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.edu wrote:
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.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 >>>
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