Re: [HCP-Users] Downloading movement regressors from HYA release

Thank you very much! Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Researcher Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: "Hodge, Michael" Date: Thursday, May 30, 2019 at 7:24 AM To: "Harms, Mich

[HCP-Users] Item data for NIH Emotion battery

Dear Experts, I would like to access the item-level data for the NIH Emotion battery of the young adult release. How can I do that? Thank you, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Researcher Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.

Re: [HCP-Users] Downloading movement regressors from HYA release

I did and actually some subjects worked, but not these ones: 101006 159441 926862 927359 942658 I still get a “cannot find file” error (10.4.5). Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Researcher Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.

Re: [HCP-Users] Downloading movement regressors from HYA release

942658 Is that normal? Thank you, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Researcher Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: "Harms, Michael" Date: Wednesday, May 15, 2019 at 9:31 AM To: Leona

[HCP-Users] Downloading movement regressors from HYA release

for this? These are the IDs: '127226' '130114' '169040' '329844' '908860' '971160' Thank you, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5

Re: [HCP-Users] ICA FIX output missing

) this = read_gifti_file_standalone(varargin{1},giftistruct); Error in ciftiopen (line 31) cifti = gifti([tmpfile '.gii']); Error in fix_3_clean (line 46) BO=ciftiopen('Atlas.dtseries.nii',WBC); }^H Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu

Re: [HCP-Users] ICA FIX output missing

in ciftiopen (line 31) cifti = gifti([tmpfile '.gii']); Error in fix_3_clean (line 46) BO=ciftiopen('Atlas.dtseries.nii',WBC); }^H Would you have any thoughts on this? Thank you, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto

Re: [HCP-Users] ICA FIX output missing

the TaskfMRIAnalysis scripts to get my “activations”. Thank you, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: "Harms, Michael" Date: Monday, February 25,

[HCP-Users] ICA FIX output missing

. A related question I would have is what filter you would recommend for task data. My intention is to use a GLM on the cleaned data, so is 2000 (linear detrending) ok, since then a lower high-pass will be applied in the GLM step? Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab

Re: [HCP-Users] Regress confounds out of CIFTIs

Dear Matt, Looks like I really need to improve my linear algebra. Thank you very much! Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: "Glasser, Matthew"

[HCP-Users] Regress confounds out of CIFTIs

by rerunning the surface preprocessing step. Would you have any suggestions? Thank you, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5

Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis

alternative suggestions on how to handle multi-session data at the group level? Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: Leonardo Tozzi Date: Wed

Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis

It worked! Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: "Glasser, Matthew" Date: Tuesday, January 8, 2019 at 3:52 PM To: Leonard

Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis

ant here and where I should point this variable: I am using the ciftiopen and ciftisave functions to open and read cifti files. Would you have any suggestion on what the FSL_FIX_CIFTIRW variable should be so that I can write the cleaned timeseries? Thank you very much, Leonardo Tozzi, MD,

Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis

artifacts, then run MELODIC ICA on the cleaned data at the group level to get some group components and then get the individual components with double regression? Or is there some problem you see in running an ICA after an ICA? Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab

[HCP-Users] Identifying noise components in group MELODIC on ciftis

data. Also, I would probably need to retrain the classifier, since we are conducting our experiment at a different site and on a GE magnet, correct? I would appreciate any pointers on how to best proceed with this matter. Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral

[HCP-Users] Binary label from surface

. Thank you, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 ___ HCP-Users mailing list HCP-Users@humanconnectome.or

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

make the same call as before, with the –avoid flag for the CSF but I guess I would still at least need to input the GrayOrdinates.txt which is still a list of seeds (-x option). How would I obtain the seed list for the grayordinates? Thank you, Leonardo Tozzi, MD, PhD Williams PanLab

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

and Connectomes/GrayOrdinates.txt ? Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: Timothy Coalson Date: Friday, November 9, 2018 at 5

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

matrix by taking the upper triangle. I think it should track from all my ROIs to all my ROIs. Concerning wb_command -probtrackx-dot-convert, it requires a few inputs but I am not sure what files to use. I hope this adds more information, thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab

[HCP-Users] White matter and CSF masks after minimal HCP processing

/tfMRI_EMOTION_LR . Would this be acceptable, for example in the case in which I were to download only the task data from your release (so I wouldn’t have the original T1s)? If not, is there another approach you would recommend? Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral

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

or any other suggestion to check the positioning of the seeds and the tractography results? Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: Sta

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

will try going through the steps and see if I manage to make it work. Thank you, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: Stamatios Sotiropoulos Date: Wednesday, Octo

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

subject’s parcellation into a series of NIFTI files in native/standard space and input these as ROIs into probtrackx? In this case, could you recommend the correct series of workbench commands? I am also open to other software recommendations besides the FSL suite. Thank you very much, Leonardo

[HCP-Users] Visualizing pconn.nii as graph

for me or have any tips on achieving what I am trying to do in an optimal way. Thank you very much. Yours sincerely, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5

[HCP-Users] Cortical labels persisting when merging cortical and subcortical regions to create parcellation

displayed in the workbench? Are they being “carried over” as labels that do not actually correspond to any greyordinates? Should I be worried that these “Phantom labels” might affect my analyses? Thank you very much. Yours faithfully, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow

[HCP-Users] Error writing .ptseries file in Matlab

something strange about them. Thank you very much. Yours faithfully, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 ___ HCP

[HCP-Users] Using Glasser parcellation for task activations

be an acceptable solution. Thank you very much. Yours faithfully, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 ___ HCP-Users mailing li

[HCP-Users] Index error in diffusion preprocessing

provide some pointers so make this edit as small as possible (I would like to avoid “shuffling” my scans, bvals and bvecs before launching the preprocessing). Thank you very much. Yours faithfully, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto

[HCP-Users] index.txt file truncated before run_eddy

AP and PA and for each we have a file with 81 and one with 83 directions. So, the number of volumes in Pos_Neg.nii.gz seems to be correct (81+83+81+83=328), but the index file is somehow truncated. Would anyone have some insight in why that could be the case? Thank you very much. Yours faithfully, Leon