Hi Douglas,  

I don’t receive any emails from anyone, I only receive the the digest which is what I “reply” to. So I am not sure what you mean by “try responding to the email that I sent.”  This is why I attempted to email you directly as I thought that is what you were asking for. 

I hope to have straightened things out by finding each part of our conversation and pasting them below (in reverse order). If you have further questions, please let me know. 

Sincerely,
Sherryse 




Message: 9
Date: Fri, 09 May 2014 17:36:36 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Viewing functional data on the inflated
brain
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <536D4A64.5000400@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed


both of what? Sorry, it looks like the thread was garbled below or
somehow the digest got into it. Try responding to the email that I sent
to keep things in order




On 05/09/2014 05:09 PM, Sherryse Corrow wrote:
Thanks Douglas.  Yes, both of those exist.

 Wed, 07 May 2014 12:51:02 –0700

It is looking for subject P143 in /usr/local/freesurfer/subjects

Does it exist? If so, does
/usr/local/freesurfer/subjects/P143/mri/brainmask.mgz
Exist?

 Wed, 07 May 2014 11:00:54 -0700

Thanks Douglas.  We tried that . . . The registration matrix that we need
is not created. Here is the output log file (attached). I am a bit new to
this so I am hoping it has the information you need. After taking a quick
glance at the log file, we noticed there are errors in the log file.
Step by step, this is what we did after we ran recon-all:
Reg-feat2anat ‹feat OurFeatDirectory.feat ‹subject P143

When we open the folder experiment.feat/reg/freesurfer, there is no
anat2exf.register.dat file.  However, there is a file called:
anat2exf.register.dat.init.

Thanks,
Sherryse


 Mon, 05 May 2014 19:58:31 –0700

Run reg-feat2anat. If that does not work, then send the command line and terminal output. Just saying that something does not work will not get you closer to a solution. We need to know what you did and what happened

Doug

 Mon, 05 May 2014 16:56:58 –0700

Hi all,

Earlier today, I posted the message listed below.   However, we discovered part 
of our issue.  When we run reg-feat2anat, there is no anat2exf.register.dat 
file created.  Therefore, we have no registration matrix to use.  Before, we 
were inadvertently using the anat2std file instead.  Any suggestions on how to 
get the anat2exf.register.dat file created?
Thanks,
Sherryse

 Mon, 05 May 2014 19:50:18 –0700

Can you tell us specifically what you have done? I mean command lines …

doug

 Mon, 05 May 2014 15:58:35 -0700

Dear FreeSurfer community,

We are having some issues registering our functional data (or masks) from FSL 
to an inflated brain in FreeSurfer.  Some of our masks, when registered to the 
inflated brain and viewed in FreeSurfer, are not showing up on the cortical 
surface.  We have followed web-tutorials for registration but are still having 
the issue.  Any suggestions?