Hi Kayle it's been a long time since I wrote that code and we've only run it a few times. If you upload your subject directory I'll take a look
cheers Bruce On Sat, 11 May 2013, Kayle Sawyer wrote: > Hi all, > > I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, but > I'm not sure if it worked. The terminal output, including commands, is > attached. It was run with version > freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509. > > On the original recon, in the rh, there is a segment of dura marked as grey > inside the pial line, at 94 111 169. The surfaces did not appear to change > substantially after I reran mris_make_surfaces with the -dura flag specifying > the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the > before and after for yourself on the attached screenshots, or if you have NMR > access, here: > /space/ficus/6/users/SNEF_edits/OB01_orig/ > /space/ficus/6/users/SNEF_edits/OB01_orig_dura/ > > I saw this output from mris_make_surfaces for the rh, so maybe -dura did > correct a different defect? > 7 non-cortical segments detected > only using segment with 1900 vertices > > Any help would be appreciated, because we have over 130 brains and the fewer > manual corrections, the better! > > Thanks, > -Kayle > > > > > From: Douglas Greve <gr...@nmr.mgh.harvard.edu> > Date: Thu, May 9, 2013 at 8:44 PM > Subject: Re: [Freesurfer] Working with MEMPRAGE > To: freesurfer@nmr.mgh.harvard.edu > > > > 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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