No, I believe my PI simply ran mri_convert on the 4 nii's,
Clearly there is a better approach? jon On May 9, 2013, at 11:04 AM, Bruce Fischl wrote: > Did you run recon-all? It will create filled.mgz in the subject/mri dir > > > > On May 9, 2013, at 11:00 AM, Jonathan Holt <whats...@umich.edu> wrote: > >> That was my suspicion, I've got them in the wrong folder. None of them are >> 'filled.mgz' though, I've only got 4 echoes (memprage_echo 1-4 .mgz) and >> nothing else. >> >> Also the exact error has it looking in >> /example/directory/subjects/memprage_echo%d.mgz/mri/filled.mgz >> >> as opposed to /example/directory/subjects/subjid/mri/filled.mgz >> >> I can rename subject directory if need be. >> >> >> On May 9, 2013, at 10:54 AM, Bruce Fischl wrote: >> >>> 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 >> >> >> _______________________________________________ >> 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
