Did you run recon-all? It will create filled.mgz in the subject/mri dir
On May 9, 2013, at 11:00 AM, Jonathan Holt whatsdac@umich.edu wrote:
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. >> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >
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