Hi all,
I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, but I'm not sure if it worked. The terminal output, including commands, is attached. It was run with version freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509.
On the original recon, in the rh, there is a segment of dura marked as grey inside the pial line, at 94 111 169. The surfaces did not appear to change substantially after I reran mris_make_surfaces with the -dura flag specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the before and after for yourself on the attached screenshots, or if you have NMR access, here: /space/ficus/6/users/SNEF_edits/OB01_orig/ /space/ficus/6/users/SNEF_edits/OB01_orig_dura/
I saw this output from mris_make_surfaces for the rh, so maybe -dura did correct a different defect? 7 non-cortical segments detected only using segment with 1900 vertices
Any help would be appreciated, because we have over 130 brains and the fewer manual corrections, the better!
Thanks, -Kayle
From: Douglas Greve greve@nmr.mgh.harvard.edu Date: Thu, May 9, 2013 at 8:44 PM Subject: Re: [Freesurfer] Working with MEMPRAGE To: freesurfer@nmr.mgh.harvard.edu
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.
