Hi Jonathan, FreeSurfer folks: Did you have success in combining 4 echoes of MEMPRAGE images into one? I went through the archives and it appears to me that you would use: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh only after the scan has been through the recon all process. My question is did you use mri-concat to combine the 4 echoes into one?
thanks, Alan On Mon, May 13, 2013 at 11:26 AM, Jonathan Holt <whats...@umich.edu> wrote: > Bruce, > > how is it that I might load multiple surfaces, loading lh after having > loaded rh makes the other disappear. this is loading manually, not from the > command line > On May 13, 2013, at 11:14 AM, Jonathan Holt wrote: > > > 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.eduwrote: > >>>>>> 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 > > > > > > _______________________________________________ > > 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 >
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