15 Jul
2013
15 Jul
'13
4:52 p.m.
Hi Alan
to use the 4 echoes you want to compute the rms. I think something like
mri_average -noconform -sqr mprage_echo?.mgz mprage_rms.mgz
should do the trick (then use mprage_rms.mgz as the input to recon-all)
cheers Bruce
On Mon, 15 Jul 2013, Alan Francis wrote:
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 whatsdac@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 <greve@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-request@nmr.mgh.harvard.edu wrote: >>>>>> Message: 35 >>>>>> Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) >>>>>> From: Bruce Fischl <fischl@nmr.mgh.harvard.edu> >>>>>> Subject: Re: [Freesurfer] Working with MEMPRAGE >>>>>> To: Jonathan Holt <whatsdac@umich.edu> >>>>>> Cc: freesurfer@nmr.mgh.harvard.edu >>>>>> Message-ID: >>>>>> <alpine.LRH.2.02.1305091043500.13418@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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