Dear Freesufers,After running recon-all -cw256 -s PT1 -all, we can find
lh.aparc.a2009s and rh.aparc.a2009s under subjects/PT1/stats. I would like to
know what is the difference between the two files?
Thanks,Yawu
Now, I get it. lh means left side. :)Yawu
From: liu...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Date: Mon, 5 Nov 2012 10:32:37 +
Subject: [Freesurfer] regional cortical thickness output
Dear Freesufers,After running recon-all -cw256 -s PT1 -all, we can find
lh.aparc.a2009s and
Hi,
I have a problem with the command for creating a frozen version of an old
freesurfer distribution.
When running the first step cp -Lr /usr/local/freesurfer/stable
/path/to/yourdirectory/freesurfer
I get the error that the -L flag is incompatible with the cp command:
bruehh01% cp -Lr /Volum
Cortical Gray matter volume + Cortical white matter + subcortical gray
volume + cerebellum
subcortical gray is:
Left_Thalamus
Right_Thalamus
Left_Thalamus_Proper
Right_Thalamus_Proper
Left_Caudate
Right_Caudate
Left_Putamen
Right_Putamen
Left_Pallidum
Right_Pallidum
Left_Hippocampus
Right_Hippoca
Sorry, I don't know anything about the UCSFFSL table.
doug
On 11/05/2012 11:41 AM, Zhiyong Xie wrote:
> Hi Doug,
> Thank you for your response. I did not find the single measurement for
> Cortical Gray matter volume and Cortical white matter from UCSFFSL
> table. looks like I need to add up all
Hi Zheng, there is something wrong with your math. When I sum up all the
columns in your table from Left-Lateral-Ventricle to CC_Anterior, I get
215952 for the first row (you get only 67548). Can you double check your
calculations?
doug
On 10/28/2012 11:53 PM, Zheng Hui wrote:
> Forgot to attac
Try using this version
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/tkregister2.bin
copy it into $FREESURFER_HOME/bin (but make a back up of the existing
tkregister2.bin first!)
doug
On 11/02/2012 03:58 PM, Eric Cunningham wrote:
> Hi folks,
> In previous threads, the command pr
Hi Forrest, I don't think I ever tried to analyze the T1s from the other
sites (in fact, I did not even know that the other sites collected T1s).
The T1s from MGH went through FS without a problem.
doug
On 11/03/2012 02:36 PM, Forrest Sheng Bao wrote:
> Hi,
>
> Has anyone (un)successfully extr
Hi Mahinda, you need to tell mri_cor2label that this is a surface with
the --surf fsaverage lh white
You can propagate this label to other subjects using mri_surf2surf.
doug
On 11/04/2012 10:08 PM, Mahinda Yogarajah wrote:
> Dear Experts,
>
> I am trying to "back-normalise" significant clusters
Hannah,
Hi! I think on the Mac, the command is:
cp -LR
that is, a capital R instead of lowercase (which is the case on linux).
I'll update the wiki page.
Nick
On Mon, 2012-11-05 at 16:30 +0100, Bruehl, Hannah wrote:
> Hi,
>
>
> I have a problem with the command for creating a frozen versi
Do run out of disk space? Also, please send terminal output in a text
file rather than as a snapshot. You can do this with
recon-all ... |& tee mylog.txt
doug
On 11/05/2012 10:21 AM, Berg, S.F. van den wrote:
>
> Dear Freesurfer experts,
>
> I have got a problem with the qcache function. I have
are you sure you are using the new version?
On 11/05/2012 02:38 PM, Eric Cunningham wrote:
> tried the new version, and it errored out at the same step
>
> ERROR: Option --lta-inv unknown
>
> thanks again for your help!
>
> On Mon, Nov 5, 2012 at 8:16 AM, Douglas N Greve
> mailto:gr...@nmr.mgh.ha
I'm not sure that was the right thing to do. There should be two files:
tkregister2 and tkregister2.bin. tkregister2 is just a script that calls
tkregister2.bin after setting up some environment variables. Try keeping
the original file name.
doug
On 11/05/2012 03:43 PM, Eric Cunningham wrote:
>
Dear Doug,
Thanks for quick reply. Does it make a difference if I use mri_label2label
instead of mri_surf2surf for label propagation after I have used mri_cor2label
? Thanks.
M
On 5 Nov 2012, at 03:08, Mahinda Yogarajah wrote:
> Dear Experts,
>
> I am trying to "back-normalise" significa
oops, sorry, I mean label2label not surf2surf
doug
On 11/05/2012 03:48 PM, Mahinda Yogarajah wrote:
> Dear Doug,
>
> Thanks for quick reply. Does it make a difference if I use
> mri_label2label instead of mri_surf2surf for label propagation after I
> have used mri_cor2label ? Thanks.
>
> M
>
>
>
Hello,
I'm getting started with freesurfer. I've played around with some of
the tutorial data for fs-fast
(http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1) and was
able to follow along and successfully carry out the preprocessing
exercises (which sufficed for my purposes), which a
Hi Chris, it should have been done with preproc-sess. What was your
preproc-sess command line? At some point, I had it set up so that it
would go to the bold directory by default unless you used "-fsd rest".
Newer versions require you to specify the FSD specifically.
doug
On 11/5/12 9:38 PM,
OK, I see the problem. I should have told you to put tkregsiter2.bin
into /apps/fs510/tktools/ (after making a copy of the one there).
doug
On 11/5/12 5:00 PM, Eric Cunningham wrote:
[e4fs@cluster bin]$ ls -l `which tkregister2.bin`
-rwxr-xr-- 1 jsadinol fs 21663433 May 22 2011 /apps/fs5
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