I'm surprised it would work well if they are not float. You'll lose a lot of precision On Mon, 13 May 2013, Jonathan Holt wrote:
> 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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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 >>> >>> >>> > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
