External Email - Use Caution
Dear colleagues,
The step "contrasurfreg" is still documented for recon-all: https://secure-web.cisco.com/1sNdAy_WhD93Ud31GJEbFbtzD8zuHWnO6zQotNCGvSLXYBn... (btw, this page has typos, in some places it's spelled "contasurfreg", with a missing R)
But when executing recon-all, it doesn't accept the flag "-contrasurfreg":
========================================= ftadel@dogberry:~$ recon-all -all -contrasurfreg -subjid ICBM152_2022 ERROR: Flag -contrasurfreg unrecognized. -contrasurfreg Linux dogberry.bic.mni.mcgill.ca 5.4.185-i686-64-smp #1 SMP Thu Mar 17 21:53:59 EDT 2022 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s exited with ERRORS at Wed Nov 2 11:23:56 EDT 2022
For more details, see the log file To report a problem, see http://secure-web.cisco.com/1BjL8hP7NAz0x_d96RT5d6D0oOfiwH5zFjFw_sEeLHgXo3J0... =========================================
Am I missing something here?
Thanks Francois
External Email - Use Caution
Hello,
Does anybody know what happened to the recon-all option -contrasurfreg. It is still documented, but recon-all crashes when trying to use it ("ERROR: Flag -contrasurfreg unrecognized.")
How can we obtain the files lh.rh.sphere.reg and rh.lh.sphere.reg with FreeSurfer 7.X?
Thanks, Francois
I think I took it out because it was a bad idea (can't really remember). If you want to do cross-hemi analysis, better to use the xhemi tool https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 11/7/2022 8:46 AM, Francois Tadel, Mr [Affiliate] wrote:
External Email - Use CautionHello,
Does anybody know what happened to the recon-all option -contrasurfreg. It is still documented, but recon-all crashes when trying to use it ("ERROR: Flag -contrasurfreg unrecognized.")
How can we obtain the files lh.rh.sphere.reg and rh.lh.sphere.reg with FreeSurfer 7.X?
Thanks, Francois
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Douglas,
If I want to obtain outputs similar to -contrasurfreg, is it correct to execute the following commands?
surfreg --s subjid --t fsaverage_sym --lh --no-annot --o rh.sphere.reg surfreg --s subjid --t fsaverage_sym --rh --no-annot --o lh.sphere.reg
Thanks Francois
Le 09/11/22 à 15:11, Douglas N. Greve a écrit :
I think I took it out because it was a bad idea (can't really remember). If you want to do cross-hemi analysis, better to use the xhemi tool https://secure-web.cisco.com/12h2xYVNRK1us6DTqUfMZepui3ASWZKcLYMsX_0mSjM4TFS...
On 11/7/2022 8:46 AM, Francois Tadel, Mr [Affiliate] wrote:
Hello,
Does anybody know what happened to the recon-all option -contrasurfreg. It is still documented, but recon-all crashes when trying to use it ("ERROR: Flag -contrasurfreg unrecognized.")
How can we obtain the files lh.rh.sphere.reg and rh.lh.sphere.reg with FreeSurfer 7.X?
Thanks, Francois
I don't remember what contrasurfreg output was. Can you elaborate?
On 11/9/2022 1:07 PM, Francois Tadel, Mr [Affiliate] wrote:
External Email - Use CautionHi Douglas,
If I want to obtain outputs similar to -contrasurfreg, is it correct to execute the following commands?
surfreg --s subjid --t fsaverage_sym --lh --no-annot --o rh.sphere.reg surfreg --s subjid --t fsaverage_sym --rh --no-annot --o lh.sphere.reg
Thanks Francois
Le 09/11/22 à 15:11, Douglas N. Greve a écrit :
I think I took it out because it was a bad idea (can't really remember). If you want to do cross-hemi analysis, better to use the xhemi tool https://secure-web.cisco.com/12h2xYVNRK1us6DTqUfMZepui3ASWZKcLYMsX_0mSjM4TFS...
On 11/7/2022 8:46 AM, Francois Tadel, Mr [Affiliate] wrote:
Hello,
Does anybody know what happened to the recon-all option -contrasurfreg. It is still documented, but recon-all crashes when trying to use it ("ERROR: Flag -contrasurfreg unrecognized.")
How can we obtain the files lh.rh.sphere.reg and rh.lh.sphere.reg with FreeSurfer 7.X?
Thanks, Francois
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Francois Tadel, Mr [Affiliate]