$ 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 whatsdac@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 <fischl@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-request@nmr.mgh.**harvard.edufreesurfer-request@nmr.mgh.harvard.eduwrote:
> Message: 35 > Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Working with MEMPRAGE > To: Jonathan Holt whatsdac@umich.edu > Cc: freesurfer@nmr.mgh.harvard.edu > Message-ID: > <alpine.LRH.2.02.**1305091043500.13418@gate.nmr.** > mgh.harvard.edualpine.LRH.2.02.1305091043500.13418@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/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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