That was my suspicion, I've got them in the wrong folder. None of them are 'filled.mgz' though, I've only got 4 echoes (memprage_echo 1-4 .mgz) and nothing else.
Also the exact error has it looking in /example/directory/subjects/memprage_echo%d.mgz/mri/filled.mgz
as opposed to /example/directory/subjects/subjid/mri/filled.mgz
I can rename subject directory if need be.
On May 9, 2013, at 10:54 AM, Bruce Fischl wrote:
is your SUBJECTS_DIR set properly? You need to put the memprage echoes in the subject's mri dir On Thu, 9 May 2013, Jonathan Holt wrote:
Oh, simple mistake!
However, now it spit's an error saying I need filled.mgz?
On May 9, 2013, at 10:44 AM, Bruce Fischl wrote:
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 >> > > > 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 . 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. >
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