No,
I believe my PI simply ran mri_convert on the 4 nii's,
Clearly there is a better approach?
jon On May 9, 2013, at 11:04 AM, Bruce Fischl wrote:
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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