I'm going to check with more ram dedicated.
Many Thanks
Lorenzo Busti
2011/12/5 Nick Schmansky
> 1.5GB is probably not enough. typically we recommend that recon-all
> have at least 3GB available to it, which can be very hard to do on a
> virtual machine (since windows takes 1GB, the vm linux
Dear all,
I have successfully run the freesurfer-steps for my subject and completed it
without errors. After that I started MNE to create my BEM meshes. The manual
tells me, for MNE to do that, the mri_watershed routine from freesurfer is
used. Also, this runs fine, as far as the four surfaces
hi everyone
i have made an annotation file from somme labels and i want
to make a mask from the result (from the annotation file). i mean i want keep
just the part of the brain covered by the annotation file in order to transform
it by mri_convert to nifti format and make my ma
you can use mri_mask for this
cheers
Bruce
On Tue, 6 Dec 2011, LAOUCHEDI MAKHLOUF wrote:
hi everyone
i have made an annotation file from somme labels and i want
to make a mask from the result (from the annotation file). i
mean i want keep just the part of the brain covered by
Dear FreeSurfers,
Anyone out there know of a list of talairach coordinates for FreeSurfer
cortical regions (MNI? I suppose)?
Thanks!
Carl
--
<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>
Carl M. Anderson, Ph.D. (mail stop 204)
Assistant Professor of Psychiatry,
Harvard M
Dear freesurfers,
I have created labels by using the command: mri_annotation2label command
(aparc.a2009s): Are these new labels only for the subject I mentioned in
the last command or can I use them for other subjects aswell (e.g. in order
to measure Volumetry of the auditory Cortex)?
THX, Greets
Hi Carl, Do you mean a centroid? I don't know of a list. You could run
mri_annotation2label to break the annotation up into individual label
files. These files are text and have XYZ in MNI305 space. You could then
compute the centroid from that.
doug
Carl Anderson wrote:
> Dear FreeSurfers,
>
>
Only for the subject specified on the command line.
doug
Klein, Holger wrote:
> Dear freesurfers,
>
> I have created labels by using the command: mri_annotation2label
> command (aparc.a2009s): Are these new labels only for the subject I
> mentioned in the last command or can I use them for othe
In this case you have 4 class variables and 3 continuous, so you'll have
16 regressors (and so 16 elements in your contrast). Your actual
contrast vector depends on the order of your class variables in the
fsgd. Assuming that the order is MP, FP, MV, FV, then the regressors
will have the follo
Dear list,
I am having the following memory allocation problem when running
mri_surf2surf. Can't find any mention of this error on the list or the
internet - sorry if I've missed anything.
mri_surf2surf --cortex --fwhm 5. --hemi lh --sval
/home/jdg45/lh.pial_converted.mgz --tval
/home/jdg45/C
Hi John,
It seems weird that you are using .mgz files (this suffix is for
volume files) with mri_surf2surf (whose inputs should be surfaces).
Also, it seems that several of the options you are trying I don't
believe exist at least according to the wiki (e.g. -cortex -fwhm). Are
you sure you are us
What is lh.pial_converted.mgz? How big is it? what do get if you run
mri_info on it?
doug
John Griffiths wrote:
> Dear list,
>
> I am having the following memory allocation problem when running
> mri_surf2surf. Can't find any mention of this error on the list or the
> internet - sorry if I've
surf2surf actually takes surface overlays (not surfaces themselves) as
input, and they can be in any format that FS reads. The wiki is probably
not up-to-date as those options are ok.
doug
Daniel Wakeman wrote:
> Hi John,
>
> It seems weird that you are using .mgz files (this suffix is for
> vo
Dear All,
1) On the FS Diffusion Tutorial webpage I found for the Group Analysis the
following scrip: GroupAnalysis.csh with the following instruction:
# Assemble input for group analysis
set type = CVS-to-avg35# alternatively could be 'TAL-to-avg35' or
'MNI-to-avg35'
Can you please e
Hi Doug,
It seems that there are still problems related to using -per-session.
Preproc-sess now finishes apparently fine (correct file names are
generated, i.e., fmc.*) but the analyses again defaults to using -per-run
at mkanalysis-sess.
Specifically, mkanalysis-sess creates an analysis.info fil
Dear All:
I was using dtrecon on my DTI data and by default it will register my
diffusion data (fa) on the TAL space so i got the fa-tal.nii file and the
fa-tal-nii.reg the file which encodes the transformation while registering to
the TAL space.
Can you please advise me what is the best way
Hi Antonella,
> 1) On the FS Diffusion Tutorial webpage I found for the Group Analysis the
> following scrip: GroupAnalysis.csh with the following instruction:
>
> # Assemble input for group analysis
> set type = CVS-to-avg35# alternatively could be 'TAL-to-avg35' or
> 'MNI-to-avg35'
> Can
Hi,
I am using TRACULA for the first time, and I am having trouble locating
$FREESURFER/HOME/trctrain/trainlist.txt..of 33 normal subjects to enter in
for set trainfile command. This is what my Freesurfer home directory looks
like:
cpdla@ba3:/software/Freesurfer/5.0.0$ ls
ASegStatsLUT.txt FreeSur
Hi - It's $FREESURFER_HOME/trctrain/trainlist.txt. Note the underscore. In
any case this is the default, so you don't have to specify trainfile in
your dmrirc unless you're using something else.
a.y
On Tue, 6 Dec 2011, C. Paula de los Angeles wrote:
Hi,
I am using TRACULA for the first ti
i dont think those files are in v5.0.0. you will need to download v5.1.
n.
On Tue, 2011-12-06 at 17:12 -0500, C. Paula de los Angeles wrote:
> Hi,
>
> I am using TRACULA for the first time, and I am having trouble
> locating $FREESURFER/HOME/trctrain/trainlist.txt..of 33 normal
> subjects to e
Oh yeah, that too. Tracula came out in 5.1.
On Tue, 6 Dec 2011, Nick Schmansky wrote:
> i dont think those files are in v5.0.0. you will need to download v5.1.
>
> n.
>
> On Tue, 2011-12-06 at 17:12 -0500, C. Paula de los Angeles wrote:
>> Hi,
>>
>> I am using TRACULA for the first time, and I
> thanks! it worked when i updated to 5.1
>>
>> On Tue, Dec 6, 2011 at 6:13 PM, Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu> wrote:
>>
>>>
>>> Oh yeah, that too. Tracula came out in 5.1.
>>>
>>>
>>> On Tue, 6 Dec 2011, Nick Schmansky wrote:
>>>
>>> i dont think those files are in v5.0.0.
Hello,
I'm having a problem with dt_recon on data scanned by Siemens TrioTim.
I'm using v4.5.0, with Mac OS 10.6.8.
dt_recon ran for a while, and stopped with an error "ERROR: cannot extract
sWiPMemBlock.alFree[8] from
/Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat"
I fo
Hi.
I am running into the following error:
ERROR: fio_pushd: /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/mni
ERROR: must specify brain mask volume for output subject .
I googled this error and it seems like you suggested this to someone else :
"As for your error, it looks like maybe the
Thank you Doug,
> Hi Yuko, I think you must have an older version of glmfit-sim some how.
> I've put a newer version here:
I replaced the /bin/mri_glmfit-sim, but got the same error.
[ERROR 1]
In line 292:
set csdCache =
$CacheDir/$subject/$hemi/$CacheLabel/fwhm$fwhmStr/$simsign/th$threshStr/
25 matches
Mail list logo
