Hi Jonathan, FreeSurfer folks:
Did you have success in combining 4 echoes of MEMPRAGE images into one? I
went through the archives and it appears to me that you would use:
mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh only after the scan
has been through the recon all process. My question is did you use
mri-concat to combine the 4 echoes into one?
thanks,
Alan
On Mon, May 13, 2013 at 11:26 AM, Jonathan Holt <whats...@umich.edu> wrote:
Bruce,
how is it that I might load multiple surfaces, loading lh after
having loaded rh makes the other disappear. this is loading
manually, not from the command line
On May 13, 2013, at 11:14 AM, Jonathan Holt wrote:
> Hi all,
>
> last question promise. Successfully completed
mris_make_surfaces for both hemispheres. in my day-to-day
editing I open tkmedit thusly:
>
> tkmedit <subjid> brainmask.mgz -aux
$SUBJECTS_DIR/subjid/mri/wm.mgz -surface
$SUBJECTS_DIR/subjid/surf/lh.white -aux-surface
$SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg
>
> this works for mprage subjects. In evaluating and possibly
editing MEMPRAGE subjects, which surfaces should I have opened
in tkmedit, as there seem to be many more this time around.
>
> best,
> jon
> On May 11, 2013, at 6:49 PM, Bruce Fischl wrote:
>
>> Hi Kayle
>>
>> it's been a long time since I wrote that code and we've only
run it a few
>> times. If you upload your subject directory I'll take a look
>>
>> cheers
>> Bruce
>> On Sat, 11 May
>> 2013, Kayle Sawyer wrote:
>>
>>> 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 <gr...@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-requ...@nmr.mgh.harvard.edu wrote:
>>>>>> Message: 35
>>>>>> Date: Thu, 9 May 2013 10:44:23 -0400 (EDT)
>>>>>> From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
>>>>>> Subject: Re: [Freesurfer] Working with MEMPRAGE
>>>>>> To: Jonathan Holt <whats...@umich.edu>
>>>>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>>>>> Message-ID:
>>>>>>
<alpine.lrh.2.02.1305091043500.13...@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
>>>>>>>>>>>
>>>>>
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>>>>>
>>>>>
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