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 wrote:
>
> 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
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 wramygdala.R.001.la
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
wrote:
What were your mri_cor2label and tk
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 t
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 that
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 :
> There are 3 missing fsl files from the
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 t
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. Hope
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
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.
> O
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
wrote:
Hi Cherisse, i don't understand what you have done. Is the mask a volume
mask or surface mask? In
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:
>
> https://mail.nmr
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
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
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 wa
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 s
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 --noe
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 comp
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
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 Taylor
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
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 (r/lh.aparc.a
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 Free
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 ... Logged
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
l
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 patience!
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) focuses
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 a
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 wh
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 Ruthger
no, they are not the same. mris_expand generates a smooth
non-self-intersecting surface, which is definitely not guaranteed by
simple projection.
cheers
Bruce
On Fri, 4 Apr 2014, Righart, Ruthger wrote:
Hi Markus,
Thank you, excellent tool and gives exactly what I was searching f
Hi Markus,
Thank you, excellent tool and gives exactly what I was searching for!
Is the resulting surface the same for mris_expand taken at 50% as the
one that is used in mri_vol2surf with flag projfrac 0.5? I wondered if
something is done differently as processing time for mris_expand is much
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