how are the echoes stored now? If they are in separate series just convert the individually. If in a single multi-frame file, use
foreach echo (0 1 2 3)
mri_convert -nth $echo <input> echo${echo}.mgz
end
cheers
Bruce
On Fri, 10 May 2013, 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
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>>>
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>
>
>
>
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