Re: [Freesurfer] fsaverage6 ?h.cortex.flat.patch files
Thank you very much for this!
On Fri, Sep 14, 2018 at 2:53 PM, Hoopes, Andrew
wrote:
> Hi Lauren,
>
>
>
> You can find the new write_patch.m function here -
> https://github.com/freesurfer/freesurfer/blob/dev/matlab/write_patch.m
>
>
>
> You can install it with:
>
>
>
> curl https://raw.githubusercontent.com/freesurfer/freesurfer/dev/
> matlab/write_patch.m > write_patch.m
>
> cp write_patch.m ${FREESURFER_HOME}/matlab
>
>
>
> best
>
> Andrew
>
>
>
>
>
> *From: * on behalf of "Dinicola,
> Lauren"
> *Reply-To: *FS Help
> *Date: *Monday, August 13, 2018 at 9:19 AM
> *To: *FS Help
> *Subject: *Re: [Freesurfer] fsaverage6 ?h.cortex.flat.patch files
>
>
>
> Thank you!
>
>
>
> On Sun, Aug 12, 2018 at 6:49 PM, Bruce Fischl
> wrote:
>
> oh, maybe we never got around to writing a write_patch.m. We'll put one
> together and send it to you
> Bruce
>
>
> On Sun, 12 Aug 2018, Dinicola, Lauren wrote:
>
> Hi Dr. Fischl,
> Thank you so much for this response. This is a great idea, but I have not
> yet been successful with
> writing out the adjusted structure to a ?h.cortex.flat.patch file.
> Is there a specific command for writing a patch?
>
> Thank you again,
>
> Lauren
>
> On Wed, Aug 8, 2018 at 3:04 PM, Bruce Fischl
> wrote:
> sorry, no. You could create them fairly easily from fsaverage7,
> since the
> fsaverage6 is a subset of the vertices in 7. Just pick out the
> locations of
> the fsaverage6 vertices from the fsaverage7 flat map and write it
> out as a
> flat map (easy to do in matlab for example)
>
> On Wed,
> 8 Aug 2018, Dinicola, Lauren wrote:
>
> > Hi all,
> > We are hoping to visualize flat maps of surface data sampled to
> fsaverage6. Do
> 'flat.patch' files
> > exist already for fsaverage6?
> >
> > Thank you for any help,
> >
> > Lauren DiNicola
> >
> >
> ___
> 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.
Re: [Freesurfer] Parcellations (e.g., labels for Brodmann Areas) for Connectome Workbench?
Hi Doug, I actually got this to work by just changing .aparc.gii to .label.gii & opening using the workbench; please disregard, and I apologize for taking your time. All the best, Lauren On Thu, Sep 6, 2018 at 2:47 PM, Dinicola, Lauren wrote: > Hi Doug, > > I have successfully converted an individual BA label to a .label.gii file > and opened it; I have not been able to open the Gifti .aparc.annot file > after attempting to convert the .annot file in Connectome Workbench. So I > am wondering if a full parcellation already exists in dlabel.gii format. > > Thank you again, > > Lauren > > On Thu, Sep 6, 2018 at 12:32 PM, Douglas N. Greve > wrote: > >> what is the compatible format? >> >> On 09/06/2018 11:54 AM, Dinicola, Lauren wrote: >> > Hi all, >> > >> > I have been searching for the Freesurfer label or annot files for >> > fsaverage in the formats compatible with Connectome Workbench and have >> > not yet found them. Are these available? >> > If not, is there a way to convert all the BA labels to then convert >> > them to borders for viewing on fsaverage? I tried mris_convert -annot >> > but was unsuccessful opening the output files. >> > >> > Thank you very much for any help. >> > >> > Lauren >> > >> > >> > ___ >> > 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 >> >> >> 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.
Re: [Freesurfer] Parcellations (e.g., labels for Brodmann Areas) for Connectome Workbench?
Hi Doug, I have successfully converted an individual BA label to a .label.gii file and opened it; I have not been able to open the Gifti .aparc.annot file after attempting to convert the .annot file in Connectome Workbench. So I am wondering if a full parcellation already exists in dlabel.gii format. Thank you again, Lauren On Thu, Sep 6, 2018 at 12:32 PM, Douglas N. Greve wrote: > what is the compatible format? > > On 09/06/2018 11:54 AM, Dinicola, Lauren wrote: > > Hi all, > > > > I have been searching for the Freesurfer label or annot files for > > fsaverage in the formats compatible with Connectome Workbench and have > > not yet found them. Are these available? > > If not, is there a way to convert all the BA labels to then convert > > them to borders for viewing on fsaverage? I tried mris_convert -annot > > but was unsuccessful opening the output files. > > > > Thank you very much for any help. > > > > Lauren > > > > > > ___ > > 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 > > > 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] Parcellations (e.g., labels for Brodmann Areas) for Connectome Workbench?
Hi all, I have been searching for the Freesurfer label or annot files for fsaverage in the formats compatible with Connectome Workbench and have not yet found them. Are these available? If not, is there a way to convert all the BA labels to then convert them to borders for viewing on fsaverage? I tried mris_convert -annot but was unsuccessful opening the output files. Thank you very much for any help. Lauren ___ 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.
Re: [Freesurfer] fsaverage6 ?h.cortex.flat.patch files
Thank you! On Sun, Aug 12, 2018 at 6:49 PM, Bruce Fischl wrote: > oh, maybe we never got around to writing a write_patch.m. We'll put one > together and send it to you > Bruce > > On Sun, 12 Aug 2018, Dinicola, Lauren wrote: > > Hi Dr. Fischl, >> Thank you so much for this response. This is a great idea, but I have not >> yet been successful with >> writing out the adjusted structure to a ?h.cortex.flat.patch file. >> Is there a specific command for writing a patch? >> >> Thank you again, >> >> Lauren >> >> On Wed, Aug 8, 2018 at 3:04 PM, Bruce Fischl >> wrote: >> sorry, no. You could create them fairly easily from fsaverage7, >> since the >> fsaverage6 is a subset of the vertices in 7. Just pick out the >> locations of >> the fsaverage6 vertices from the fsaverage7 flat map and write it >> out as a >> flat map (easy to do in matlab for example) >> >> On Wed, >> 8 Aug 2018, Dinicola, Lauren wrote: >> >> > Hi all, >> > We are hoping to visualize flat maps of surface data sampled to >> fsaverage6. Do >> 'flat.patch' files >> > exist already for fsaverage6? >> > >> > Thank you for any help, >> > >> > Lauren DiNicola >> > >> > >> ___ >> 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.
Re: [Freesurfer] fsaverage6 ?h.cortex.flat.patch files
Hi Dr. Fischl, Thank you so much for this response. This is a great idea, but I have not yet been successful with writing out the adjusted structure to a ?h.cortex.flat.patch file. Is there a specific command for writing a patch? Thank you again, Lauren On Wed, Aug 8, 2018 at 3:04 PM, Bruce Fischl wrote: > sorry, no. You could create them fairly easily from fsaverage7, since the > fsaverage6 is a subset of the vertices in 7. Just pick out the locations > of > the fsaverage6 vertices from the fsaverage7 flat map and write it out as a > flat map (easy to do in matlab for example) > > On Wed, > 8 Aug 2018, Dinicola, Lauren wrote: > > > Hi all, > > We are hoping to visualize flat maps of surface data sampled to > fsaverage6. Do 'flat.patch' files > > exist already for fsaverage6? > > > > Thank you for any help, > > > > Lauren DiNicola > > > > > ___ > 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.
Re: [Freesurfer] fsaverage6 ?h.cortex.flat.patch files
Thank you so much for this response! I appreciate the help. Lauren On Wed, Aug 8, 2018 at 3:04 PM, Bruce Fischl wrote: > sorry, no. You could create them fairly easily from fsaverage7, since the > fsaverage6 is a subset of the vertices in 7. Just pick out the locations > of > the fsaverage6 vertices from the fsaverage7 flat map and write it out as a > flat map (easy to do in matlab for example) > > On Wed, > 8 Aug 2018, Dinicola, Lauren wrote: > > > Hi all, > > We are hoping to visualize flat maps of surface data sampled to > fsaverage6. Do 'flat.patch' files > > exist already for fsaverage6? > > > > Thank you for any help, > > > > Lauren DiNicola > > > > > ___ > 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] fsaverage6 ?h.cortex.flat.patch files
Hi all, We are hoping to visualize flat maps of surface data sampled to fsaverage6. Do 'flat.patch' files exist already for fsaverage6? Thank you for any help, Lauren DiNicola ___ 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.
