Dear all,
I have read the troubleshooting in the website
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints_tktools. I
want to know if thereis a similar method to remove skull part in GM? I donot
want to use -gcut and watershed option. I think control point method is better
than
Hi Skyler - I would *highly* recommend using the version of tracula in
5.3, as there have been improvements in both performance and speed.
You can check the DWI to anatomical registration by overlaying the
aparc+aseg from the dlabel/diff directory (which is in diffusion space) on
the FA map.
Thank you very much for all the help.
> On Dec 2, 2013, at 11:27 AM, Douglas N Greve
> wrote:
>
>
>> On 12/01/2013 11:40 PM, Arash Nazeri wrote:
>> Hi all,
>>
>> I wanted to make sure how one could assign intensities from the
>> subjacent white matter voxels to the cortical surfaces using mr
when you say there is some skull considered to be gray matter, do you
mean in the aseg or does the pial surface contain it? If it's the aseg
then it probably doesn't matter as we don't use the asegs for cortical
stuff in any case
cheers
Bruce
On Tue, 3 Dec 2013, Rujing Zha wrote:
Dear Louis,
Dear Louis,
Thanks for your helpful prompt in advance.
I see. In my case, there is a not properly stripping, there is a not properly
gray matter(there are a some skull considered as gray matter). Did you mean I
can draw the segmentation without considering the skull stripping? And a bad
brainmas
Hi Louis,
Thanks for your helpful suggestion.
Maybe I just click the "slice -/+" module if I want to view all the slices of
one subject's volume in tkmedit. But I do not want to click the button
continuously to view all the slices. I want to press a button/key once, then I
can see all the slice
Hi Martin,
In November 27 I posted a similar question, which later I found a solution.
See if it works for you.
Hi Lilla,
> Thank you for your reply. I have boost installed, yet it is not the
> version required (v. 1.49). Although, even after installing an older
> version such as the 1.41 it is n
Hi Skyler - Are you using freesurfer 5.1 or 5.3?
Most likely this issue is due to poor registration, either from the
individual DWI to the individual T1, or from the individual T1 to the
template space. Or it could be that there is a problem with the
aparc+aseg.
a.y
On Mon, 2 Dec 2013, Sky
Hi all,
I've been running DTI using tracula (fs version 5) for over 1 week on 2
subjects. It appears that it is having difficulty finding satisfactory control
point fit and has attempted over 1600 tries. Any help is greatly appreciated.
See error below:
INFO: Distances between consecutive poin
Hi Zeke,
Thanks a lot for explanation. I think I will install centOS into a virtual
machine for quick solution. I only need it to run CVS.
Thanks and best regards,
Martin
Sent from my iPad
> On 2.12.2013, at 22:50, Z K wrote:
>
> Martin,
>
> Upx (http://upx.sourceforge.net) is an executabl
Martin,
Upx (http://upx.sourceforge.net) is an executable packaging utility we
run on all our binaries before shipping to reduce their overall size.
One consequence of upx is that it changes the way the "file" and "ld"
commands process the binaries. In this case it makes the "file" command
say
Hi,
so far that wiki page only had the commands for cross sectional runs. I
added the commands for the longitudinal runs (see my mail and also the
one for the surface mapping) to that page for future reference.
Best, Martin
On 12/02/2013 03:21 PM, Douglas N Greve wrote:
> For #2 you can use th
Doug,
Thank you for your very helpful suggestion. Indeed, doing so made it so I
could quickly take any parts (or all) of each Greicius network and put them
in individual subject space.
In case this may help anyone else, the final series of commands were (in
this case, for the whole anterior salie
For #2 you can use the method described here
http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 12/02/2013 03:01 PM, Martin Reuter wrote:
> Hi Ivan,
>
> 1) it means that the voxel sizes across your images are different. Do
> mri_info on the images to see what's going on. Usually t
Hi David - I am not convinced that all the regisrtrations have worked well
for this subject. The fact that some of the coordinates of the control
points, which are mapped from template to individual space, are negative
in individual space (see INFO messages in log file), means that some part
Tank you very much.
A-Do you mean the partial correlation coeff (PCC) at each voxel averaged over
region? Finally a linear regression is done between cortical thickness of a
composite region and NPS. However the authors discuss every individual region
as related to disease. So a table with parti
Hi Ivan,
1) it means that the voxel sizes across your images are different. Do
mri_info on the images to see what's going on. Usually this is no
problem if the differences are tiny. Just a warning.
2) yes, the longs are all in the same space as the base, you can map
images to the rawavg from
Hi Rujing,
Even if there is some skull/dura left after the skullstrip step in
recon-all, it still may not negatively impact the surfaces. It might be
worth running the remaining recon-all steps to see how the surfaces turn
out.
If you want to swap-in a better skullstripped volume into the re
Hi Zeke,
Thanks for response. Well it was the first thing for me to try to compile boost
on gentoo, which went fine. However the libraries were not compatible. Gentoo
has 1.52 version, while the one needed is about 4 years old.
When I do "ldd mris_resample" I get "not a dynamic executable" and
Hi Rujing,
You can use a tcl script to take several snapshots in tkmedit, then you
could use the convert command (part of ImageMagick distro) or
something similar to create an animated gif. With the convert command you
would use the -adjoin and -delay flags. You could use one of the tcl
scri
On 12/02/2013 02:22 PM, std...@virgilio.it wrote:
> Hi list,
>
> I have some questions, please.
>
> I performed linear regression by qdec to find the regions where the
> cortical thinning correlates with neuropsychological test (NPS),
> taking in account 3 nuisance factors.
>
> A- I individuated
Yes, that's correct! Thanks for the follow up
~koene
On 12/2/13 2:27 PM, Louis Nicholas Vinke wrote:
> Hi Koene,
> It looks like Nick copied that volume over on 11/27. Thanks for
> pointing that out.
> -Louis
>
> On Tue, 26 Nov 2013, Koene Van Dijk wrote:
>
>> Hi there,
>>
>> We've been using t
Hi Koene,
It looks like Nick copied that volume over on 11/27. Thanks for pointing
that out.
-Louis
On Tue, 26 Nov 2013, Koene Van Dijk wrote:
> Hi there,
>
> We've been using this local version of Freesurfer:
> /cluster/freesurfer/centos6_x86_64/stable5
>
> And this file was relevant:
> /clust
yep, you should be able to do that
On 12/02/2013 02:08 PM, Clark Fisher wrote:
> Thanks for the reply. That makes sense. With your modified approach, maybe
> I could even work the scalings into the contrast weights? Thanks for the
> feedback.
>
> -Clark
>
>
> On Dec 2, 2013, at 12:50 PM, Doug
Hi list,
I have some questions, please.
I performed linear regression by qdec to find the regions where the cortical
thinning correlates with neuropsychological test (NPS), taking in account 3
nuisance factors.
A- I individuated some posterior regions and now I'd like to build a table with
part
Thanks for the reply. That makes sense. With your modified approach, maybe I
could even work the scalings into the contrast weights? Thanks for the
feedback.
-Clark
On Dec 2, 2013, at 12:50 PM, Douglas N Greve wrote:
>
> Hi Clark, I think Approach A should work ok. As you imply, there co
Hi Clark, I think Approach A should work ok. As you imply, there could
be different scalings, so take that into account somehow. A slightly
modified approach would be do define a different set of conditions for
each subject in the paradigm file. They create a contrast with
mkcontrast-sess that
Hi Doug (and other Freesurfers),
Hope you had a pleasant Thanksgiving. My thread last left off before everyone
left for the holidays. I just wanted to re-raise this question, as it's still
a pressing one for me.
Thanks,
Clark
On Nov 27, 2013, at 11:06 AM, Clark Fisher
mailto:cfis...@rockef
The problem is in the noE4female group. You only have 3 subjects and the
zAPOB and thickness are nearly equal and opposite in sign. The
correlation between these two regressors exceeds .96. This is probably
spurious, but it is killing the design matrix.
doug
On 12/02/2013 11:44 AM, Gabriel Go
There you are!Hope it helps- Mensaje original -De: Douglas N Greve Fecha: Lunes, 2 de Diciembre de 2013, 5:09 pmAsunto: Re: [Freesurfer] glmfit error on v5.1A: freesurfer@nmr.mgh.harvard.edu> Can you send the matrix that it creates?> > On 12/02/2013 06:09 AM, Gabriel Gonzalez Escamilla wrot
Martin,
libboost is not a static library, it is a shared library. It comes by
default on centOS platforms and freesurfer compiles against it during
the the build process. Typing 'ldd mris_resample' and examining the
output confirms this:
$>ldd mris_resample
linux-vdso.so.1 => (0x7fffd2773
On 12/01/2013 11:40 PM, Arash Nazeri wrote:
> Hi all,
>
> I wanted to make sure how one could assign intensities from the
> subjacent white matter voxels to the cortical surfaces using mri_vol2surf.
>
> Based on the documentation page --projfrac, if used with negative
> values, would assign whit
On 12/02/2013 09:05 AM, Yolanda Vives wrote:
> Dear FreeSurfer experts,
>
> I am performing a DODS analysis with QDEC to compare cortical
> thickness of patients and controls and I have some questions regarding
> the nuisance factors age and global cortical thickness.
>
> 1.- Should I demean bot
Can you send the matrix that it creates?
On 12/02/2013 06:09 AM, Gabriel Gonzalez Escamilla wrote:
> Dear Freesurfer experts,
>
> Sorry for the inconvenience but I posted this message last week, but I
> did not receive any answer. I really need to keep going on with my
> analyses.
>
>
> I have r
hi - thanks , not sure though...the no_dif brain mask
seems ok, if that is what you meant...
I did re-run the processing and
in the last run I can not see the WARN you mentioned
the latest preprocessing output from the preprocessing can be
found here: https://dl.dropboxusercontent.com/u/8209026/
Dear FreeSurfer experts,
I am performing a DODS analysis with QDEC to compare cortical thickness of
patients and controls and I have some questions regarding the nuisance
factors age and global cortical thickness.
1.- Should I demean both variables or only the age?
2.- Which of the following opt
Dear all,
Part of subjects 3d images cannot be stripped skull and neck properly in
recon-all default. I have got the brain volume mask, how I can using the
existing proper mask to help strip skull in recon-all and next workflow?
Thanks.Any reply will be appreciated.
All the best.
2013-12-02
R
Dear Freesurfer experts,Sorry for the inconvenience but I posted this message last week, but I did not receive any answer. I really need to keep going on with my analyses.I have runned the following command line:mri_glmfit --surf PLI_MCI_sample7_avg lh --C /root/trabajo/freesurfer/subjects/PLI
Hi Emily - Sorry for responding late due to traveling.
Does bedpostx not run at all, or does it stop half-way? What files if any
have been created in the dmri.bedpostX directory?
a.y
On Wed, 20 Nov 2013, ebell...@uwm.edu wrote:
> Hello,
>
> I am finding that my bedposting is not completing su
Hi Sal - I apologize for the late response due to traveling.
With tracula we have certainly used 30 direction data. It shouldn't be a
problem, since tracula fits the ball-and-stick model of diffusion of
Behrens et al 2007, which has been shown to give reasonable results
fitting 2 crossing fibe
Hi David - Sorry for the delayed response due to traveling.
There's a warning about the right ILF in the log file that may offer a
clue:
WARN: Initial control point 37 56 -6 is not in DWI volume - is DWI cropped?
WARN: Replacing with closest point in volume (37 56 0)
WARN: Initial control poi
Hi Bruce,
Thank you for your response. Now at least I know what went wrong; I'll
try your solution.
Thanks!
Anita
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