Thanks Bruce.
On Mon, Jul 15, 2013 at 4:52 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > 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 <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.edu<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<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<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<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 <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<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<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<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<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.
