Re: [HCP-Users] Probabilistic tractography for dense connectome

wrote: Is that because this is a native space grayordinates instead of an MNI space grayordinates and thus the masks are subject specific? Matt. From: Aaron C mailto:aaroncr...@outlook.com>> Date: Wednesday, May 1, 2019 at 12:27 PM To: Stamatios Sotiropoulos mailto:stamatios.sotiropou...@nott

Re: [HCP-Users] Probabilistic tractography for dense connectome

s@humanconnectome.org> Cc: Stamatios Sotiropoulos Subject: Re: [HCP-Users] Probabilistic tractography for dense connectome Not as far as I am aware, but Stam might know. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Aaron C mailto:aaroncr...@outlook.com>> D

Re: [HCP-Users] Diffusion connectivity matrix with cortical and subcortical parcellation

Hi The HCP course tractography practical would be a good way to start (see page 386 onwards): https://wustl.app.box.com/s/wna2cu94pqgt8zskg687mj8zlmfj1pq7 Briefly, if you have a number of surfaces (need to convert them to ASCII using surf2surf) and subcortical volumes you can merge them into

Re: [HCP-Users] Diffusion connectivity matrix with cortical and subcortical parcellation

Hi The HCP course tractography practical would be a good way to start (see page 386 onwards): https://wustl.app.box.com/s/wna2cu94pqgt8zskg687mj8zlmfj1pq7 Briefly, if you have a number of surfaces (need to convert them to ASCII using surf2surf) and subcortical volumes you can merge them into

Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation

Hi Karthik You need to run —network —omatrix1, and I would add —loopcheck. Have a look at the HCP course tractography practical for the different options in getting connectomes. Cheers Stam On 1 Sep 2017, at 21:30, Glasser, Matthew > wrote: I

Re: [HCP-Users] dMRI: Error while running "run_eddy.sh"

n "eddy_cuda". Unfortunately, the same error came up. It looks like "eddy_cuda" cannot be run on the most recent version of Mac because of CUDA incompatibility. Do you have any other idea to solve this issue? Thanks. Sang-Young On Aug 22, 2017, at 3:49 PM, Stamatios Sotiropoulos <s

Re: [HCP-Users] dMRI: Error while running "run_eddy.sh"

Hi you need to install CUDA 7.5 and have LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda/lib64 export LD_LIBRARY_PATH in your ~/.bashrc, assuming that /usr/local/cuda is where you have installed CUDA, otherwise replace accordingly. Cheers Stam On 22 Aug 2017, at 20:01, Glasser, Matthew

Re: [HCP-Users] bedpostx parameters for HCP data

Hi Jan something like: bedpostx_gpu T1w/Diffusion -n 3 -b 3000 -model 3 -g —rician Model3 is available in bedpostx as of FSL 5.09. Probably also best to download the latest patch. Best wishes Stam > On 16 Nov 2016, at 13:13, Jan Schreiber wrote: > > Dear HCP

Re: [HCP-Users] error running bedpostx

Hi If the problem is in fslslice, this is likely a memory problem. Depending on how strict your queueing software is and what are the memory limits for each queue, it may kill or not the preproc job if it thinks it asks too much memory. Notice that the HCP data are an order of magnitude larger

Re: [HCP-Users] Script for DTIV1_to_Workbench.sh

r the script is not available, if in case you have the script please kindly forward it.ThanksVasudevOn 29 February 2016 at 17:29, Stamatios Sotiropoulos <stamatios.sotiropou...@ndcn.ox.ac.uk> wrote: Hi This should be included in the HCP course material. Ideally in the future the Connectome Workbe

Re: [HCP-Users] Script for DTIV1_to_Workbench.sh

Hi This should be included in the HCP course material. Ideally in the future the Connectome Workbench could directly support such functionality. Best Stam On 29 Feb 2016, at 11:51, Dev vasu > wrote: Dear

Re: [HCP-Users] FSL - rseed option in probtrackx2

Hi Matthew Probtrackx uses a standard C function for generating random numbers, like rand(). Unfortunately, I think that the C/C++ standard does not guarantee that running rand() on different machines will give you the same random sequence, so there is no way to be sure that this will happen.

Re: [HCP-Users] NaNs after merging dconn files

Hi Matthew No, they are not meant to be there. Can you open and display the dconn file in workbench? FYI, there will be a new FSL release sometime this or the next week. It will have some bug fixes in probtrackx2 and some new features. It may be the case that this problem disappears with the

Re: [HCP-Users] Odd BedpostX results

Hi Matthew Remind me where did you find a binary for running this command? This has not been in any FSL releases yet, so I am not sure what you ran there. We plan to include a binary with model3 in the next FSL release. Cheers Stam On 30 Jun 2015, at 08:46, Matthew George Liptrot

Re: [HCP-Users] Tractography and fdt_matrix_merge

Hi Matthew As you noticed these are in-progress, therefore contain non-released pipelines and code. We do not support unreleased code, but if you want I can send you a binary (notice that we are still debugging/developing some aspects of this pipeline). Cheers Stam On 7 Apr 2015, at 10:03,

Re: [HCP-Users] Processing Diffusion MRI Data

stage. I have not run bedpostx before today on this subject, so I'm confused why this is occurring. Is there something I'm missing? Thanks, Derek From: Stamatios Sotiropoulos stamatios.sotiropou...@ndcn.ox.ac.ukmailto:stamatios.sotiropou...@ndcn.ox.ac.uk Sent

Re: [HCP-Users] Processing Diffusion MRI Data

, Matthew [mailto:glass...@wusm.wustl.edu] Sent: Tuesday, February 17, 2015 12:55 PM To: Archer,Derek B; Stamatios Sotiropoulos; hcp-users@humanconnectome.orgmailto:hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Processing Diffusion MRI Data Are you running the command on ${StudyFolder

Re: [HCP-Users] Processing Diffusion MRI Data

the current bedpostx_gpu (under 5.0.7/8) not support these flags? a previous discussion on the fsl mailing list suggested that it did. cheers, satra On Tue, Feb 17, 2015 at 10:26 AM, Stamatios Sotiropoulos stamatios.sotiropou...@ndcn.ox.ac.ukmailto:stamatios.sotiropou...@ndcn.ox.ac.uk wrote: Hi Derek

Re: [HCP-Users] Processing Diffusion MRI Data

the –g option? Do I need a newer version of FSL? Thanks, Derek Archer From: Stamatios Sotiropoulos [mailto:stamatios.sotiropou...@ndcn.ox.ac.uk] Sent: Monday, February 16, 2015 12:48 PM To: Archer,Derek B Cc: hcp-users@humanconnectome.orgmailto:hcp-users@humanconnectome.org Subject: Re: [HCP-Users

Re: [HCP-Users] Processing Diffusion MRI Data

Hi Derek Please notice that model=3 is not officially released yet in FSL. Also, there should be a future HCP release in the near future including bedpostx results, with the optimal parameters. Stam On 16 Feb 2015, at 16:25, Archer,Derek B arche...@ad.ufl.edumailto:arche...@ad.ufl.edu

Re: [HCP-Users] speckled FA with dtifit on b1000 shell

Hi Joe I suspect that the data you have extracted are not consistent. Have you added b=0 images? Do these correspond to the right entries in the bvals file? I bet your dti_S0 will not look like a b=0, which would indicate that the sequence in your data file and the corresponding bvals do not

Re: [HCP-Users] Problem running the HCP DTI data in a high performance cluster

Hi Nele Do you run that in parallel or on a single node? In any case you need enough memory to be able to process HCP data. Bedpostx calls fsl_sub to send jobs to the cluster queue. If your cluster’s default memory allocation limits are low, you can easily run out of memory. You could

Re: [HCP-Users] Coordinate of CIFTI files

Exactly what Matt says, you do not need to transform the data. Stam On 8 Aug 2013, at 02:08, Glasser, Matthew wrote: Stam may be able to answer this better than me. I think what you would do is to provide probtrackx the native to MNI (and MNI to native) warps and use the MNI space 32k