Hi Justin,
This is quite similar to a question I had asked previously:
https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33421.html
I believe the solution is to generate a 14000 vertex template, and then
appy mri_surf2surf to all 10 subjects, which will map the vertices of
all 10
hi folks,
we are setting up freesurfer on a new cluster and trying to be as modular
as possible in terms of dependencies. at present we are only installing
5.3.0 + tracula updates.
will libnetcdf (required by tracula) be included in freesurfer? or is it
considered a dependency?
and talking of
Hi,
I have a question about how to calculate the COV for the MNE software. As I
understand it from Section 4.17 of the 2.7.3 MNE manual, if one is averaging
together COV matrices, one weights them by the number of observations going
into each one. I also see from Section 4.17.2 that these
Job description:
National University of Singapore (NUS) is a leading global university
centre in Asia. It offers a global approach to education and research,
with a focus on Asian perspectives and expertise. Computation functional
anatomy laboratory at NUS (http://www.bioeng.nus.edu.sg/cfa)
Hi Vincent - I suspect that this problem would be fixed by some recent
changes that I've implemented for the longitudinal stream of tracula, and
that I'm in the process of testing. As soon as we can get a new dev
version built, I'll let you know so you can test it.
Thank you for your
Hi Satra - We've been talking about a 5.3.1, yes. On my end, it would
include the tracula updates that are currently available and possibly some
more (I've been working on some improvements to longitudinal tracula).
Not sure about libnetcdf but this is a good time to add things to the wish
Dear Freesurfers,
As discovered here,
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35160.html
it seams that some Mac OSX installations suffered from incomplete files.
I just veryfied that I had downloaded the complete image and wget says yes:
Logging in as anonymous ...
There are 3 missing fsl files from the OSX snow leopard installation.
They can be downloaded from here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/fsl
Copy them into your $FREESURFER_HOME/bin directory.
-Zeke
On 04/04/2014 12:32 PM, Markus Gschwind wrote:
Dear
Hi Shantanu,
Thanks for your reply. My command line in tksurfer was:
~$ tksurfer TGT_N61AvgSubject rh inflated -annotation
/Data/freesurfer/subjects/TGT_N61AvgSubject/label/rh.Comp2RH_TGTN61_Apr3.annot
You can also do the same for the pial surface.
The original ctab file
Hi Cherisse, i don't understand what you have done. Is the mask a volume
mask or surface mask? In mri_cor2label, you can specify a surface to get
surface vertex numbers.
doug
On 04/02/2014 07:03 PM, Cherisse Onuigbo wrote:
Hello
I was wondering how to create a label from a binary mask. I
Try excluding the following line from your ctab
0 Unknown 0 0 00
The list in the ctab should match that of the labels you are passing on
the command line (it is ok to have more in the ctab than on the command
line)
doug
On 04/02/2014 01:05 PM, Laura
Don't use --projopt and it won't segfault
On 04/03/2014 02:08 AM, Joerg Pfannmoeller wrote:
The command is:
mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat --trgsubject
subjid --interp nearest --projopt /.../map001 --hemi rh --o
/.../f001_surf.nii --noreshape --cortex
I'm not sure, when I run it it results in different xyz. What version
are you using?
I've put a copy of my version (for linux) here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surfcluster
doug
On 04/03/2014 03:56 AM, Joerg Pfannmoeller wrote:
Hi,
I am trying to
First run this
tkregister2 --mov hipposubfield.mgz --reg hsf.reg.dat --s subject
--regheader --fstarg
It will bring up the tkregister2 GUI and just double check that the
subfields are where they need to be. Hit Save Reg and exit. In the
future, you can run the tkregister2 command with
The QDEC output does not quite report what you want to report. I would
run mri_glmfit-sim using --glmdir /path/to/qdec/folder and the same
parameters as you used for the monte carlo simulation. this will produce
several files including a summary/table file with the MNI305 coordinates
of most
They are not exactly the same. However, if you run mri_vol2surf with
--surf white50 --projfrac 0 it will be identical (where white50 is the
surface create with mris_expand)
doug
On 04/04/2014 05:34 AM, Righart, Ruthger wrote:
Hi Markus,
Thank you, excellent tool and gives exactly what I was
You can use mris_label2annot to create an annotation and then control
the colors via the ctab
doug
On 04/03/2014 09:13 AM, Rudolph Pienaar wrote:
Hi all --
I have a process that generates a list of ROIs (from aparc.annot) based
on some cost condition. I wanted to view these labeled ROIs in
This is a question for Ruopeng (who is the author of freeview, and
cc'ed). Can you upload the subject and the annot file so that he can
replicate the problem?
doug
On 04/03/2014 06:55 PM, Laura Taylor wrote:
Hi Again Doug,
I was able to get what I was looking for after I modified my ctab
Hi Omar, there is a bug in that version off mni152reg. Use the version
in dev instead
doug
On 04/03/2014 03:50 PM, Omar Singleton wrote:
Hi Freesurfers,
I am trying to convert a volume from MNI152 to subject space. I tried to
do what this previous question suggested:
My mask is a volume mask. When I run the function normally, the vertices that
are in the text file do not fall in the region of my mask.
On Friday, April 4, 2014 2:28 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
Hi Cherisse, i don't understand what you have done. Is the mask a volume
How are you checking the vertex coordinates? You can't use SPM, you'll
have to use tkmedit or freeview
On 04/04/2014 04:04 PM, Cherisse Onuigbo wrote:
My mask is a volume mask. When I run the function normally, the
vertices that are in the text file do not fall in the region of my mask.
On
Great, thank you!
Do you maybe know if these changes will only affect the center
variables? I have almost completed my soon-due report about the
longitudinal analysis of weighted average variables (overall not
byvoxel along the MAP) and now I fear that results are maybe not correct
because
Can you upload the y.mgh file and fsgd file so that I can try to
replicate it? What platform are you running on and what version of FS?
doug
On 04/02/2014 06:34 PM, Tudor Popescu wrote:
Hi Doug
Sorry, again I wasn't sure whether you'd noticed my reply amonst the
latest list messages.
Hi Vincent - Overall measures for the whole tract would not be affected
by this type of error.
a.y
On Fri, 4 Apr 2014, Vincent Brunsch wrote:
Great, thank you!
Do you maybe know if these changes will only affect the center
variables? I have almost completed my soon-due report about the
Thank you Zeke,
What about these?
/usr/local/freesurfer/bin/bet.fsl
/usr/local/freesurfer/bin/flirt.fsl
/usr/local/freesurfer/bin/slicetimer.fsl
They are not there neither compared to the ubuntu install.
Best,
Markus
2014-04-04 19:05 GMT+02:00 Z K zkauf...@nmr.mgh.harvard.edu:
There are
I first checked it in tkmedit, but I didn't see the region in green as I went
through the slices. I also put another label in there just to check if I was
displaying labels correctly and others showed up. Then I used the display
function in spm and input the coordinates there, but it showed
What were your mri_cor2label and tkmedit command lines? SPM will never
work properly for what you are trying to do.
On 04/04/2014 04:42 PM, Cherisse Onuigbo wrote:
I first checked it in tkmedit, but I didn't see the region in green as
I went through the slices. I also put another label in
mri_cor2label --c wramygdala.R.001.nii --id 1 --l wramygdala.R.001.label
tkmedit Subjects_for_Cherisse/S001 T1.mgz -aux brainmask.mgz -seg aseg.mgz
And then I added the label using the drop down menu.
On Friday, April 4, 2014 3:45 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
What were
Try this first
mri_cor2label --c aseg.mgz --id 17 --l lh.hippo.label
Then load lh.hippo.label
If wramygdala.R.001.nii is not in the conformed space, your command will
not work
On 04/04/2014 05:17 PM, Cherisse Onuigbo wrote:
mri_cor2label --c wramygdala.R.001.nii --id 1 --l
Thanks Doug, I've FileDropped you the zip. Running FS 5.3.0 on Virtualbox
4.2.12 (Ubuntu guest, Windows host)
T
On 4 April 2014 22:09, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
Can you upload the y.mgh file and fsgd file so that I can try to replicate
it? What platform are you running
30 matches
Mail list logo
