Hi Bruce,
Thank you so much, sorry to replay so late.
I also read your conversation with Jonathan regarding 3D to 2D
transformation, it is very helpful.
On 06/22/2015 11:45 AM, Bruce Fischl wrote:
sure, the average subject has a sphere and you can do it there. Or you
can flatten and use eucli
Yay !!! It works finally.
So the problem in the first place is: I got the wrong version of shared
library :)
Thank you so much.
2015-07-01 14:58 GMT+07:00 Jalmar Teeuw :
> Yes, the sudo prefix is optional, but may be required otherwise you get a
> 'not authorized' message (i.e. you need administ
Dear Freesurfer team:
I am here want to ask for your help for some problems in Freesurfer
when I was processing my data.
As described below, Freesurfer report :
ERROR! FOV=320.000 > 256
Include the flag -cw256 with recon-all!
Inspect orig.mgz to
leopard i686 stable pub v5.1.0
As an aside I watched your introductory videos and found you to be very
knowledgeable, well-spoken and very helpful in understanding some of the
amazing things you guys are doing for analysis. Really cool to be emailing
you and getting help from the pros.
Thanks
Jo
How did you create the ROIs?
On 07/01/2015 12:25 PM, Martin Hebart wrote:
> Dear members of the list,
>
> I'm new to Freesurfer, so please excuse me asking possibly basic
> questions. I have spent quite some time on the wiki and searching
> through the emails before writing to the list, but I mi
Hi Joe
what FS version are you using? That certainly looks like a bug, but maybe
it's one we've fixed already?
Bruce
On Wed, 1 Jul 2015, joseph veliz wrote:
> Hello Freesrufers,
>
> There are voxels in random areas of the aparc+aseg.mgz that are categorized
> as 'unknown'.
>
> I read an ear
Michael, can you send me the label in fsaverage space?
doug
On 06/16/2015 05:00 PM, Michael Kranz wrote:
> Hi guys,
>
> I have created a custom surface label in the fsaverage template. I
> then used mri_label2label to map onto an individual subject. Despite
> the fsaverage label looking ok, the
Is it registered to the surface? If so, you can use mri_vol2surf to
sample it onto the surface then display it as an overlay.
cheers
Bruce
On Wed, 1 Jul
2015, Worker, Amanda wrote:
Hi,
I am trying to find a way to overlay a .nii file for a single blob of
activation - simply to visualise t
Dear members of the list,
I'm new to Freesurfer, so please excuse me asking possibly basic questions.
I have spent quite some time on the wiki and searching through the emails
before writing to the list, but I might have missed some important
information.
I would like to work on anatomical ROIs c
Hi,
I am trying to find a way to overlay a .nii file for a single blob of
activation - simply to visualise the region of the blob with the cortical
surface.
Is there a way to do this in either freeview or tksurfer? The blob is in nifti
format and the surface is in the usual .mgh format.
T
Hi Xiaowei,
Can you please try copying the 3 attached files to $FREESURFER_HOME/bin (they
are the linux version of the ones I sent to Angela earlier today) and, running
the command below, and then trying to re-run the subfield segmentation code?
chmod u+x $FREESURFER_HOME/bin/run_segmentSubject*.
Hi all,
I am also running hippocampal subfields segmentation with V6 develop version,
and I got the error as following:
#
#@# Hippocampal Subfields processing (T1 only) left Tue Jun 30 23:06:21 PDT 2015
/home/xzhuang/Downloads/freesurfer/bin/segmentS
I’m trying to extract the surface area measurements for each subject from
clusters generated by Monte Carlo analysis within qdec. From previous posts I
came up with the following command:
mri_segstats --annot fsaverage lh mc-z.abs.th20.sig.ocn --i y.mgh --avgwf
lh-Diff-HV-WAGR-Intercept-area.d
thanks, that solved my problem!
Angela
> Sorry, I forgot to mention that you should change the permissions of the
> files. Please run the following command:
> chmod u+x $FREESURFER_HOME/bin/run_segmentSubject*.sh
> Cheers,
> Eugenio
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.
Sorry, I forgot to mention that you should change the permissions of the files.
Please run the following command:
chmod u+x $FREESURFER_HOME/bin/run_segmentSubject*.sh
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/L
Thank you Eugenio, but the problem is still present (attached the log).
Thank you for any help!
Angela
#@# Hippocampal Subfields processing (T1 only) left Wed Jul 1 13:04:47
CEST 2015
\n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh
/Users/angelafavaro/Desktop/prova/freesurfer/
Hi Angela,
I think this is a problem I fixed in the development version a couple of days
ago. Can you please just try saving the attached 3 files in the directory
$FREESURFER_HOME/bin/ replacing the ones that are there?
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeig
Hi there,
I am using Freesurfer in children which means lots of manual editing. I got
very nice results with doing the recommended reconstruction
(https://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction) .
However, I got a problem with the volumes: Gray Matter and White Matter:
When
Hi all,
I have tried to run the new hippocampal segmentation module (after running
the dev version of FS 6. The module did not work and this message error
appears (please find attached the log).
DYLD_LIBRARY_PATH is
/Users/angelafavaro/Desktop/prova/freesurfer/lib/gcc/lib:.:/Users/angelafavaro/De
Yes, the sudo prefix is optional, but may be required otherwise you get a 'not
authorized' message (i.e. you need administrative privileges to install
software and libraries); note 'libXp' is case-sensitive!
sudo yum install libXp.x86_64
The library will be installed at /usr/lib64/libXp.so.6
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