$ 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<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> >>> >>> >>> >>> >
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