Dear FS experst,
I used the command mri_surfcluster. For one analysis, I obtained 6 clusters
with one huge of 473 cm2 which corresponds to several sub-clusters because it
was expanded through a large part of the cortex (covering several anatomical
regions). Is there a way to separate one
Hi Octavian
does your data show in the proper orientation in freeview/tkmedit?
Analyze is a dangerous format as it doesn't contain direction cosine info
and hence even if it looks right you may have left/right swapped and not
know it.
I don't think the spherical stuff needs tal, so if it
Hi Bruce,
if i have analyse format which is the right orientation to enter the data
in freesurfer. Radiologically (r/l) or vise versa?
John
On Thu, Nov 6, 2014 at 3:21 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
Hi Octavian
does your data show in the proper orientation in
Dear all,
I'm trying to run a retinotopy analysis in several subjects but it crashed
with an error in one subject. I ran this command line:
selxavg3-sess -a rtopy.HS.rh -s SUBJ09
and this is the last part of the output with the error message.
Any help would be much appreciated.
Best
Francesca
This server cannot run any X11 for security reasons.
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
On Wed,
Hi Bruce.
I believe Tksurfer, even with renderoffscreen, requires X11.
I suppose I could export one slice of T1 data and the same Slice of Aseg
data and make a script to superimpose both. Not sure which of the cmd line
tools to use for this slice export.
Anthony,
Im a few hours in running bert on Yosemite with no issue so far. Could
you please send me you log file for the case below? Thanks.
-Zeke
On 11/06/2014 12:02 AM, Anthony Dick wrote:
Hello Zeke,
I have tried giving permissions to multiple folders (freesurfer, bin,
Documents, bert
Hi PPJ
I think mri_extract will do the trick.
cheers
Bruce
On Thu, 6 Nov 2014, Pedro Paulo de
Magalhães Oliveira Junior wrote:
Hi Bruce.
I believe Tksurfer, even with renderoffscreen, requires X11.
I suppose I could export one slice of T1 data and the same Slice of Aseg
data and make a
Hello,
I am trying to run the second step of the TRACULA processing which is:
trac-all -bedp -c /home/...
I am currently using freesurfer v5.3.0 and I get the following error:
WARN: Running FSL's bedbost locally - this might take a while
WARN: It is recommended to run this step on a cluster
I subscribe to the question above. Also, is there a flag that would make
recon throw a warning about tailarach registration issue, but not stop the
routine?
Thank you,
Octavian
On Thu, Nov 6, 2014 at 7:30 AM, John Epiktitos epikti...@gmail.com wrote:
Hi Bruce,
if i have analyse format which
Can you send me
/usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh/Xtmp.mat
On 11/06/2014 09:53 AM, Francesca Strappini wrote:
Dear all,
I'm trying to run a retinotopy analysis in several subjects but it
crashed with an error in one subject. I ran this command
Do you mean cluster-wise threshold or cluster-forming threshold?
On 11/06/2014 01:12 AM, Bronwyn Overs wrote:
Dear Freesurfer Mailing list,
While running a glm anlaysis with monte carlo correction (using
cluster wise thresholds of .05 .01), I encountered the following issue:
When
On 11/06/2014 12:53 AM, Alshikho, Mohamad J. wrote:
Dear Bruce,
My questions is just to learn and to improve my understanding.
The commands recon-all and dt-recon are routinely generating the
statistics at the end of there running and we can check the results
in aseg.stats (the
So I am trying to use TKregister2 and I keep having this error pop up. I
tried looking online for a solution. I tried adding export
LIBGL_ALWAYS_INDIRECT=y to my .cshrc file but it did not help. I saw the
question asked several times but never any answer to the significance of
it, but I am
Hi Adam,
I know in your past email you mentioned that you do not think control
points could fix the situation, could you tell me why you think that? Have
you tried adding some and it failed?
I took a look at your data and the wm value seems pretty low (low 70-80s)
around the area near where
Dear FS Experts,
I'm trying to work with the DTI Siemens (non MGH) and is not working. An error
occurs in step Tensor Fit”.
II tried a solution that have worked as substitute bvecs values before this
step manual (by original bvecs) and it works great (is meant by: continued)!.
Surely I'm
Nicholas,
You probably encountered this page which describes your issue:
https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_GUIs_troubleshooting
And it seems you've already attempted the recommended solution.
Unfortunately that is the only way I have ever solved this issue, but I
do know it
I am using remote desktop connection, so I am putting it into the terminal
on the Linux computer itself. Does the notation need to change at all if I
am using TCSH and not BASH?
On Thu, Nov 6, 2014 at 1:36 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote:
Nicholas,
You probably encountered this
Well it should give an error if your not setting it correctly, but yes
the syntax IS different for tcsh.
setenv LIBGL_ALWAYS_INDIRECT y
-Zeke
On 11/06/2014 02:46 PM, Nicholas Heugel wrote:
I am using remote desktop connection, so I am putting it into the
terminal on the Linux computer
So the system I am working on only recently was setup, is it possible the
problem is that there is no LIBGL library on the system? What would the
name of the folder for the library be? and where would I download libGL if
it is not on the system?
On Thu, Nov 6, 2014 at 1:54 PM, Z K
If OpenGL was not installed you would get a completely different error.
The error you are getting is a very specific error relating to a
compatibility issue between Exceed OpenGL and Mesa GLX. In every
instance that I am aware of, setting the environment variable below has
solved the issue.
Hi!
I have several external regressors in my analysis that I configure with
-taskreg in mkanalysis-sess (something like -notask -taskreg nameoffile 6).
I was wondering how to set up mkcontrast-sess to contrast these regerssors
given that I do not have a paradigm file for them.
Can I just do
So I did what you suggested above, where I verified via the ECHO that the
environmental variable was set properly, and it echoes back y. But when I
run tkregister it still gives me the same error.
On Thu, Nov 6, 2014 at 2:23 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote:
If OpenGL was not
It was all done in the terminal one line at a time from what you had
emailed me.
On Thu, Nov 6, 2014 at 2:31 PM, Nicholas Heugel nheuge...@gmail.com wrote:
So I did what you suggested above, where I verified via the ECHO that the
environmental variable was set properly, and it echoes back y.
Hi Ani,
I actually did end up fixing the insula mis-segmentation using either control
points or WM edits for many subjects (I think the one I sent you too, not
sure). However, I did notice that in some subjects, the edits will push the wm
line out a little too much such that minor part of the
Hi Adam,
Well that is good to hear! So you are all set with this problem then?
-Ani
On Thu, 6 Nov 2014, Adam Mezher wrote:
Hi Ani,
I actually did end up fixing the insula mis-segmentation using either control
points or WM edits for many subjects (I think the one I sent you too, not
Doug and Bruce.
Many thousands of thanks
Mohamad
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, November 06, 2014 12:12 PM
To:
Then I am sorry but there is nothing else I can suggest at this time.
Getting various GUI based application to work and display properly over
remote connections can sometimes be a difficult task given the all the
variables involved. It is outside the scope of my ability to ensure this
works
Thanks Bruce,
So I just need a warp field in .m3z format. Cool. As this distortion
correction is proprietary, we don't actually get the warp fields, which is
silly. But I was thinking since scanner distortions are subtle and
coarse, it should be sufficient to nonlinearly register the
two
I will look into free view. I screen share with the Linux cluster, so I should
be able to install and run free view. Thanks for your assistance.
-Original Message-
From: Z K zkauf...@nmr.mgh.harvard.edu
Sent: 11/6/2014 3:45 PM
To: Freesurfer support list
I believe it is the cluster-forming threshold. I was running the following:
mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache
1.3 abs --cwpvalthresh 0.05 --2spaces
mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache 2
abs --cwpvalthresh 0.05 --2spaces
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