
Hi Vidhu, You could use mri_vol2label or mri_binarize ( check freesurfer site or help in terminal for details ) Cheers
On Tue, Oct 3, 2017 at 11:05 AM Vidhu Agrawal mail2vidhu.alld@gmail.com wrote:
Respected Sir,
I meant to ask that if i want to separate for example hippocampus and view as a separate volume what code should i implement?
On Mon, Oct 2, 2017 at 6:44 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote:
what do you mean by separate? Extract into a separate volume? If so, you can use mri_extract_labels or mri_binarize with the --match flag.
cheers Bruce On Mon, 2 Oct 2017, Vidhu Agrawal wrote:
how to separate any sub cortical region in 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 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 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.
use, for example,
mri_binarize --i aseg.mgz --match 17 --o left-hippo.mgz
The 17 is the index for left hippo as found in $FREESURFER_HOME/FreeSurferColorsLUT.txt
On 10/3/17 6:48 AM, Vidhu Agrawal wrote:
Respected Sir,
A segment.dat file is formed and when i am running:
mri_label2vol --label lh-avg_central_sulcus.label --temp 1.nii --reg segment.dat --fillthresh .5 --o cent-lh.nii.gz
Then error is coming:
Error reading betplaneres from segment.dat
On Tue, Oct 3, 2017 at 4:13 PM, Vidhu Agrawal <mail2vidhu.alld@gmail.com mailto:mail2vidhu.alld@gmail.com> wrote:
Respected sir, I have run the code: mri_label2vol --label lh-avg_central_sulcus.label --temp 1.nii --reg register.dat --fillthresh .5 --o cent-lh.nii.gz it is giving error: Loading registration from register.dat regio_read_register(): No such file or directory Could not open register.dat *There is no such directory formed after recon-all.* On Tue, Oct 3, 2017 at 1:08 PM, Fereshte <fereshte.ramezani@gmail.com <mailto:fereshte.ramezani@gmail.com>> wrote: Hi Vidhu, You could use mri_vol2label or mri_binarize ( check freesurfer site or help in terminal for details ) Cheers On Tue, Oct 3, 2017 at 11:05 AM Vidhu Agrawal <mail2vidhu.alld@gmail.com <mailto:mail2vidhu.alld@gmail.com>> wrote: Respected Sir, I meant to ask that if i want to separate for example hippocampus and view as a separate volume what code should i implement? On Mon, Oct 2, 2017 at 6:44 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: what do you mean by separate? Extract into a separate volume? If so, you can use mri_extract_labels or mri_binarize with the --match flag. cheers Bruce On Mon, 2 Oct 2017, Vidhu Agrawal wrote: > how to separate any sub cortical region in 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> 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> 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
yes, you can do that with either of the binaries I mentioned
cheers Bruce On Tue, 3 Oct 2017, Vidhu Agrawal wrote:
Respected Sir,
I meant to ask that if i want to separate for example hippocampus and view as a separate volume what code should i implement?
On Mon, Oct 2, 2017 at 6:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: what do you mean by separate? Extract into a separate volume? If so, you can use mri_extract_labels or mri_binarize with the --match flag.
cheers Bruce On Mon, 2 Oct 2017, Vidhu Agrawal wrote: > how to separate any sub cortical region in 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@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas Greve -
Fereshte -
Vidhu Agrawal