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.edumailto:greve@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Viewing functional data on the inflated brain To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Message-ID: <536D4A64.5000400@nmr.mgh.harvard.edumailto: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.
Douglas N Grevehttp://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N+Greve%22 Wed, 07 May 2014 12:51:02 –0700http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20140507
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?
Sherryse Corrowhttp://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Sherryse+Corrow%22 Wed, 07 May 2014 11:00:54 -0700http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20140507
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
Douglas Grevehttp://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+Greve%22 Mon, 05 May 2014 19:58:31 –0700http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20140505
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
Sherryse Corrowhttp://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Sherryse+Corrow%22 Mon, 05 May 2014 16:56:58 –0700http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20140505
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
Douglas Grevehttp://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+Greve%22 Mon, 05 May 2014 19:50:18 –0700http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20140505
Can you tell us specifically what you have done? I mean command lines …
doug
Sherryse Corrowhttp://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Sherryse+Corrow%22 Mon, 05 May 2014 15:58:35 -0700http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20140505
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?