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 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.
