Hi all, last question promise. Successfully completed mris_make_surfaces for both hemispheres. in my day-to-day editing I open tkmedit thusly:
tkmedit <subjid> brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz -surface $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg this works for mprage subjects. In evaluating and possibly editing MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as there seem to be many more this time around. best, jon On May 11, 2013, at 6:49 PM, Bruce Fischl wrote: > 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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