> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
> [gr...@nmr.mgh.harvard.edu]
> Sent: Wednesday, September 28, 2016 5:42 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Co-registering di
...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, September 28, 2016 5:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Co-registering different source data
Is Testing1.label a surface-based label? If so, use
esurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Wednesday, September 28, 2016 4:35 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Co-registering different source data
>
> which lh.infl
esurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Wednesday, September 28, 2016 4:35 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Co-registering different source data
>
> which lh
28, 2016 4:35 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Co-registering different source data
which lh.inflated and rh.inflated did you load? That is, for which
subject?
On Wed, 28 Sep 2016, Crawford, Anna wrote:
> I just opened freeview (just typed freeview into the command l
eesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Wednesday, September 28, 2016 4:27 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Co-registering different source data
>
> what was your freeview command line, an
: [Freesurfer] Co-registering different source data
what was your freeview command line, and what did you do to make it crash?
On Wed, 28 Sep 2016, Crawford, Anna wrote:
> Thank you! that seemed to have worked. I thought I had tried that before, but
> must not that. The input/output is
rvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve
> [gr...@nmr.mgh.harvard.edu]
> Sent: Wednesday, September 28, 2016 4:08 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Co-registering different source data
>
> Try giv
, 2016 4:08 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Co-registering different source data
Try giving it the full path to the label, ie,
--srclabel
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label
On 9/28/16 3:47 PM, Crawford, Anna wrote:
>
; [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Wednesday, September 28, 2016 3:11 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Co-registering different source data
>
> Hi Anna
>
> sorry, I've lost
] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Wednesday, September 28, 2016 3:11 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
sorry, I've lost track of where this is at. Can you send us the full
screen output of the command you
; [dgwake...@gmail.com]
> Sent: Tuesday, September 27, 2016 12:04 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Co-registering different source data
>
> I think you SUBJECTS_DIR might be set incorrectly,
>
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/
...@nmr.mgh.harvard.edu] on behalf of dgw [dgwake...@gmail.com]
Sent: Tuesday, September 27, 2016 12:04 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Co-registering different source data
I think you SUBJECTS_DIR might be set incorrectly,
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label
I
> Anna
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of dgw
> [dgwake...@gmail.com]
> Sent: Tuesday, September 27, 2016 11:52 AM
> To: Freesurfer support list
> Subject: Re: [F
: [Freesurfer] Co-registering different source data
what is the output of "ls"?
On 9/27/16 11:50 AM, Crawford, Anna wrote:
> Thank you. That worked for changing the default directory. When I run
> mri_label2label, I am still getting the same error that there is no such file
...@nmr.mgh.harvard.edu] on behalf of dgw [dgwake...@gmail.com]
Sent: Tuesday, September 27, 2016 11:36 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Co-registering different source data
Anna, if you are using bash the command is:
export SUBJECTS_DIR=
On 9/27/16 11:31 AM, Crawford, Anna wrote
the label.
>
> Anna
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of dgw
> [dgwake...@gmail.com]
> Sent: Tuesday, September 27, 2016 11:36 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Co-regi
> From: Crawford, Anna
> Sent: Tuesday, September 27, 2016 11:12 AM
> To: Freesurfer support list
> Subject: RE: [Freesurfer] Co-registering different source data
>
> If I don't use --sd it uses the default subject directory (SUBJECTS_DIR
> /tools/freesurfer/subje
of Douglas Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, September 27, 2016 10:50 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Co-registering different source data
Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that
is already set properly, then do not use
ssing information?
>>
>> Thank you,
>> Anna
>> ________________
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Monday,
To: Freesurfer support list
Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
freeview now checks (in the dev version I believe) if the label has been
sampled onto the surface and won't crash, but you need to use
mri_label2label to sample it onto the surface before loading it onto
ember 26, 2016 4:23 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Co-registering different source data
>
> Hi Anna
>
> scuba is very old and deprecated. Try using freeview instead
>
> cheers
> Bruce
> On Mon, 26 Sep
> 2016, Crawford, Anna
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, September 26, 2016 4:23 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Co-registering different source data
ard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, September 26, 2016 1:52 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Co-registering different source data
>
> yes, create a volume ROI and you can map it onto the surface using
> mri_vo
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, September 26, 2016 1:52 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Co-registering different source data
yes
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, September 26, 2016 1:16 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Co-registering different source data
>
> can you explain what the ROI is suppo
is...@nmr.mgh.harvard.edu]
> Sent: Monday, September 26, 2016 10:44 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Co-registering different source data
>
> Hi Anna
>
> I'm not exactly sure what you mean, but if you register EEG electrodes to
> the white or
rd.edu]
> Sent: Monday, September 26, 2016 10:44 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Co-registering different source data
>
> Hi Anna
>
> I'm not exactly sure what you mean, but if you register EEG electrodes to
> the white or pial surface, then y
] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, September 26, 2016 10:44 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Co-registering different source data
Hi Anna
I'm not exactly sure what you mean, but if you register EEG electrodes to
the white or pial surface
Hi Anna
I'm not exactly sure what you mean, but if you register EEG electrodes to
the white or pial surface, then you can visualize them on the inflated
surface trivially. That is, you can create your ROI on any surface of the
same hemisphere/subject and visualize it on any other
cheers
Bruce
Hello,
I am trying to create a new surface area on the inflated brain given by
freesurfer using recon-all. I make to create my own ROI that is co-registered
onto this surfer. Ultimately, I want to be able to take information from a
different data source such as EEG and have it co-registered
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