label file from freesurfer 5.3

List overview All Threads
Download

newer

older

recon-all errors

Mapping Vertices from Subject to...

Daniel Yang

31 May 2017 31 May '17

1:36 p.m.

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

Show replies by date

Bruce Fischl

31 May 31 May

1:37 p.m.

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

Daniel Yang

1:39 p.m.

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?

Bruce Fischl

1:42 p.m.

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: danielyang@gwu.edu
  On May 31, 2017, at 1:37 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> 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.

Daniel Yang

1:47 p.m.

Thank you. I just sent it to your mailbox.

Bruce Fischl

1:52 p.m.

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: danielyang@gwu.edu
  On May 31, 2017, at 1:42 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> 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: danielyang@gwu.edu

       On May 31, 2017, at 1:37 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> 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.

Daniel Yang

1:57 p.m.

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: danielyang@gwu.edu mailto:danielyang@gwu.edu > On May 31, 2017, at 1:52 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu 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: danielyang@gwu.edu >> >> On May 31, 2017, at 1:42 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu 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: danielyang@gwu.edu >> >> On May 31, 2017, at 1:37 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu 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.

Bruce Fischl

3:24 p.m.

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: danielyang@gwu.edu

  On May 31, 2017, at 1:52 PM, Bruce Fischl
  <fischl@nmr.mgh.harvard.edu> 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: danielyang@gwu.edu

       On May 31, 2017, at 1:42 PM, Bruce Fischl
  <fischl@nmr.mgh.harvard.edu> 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: danielyang@gwu.edu

            On May 31, 2017, at 1:37 PM, Bruce Fischl
  <fischl@nmr.mgh.harvard.edu> 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.

Daniel Yang

4:49 p.m.

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: danielyang@gwu.edu mailto:danielyang@gwu.edu > On May 31, 2017, at 3:24 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu 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: danielyang@gwu.edu >> >> On May 31, 2017, at 1:52 PM, Bruce Fischl >> fischl@nmr.mgh.harvard.edu 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: danielyang@gwu.edu >> >> On May 31, 2017, at 1:42 PM, Bruce Fischl >> fischl@nmr.mgh.harvard.edu 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: danielyang@gwu.edu >> >> On May 31, 2017, at 1:37 PM, Bruce Fischl >> fischl@nmr.mgh.harvard.edu 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.

3290

Age (days ago)

3290

Last active (days ago)

freesurfer@nmr.mgh.harvard.edu

8 comments

2 participants

tags (0)

participants (2)

Bruce Fischl
Daniel Yang