is your SUBJECTS_DIR set properly? You need to put the memprage echoes in the subject's mri dir On Thu, 9 May 2013, Jonathan Holt wrote:
> Oh, simple mistake! > > However, now it spit's an error saying I need filled.mgz? > > > On May 9, 2013, at 10:44 AM, Bruce Fischl wrote: > >> it needs to be: >> >> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh >> >> note the "4" which tells it how many echoes to read >> >> On Thu, 9 May 2013, Jonathan Holt wrote: >> >>> I input: >>> >>> mris_make_surfaces -dura memprage_echo%d.mgz subjid lh >>> >>> it returns: >>> >>> detecting dura using 0 echos from memprage_echo%d.mgz >>> >>> >>> Should I execute the command in the same directory as the mgz's? Should >>> they be set up or placed in a specific directory? I also, as with >>> recon-all, exported the proper subject directory beforehand. >>> >>> >>> On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: >>> >>>> can you send me the full command line? It should say 4 echoes, not 0 >>>> On Thu, 9 May 2013, Jonathan Holt wrote: >>>> >>>>> Thanks Bruce, >>>>> >>>>> should the hemisphere's be processed separately, or how do I signify lh >>>>> and rh simultaneously? >>>>> >>>>> Also, should the fact that after running mris_make_surfaces, it says >>>>> "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? >>>>> I've got 4 different echos, all mgzs in the directory. I have a feeling >>>>> I'm doing this incorrectly. >>>>> >>>>> jon >>>>> On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: >>>>> >>>>>> Hi Jon >>>>>> >>>>>> yes, the subject and hemi need to be defined (they are required >>>>>> parameters) >>>>>> Bruce >>>>>> On Wed, 8 May 2013, Jonathan Holt wrote: >>>>>> >>>>>>> Hi all, >>>>>>> combed through the mail archives to figure out how to work with multi >>>>>>> echo >>>>>>> mprage, found what I need but I wanted to confirm which of these two >>>>>>> commands is the appropriate >>>>>>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh >>>>>>> mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and >>>>>>> hemispheres need to be specified as per the 1st line? >>>>>>> jon >>>>>>> >>>>>> >>>>>> >>>>>> 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 >>>>> >>>>> >>>>> >>> >>> >>> >>> > > > _______________________________________________ > 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
