[Freesurfer] label file from freesurfer 5.3
Dear FreeSurfer experts, When I tried to use FreeSurfer 6.0.0’s freeview to open a label file generated by FreeSurfer 5.3, I could not see anything. Is it incompatibility issue going on here? Thanks, Daniel ___ 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] label file from freesurfer 5.3
Good to know, then, it must be the way I interact with FS 6.0.0 that is wrong. It’s a surface label. Can I send you the label file to see if you could view that in FS 6.0.0’s freeview using command line? -- Y.J. Daniel Yang, Ph.D. Assistant Research Professor Autism and Neurodevelopmental Disorders Institute The George Washington University and Children’s National Health System E-mail: daniely...@gwu.edu <mailto:daniely...@gwu.edu> > On May 31, 2017, at 1:37 PM, Bruce Fischl wrote: > > no, the label format should be backwards compatible. Was it a surface or > volume label? > On Wed, 31 May 2017, Daniel Yang wrote: > >> Dear FreeSurfer experts, >> >> When I tried to use FreeSurfer 6.0.0’s freeview to open a label file >> generated by FreeSurfer 5.3, I could not see anything. >> >> Is it incompatibility issue going on here? >> >> Thanks, >> Daniel >> >> >> ___ >> 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] label file from freesurfer 5.3
Thank you. I just sent it to your mailbox. -- Y.J. Daniel Yang, Ph.D. Assistant Research Professor Autism and Neurodevelopmental Disorders Institute The George Washington University and Children’s National Health System E-mail: daniely...@gwu.edu <mailto:daniely...@gwu.edu> > On May 31, 2017, at 1:42 PM, Bruce Fischl wrote: > > sure, but I'll need the subject as well (at least one surface) > On Wed, 31 May 2017, Daniel Yang wrote: > >> Good to know, then, it must be the way I interact with FS 6.0.0 that is >> wrong. >> It’s a surface label. >> Can I send you the label file to see if you could view that in FS 6.0.0’s >> freeview using command line? >> -- >> Y.J. Daniel Yang, Ph.D. >> Assistant Research Professor >> Autism and Neurodevelopmental Disorders Institute >> The George Washington University and Children’s National Health System >> E-mail: daniely...@gwu.edu >> >> On May 31, 2017, at 1:37 PM, Bruce Fischl >> wrote: >> no, the label format should be backwards compatible. Was it a surface or >> volume label? >> On Wed, 31 May 2017, Daniel Yang wrote: >> >> Dear FreeSurfer experts, >> >> When I tried to use FreeSurfer 6.0.0’s freeview to open a label file >> generated by FreeSurfer 5.3, I could not see anything. >> >> Is it incompatibility issue going on here? >> >> Thanks, >> Daniel >> >> ___ >> 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 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] label file from freesurfer 5.3
Thanks, Bruce! It works now. Is it possible I can convert all the negative values in the label to something like 1? Best, Daniel -- Y.J. Daniel Yang, Ph.D. Assistant Research Professor Autism and Neurodevelopmental Disorders Institute The George Washington University and Children’s National Health System E-mail: daniely...@gwu.edu <mailto:daniely...@gwu.edu> > On May 31, 2017, at 1:52 PM, Bruce Fischl wrote: > > Hi Daniel > > it's because the values in your label are all negative and the default > threshold is 0. Set it to -20 or something and you will see the label > > cheers > Bruce > On Wed, 31 May 2017, Daniel Yang wrote: > >> Thank you. I just sent it to your mailbox. >> -- >> Y.J. Daniel Yang, Ph.D. >> Assistant Research Professor >> Autism and Neurodevelopmental Disorders Institute >> The George Washington University and Children’s National Health System >> E-mail: daniely...@gwu.edu >> >> On May 31, 2017, at 1:42 PM, Bruce Fischl >> wrote: >> sure, but I'll need the subject as well (at least one surface) >> On Wed, 31 May 2017, Daniel Yang wrote: >> >> Good to know, then, it must be the way I interact with FS 6.0.0 that is >> wrong. >> It’s a surface label. >> Can I send you the label file to see if you could view that in FS >> 6.0.0’s freeview using command line? >> -- >> Y.J. Daniel Yang, Ph.D. >> Assistant Research Professor >> Autism and Neurodevelopmental Disorders Institute >> The George Washington University and Children’s National Health System >> E-mail: daniely...@gwu.edu >> >> On May 31, 2017, at 1:37 PM, Bruce Fischl >> wrote: >> no, the label format should be backwards compatible. Was it a surface >> or volume label? >> On Wed, 31 May 2017, Daniel Yang wrote: >> >> Dear FreeSurfer experts, >> >> When I tried to use FreeSurfer 6.0.0’s freeview to open a label >> file generated by FreeSurfer 5.3, I could not see anything. >> >> Is it incompatibility issue going on here? >> >> Thanks, >> Daniel >> >> ___ >> 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 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] label file from freesurfer 5.3
Thank you so much for your help! -- Y.J. Daniel Yang, Ph.D. Assistant Research Professor Autism and Neurodevelopmental Disorders Institute The George Washington University and Children’s National Health System E-mail: daniely...@gwu.edu <mailto:daniely...@gwu.edu> > On May 31, 2017, at 3:24 PM, Bruce Fischl wrote: > > sure. Easy enough to do in matlab. > On Wed, 31 May 2017, Daniel Yang wrote: > >> Thanks, Bruce! It works now. >> Is it possible I can convert all the negative values in the label to >> something like 1? >> Best, >> Daniel >> -- >> Y.J. Daniel Yang, Ph.D. >> Assistant Research Professor >> Autism and Neurodevelopmental Disorders Institute >> The George Washington University and Children’s National Health System >> E-mail: daniely...@gwu.edu >> >> On May 31, 2017, at 1:52 PM, Bruce Fischl >> wrote: >> Hi Daniel >> it's because the values in your label are all negative and the default >> threshold is 0. Set it to -20 or something and you will see the label >> cheers >> Bruce >> On Wed, 31 May 2017, Daniel Yang wrote: >> >> Thank you. I just sent it to your mailbox. >> -- >> Y.J. Daniel Yang, Ph.D. >> Assistant Research Professor >> Autism and Neurodevelopmental Disorders Institute >> The George Washington University and Children’s National >> Health System >> E-mail: daniely...@gwu.edu >> >> On May 31, 2017, at 1:42 PM, Bruce Fischl >> wrote: >> sure, but I'll need the subject as well (at least one >> surface) >> On Wed, 31 May 2017, Daniel Yang wrote: >> >> Good to know, then, it must be the way I interact >> with FS 6.0.0 that is wrong. >> It’s a surface label. >> Can I send you the label file to see if you could >> view that in FS 6.0.0’s freeview using command line? >> -- >> Y.J. Daniel Yang, Ph.D. >> Assistant Research Professor >> Autism and Neurodevelopmental Disorders Institute >> The George Washington University and Children’s >> National Health System >> E-mail: daniely...@gwu.edu >> >>On May 31, 2017, at 1:37 PM, Bruce Fischl >> wrote: >> no, the label format should be backwards compatible. >> Was it a surface or volume label? >> On Wed, 31 May 2017, Daniel Yang wrote: >> >>Dear FreeSurfer experts, >> >>When I tried to use FreeSurfer 6.0.0’s freeview >> to open a label file generated by FreeSurfer 5.3, I could >> not see anything. >> >>Is it incompatibility issue going on here? >> >>Thanks, >>Daniel >> >>___ >>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
[Freesurfer] fwhm in area analysis
Hi FreeSurfer experts,
When I specify fwhm=15 to analyze area, mri_surfcluster said that it cannot
find fwhm31 in fsaverage/${hemi}/cortex/fwhm31/...
This did not happen when I used FreeSurfer 5.3.0
I am wondering if FreeSurfer 6.0.0 pre-smooths the surface area?
Thanks,
Daniel
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
Re: [Freesurfer] fwhm in area analysis
Hi FreeSurfer experts,
I am wondering if I use fwhm=15 to analyze area, mri_surfcluster reported
that it cannot find fwhm31 in fsaverage/${hemi}/cortex/fwhm31/...
is this normal?
When I use fwhm=10, everything seems to be okay.
Best,
Daniel
On Tue, Sep 26, 2017 at 8:57 PM, Daniel Yang
wrote:
> Hi FreeSurfer experts,
>
> When I specify fwhm=15 to analyze area, mri_surfcluster said that it
> cannot find fwhm31 in fsaverage/${hemi}/cortex/fwhm31/...
>
> This did not happen when I used FreeSurfer 5.3.0
>
> I am wondering if FreeSurfer 6.0.0 pre-smooths the surface area?
>
> Thanks,
> Daniel
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
Re: [Freesurfer] fwhm in area analysis
Hi FreeSurfer experts,
To follow up on my early post, I am wondering if I use fwhm=15 to analyze
area, mri_surfcluster reported that it cannot find fwhm31 in
fsaverage/${hemi}/cortex/fwhm31/...
is this normal?
When I use fwhm=10, everything seems to be okay.
Best,
Daniel
On Tue, Sep 26, 2017 at 8:57 PM, Daniel Yang
wrote:
> Hi FreeSurfer experts,
>
> When I specify fwhm=15 to analyze area, mri_surfcluster said that it
> cannot find fwhm31 in fsaverage/${hemi}/cortex/fwhm31/...
>
> This did not happen when I used FreeSurfer 5.3.0
>
> I am wondering if FreeSurfer 6.0.0 pre-smooths the surface area?
>
> Thanks,
> Daniel
>
___
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.
