9:32 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fsaverage for ROI analysis of children
Can you back up and tell us what it is you are trying to do? Where did the ROI
come from and how did you create it?
doug
On 11/3/14 8:56 AM, Smith, Michael wrote:
Hello all,
I have been conduct
ildren
Did you make the from the ?h.aparc.annot of fsaverage? If so, why not make the
label from the ?h.aparc.annot from the individual subject and then calculate
the thickness from that?
doug
On 11/3/14 9:44 AM, Smith, Michael wrote:
Hi Doug,
We are trying to look at the cortical thickness of a few
us what it is you are trying to do? Where did the ROI
come from and how did you create it?
doug
On 11/3/14 8:56 AM, Smith, Michael wrote:
Hello all,
I have been conducting an ROI analysis and following the cortical thickness ROI
tutorial found here:
https://surfer.nmr.mgh.harvard.edu/fswiki/
Hello all,
I have been conducting an ROI analysis and following the cortical thickness ROI
tutorial found here:
https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness. After
going through this tutorial with a few of my subjects I’ve noticed the ROI when
registered to the fsavera
Subject: Re: [Freesurfer] Creating an ROI mask for Cortical Thickness Analysis
Hi Michael
you can use mri_annotation2label to extract a specific label from the aparc
file and go from there.
cheers
Bruce
On Thu, 23 Oct 2014, Smith, Michael wrote:
> I guess I'm not entirely sure how to do t
tober 22, 2014 4:21 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Creating an ROI mask for Cortical Thickness Analysis
Why not just get it from the ?h.aparc.stats file?
On 10/22/2014 03:43 PM, Smith, Michael wrote:
> Hello Freesurfer's
>
> I am trying to l
Hello Freesurfer’s
I am trying to look at the cortical thickness for a specific ROI on the
cortical surface (Primary Auditory Cortex: transverse temporal gyri). I found
a specific tutorial
(https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness) however
the tutorial assumes I al
you submitted to recon all. Recon-all will try to average these
together, and since they have such different contrasts, you will end up with a
poor template for surfaces later on.
Try running recon-all again without the T2 and see if that helps.
-Ani
On Wed, 2014-10-08 at 17:21 +0000, Smith, Mic
t;
>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 Fischl" wrote:
>>
>>> can you s
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
>&
cify the range of allowable intensities for gray and white matter.
>If
>you upload the subject to our ftp site (the whole subject directory
>tarred
>and gzipped) we will take a look
>
>cheers
>Bruce
>
>On Mon, 6 Oct 2014, Smith, Michael wrote:
>
>> Hi,
>
do see license.txt which should work.
>
>Can you try just renaming (or copying) the file "license.txt" to
>".license" and see what happens? This can be done with the following
>command:
>
>cd /Applications/freesurfer
>cp license.txt .license
>
>Give t
Zeke,
Attached is a screenshot. Thanks!
On 10/1/14, 11:03 AM, "Z K" wrote:
>Hello Micheal,
>
>Can you please provide me the output when you 'cd' into the
>FREESURFER_HOME directory and type the command 'ls -a'
>
>-Zeke
>
>
>On 10/01/2014
Hello Freesurfer Team!
I’ve been having an issue using the tkmedit function in freesurfer. I get the
following error:
ERROR: FreeSurfer license file /Users/smig9x/Applications/freesurfer//.license
not found.
If you are outside the NMR-Martinos Center,
go to http://surfer.nmr.mgh.harvard.
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