Hi, thanks for the help!
These are the outputs:
1) What is the output of the following:
ls -ld $FREESURFER_HOME/bin
drwxrwxrwx 1 francesca francesca 118784 May 14 2013
/media/Shared_Data/freesurfer/bin
2) After sourcing FreeSurfer, what happens when you type:
tkmedit -f
Dear Doug,
thank you for your answer. I added --target fsaverage_sym but it still
fails:
MRISread($SUBJECTS_DIR/fsaverage_sym/surf/lh.fsaverage_sym.sphere.reg):
could not open file.
This seems to happen because in the folder fsaverage_sym/surf there is no
lh.fsaverage_sym.sphere.reg; in this
Sorry Rujing, I don't think we ever implemented that (although we should)
On Wed, 14 May 2014, charujing123 wrote:
Hi FS experts and users
I want to change the background color of tksurfer from black to white. However
I cannot find
the drop-down list. Is there anyone who can tell me to
Hi Qiongmin
1) The command you ran resamples the thickness from being a scalar field
over the subject surface to being a scalar field over the fsaverage
surface. If you load fsaverage (say inflated) in tksurfer or freeview you
should then be able to load the overlay onto it.
2) We provide
Hi Francesca,
you need to make sure that the current user has read and execute
permissions of the Freesurfer files. Either make sure that the
FreeSurfer directory is in the same group as the user and give group
rights, or give read and execute rights to everyone.
source freesurfer first
cd
Ok, thank you!
I sourced freesurfer and then I tried:
cd $FREESURFER_HOME
sudo chmod -R a+rX *
But I still get the same error:
shalim-ubunut:/media/Shared_Data/freesurfer freeview
/media/Shared_Data/freesurfer/bin/freeview: Permission denied.
shalim-ubunut:/media/Shared_Data/freesurfer sudo
Francesca,
Is this a dual boot system (do you have multiple operating systems
installed on it)?
Are you running FreeSurfer in a virtual machine?
It sounds like another operating system may be controlling the
permissions of the /media/Shared_Data directory.
D
On Wed, May 14, 2014 at 9:51 AM,
Yes, it's a dual boot system (Windows7 and Ubuntu 12.04 LTS)
I'm running FreeSurfer on Ubuntu.
Shared_Data is shared between Windows and Ubuntu.
I can try to install FreeSurfer on Linux /usr/local if you think that this
can help.
Thanks!
Francesca
2014-05-14 17:09 GMT+03:00 dgw
Hello all,
I generated the lgi.stats file for all my subjects and in one of them I
got this warning:
mris_anatomical_stats -a aparc.annot -t pial_lgi -f
SUBJ/stats/lh.aparc_lgi.stats SUBJ lh
computing statistics for each annotation in aparc.annot.
using thickness file pial_lgi.
reading
ok, thank you!
Francesca
On Wednesday, May 14, 2014, dgw dgwake...@gmail.com wrote:
It doesn't need to be in /usr/local (I'm not sure if the FreeSurfer
team has a preferred install location), but it is probably simpler
(read: there may be some complex way to get it to work on a shared
There is not a way to change the background color without reprogramming
the interface
On 05/14/2014 12:01 AM, charujing123 wrote:
Hi FS experts and users
I want to change the background color of tksurfer from black to white.
However I cannot find the drop-down list. Is there anyone who can
Hi Bruce and Doug,
Ok, I see. That's all right.
All the best.
Rujing Zha
2014-05-14
charujing123
发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu
发送时间：2014-05-14 20:22
主题：Re: [Freesurfer] change background color in tksurfer
收件人：Freesurfer support listfreesurfer@nmr.mgh.harvard.edu
抄送：
Sorry
That probably means that the subject is out of synch. Try viewing the
subject's surface tksurfer or freeview and load the annotation.
doug
On 05/14/2014 10:25 AM, _andre...@sapo.pt wrote:
Hello all,
I generated the lgi.stats file for all my subjects and in one of them
I got this warning:
On 05/13/2014 11:19 PM, Caka wrote:
Dear Doug and all, I have already done two things: (1) 'recon-all’ to
the segmentation for 140 subjects; (2) surface registration to
fsaverage template for 1 subject using: mri_surf2surf --hemi lh
--srcsubject sub001 --srcsurfval thickness --src_type curv
Is the mean thickness in the ?h.aparc.stats file? Something like
# Measure Cortex, MeanThickness, Mean Thickness, 2.27227, mm
On 05/13/2014 05:18 PM, amirhossein manzouri wrote:
Hi,
The same result! the last is insula !
Best regards,
Amirhossein Manzouri
On Mon, May 12, 2014 at 5:05
Hi Bruce,
Thanks again for your help so far. I had a few follow up questions:
1) As far as mapping the average thickness to fsaverage coords, when I was
constructing the average thickness map I used mris_preproc with --target
fsaverage (and then mri_concat), so it's already in fsaverage
Yes!
On May 14, 2014 7:16 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
Is the mean thickness in the ?h.aparc.stats file? Something like
# Measure Cortex, MeanThickness, Mean Thickness, 2.27227, mm
On 05/13/2014 05:18 PM, amirhossein manzouri wrote:
Hi,
The same result! the last
Hi Freesurfers,
I'm confused about surface vertices labels. One of the tutorial mentions
that: There is a one-to-one correspondence between surfaces which allows
the user to cross-reference vertices from one surface to another (even
across subjects) and to the volume. So there is a map between
Hello Freesurfer users,
Does anyone know a command to automatically expand (grow/dilute) a label
file along the surface, e.g. add neighbouring vertices to the label?
Thanks,
Martha Shiell
Ph.D. Candidate, Neuroscience
McGill University
___
Freesurfer
Hi Martha
you can dilate the label in either tksurfer (tools-label-dilate label)
or in the dev version of mri_label2label (which you will need to
download)
cheers
Bruce
On Wed, 14 May 2014, Martha Shiell wrote:
Hello Freesurfer users,
Does anyone know a command to automatically expand
Dear FreeSurfer group,
If I want to extract frontal WM volume, is it something doable in FreeSurfer?
Much obliged,
Daniel
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The
You can choose the areas that you want to define frontal from
wmparc.mgz and add up the volumes. If you have another way to define
frontal, then you'd have to tell us what that is.
doug
On 05/14/2014 05:37 PM, Yang, Daniel wrote:
Dear FreeSurfer group,
If I want to extract frontal WM
Hi Doug,
Do you mean wmparc.stats? If yes, that is my understanding of the only way (so
far) to estimate WM volume by FreeSurfer too, and you already told me (before)
that it is only 5mm from white surface down into the brain center, correct??
I don't have a better way to do this so far.
If
On 05/14/2014 06:26 PM, Yang, Daniel wrote:
Hi Doug,
Do you mean wmparc.stats? If yes, that is my understanding of the only
way (so far) to estimate WM volume by FreeSurfer too, and you already
told me (before) that it is only 5mm from white surface down into the
brain center, correct??
Hello freesurfer, thanks for your message. I am doing the recon-all for T1
and T2* structural dataset now I have in all 8 files in the order of
(T2T1T2DTIT@T2*T2). I am doing a data analysis of another subject and
we have one T1 file s600a1001.mgz. Since my shell is a bash shell, I am
running
You should set your SUBJECTS_DIR variable to the directory with all the
subjects. Edit the .bashrc/.tcshrc/.cshrc by replacing the current one
with
SUBJECTS_DIR /User/sampada/Desktop/Vaibhav2/
and then run recon-all
S.
On Wed, May 14, 2014 7:47 pm, Dr Sampada Sinha wrote:
Hello freesurfer,
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