I ran mri_convert on the RMS'd nifti, then recon-all on that. I don't understand how I can go from 1 RMS'd mgz back to 4 separate echos?
jon On May 10, 2013, at 12:41 PM, Bruce Fischl wrote: > did you run recon-all -all all the way through? you should name your echoes > something different like echo1.mgz, echo2.mgz... then specify -dura > echo%d.mgz 4 > > cheers > Bruce > > > On Fri, 10 May 2013, Jonathan Holt wrote: > >> $ export SUBJECTS_DIR=/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer $ >> mris_make_surfaces -dura 001%d.mgz 4 s_MEMPRAGE lh >> it's entirely possible I'm specifying the wrong mgz? After running recon-all >> on the >> RMS the usual directories were created, etc... including 001.mgz which is in >> s_MEMPRAGE/mri/orig. >> On Fri, May 10, 2013 at 12:39 PM, Jonathan Holt <whats...@umich.edu> wrote: >> $ export SUBJECTS_DIR=/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer$ >> mris_make_surfaces -dura 001%d.mgz 4 s_MEMPRAGE lh >> it's entirely possible I'm specifying the wrong mgz? After running recon-all >> on >> the RMS the usual directories were created, etc... including 001.mgz which is >> in s_MEMPRAGE/mri/orig. >> On Fri, May 10, 2013 at 12:33 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> can you send details about the steps you carried out including full >> command lines? >> On Fri, 10 May 2013, Jonathan Holt wrote: >> >> I've gotten as far as running the mris_make_surfaces on >> the RMS, but after running for a bit it stopped with >> this error >> >> mghRead (file/path/s_MEMPRAGE/mri/0010.mgz -1): coult >> not open file >> mris_make_surfaces: could not read 0th echo for dura >> localization from file/path/s_MEMPRAGE/mri/0010.mgz >> >> for reference, the RMS file name is 001.mgz >> >> jon >> On May 9, 2013, at 8:44 PM, Douglas Greve wrote: >> >> 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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