On 06/05/2013 11:49 AM, Tudor Popescu wrote:
>
> C) When running mri_surf2surf, I get an error saying
> that file
> /surf/lh.white cannot be opened. The 'average' folder
> produced
> after I ran make_average_subject does not contain a
> /surf/lh.white file, only a /surf/lh.white_avg file! I
> didn’t
> find a log file from make_average_subject so i don’t
> know if
> it gave any errors..
>
> It's extremely helpful to have command lines ...
>
>
> Sorry, my commands were:
> make_average_subject --subjects C01 C02 C03 C04 C05 C06 C07
> C08 C09 C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 M01 M02 M03
> M04 M05 M06 M07 M08 M09 M10 M11 M12 M13 M14 M15 M16 M17 M18 M19
> mri_surf2surf --hemi lh --s average --sval lh.thickness.mgh
> --fwhm 10 --tval lh.thickness.10.mgh
>
> It might be a version problem. You can create a symbolic link from
> lh.white_avg to lh.white
>
>
> Under fsaverage/surf there is both an lh.white and an lh.white_avg
> file, while under average/surf there's only lh.white_avg. I repeated
> the mri_surf2surf command above with "--s fsaverage" instead of "--s
> average" (since I understand in this case it's the same thing), and
> then it ran to completion.
It should be close but probably not exact.
>
> Also, it's not clear from the wiki what flag should an ROI's
> label/mask be specified into mri_surf2surf with, prior to a ROI
> analysis. The --cortex flag seems to always be required anyway, and
> --sval seems to be design-related ("--sval
> lh.gender_age.thickness.00.mgh" in the group tutorial)! Should the
> same flag then also be used to specify the ROI in mri_glmfit, the
> command that follows mri_surf2surf?
Look at the mri_surf2surf --help
doug
>
> Thanks!
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________
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.
