it doesn't matter what you name them as long as you tell mris_make_surfaces. Store them in the subject's mri dir On Fri, 10 May 2013, Jonathan Holt wrote:
> will convert individually, should they eventually be stored in the same > directory as the RMS'd mgz, with the same file name + invidivual numbers? > > after which I'd proceed with mris_make_surfaces? > > > jon > On May 10, 2013, at 12:48 PM, Jonathan Holt wrote: > >> 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. 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. >>>> >>>> _______________________________________________ >>>> 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
