Hi Doug,
Removing -i fmc did not help, and I still get the same error.
By looking at the rawfunc2surf-sess script, it looks like specifying an
argument for -surfreg makes ExpKeyNeeded = 1. Can I just specify something
for -expkey? Is this something that is used only in the name of log file?
Than
Hello Freesurfers
A bit new to the program, so I hope the following makes sense. We would
like to do a bottom-up vertex-by-vertex analysis to see where functional
activation correlates with thickness. We've done our functional analyses
through SPM and can get those maps into tksurfer. Most of the
Try it without -i fmc
On 10/08/2014 04:38 AM, Reza Rajimehr wrote:
> One more question:
>
> I tried to run:
>
> rawfunc2surf-sess -s oz_fparc -i fmc -trgsubject F99 -surfreg
> iter05.sphere.reg -fwhm 2 -per-session
>
> And I got this:
>
> ERROR: experts key needed (-expkey)
>
> Not sure what thi
I don't think you want to run with -nocanorm. Just commenting out the
addition of the -f $ControlPointsFile should be sufficient. Right Nick?
On
Wed, 8 Oct 2014, Marx, Gabe wrote:
Hi Bruce,
I appreciate the response!
I am sorry, I am a bit confused. The release notes state:
"An option is t
Hi Bruce,
I appreciate the response!
I am sorry, I am a bit confused. The release notes state:
"An option is to disable the running of mri_ca_normalize when re-running the
-autorecon2 or -autorecon2-cp stage after adding control points by adding the
flag -nocanorm to the end of recon-all. We w
I will try that.
Have a good day!
Date: Wed, 8 Oct 2014 14:07:38 -0400
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Mismatched dimensions with T1 and Flair inputs
you would have to first run recon-all -all on the T1
On Wed, 8 Oct 2014,
Vilde wrot
i saw this problem on one redhat installation, not on any others, seems
something with the X library orientation
information and openGL
greg
On 10/08/14, Jamie Hanson wrote:
> Hi Freesurfer List,
>
>
> I had a (hopefully quick) question about surface viewers and data orientation
> in tksurfe
Hi Freesurfers,
I am trying to make an atlas using the GCA algorithm and the error message
I just got is asking for the talairach.xfm file. The scans I am using were
originally run through freesurfer 3.1 and talairach processing was not
done. What do you suggest I do to use these scans in my new a
Hello Lee - thanks so much for your response. I looked into the document
you referred me to and found a section on GE protocols here (page 3):
http://martinos.org/~andre/FreeSurfer_recommended_morphometry_protocols.pdf
I would appreciate your input on a few details.
First, the document indicates
you would have to first run recon-all -all on the T1
On Wed, 8 Oct 2014,
Vilde wrote:
Thank you Bruce!
If I understand you correctly, would the command be
Recon-all -s subj_name -FLAIRpial.nii ?
Or would I first have to do recon-all with only T1 as input and then do
another command after it
Thank you Bruce!
If I understand you correctly, would the command be
Recon-all -s subj_name -FLAIRpial.nii ?
Or would I first have to do recon-all with only T1 as input and then do another
command after it has finished running? And in that case, what would that
command be?
Best,
Vilde
Date:
Ah, sorry for some reason it just wasn’t clicking before. I was able to
upload a dataset. Thanks!
On 10/8/14, 10:59 AM, "Bruce Fischl" wrote:
>Hi Michael
>
>you need to follow the directions on this page:
>
>http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
>
>in particular, make sure y
Hi Vilde
no, you can't give recon-all a flair directly, it needs a T1 do do the
recon on. You use the flair at the end to do a post-hoc deformation using
-flairpial I believe
cheers
Bruce
On Wed, 8 Oct 2014, Vilde wrote:
Dear mailing list,
I am trying to do a recon-all with two nifti inp
Dear mailing list,
I am trying to do a recon-all with two nifti inputs: A T1 and a Flair, for pial
surface refinement. This results in an error message saying the dimensions are
mismatched. (The third dimension of the T1 and Flair are different by one
slice. ) I do not, however, have a problem r
Hi Gabe
this wasn't really a bug per-se, just induced some behavior that people
didn't like. You can't skip the mri_ca_normalize step or the aseg won't be
accurate. The aseg patch I believe just starts autorecon2-cp after the aseg
hs been created, but Nick or Zeke can correct me if I'm wrong.
Hi Michael
you need to follow the directions on this page:
http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
in particular, make sure you change directories before trying to put
cheers
Bruce
On Wed,
8 Oct 2014,
Smith,
Michael wrote:
See attached
On 10/8/14, 10:46 AM, "Bruce Fisc
See attached
On 10/8/14, 10:46 AM, "Bruce Fischl" wrote:
>can you send us the details of your ftp command?
>On Wed, 8 Oct 2014, Smith,
>Michael wrote:
>
>> Hi Bruce,
>>
>> Do I not have permission to transfer files to the remote machine? I can
>> login fine as an anonymous user but when I attemp
Hi Stefano,
what would the format of the txt file be? Probably your best bet would be
to do it in matlab
Bruce
On Tue, 7 Oct 2014,
std...@virgilio.it wrote:
Hi list,
I need to extract the cortical and subcortical masks created by using
recon-all as .txt. I would work on the txt to import
can you send us the details of your ftp command?
On Wed, 8 Oct 2014, Smith,
Michael wrote:
Hi Bruce,
Do I not have permission to transfer files to the remote machine? I can
login fine as an anonymous user but when I attempt to use the put command
it says it could not create the file.
On 10/7
Hi Bruce,
Do I not have permission to transfer files to the remote machine? I can
login fine as an anonymous user but when I attempt to use the put command
it says it could not create the file.
On 10/7/14, 7:33 PM, "Bruce Fischl" wrote:
>Hi Michael
>
>sure, the T2 can help if you have it (altho
Please remove this mail. This problem was already solved.
On Tue, 7 Oct 2014 16:55:16 +0200
pfannmo...@uni-greifswald.de wrote:
> Dear FreeSurfer experts,
>
> I computed distances on the cortex surface of fsaverage using mris_pmake. The
> exact syntax of the distance computation was:
>
> mris
One more question:
I tried to run:
rawfunc2surf-sess -s oz_fparc -i fmc -trgsubject F99 -surfreg
iter05.sphere.reg -fwhm 2 -per-session
And I got this:
ERROR: experts key needed (-expkey)
Not sure what this flag is.
Reza
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