Hi Derek,
Did you or the administrators change something in bedpostx script ?
I cannot find these error messages in FSL 5.0.8.
Moises.
On 3 April 2015 at 01:27, Archer,Derek B wrote:
> Hi Stam,
>
>
> I got the FSL version updated (5.0.8) on the cluster, and am attempting
> to process this d
Hi Maarten,
you can use Matrix3:
--omatrix3 --target3='seeds' --lrtarget3='wholebrain'
Best,
Moises.
On 10 July 2015 at 11:12, Maarten Vaessen wrote:
> Thanks for the reply. I am using FSL v5.0.8, but have also tried with
> 5.0.6.
>
> Does that mean that there is no way to do seed-to-wholebra
gt; --lrtarget3=../fsaverage_LR32k/102816.L.white.32k_fs_LR.surf.gii -P 50
> --forcedir --dir=./test_surf_track_STS_Lwhite -s
> ../Diffusion.bedpostX/merged -m nodif_brain_mask.nii.gz
> --seedref=nodif_brain_mask.nii.gz
>
> Any idea what this means?
>
> -M
>
>
>
>
>
Hi Karthik,
It depends on your processor and on the parameters that you use.
One large slice of HCP diffusion data takes about 4 hours on a single CPU
core (modern processors have several cores) using the default parameters
(2250 MCMC iterations, 2 fibres estimation).
HCP data has about 90 slice
Regards,
>
> Karthik
>
>
>
> *From:* Glasser, Matthew [mailto:glass...@wustl.edu]
> *Sent:* Thursday, January 26, 2017 5:49 AM
> *To:* Moises Hernandez Fernandez ;
> Gopalakrishnan, Karthik
> *Cc:* hcp-users@humanconnectome.org
>
> *Subject:* Re: [HCP-Users]
t kind of memory usage should I anticipate when I run
> this for HCP diffusion data?
>
>
>
> Regards,
>
> Karthik
>
>
>
> *From:* Moises Hernandez Fernandez [mailto:mois...@fmrib.ox.ac.uk]
> *Sent:* Friday, January 27, 2017 3:37 PM
> *To:* Gopalakrishnan, Karth
gt; *From:* Niels Bergsland [mailto:npbergsl...@bnac.net]
> *Sent:* Tuesday, January 31, 2017 4:19 AM
> *To:* Gopalakrishnan, Karthik
> *Cc:* Moises Hernandez Fernandez ;
> hcp-users@humanconnectome.org
>
> *Subject:* Re: [HCP-Users] Running bedpostx on HCP diffusion data
&g
Hi Su,
I suggest that you review the output log files. The slices that have
failed should have an error message inside (probably because an excess
of some limit).
Cheers,
Moises.
Quoting "Glasser, Matthew" :
Do you know that your cluster is not killing some of the jobs? Which
slices are m
I had the same problem in the past... try:
*c3d_affine_tool -itk ANTSmat.txt -ref myref -src mysrc -ras2fsl -o
FSLmat.txt *
However, as Tim said, this tool only converts the affine, not the warp.
Moises.
On 2 February 2018 at 18:33, Timothy Coalson wrote:
> I haven't finished figuring this o
