Re: [Freesurfer] viewing subcortical structures
Thanks! I don't have mri_binarize though. Is it included in 3.0.3? I am currently running stable 3.0.1 >>> Doug Greve <[EMAIL PROTECTED]> 7/17/2006 7:14 pm >>> One way to do it is with mri_binarize: mri_binarize --i aseg.mgz --min 1.5 --max 2.5 --o wm-lh.mask.nii This will find all the voxels whose value is between 1.5 and 2.5 and set them to 1 in the output. In this case, it will make a binary mask of the left cerebral white matter as that has a code of 2 (from FreeSurferColorLUT.txt). The output can be saved in any mri_convert output format (ie, mgh, mgz, analyze, nifti, etc). doug Sasha Wolosin wrote: >Dear all, > Does aseg save out masks of the various subcortical regions measured? > If so, is it possible to visualize and/or edit these in tkmedit/scuba, >or export them to an external format? >Thanks, >Sasha > > > >Disclaimer: >The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. >___ >Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] viewing subcortical structures
It is relatively new. You can get it from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize doug On Tue, 18 Jul 2006, Sasha Wolosin wrote: Thanks! I don't have mri_binarize though. Is it included in 3.0.3? I am currently running stable 3.0.1 Doug Greve <[EMAIL PROTECTED]> 7/17/2006 7:14 pm >>> One way to do it is with mri_binarize: mri_binarize --i aseg.mgz --min 1.5 --max 2.5 --o wm-lh.mask.nii This will find all the voxels whose value is between 1.5 and 2.5 and set them to 1 in the output. In this case, it will make a binary mask of the left cerebral white matter as that has a code of 2 (from FreeSurferColorLUT.txt). The output can be saved in any mri_convert output format (ie, mgh, mgz, analyze, nifti, etc). doug Sasha Wolosin wrote: Dear all, Does aseg save out masks of the various subcortical regions measured? If so, is it possible to visualize and/or edit these in tkmedit/scuba, or export them to an external format? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] viewing subcortical structures
thanks. Regarding subcortical segmentation in general, if I am using a Philips scanner should I be using the flag -cross-sequence when calling mri_ca_label? >>> Doug Greve <[EMAIL PROTECTED]> 7/18/2006 10:54 am >>> It is relatively new. You can get it from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize doug On Tue, 18 Jul 2006, Sasha Wolosin wrote: > Thanks! I don't have mri_binarize though. Is it included in 3.0.3? I > am currently running stable 3.0.1 > > Doug Greve <[EMAIL PROTECTED]> 7/17/2006 7:14 pm >>> > One way to do it is with mri_binarize: > > mri_binarize --i aseg.mgz --min 1.5 --max 2.5 --o wm-lh.mask.nii > > This will find all the voxels whose value is between 1.5 and 2.5 and > set > them to 1 in the output. In this case, it will make a binary mask of > the > left cerebral white matter as that has a code of 2 (from > FreeSurferColorLUT.txt). > > The output can be saved in any mri_convert output format (ie, mgh, mgz, > > analyze, nifti, etc). > > doug > > > Sasha Wolosin wrote: > >> Dear all, >> Does aseg save out masks of the various subcortical regions > measured? >> If so, is it possible to visualize and/or edit these in > tkmedit/scuba, >> or export them to an external format? >> Thanks, >> Sasha >> >> >> >> Disclaimer: >> The materials in this e-mail are private and may contain Protected > Health Information. Please note that e-mail is not necessarily > confidential or secure. Your use of e-mail constitutes your > acknowledgment of these confidentiality and security limitations. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying, distribution, or the taking of any action in > reliance on the contents of this information is strictly prohibited. If > you have received this e-mail in error, please immediately notify the > sender via telephone or return e-mail. >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] viewing subcortical structures
no, you should use -align (which I think is the default now) On Tue, 18 Jul 2006, Sasha Wolosin wrote: thanks. Regarding subcortical segmentation in general, if I am using a Philips scanner should I be using the flag -cross-sequence when calling mri_ca_label? Doug Greve <[EMAIL PROTECTED]> 7/18/2006 10:54 am >>> It is relatively new. You can get it from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize doug On Tue, 18 Jul 2006, Sasha Wolosin wrote: Thanks! I don't have mri_binarize though. Is it included in 3.0.3? I am currently running stable 3.0.1 Doug Greve <[EMAIL PROTECTED]> 7/17/2006 7:14 pm >>> One way to do it is with mri_binarize: mri_binarize --i aseg.mgz --min 1.5 --max 2.5 --o wm-lh.mask.nii This will find all the voxels whose value is between 1.5 and 2.5 and set them to 1 in the output. In this case, it will make a binary mask of the left cerebral white matter as that has a code of 2 (from FreeSurferColorLUT.txt). The output can be saved in any mri_convert output format (ie, mgh, mgz, analyze, nifti, etc). doug Sasha Wolosin wrote: Dear all, Does aseg save out masks of the various subcortical regions measured? If so, is it possible to visualize and/or edit these in tkmedit/scuba, or export them to an external format? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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
[Freesurfer] Expanding pial outline
I ran two brains through autorecon2 and the pial line is drawn too close at many parts and cuts off parts of the brain. I looked through the website and only saw instructions for how to remove stuff and make the pial line smaller. I was wondering if there is a command I can run to expand the pial line or what is the best way to edit the files so more brain is included. I was looking at the threshold tools and couldn't see a way to convert say anything with a value of 30-40 to 60, so I was wondering if that was also possible. Thanks -- -Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Expanding pial outline
can you send a snapshot of what you mean? Make sure that it's not the skull stripping removing things (look at the brainmask.mgz volume) On Tue, 18 Jul 2006, Jake Freimer wrote: I ran two brains through autorecon2 and the pial line is drawn too close at many parts and cuts off parts of the brain. I looked through the website and only saw instructions for how to remove stuff and make the pial line smaller. I was wondering if there is a command I can run to expand the pial line or what is the best way to edit the files so more brain is included. I was looking at the threshold tools and couldn't see a way to convert say anything with a value of 30-40 to 60, so I was wondering if that was also possible. Thanks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
