Does Freesurfer's GPU bits care about single or double precision?
Cheers, satra
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The information in this e-mail is intended only for t
Dear Freesurfer experts,
I have recently installed Freesurfer onto a VirtualBox Linux environment, and
had no problems running the supplied practice subject, 'Bert', all the way
through reconstruction. However, when I started trying to analyze my own
subject's, recon-all keeps exiting just aft
Hi all,
I am trying to compute differences between 2 runs of my same set of
subjects (repeatability) using the steps from the paired analysis wiki page.
After I finish the mris_preproc and the mri_surf2surf steps, when I do the
glmfit, should I be using the osgm option ? Since it is the sa
Hi David - Can you please send us the trac-all.log file for this subject?
Without seeing where it stopped and what error messages there are it's
hard to guess what's going on.
Thanks,
a.y
On Fri, 15 Nov 2013, David Soto wrote:
Hi -
trac-all completed in all my Ps except one
and I notice
Hi experts,
I came across an error in the third stage of reconstruction using
freesurfer. I am rerunning freesurfer on windows 7 64 bit:
freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full
I have following error:
#@# Sphere rh Fri Nov 15 14:28:04 EST 2013
/home/virtualuser/freesurfer/sub
Hi Jonathan
yes, checkout our wiki which lists our upload site. Tar and gzip the
subject and put it at:
https://gate.nmr.mgh.harvard.edu/filedrop2/
Bruce
On Fri, 15 Nov 2013,
Jonathan DuBois wrote:
Hi Bruce,
Thanks for getting back to me. Unfortunately, we don't have a FLAIR/T2 for
this
use this version
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/reg-feat2anat
On 11/15/2013 02:04 PM, Greg Reckless wrote:
> I am having the same problem with a newer version of tcshell and
> reg-feat2anat as discussed in threads below. Has this been resolved?
> If not, could a wor
I am having the same problem with a newer version of tcshell and
reg-feat2anat as discussed in threads below. Has this been resolved?
If not, could a working link to the updated version mentioned previously
be reposted.
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-June/030473.ht
Can you convert the two to mgz or nii with mri_convert and then run
tkregister2? If they were acquired in the same session, then the
geometric information in the header should bring them into close
registration regardless of voxel size, orientation, field of view, etc.
mri_convert should pres
Yes, they were acquired in the same session, but using a slightly different
FOV. They were converted from dicom to nifti using dcm2nii and then used
for FS analysis.
The axis orientation of the images is the same. Extensive image analysis
(including registration of FLAIR and T1 using FLIRT) has be
Have you checked this wiki page?
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 11/15/2013 01:45 AM, Octavian Lie wrote:
> Dear All,
> I need to export a T1.mgz and N points (Nx3 coordinates .mat file) of
> the same volume in SPM12b. N are actually intracranial electrodes.
> For t
were these acquired in the same session? If so, were they converted to
mgz directly from dicom?
On 11/15/2013 10:15 AM, Martijn Steenwijk wrote:
> I digged further into this.
>
> The scale difference previously reported is not true. It is only a
> translation error.
>
> It looks like that the o
Hello experts,
Could you please help me? I have already checked perl is in usr/bin/perl.
Sincerely, Bernardo.
nu_correct.mni.log is:
tmpdir is ./tmp.mri_nu_correct.mni.2629
/Users/bernardomartins/Desktop/manoel/manoel/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2629/nu0.mnc -odt float
mri_
Hi Anna,
Yes, search for 'build-stamp' in the recon-all.log. There's also the
build-stamp.txt in the scripts dir, but the recon-all.log will tell you if
different versions were run by looking at the build-stamp for each
invocation in the log.
-Louis
On Fri, 15 Nov 2013, Anna Jonsson wrote:
>
CentOS4. Their is a 32bit and 64bit build of freesurfer CentOS4.
Download and install the version compatible with your platform.
-Zeke
On 11/15/2013 12:52 AM, Rujing Zha wrote:
> Dear all,
> In CentOS5,which freesurfer5.3 version(centos4 or centos6?) can be
> compatible?
> Thanks!
> All the best
> Hi Bruce,
>
> Yes - of course that helps :)
>
> I did not even know that it was a hard question!
>
> I had noticed that some results from freesurfer, and other segmentation
> techniques, subsequently fail manual QC.
>
> Do you think that there would be value in some kind of parameter sensitivity
I digged further into this.
The scale difference previously reported is not true. It is only a
translation error.
It looks like that the orig.mgz has (0,0,0) in the center of the image;
while FLAIRraw (after header-only registration) has the origin at index
(0,0,0) - so in one of the corners of t
Hi, I am trying to find a list of all the labels available for FreeSurfer 5.3
and am having a hard time finding it.
Any suggestions?
Thank you,
regards,
Elisabetta del Re
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Hi Bruce;
Thanks you very much... It rans ok...
Sincerely,
Gonzalo Rojas Costa
Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel:
Hi Jonathan
it really depends on the characteristics of the dysplasia. We have some
experience with this and in general FS does really well, but if it's a
large region of cortex that is 8mm thick things will probably fail. Do you
have a highres FLAIR/T2? That can help.
If you upload the subj
Hi Mark
that's a tough question to answer, as it depends on the parameter. I'm
sure that the answer is "yes" for some, but in general we try very hard to
adaptively estimate our parameters, which is why our tools work well on a
wide variety of T1-weighted acquisitions. We also have a test suit
Hi Gonzalo
recon-all -s -balabels
should do the trick
cheers
Bruce
On Fri, 15 Nov 2013, Gonzalo Rojas Costa
wrote:
>
> Hi:
>
> I have some freesurfer processed studies I used 5.1 version, and now I
> found that it don't has the brodmann area labels and statistics generated in
> some stu
Hi:
I have some freesurfer processed studies I used 5.1 version, and now I
found that it don't has the brodmann area labels and statistics generated
in some studies... How can I create it without doing again the complete
recon-all ?
Sincerely,
Gonzalo Roj
Hi -
trac-all completed in all my Ps except one
and I noticed that the dlabel/diff output does not contain all the files
I assessed whether it could be do to poor registration, by checking
the aparc+aseg
file and looks allright
I also checked the registration of FA maps to standard space by
fr
Dear all,
Thanks for all the input. Doug, concerning your suggestion
tkregister2 --mov FLAIRraw.mgz --targ orig.mgz --regheader --reg junk
Using this, the axes orientationseem to be correct, but scaling and
translation of registered FLAIRraw seem to be way off. (registered FLAIRraw
is much larger
Hi:
Which is the freeview newest version ?... the one that is included in
freesurfer 5.3.0 package ?...
Sincerely,
Gonzalo Rojas Costa
Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clínica las Condes
Lo Fontecilla 4
Good morning Dr Vinke,
did you have the chance to take a look at the subject I uploaded a few days
ago?
thanks again.
Kind regards,
Pietro
--
Pietro De Rossi, MD
-
Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento
NESMOS (Neuroscie
Dear list members,
I was wondering where in the Freesurfer output the information on which
freesurfer version has been used to process scans is located? eg
recon-all.log?
Thank you,
Kind Wishes,
Anna
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