10 May
2013
10 May
'13
12:41 p.m.
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 whatsdac@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 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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