you can use file->aux-surfaces->load aux main surface (or something like that). Or use freeview.
cheers Bruce On Mon, 13 May 2013, Jonathan Holt 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.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 >> >> >> _______________________________________________ >> 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
