Hi Jon you need to run recon-all all the way through, then run the command I sent you with the echoes in the mri dir
cheers Bruce On Thu, 9 May 2013, Jonathan Holt wrote: > 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. 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