I'll definitely do that next time... although it didn't seem to pose any noticeable issues this time around?
jon On May 13, 2013, at 3:52 PM, Bruce Fischl wrote: > p.s. make sure that the echoes are in float format, not uchar/int/short (you > need to use -odt float in the mri_convert command line) > On Mon, 13 May 2013, Bruce Fischl wrote: > >> 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. 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