can you send details about the steps you carried out including full command lines? On Fri, 10 May 2013, Jonathan Holt wrote:
> 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. 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