Hi Michael
This is a Mac specific problem. You can reduce the number of a priori tracts
used by reducing the entries in the list found in
freesurfer/trctrain/trainlist.txt. On my Mac it works with 26 a priori
tracts.
Cheers
Jürgen
On [DATE], Michael Scheel [ADDRESS] wrote:
Dear FS experts,
Hi Freesurfer experts,
Compiling FreeSurfer with GPU support failed with the error message
which is added to the end of this email.
The current build environment is as follows:
GeForce GTX 690
CUDA Toolkit 4.2
CentOS 6.3
I wonder if there are any specific requirements for building
CUDA-enabled
Hi Doug,
Thanks for your suggestion, but it didn't work out either.
Ed
On 16 Jul 2012, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
Message: 18
Date: Mon, 16 Jul 2012 11:32:06 -0400
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] How to register FLAIR to
Hi Michael and Jürgen - This issue has been resolved, see Updates:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula
It had to do with the original mac executables having been compiled on an
older version of MacOS, which was not smart about utilizing all the memory
on your computer. If
On Tue, Jul 17, 2012 at 4:54 AM, Akio Yamamoto
yamam...@tkl.iis.u-tokyo.ac.jp wrote:
Compiling FreeSurfer with GPU support failed with the error message
which is added to the end of this email.
The current build environment is as follows:
GeForce GTX 690
CUDA Toolkit 4.2
CentOS 6.3
I
Hi all,
I think I found the problem. I reduced the number of train files in the
trainlist.txt file and it ran without errors. Maybe I will need more memory
to run with all train files.
thanks
2012/7/16 Rui Lavrador ruilavra...@gmail.com
-- Forwarded message --
From: Rui
Hi all,
Using previous versions of FreeSurfer, we have used the eTIV as a covariate for
our volumetric analyses. We have been using the eTIV numbers from 5.1.0 for new
studies. What would you recommend using for subjects who have been run with
5.1.0? Can you make the template available
Hi Sue
you could take the eTIV from 5.0 and the aparc stats from 5.1.0. I
believe we already distribute the updated template but it's not used. Nick:
do you want to send around a patch to recon-all that people can use before
5.2 comes out?
thanks
Bruce
On
Tue, 17 Jul 2012, Susan Ruiz
Hi Ed, can you upload the FS analysis of the subject and the FLAIR so I
can take a look?
doug
On 7/17/12 5:21 AM, Ed Gronenschild wrote:
Hi Doug,
Thanks for your suggestion, but it didn't work out either.
Ed
On 16 Jul 2012, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu
Does fslregister work by itself?
On 7/17/12 10:39 AM, Ed Gronenschild wrote:
Hi Doug,
I've found a solution to the problem: I converted T1.mgz and
FLAIR.mgz to nii.gz and then applied flirt directly with the
same options as in flsregister called by bbregister,
so
flirt -cost corratio -dof 6
This is computed by computing the volume inside the pial surface and
subtracting the volume inside the white surface (and accounting for
small amounts in the unknown region).
doug
On 07/17/2012 04:47 AM, Emelie Andersson wrote:
Thank You Douglas,
May I ask if You know how the numbers were
Try the pctsurfcon program
doug
On 07/17/2012 11:44 AM, Fred Lado wrote:
I found a thread (with same subject line) in the archive that referred
to Freesurfer tools to measure white-gray contrast, but I could not
find anything further on where the information resides. Is there a
way to
Hi,
In the longitudinal tutorial it states that: In order to analyze your
longitudinal data, you have different options. You could, e.g., open the stats
text files in each tpN.long.templateID/stats/ dir, containing statistics such
as volume of subcortical structures or thickness averages for
On 07/16/2012 09:30 PM, Meng Li wrote:
Dear professor,
Thanks for your reply.
You said that when drawing conclusions from both hemispheres then I
need to use .025, but I found that in qdec interface, the default
value of -cwpvalue is 0.05. So are they inconsistent?
This would be
Hi freesurfer experts,
I want to use a volume based MNI152 ROI in Freesurfer, when I check it over
fsaverage with the following command the ROI is not in the correct position...:
tkmedit fsaverage T1.mgz -overlay ROI45.nii -overlay-reg
$FREESURFER_HOME/average/mni152.register.dat
And I have
Hi Gari,
Does it appear in the right place if you run
tkmedit -f $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz -overlay ROI45.nii
doug
On 07/17/2012 01:20 PM, Garikoitz Lerma Usabiaga wrote:
Hi freesurfer experts,
I want to use a volume based MNI152 ROI in Freesurfer, when I check it
over
Hi Anson,
'conversion' means to extract the values from that file (for the
specific structure(s)) and put them into a format that can be read by
your program (SPSS). For the stats you would not use qdec anyway (you
could use mri_glmfit).
You may want to check out asegstats2table and
Hi Rui - Just keep in mind that when you're removing lines from
trainlist.txt, you're removing subjects from the atlas. So instead of
using a tract atlas that's based on 33 subjects, you are now using a tract
atlas based on as many subjects as the lines that remain in trainlist.txt.
a.y
On
Hello,
I have successfully developed an automated algorithm combining pixel
intensity-based and shape based approaches to segment the lateral ventricles. I
have applied my algorithm to a small data set of 1.5 T1 ADNI images consisting
of 24 AD (subjects with Alzheimer Disease) 19 MCI (subjects
Hi John
have you checked with the ADNI folks? I think they have FreeSurfer
segmentation on many if not most of their subjects. We place no
connectivity constraints on the ventricular segmentations because they get
so thin that indeed sometimes 1mm data cannot resolve the connections. So
Thanks Doug,
I've done it with the one in SPM:
tkmedit -f $SPM8_DIR/canonical/avg152T1.nii -overlay ROI45.nii -fthresh 0.5
is this ok or should I test it with the one from FSL as well? My partner is
working with SPM and MarsBar.
Both in FS and in SPM the ROI is the same, troubles start when I
Hi Natacha,
make-all does not work for base and long. The easiest is to delete the
base (unless you made edits of course), and rerun the base from scratch.
You can also look at scripts/recon-all.log and see where it stopped,
then use flags like -autorecon2 -autorecon3 (or more fine steps) to
Hi Elisabeth,
don't mix versions. There is lots of stuff that can go wrong (files that
don't exist in 4.5 cross that the longitudinal stream expects etc.).
Since the longitudinal stream has been improved significantly since 4.5
(more reliability, several bug fixes etc) I'd recommend to re-run
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