the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug
On 5/9/13 6:48 PM, Bruce Fischl wrote: > Hi Kayle > > you would run recon-all on the RMS, then run the dura stuff posthoc. > > cheers > Bruce > On Thu, > 9 May 2013, Kayle Sawyer wrote: > >> Hi all, >> >> Can the MEMPRAGE be specified in recon-all with the -i flag? We have been >> using the MEMPRAGE RMS scans and discarding the multiecho scans. If we >> instead specify the multiecho scans for recon-all, do we need to give any >> additional parameters (e.g. the number of echoes) for it to utilize the 4 >> echoes to detect dura and refine pial surfaces in mris_make_surfaces, as >> described below? Or would we have to run recon-all with the RMS, then after >> it finishes re-run mris_make_surfaces manually with the -dura flag to refine >> the pial surface? >> >> Also, I'd like to make sure we are using dcmunpack properly. We take the > scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run > number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz > file, and the RMS gets put into a separate mgz file. >> Thanks, >> -Kayle >> >> On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: >>> Message: 35 >>> Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) >>> From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> >>> Subject: Re: [Freesurfer] Working with MEMPRAGE >>> To: Jonathan Holt <whats...@umich.edu> >>> Cc: freesurfer@nmr.mgh.harvard.edu >>> Message-ID: >>> <alpine.lrh.2.02.1305091043500.13...@gate.nmr.mgh.harvard.edu> >>> Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII >>> >>> 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 >>>>>>>> >> >> _______________________________________________ >> 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 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.
