FYI: In the -prep and -path sections I can run a 77 direction DWI on 33
training subjects with 8Gb RAM, Ubuntu 12.04 but it spills over into the
swap memory. The -bedp section is not a memory hog at all.
Cheers,
Sean
On 3/05/13 4:51 PM, "Jürgen Hänggi" wrote:
>Hi Daria
>
>We had the same
Hi,
Given the issues discovered with 5.2, we're now wondering whether we should
just go back to 5.1 or wait until 5.3 (under a bit of time pressure).
Can I just clarify the how the capability of 5.2 (and 5.3) to run subjects with
single time points in longitudinal analysis (by creating an artif
Hi Gonzalo
version 5.3 is midway through the QA process. We can give you a beta of
it in the next couple of days if you want
Bruce
On Thu, 2 May 2013, Gonzalo Rojas
Costa wrote:
Hi Bruce:
And, where is version 5.3 ?... in the "nightly dev builds" ?...
Sincerely,
Gonzalo Rojas Costa
O
Hello all,
I am facing a problem whereby after running GLMfit and cluserwise
correction for multiple comparisons using the monte-carlo method, I was
unable to generate any clusters. I do have significant images produced for
the glmfit.
All procedures were done according to the tutorial to match t
Hi Sarah.
I cannot comment on 5.1 vs waiting for 5.3.
About the single time point. The reason is not that we need the base. We just
want to make sure that that image undergoes the same processing steps as all
other images to avoid a processing bias.
Mixed effects models allow inclusion of subje
What effect, if any, would the implantation of a Vagus Nerve Stimulator
have on registration?
Thank you,
Beth
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The information in this
Hi Beth
it depends on what kinds of artifacts it causes. I would think it would
be ok, but don't have any experience.
Bruce
On Fri, 3 May 2013, Jerskey, Beth
wrote:
> What effect, if any, would the implantation of a Vagus Nerve Stimulator have
> on registration?
> Thank you,
> Beth
>
>
>
___
Sarah,
Hi, to help you decide, since I dont know what your study entails or the
timeline, this is some info:
- bug in 5.2 affects just white and pial surface placement, so thickness
and area data will be off. surface registration, and its off-shoot data,
like aparc labels and inter-subject surfa
Hi freesurfer,
I have a label and each vertex in this label has a probability value.
My problem is that how to determine the peak vertex (or the center of gravity)
of this label and get the coordinates.
And I also want to know, in the tksurfer interface, whether the vertex index
has a correspo
Is there a way to correct fmri data for epi distortions in freesurfer? Or
does the data need to be first fun through FSL's B0 unwarping?
Corinna
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Hello Freesurfers,
I would like to use mri_cor2label for areas of the cortext defined in
the FreeSurferColorLUT.txt. There are many ROIs whose IDs are >255,
the numerical limit imposed on mri_cor2label. How can I define labels
using these larger-numbered ROIs? I am specifically interested in
Hi Corinna
yes, we use the FSL tools for B0 correction.
cheers
Bruce
On Fri, 3 May 2013, Corinna
Bauer wrote:
> Is there a way to correct fmri data for epi distortions in freesurfer? Or
> does the data need to be first fun through FSL's B0 unwarping?
>
> Corinna
>
>
__
Hi Anastasia,
Thank you for your response. I think I figured out what was the problem: The
delimiter for the 3 column .bvec file MUST be SPACE/TAB, otherwise the program
fails to reshape it correctly. In my case the delimiter was "," and the program
was reading only the 1st column of it.
I ha
Hi Corinna, are you using FSFAST? If not, are you still going to the
surface?
doug
On 05/03/2013 11:07 AM, Corinna Bauer wrote:
> Is there a way to correct fmri data for epi distortions in freesurfer?
> Or does the data need to be first fun through FSL's B0 unwarping?
>
> Corinna
>
>
>
Hi Jeff, are you sure that mri_cor2label does not take ids > 255? I just
ran it without a problem.
doug
On 05/03/2013 11:30 AM, jwa...@nmr.mgh.harvard.edu wrote:
> Hello Freesurfers,
> I would like to use mri_cor2label for areas of the cortext defined in
> the FreeSurferColorLUT.txt. There
Can you send the command line and terminal output and the version of FS
you are using?
doug
On 05/03/2013 09:01 AM, Joshua deSouza wrote:
> Hello all,
>
> I am facing a problem whereby after running GLMfit and cluserwise
> correction for multiple comparisons using the monte-carlo method, I
> was
On 05/03/2013 10:00 AM, limengsecret wrote:
> Hi freesurfer,
> I have a label and each vertex in this label has a probability value.
what format are you using for the label? Is it a freesurfer .label file?
> My problem is that how to determine the peak vertex (or the center of
> gravity) of this
Create the B0 voxel shift map. Call it b0dcmap.nii.gz and put it in
the bold folder, eg:
epidewarp.fsl \
--mag mag.nii.gz \
--dph dphase.nii.gz \
--tediff YOUR_TE_DIFF --esp YOUR_ESP \
--vsm bold/b0dcmap.nii.gz
When you run mkanalysis-sess and preproc-sess, add "-b0dc" to the
command lin
thanks Doug, I will give that a try.
On Fri, May 3, 2013 at 12:27 PM, Douglas N Greve
wrote:
> Create the B0 voxel shift map. Call it b0dcmap.nii.gz and put it in
> the bold folder, eg:
>
> epidewarp.fsl \
> --mag mag.nii.gz \
> --dph dphase.nii.gz \
> --tediff YOUR_TE_DIFF --esp YOUR_ESP \
Should the phase image be in rads? and does the magnitude image need to be
skull-stripped first?
On Fri, May 3, 2013 at 12:30 PM, Corinna Bauer wrote:
> thanks Doug, I will give that a try.
>
>
> On Fri, May 3, 2013 at 12:27 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> Create
It needs to be 0 to 4095, see below
--ph phasevolid
Phase volume from the B0 fieldmap (if the phases from Echo1, Echo2 are
available instead of their difference). These are assumed to be scaled
between 0 to 4095 for -pi to pi. Eg, ph.ext, where ext is either nii,
nii.gz, or img. Not with --comple
oh great. Is there a way to get this to work with FSL 5?
On Fri, May 3, 2013 at 1:11 PM, Douglas N Greve
wrote:
> It needs to be 0 to 4095, see below
>
> --ph phasevolid
>
> Phase volume from the B0 fieldmap (if the phases from Echo1, Echo2 are
> available instead of their difference). These are
What is going wrong when you run FSL 5?
On 05/03/2013 01:38 PM, Corinna Bauer wrote:
> oh great. Is there a way to get this to work with FSL 5?
>
>
> On Fri, May 3, 2013 at 1:11 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> It needs to be 0 to 4095, see below
>
> --
What is your cmd line? Can you run it with --debug as the first arg,
capture the output, and send it to me? eg,
dewarp.fsl --debug ... |& tee dng.log
On 05/03/2013 01:43 PM, Corinna Bauer wrote:
> I get this:
>
> FSLVersion 5.0.2
> FSLVerMaj 5
> FSL Version is 5.0.2, must be 3.X or 4.X
>
>
>
I can't remember why I excluded version 5. I put another version
herethat will accept v5
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl
try it and let me know if it works
On 05/03/2013 02:13 PM, Corinna Bauer wrote:
>
> /usr/local/freesurfer/subjects/symmetry/functi
It might have something to do with the complex input. I don't have
complex data handy. Can you upload yours to our filedrop?
On 05/03/2013 02:40 PM, Corinna Bauer wrote:
> I replaced the epidewarp.fsl file in the bin folder. Tried it again
> and got this:
>
> /usr/local/freesurfer/subjects/symm
It should actually run all the way through. If your field maps have the
same geometry as your fmri volumes, and your fmri runs have correct
geometry, then you can run
mri_convert imag_fmap2300.nii imag_fmap2300.geo.nii --in_like fmri.nii
Also note that you are just creating a voxel shift map w
Hi Bruce:
Ok... I am interested in the 5.3 beta version...
Sincerely,
Gonzalo Rojas Costa
On Fri, May 3, 2013 at 8:41 AM, Bruce Fischl wrote:
> Hi Gonzalo
>
> version 5.3 is midway through the QA process. We can give you a beta of it
> in the next couple of days if you want
>
> Bruce
>
ok, I think Nick posted a link of where the beta will be (or if not, he
will)
Bruce
On Fri, 3 May 2013, Gonzalo Rojas Costa wrote:
Hi Bruce:
Ok... I am interested in the 5.3 beta version...
Sincerely,
Gonzalo Rojas Costa
On Fri, May 3, 2013 at 8:41 AM, Bruce Fischl wrote:
Hi Gonzalo
If they don't match, then this is beyond the scope of the tools as they
currently exist.
On 05/03/2013 04:40 PM, Corinna Bauer wrote:
> volume sizes don't match.
>
> INFO: could not find
> fieldmap/20130409_153340FieldMappings011a001x1.mat file for direction
> cosine info.
> INFO: use Analyze
this link is here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/
the centos6_x86_64 build is there now. the others will appear as they
finish their builds, which can take quite a bit of time... so check back
every day or so
n.
> ok, I think Nick posted a link of where t
Hi, Nick.
Recently, you sent me a test version of tkmedit to test under Fedora 18
to address the glibc problem. That tkmedit worked great and you said we
would have a new version of the whole package in brief. Is this 5.3 BETA
the versio addressing this glibc problem?
Em Sex, 2013-05-03 às 17:46
Today it was released the version 4.1.0 of iSurf BrainView for iPad, iPhone
and iPod Touch.
Major changes:
- Color scheme has been changed to match Windows 8 Version.
- Icon has been redesigned as suggested by many users.
- Now it supports the new resolution. 1136x640
- 3D engine has been redesign
Hello,
I was attempting to preprocess a scan earlier and I got an error which
seems to indicate a problem with the version of FSL:
>From this command:
preproc-sess -s nmasa_016_130111 -fsd bold -stc up -surface fsaverage lhrh
-mni305 -fwhm 5 -per-run
I get this error:
#--Using FSL's BE
Marco,
Hi, yes, this release should fix the glibc problem on fedora 18 and
hopefully unbuntu 13 as well. If you have a chance to exercise all of it
(run recon-all on a subject, and run the guis like tkmedit, tksurfer,
freeview and qdec) that would be a big help prior to our official release
after
Thanks Doug,
The command line I am running is:
mri_cor2label --c
/cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/mri/aseg.mgz
--id 1029 --l
/cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/label/suppar_ctx_LH_${identif
Hi Jeff
Don't you want the aparc+aseg not the aseg?
Bruce
On May 3, 2013, at 10:37 PM, jwa...@nmr.mgh.harvard.edu wrote:
> Thanks Doug,
>
> The command line I am running is:
>mri_cor2label --c
> /cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/mri/aseg.mg
yea, the aseg only goes to 255.
On 5/3/13 10:44 PM, Bruce Fischl wrote:
> Hi Jeff
> Don't you want the aparc+aseg not the aseg?
> Bruce
>
>
>
> On May 3, 2013, at 10:37 PM, jwa...@nmr.mgh.harvard.edu wrote:
>
>> Thanks Doug,
>>
>> The command line I am running is:
>> mri_cor2label --c
>> /clus
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