hots, 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 c
eciated, because we have over 130
brains and the fewer manual corrections, the better!
>>>
>>> Thanks,
>>> -Kayle
>>>
>>>
>>>
>>>
>>> From: Douglas Greve
>>>
gt;>> 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 brain
s, 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
>>>
;>>> 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
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_ed
>>>> 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
>&g
its/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 u
EF_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
w 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 brai
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!
>>
>> Th
ted
> 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
> Date: Thu, May 9, 2013 at 8:44 PM
> Subject:
t;>>> 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
>>>
>>>
multi echo scan gets put
>>>into one mgz
>>>file, and the RMS gets put into
>>> a separate mgz file.
>>> Thanks,
>>>
freesurfer-requ...@nmr.mgh.harvard.edu
>> wrote:
>> Message:
>> 35
>> Date:
>>
Bruce
Fischl
Subject:
Re:
[Freesurfer]
Working
urfaces 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
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 2
mber] 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
>>
y 2013 10:44:23 -0400 (EDT)
>> From: Bruce Fischl
>> Subject: Re: [Freesurfer] Working with MEMPRAGE
>> To: Jonathan Holt
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Message-ID:
>>
>> Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII
>>
freesurfer-requ...@nmr.mgh.harvard.edu wrote:
> Message: 35
> Date: Thu, 9 May 2013 10:44:23 -0400 (EDT)
> From: Bruce Fischl
> Subject: Re: [Freesurfer] Working with MEMPRAGE
> To: Jonathan Holt
> Cc: freesurfer@nmr.mgh.harvard.edu
> Message-ID:
>
> Content-Type: T
Hi Jon
you need to run recon-all all the way through, then run the command I sent
you with the echoes in the mri dir
cheers
Bruce
On Thu, 9 May 2013, Jonathan Holt wrote:
> No,
>
> I believe my PI simply ran mri_convert on the 4 nii's,
>
> Clearly there is a better approach?
>
> jon
> On May 9,
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 wrote:
>
>> Tha
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 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.
>
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/direct
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:
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, Jonat
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 mempr
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
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 s
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 d
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
> comman
34 matches
Mail list logo
