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
