$ 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.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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