Re: [HCP-Users] Workbench suddenly closes itself

Hi - have you tried using the non rh version? That *might* solve it... Cheers On 7 Apr 2014, at 15:44, Mahshid Najafi mhs...@gmail.com wrote: Hi, I have a problem with workbench. Sometimes when I try to load a label map or time series data in the workbench, it suddenly gives following

Re: [HCP-Users] High-resolution resting state networks available as template?

Indeed - and note that it is quick and easy to feed the group-PCA eigenmaps available on ConnectomeDB into MELODIC to get group-ICA maps. Cheers. On 18 Apr 2014, at 22:45, Glasser, Matthew glass...@wusm.wustl.edu wrote: We haven¹t released any HCP templates yet (at least as far as I know),

Re: [HCP-Users] Creating Group Average Resting State fMRI

Hi - One important point - you should never temporally concatenate without first demeaning the individual timeseries. Cheers. On 20 May 2014, at 10:14, Ausaf Bari aus...@gmail.com wrote: Ok that is something I tried recently actually - to merge all the runs across all the subjects and then

Re: [HCP-Users] Questions about FIX pre-processed rfMRI-data

Hi On 2 Sep 2014, at 10:28, David Hofmann davidhofma...@gmail.com wrote: after taking a look into the HCP related papers, I decided to download the FIX/pre-processed rfMRI-data for 1 subject (100307_3T_rfMRI_REST_fix). I want the ready-to-analyze-pre-processed data for the first session

Re: [HCP-Users] Dividing node timeseries

Hi On 3 Sep 2014, at 16:29, David Hofmann davidhofma...@gmail.com wrote: Hi at all, I was wondering, if it is possible to split a node time series txt-file including all sessions (4800 time points) in 4 parts (first 1200 time points are the first scan and so on) to obtain the time series

Re: [HCP-Users] gradient unwarp in preFS script

Hi guys - if the brain is centred on isocentre the gradwarp on a Skyra should be about 1-2mm max within the brain. Cheers, Steve. On 16 Oct 2014, at 16:16, Harms, Michael mha...@wustl.edu wrote: In that case, I don't know what the degree of gradient nonlinearity is for a stock Skyra.

Re: [HCP-Users] gradient unwarp in preFS script

-Skyra has totally different gradient coil and configuration than standard Skyras. Cheers. -G From: Stephen Smith [mailto:st...@fmrib.ox.ac.uk] Sent: Thursday, October 16, 2014 11:33 AM To: Harms, Michael Cc: Book, Gregory; hcp-users@humanconnectome.org Subject: Re: [HCP-Users

Re: [HCP-Users] Coordinates for node timeseries

Hi - the nodes correspond to the parcels in the associated ICA decompositions that are also part of this distribution. Cheers. On 2 Nov 2014, at 10:39, David Hofmann davidhofma...@gmail.com wrote: Hi, I downloaded the subject-specific node timeseries (txt-files), but could not find any

Re: [HCP-Users] Incorporating physiological monitoring data

on the cleaned data? Peace, Matt. From: Harms, Michael mha...@wustl.edu mailto:mha...@wustl.edu Date: Monday, February 16, 2015 at 10:42 AM To: Matt Glasser glass...@wusm.wustl.edu mailto:glass...@wusm.wustl.edu, Stephen Smith st...@fmrib.ox.ac.uk mailto:st...@fmrib.ox.ac.uk, Miriam Klein

Re: [HCP-Users] Incorporating physiological monitoring data

Hi - I think you would probably be best off taking the FIX-cleaned version of the data, and then apply additional confound regressors if they will help. Don't forget to apply the same highpass filter (to those regressors) that was applied already in the data preproc, before you use them.

Re: [HCP-Users] netmats in HCP

yup - that also affects the scaling - see FSLNets doc and the PTN release doc. Cheers. On 30 Mar 2015, at 18:17, Glasser, Matthew glass...@wusm.wustl.edu wrote: Hi Steve, What about the correction for temporal autocorrelation? Matt. From: Stephen Smith st...@fmrib.ox.ac.uk mailto:st

Re: [HCP-Users] netmats in HCP

Hi - one thing is that we estimate (z versions of) netmats separately for each 15min run and then average the 4 netmats to give a single netmat per subject. Cheers. On 30 Mar 2015, at 18:14, Yizhou Ma maxxx...@umn.edu wrote: Hi Timothy, Thank you for pointing that out. I typed that wrong

Re: [HCP-Users] Questions about the extensively processed rfMRI data

Hi On 25 Feb 2015, at 03:39, Aaron C aaroncr...@outlook.com wrote: Dear HCP users, I have some questions about the extensively processed rfMRI data of “parcellation-timeseries-netmats”. Their filenames are “groupICA_3T_Q1-Q6related468_MSMsulc.tar.gz”,

Re: [HCP-Users] Group ICA with Melodic on 20 or more subjects

Thanks Matt That's correct that the --migp option (see a recent post from me to the FSL list about this new option) inside melodic is still single-threaded. However the journal paper (linked below by Matt) includes simple matlab code for doing MIGP and that can easily be parallelised as well

Re: [HCP-Users] Parcellated Connectome

Hi - there are many factors that affect overall scaling - more below: On 10 Apr 2015, at 14:22, Nomi, Jason jxn...@miami.edu wrote: Dear Experts, I have noticed that the time-series for individual subjects from the dual regression output in the parcellated connectome (100 comp ICA) has

Re: [HCP-Users] ICA problem

Hi - what's in the report_log.html file? Cheers On 26 May 2015, at 05:22, mo mo mo7278231r...@yahoo.com wrote: Hello every one I ran FSL MELODIC single session ica on connectome project Q1- single subject preprocessed rest-fMRI data, but in the result MELODIC report page,the ICA

Re: [HCP-Users] Data processing with SPM

Hi - I think you probably need to take this query to the SPM email list I'm afraid - we haven't used SPM so far in the HCP, so don't have experience with how it performs on HCP data. Cheers, Steve. On 26 May 2015, at 04:01, 李勋 lixun2...@126.com wrote: Hi there, I've encountered a problem

Re: [HCP-Users] group-ICA spatial maps

Hi > On 3 Dec 2015, at 04:24, Bagrat Amirikian wrote: > Hi, > I have downloaded and unpacked HCP500_Parcellation_Timeseries_Netmats data. > My question is about group ICA spatial maps, specifically, about > melodic_IC.dscalar.nii and melodic_IC_ftb.dlabel.nii files in the

Re: [HCP-Users] FIX-denoised

Hi all I think Greg was making the valid point that: if you want to regress the full space of A and B out of your data, it is not correct to regress out A and then afterwards regress out B, unless A and B are orthogonal. To do it correctly you either need to combine [A B] into a single model

Re: [HCP-Users] Phase Encoding left-to-right and right-to-left

timates may be a more >> feasible option. >> >> --Greg >> >> ____ >> Greg Burgess, Ph.D. >> Staff Scientist, Human Connectome Project >> Washington University School

Re: [HCP-Users] phase encoding and group ICA

Hi - Wrt group-ICA, it makes no difference what order the data was fed into the MIGP group-PCA. Wrt the 4 chunks combined into the node timeseries in the 500-subject PTN release: the order is always the following, so you will need to take into account the information you pasted below if you

Re: [HCP-Users] Phase Encoding left-to-right and right-to-left

I think maybe we need to be explicit about exactly what we're talking about averaging? Cheers. Stephen M. Smith, Professor of Biomedical Engineering Head of Analysis, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford. OX3 9 DU, UK +44 (0) 1865 222726

Re: [HCP-Users] A question about R820 MSM-All registered dense connectome

Hi - we used the 820 subjects with the absolutely complete set of timepoints from all 4 runs, for the group-average dense connectome and group-ICA stuff. Cheers > On 3 Jun 2016, at 19:16, Aaron C wrote: > > I checked the number of subjects which completed all four

Re: [HCP-Users] HCP S900 - PTN data release

Hi - I agree that is a bit confusing - actually the PDF is linked directly from the main 900 data release page (hover over the "?) - the link is http://humanconnectome.org/documentation/S900/HCP900_GroupICA+NodeTS+Netmats_Summary_15dec2015.pdf

Re: [HCP-Users] Converting FA maps to CIFTI

Hi - so you have estimated in FA, MD, etc in grey matter? Note that CIFTI doesn't cover white matter. Cheers. > On 1 Feb 2016, at 06:01, Georg Kerbler wrote: > > Hi, > > I would like to convert FA/MD/AD/etc. images which I calculated in T1w space, > into CIFTI's, in

Re: [HCP-Users] "good" vs. "bad" components in ICA-FIX denoised rsfMRI data

wustl.edu > > > > On 3/9/16, 2:10 AM, "hcp-users-boun...@humanconnectome.org > <mailto:hcp-users-boun...@humanconnectome.org> on behalf of Stephen Smith" > <hcp-users-boun...@humanconnectome.org > <mailto:hcp-users-boun...@humanconnectome.org> on beh

Re: [HCP-Users] Negative Voxel Values signed int 16 vs uint16 issue

Hi - yes it may depend on the context/pipeline but for simplicity and safety pretty much everything we do just works in floats. Cheers > On 3 Mar 2016, at 21:18, Harms, Michael wrote: > > > Maybe Steve or MJ can chime in regarding the FSL issues, but I do recall > there

Re: [HCP-Users] "good" vs. "bad" components in ICA-FIX denoised rsfMRI data

Hi - it's the same as in standard FIX usage - the file listing bad components is called hand_labels_noise.txt - inside the ICA output folder. Cheers > On 9 Mar 2016, at 03:25, Ely, Benjamin wrote: > > Hi all, > > I’m interested in running some analyses (particularly

Re: [HCP-Users] Extracting ROI data from HCP resting state data - 2400 data points instead of 1200 ?

Hi - no we do not (in general for resting-state) ever recommend temporal contatenation like this before further analyses - for the reason you're seeing here. For example, for the HCP released netmats, we take the 4 runs, one at a time, estimate the 4 (zstat) netmats, and average those. Cheers.

Re: [HCP-Users] Exact Meaning of ICA maps in 800 subjects release

estion: would the Z-maps related to the second-last step step > (dual regression to create volumetric representations if the IC) be available > (they are not in the public release)? > > This would greatly aid in interpreting/threshold the volumetric betas. > > Thanks a lot in a

Re: [HCP-Users] HCP script used for generating group-averaged dense connectome

Hi - it *should* be part of the scripts available as part of the big PTN download. ( HCP900 Parcellation + Timeseries + Netmats (820 Subjects) ) Let me know if it's not in there. Cheers. > On 17 Jul 2016, at 06:10, Aaron C wrote: > > Dear HCP experts, > > Could I

Re: [HCP-Users] Exact Meaning of ICA maps in 800 subjects release

gt; wrote: > > Hi, > > The volumetric version! > > Thanks in advance, > > Nicola > > > ---- Original message > From: Stephen Smith <st...@fmrib.ox.ac.uk> > Date: 04/07/2016 12:37 PM (GMT+01:00) > To: Nicola Toschi <tos...@med.

Re: [HCP-Users] Exact Meaning of ICA maps in 800 subjects release

HI - do you mean the grayordinate or volumetric versions? Cheers > On 4 Jul 2016, at 11:16, Nicola Toschi wrote: > > Hi list, > > This may be more of a MELODIC question, but I would be grateful for any input: > > In the ICA release on 800+ subjects, what is the

Re: [HCP-Users] Same data / Multiple comparisons ?

Hi Tom actually the MegaTrawl latest version is here: https://db.humanconnectome.org/megatrawl/index.html But yes indeed - early on within the HCP we discussed options for trying to deal with this large-scale-multiple-comparisons-problem,

Re: [HCP-Users] Basis Function Selection

Hi - in general it's better to use smooth basis functions (eg as used by default in FLOBS) than "square" bases like default FIR bases. There's some literature on that but I can't quite remember now who published that - but it seems logical given that you're fitting smooth data - assuming (eg)

Re: [HCP-Users] MELODIC denoising vs. released ICA-FIX datasets

Hi - it sounds like maybe it's working fine within the limits of slight differences in mathematical precision between the C++ vs matlab parts of the processing - so the main question would be - have you looked in a viewer at the difference image - e.g. are the voxels with large differences

Re: [HCP-Users] ICA-FIX HP200 training data

Hi - try the following: www.fmrib.ox.ac.uk/~steve/ftp/HCP20_hp200.RData Cheers > On 7 Nov 2016, at 17:45, Ely, Benjamin wrote: > > Hi HCP team, > > I'm interested in comparing the performance of ICA-FIX using a 200s vs. 2000s > highpass filter cutoff for some

Re: [HCP-Users] global signal regression on HCP ICA FIX denoised BOLD?

Yes,. Cheers. > On 5 Jan 2017, at 11:57, Joelle Zimmermann > wrote: > > Hi HCPers, > > Is it correct that global signal regression was not done on the ICA FIX > denoised fmri BOLD data? > > Thanks, > Joelle > ___ >

Re: [HCP-Users] ICA failure with volumetric ICA-FIX denoised files

Hi - I would strongly recommend doing the group-ICA and dualregression on the CIFTI versions of the data, not volumetric. However, if you really want volumetric versions of 50-dimensional group-ICA then we could provide those that have been done via group-ICA on CIFTI data which has then been

Re: [HCP-Users] Question about the CCA calculation from "A positive-negative mode of population covariation links ..."

Hi - here's some additional code - I *think* this is the relevant code for what you're asking about. Cheers. % temporary version of vars, useful for various null tests below grotvars=inormal(vars); grotvars(:,std(grotvars)<1e-10)=[]; grotvars(:,sum(isnan(grotvars)==0)<20)=[]; % permutation

Re: [HCP-Users] tikhonov-regularized partial correlation using FSLnets

Hi This normalisation isn't directly part of the actual L2 regularisation - it is just setting the overall scaling of the covariance matrix, so that the effect of choice of regularisation parameter is not dependent on the overall scaling of the original data. The scaling is just the RMS of

Re: [HCP-Users] Matlab scripts for the HCP 820-subject PTN release

HI - this is an implementation of the variance normalisation used by MELODIC - see Beckmann TMI 2004. The idea is to remove the 30 strongest PCA components (temporarily) and use the remaining weakest components (ie residual "noise") to compute the voxelwise scalings for the variance

Re: [HCP-Users] Where are per-subject netmats?

the "subjectIDs.txt" file? > > > > Bests, > > Habib > > > On Thu, Jun 1, 2017 at 3:25 PM, Stephen Smith <st...@fmrib.ox.ac.uk > <mailto:st...@fmrib.ox.ac.uk>> wrote: > Probably clearest to use both terms for clarity, e.g. "ICA

Re: [HCP-Users] variation across connectomes

Hi Michael - I think Joelle is asking about tractography instead of func conn. I expect it will be some time before fuller sets of tractography analyses have been done. Cheers. > On 2 May 2017, at 01:17, Harms, Michael wrote: > > > Well, there’s the canonical correlation

Re: [HCP-Users] Where are per-subject netmats?

Hi - subject netmats are in the main PTN download. Cheers. > On 1 Jun 2017, at 15:05, Thomas Nichols wrote: > > Hi Jenn, > > Sorry for the slow reply on this. We tried downloading the links you pointed > us to

Re: [HCP-Users] Combining rfMRI data for different phase encoding directions

Hi - I think your main two choices are whether to run FIX on each 5min run separately, or to preprocess and concatenate each pair of scans from each session and run FIX for each of the 4 paired datasets. You could try FIX both ways on a few subjects and decide which is working better. Cheers.

Re: [HCP-Users] netmats prediction of fluid intelligence

Hi all Yes - I've discussed this with Todd and it's not immediately clear whether the difference is due to: - they used full correlation not partial - they used fewer confound regressors (IIRC) - their prediction method is *very* different (pooling across all relevant features rather than

Re: [HCP-Users] RSN masks for 32K surfaces?

HI - yes see the HCP "PTN" data release. Cheers. > On 16 Oct 2017, at 16:10, Claude Bajada wrote: > > Hello all, > > Are there any canonical resting state network masks available for the > MSMAll 32k HCP surfaces as a gifti or cifti file? If so, where can I > obtain

Re: [HCP-Users] parcellation papaya viewer

Hi The actual group-ICA maps are not thresholded - but yes there is a preset colour overlay threshold applied by default in the papaya viewer. For the latest (~1000 subjects) PTN release, the volumetric maps were created within-subject using dual-regression, and are z-stat maps from the

Re: [HCP-Users] question about noise components in PTN release

Hi that’s right in the most recent PTN release the number of “junk” components is much lower, and also less unambiguously junk- so at this point we have not tried to classify them Cheers Stephen M. Smith, Professor of Biomedical Engineering Head of Analysis, Oxford

Re: [HCP-Users] Smoothing, discarding volumes

Hi > On 3 Jan 2018, at 14:44, Tobias Bachmann > wrote: > > Dear all, > > when using the HCP's ICA+FIX data (NIfTI volume files) for a rather simple > group ICA, would you recommend further conventional preprocessing, i.e. > > 1. smoothing (about

Re: [HCP-Users] ICA-FIX

Hi - I would think the easiest and best thing to do would be just to apply more aggressive high-pass filtering to the already FIX-cleaned data. Was there a reason you didn't want to do that? It's not at all a problem that the less aggressive HP filter had already been applied before original

Re: [HCP-Users] gradient nonlinearity correction question

Hi - no, in my experience running the post-hoc correction should look virtually identical to the on-scanner correction. Note that this will not be the case for 2D (eg EPI) data because on-scanner can only be done 2D - so that won't match post-hoc 3D correction. Cheers. > On 11 Apr 2018, at

Re: [HCP-Users] Melodic ICA idle

need to be in cifti? > > Cheers :) > > Will > > > From: Glasser, Matthew <glass...@wustl.edu <mailto:glass...@wustl.edu>> > Sent: 14 March 2018 01:14:51 > To: Harms, Michael; Stephen Smith; Will Khan > Cc: hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.

Re: [HCP-Users] A question about the data in native space

Hi - you could fairly easily use the FIX bad-component timeseries to regress out noise from the native space data, yes. I don't think that data is already precomputed for you. Cheers. > On 20 Mar 2018, at 10:44, Aaron C wrote: > > Dear HCP experts, > > I have a

Re: [HCP-Users] can't find age, sex, etc in megatrawl?

Hi No I don’t think we explicitly calculated those things. Cheers. Stephen M. Smith, Professor of Biomedical Engineering Head of Analysis, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford. OX3 9 DU, UK +44 (0) 1865 610470 st...@fmrib.ox.ac.uk