I've gotten as far as running the mris_make_surfaces on the RMS, but after running for a bit it stopped with this error
mghRead (file/path/s_MEMPRAGE/mri/0010.mgz -1): coult not open file mris_make_surfaces: could not read 0th echo for dura localization from file/path/s_MEMPRAGE/mri/0010.mgz for reference, the RMS file name is 001.mgz jon On May 9, 2013, at 8:44 PM, Douglas Greve wrote: > > 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. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
