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 wrote: > > In that case, I don't know what the degree of gradient nonlinearity is for a > stock Skyra. But I'd try to

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

at the HCP-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@humanconnecto

Re: [HCP-Users] Different rsfMRI result from different timeseries' netmats

Hi Yes - "ts2" and "ts3" are different methods for estimated parcel-timeseries (ie node-timeseries) - see the documentation for more details on their differences. Indeed - if they gave the same results (as each other) we would not be distributing both as separate things! The reason we hav

Re: [HCP-Users] More questions about Fix-preprocessed rs-fMRI data

Hi The 15min runs can be concatenated in order to get one hour's worth of data from a given subject - that is the simplest way to combine the datasets in order to make the most of the full data. You can of course just work with a single 15min run for a given subject - but I would say that that

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 wrote: > Hi, > > I downloaded the subject-specific node timeseries (txt-files), but could not > find any information about

Re: [HCP-Users] Node timeseries - How many ROI's to use?

Hi - separate from your main question, in general I have a "better feeling" about netmat analysis from the 50 and 200 node datasets than the other options. Please don't ask me to defend that (or be correct about it!) - because it's just a gut feeling from having played with the datasets a lot.

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 as

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. Cheer

Re: [HCP-Users] Incorporating physiological monitoring data

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

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

Hi > On 25 Feb 2015, at 03:39, Aaron C 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”, > “NodeTimeseries_3T_Q1-Q6related468_MSMsulc_ICAd*_ts*.

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

Hi - yes I would very much hope so! Cheers. > On 28 Feb 2015, at 06:18, Aaron C wrote: > > Thank Dr. Smith very much for his very helpful answers. > > I have one more question about the extensively processed rfMRI data of > “parcellation-timeseries-netmats”. I think I saw the vitamin E caps

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 wrote: > > Hi Timothy, > > Thank you for pointing that out. I typed that wrong but I used

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 wrote: > > Hi Steve, > > What about the correction for temporal autocorrelation? > > Matt. > > From: Stephen Smith mailto:st...@fmri

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 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 a much > l

Re: [HCP-Users] Parcellated Connectome

, when I apply a strong threshold for image presentation to "clean up" > the image a little, does the time series also include those voxels that are > not visible due to high thresholding? > > Thanks again! > > Jason > > > From: Stephen Smith > S

Re: [HCP-Users] rsfc preprocessing

Well.. I would add that if you want to control the lowpass filtering with any decent degree of frequency-cutoff specificity I would not use the Gaussian lowpass filter in fslmaths, but something sharper (eg Butterworth) eg in matlab. But generally we don't recommend doing lowpass. Cheers.

Re: [HCP-Users] groupICA parcellation region names and threshold

Hi > On 17 May 2015, at 17:00, Ester Bonmatí wrote: > > Dear HCP users, > > I am using the HCP500_parcellation_timeseries_netmats dataset. > > For each parcellation (25, 50, 100, 200, 300) there is the melodic_IC_sum > thumbnail corresponding to each partition. This images are named with nume

Re: [HCP-Users] ICA problem

Hi - what's in the report_log.html file? Cheers > On 26 May 2015, at 05:22, mo mo 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 > tab is empty. >

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 wrote: > > Hi there, I've encountered a problem when dealing wit

Re: [HCP-Users] HCP PTN release: Clustered RSN on 200 ICA

Hi The call (using FSLNets) to do the hierarchical clustering is briefly mentioned in the PTN documentation - see the section on: "view hierarchical clustering of nodes" But as this is primarily just a convenient way of displaying the netmats we did not include the outputs of that in the PTN re

Re: [HCP-Users] ft_read_cifti too many grayordinates

HI Matt - thanks - so is there an option with ft_read_cifti for excluding those grayordinates that are not part of the "standard" 91k set, upon read-in? Cheers > On 20 Jul 2015, at 17:06, Glasser, Matthew wrote: > > Some of us don’t think that code should do that. You can manually remove the

Re: [HCP-Users] failure to replicate dual regression 1 results (PTN nodetimeseries)

Hi - yes this won't match - the node timeseries we released in PTN were derived using the CIFTI (surface etc) version of the data, not volumetric. Cheers. > On 31 Jul 2015, at 15:50, Yizhou Ma wrote: > > Dear HCP experts, > > I am trying to run my own dual regression on HCP's rsfMRI data. Wh

Re: [HCP-Users] auto-correlations

Hi > On 25 Aug 2015, at 18:04, Nomi, Jason wrote: > > Dear Experts, > > I was just reading in the Smith et al. (2013) paper about correcting for > autocorrelations (footnote 7) and was wondering if there were any type of > corrections you would advise. > > I am aware that I should demean, an

Re: [HCP-Users] TOPUP options with HCP scripts - Phase Encoding and Voxel Size incompatibilty with EPI

Hi AFAIK you can - in theory - use the topup-derived B0-fieldmap to unwarp the fMRI-EPI data even with these differences in acquisition. However I can't comment at all on how much work it will be to adapt the HCP scripts to make this happen. Would need advice from others on that point. Cheers

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] 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

s with 4800 time >> points will take four times as much RAM as using only 1200 time points. For >> folks with limited RAM, averaging the correlation estimates may be a more >> feasible option. >> >> --Greg >> >> _______

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 groupICA* > subdirect

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

CA, only a single number appeared. Should this > be reported as a bug in wb_view for Windows? Sorry I'm not a wb_view expert so would need someone else to comment on that. Cheers, Steve. > > 3. Thanks for the explanation. > > Cheers, > > Bagrat > > > Fro

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] group-ICA spatial maps

a > single ‘*.dscalar.nii’ file analogous to the format of the provided > unthresholded Zstats ‘melodic_IC.dscalar.nii’ files that can be viewed in > wb_view? > > Cheers, > > Bagrat > > From: Stephen Smith [mailto:st...@fmrib.ox.ac.uk > <mailto:st...@fmrib.ox.

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 order to correlate/overl

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 being some concern yea

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 smoothness estimations) >

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

gt; > On 3/9/16, 2:10 AM, "hcp-users-boun...@humanconnectome.org > <mailto:hcp-users-boun...@humanconnectome.org> on behalf of Stephen Smith" > <mailto:hcp-users-boun...@humanconnectome.org> on behalf of > st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>

Re: [HCP-Users] Listing resting-state functional data by gender

Hi - Tim's correct - the group-average connectivity HCP resource is already computed across all subjects so can't be recomputed on-the-fly for new subsets of subjects. All matlab code used to generate it is supplied though as part of the "PTN" download. Steve. > On 4 Apr 2016, at 22:24, Tim

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 resting-state > scans, but f

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 exact mathematical meaning

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

> > The volumetric version! > > Thanks in advance, > > Nicola > > > ---- Original message > From: Stephen Smith > Date: 04/07/2016 12:37 PM (GMT+01:00) > To: Nicola Toschi > Cc: hcp-users > Subject: Re: [HCP-Users] Exact Meaning of

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

they are not in the public release)? > > This would greatly aid in interpreting/threshold the volumetric betas. > > Thanks a lot in advance, > > Nicola > > On 07/06/2016 10:09 AM, Stephen Smith wrote: >> Hi >> >> Group-ICA is carried out in grayordinat

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 find the shell or MATLAB s

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, bu

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 isola

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

Hi Ely - one additoinal point - if you are wanting to apply these pipelines to your own data, you may want to change the (very unaggressive, basically just detrending as you said) approach to highpass filtering (both in general and for use pre-FIX). I haven't seen many datasets where the "slow"

Re: [HCP-Users] Extracting beta values from analyzed task-data

HI - "pe" are the beta files and "cope" are contrasts of these. Cheers. > On 16 Oct 2016, at 12:03, Vadim Axelrod wrote: > > Dear list, > > I downloaded the analyzed 3T HCP fMRI task-data. In the cope* subfolders I > can find the outputs of the contrast calculation, e.g., Zstat1.dtseries.nii.

Re: [HCP-Users] Fluctuations of the CSF in the ventricles

I suspect this simply comes down to the low TR resulting in suppressed CSF signal - not directly the use of multiband or a specific recon. Steve. > On 31 Oct 2016, at 23:38, Chris Gorgolewski > wrote: > > That's what the reference manual is suggesting as well, but it's not clear on > what

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 locally-acquired HCP-like resting

Re: [HCP-Users] Phase Encoding left-to-right and right-to-left systematically affect intra hemisphere connections

Hi - there's several images here, and I'm not sure how you estimated these connectivity patterns? Are you sure this isn't just run-run variability? Cheers. > On 11 Nov 2016, at 19:29, Xiaozhen You wrote: > > Hi HCP experts, > I noticed the very different effect from the RL or LR phase encodi

Re: [HCP-Users] 4D Intensity normalization in the fMRIVolume pipeline

Yes I think that's it. Cheers. > On 22 Nov 2016, at 04:20, Harms, Michael wrote: > > > Isn’t it more like (data/4DMean*1), so that the percentage change > relative to the mean is preserved? > > cheers, > -MH > > -- > Michael Harms, Ph.D. > --

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 > ___ > HCP-Users mailing list > HCP-Use

Re: [HCP-Users] HCP-Users Digest, Vol 8, Issue 8

I think Andreas would know about the vibration issue - it was him that solved it in the first place :-) On 14 Jul 2013, at 18:37, "Glasser, Matthew" wrote: > I believe that comes from table vibration. You might consider increasing > the TR and it may be reduced. > > Matt. > > On 7/14/13

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 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 error and > cl

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 wrote: > We haven¹t released any HCP templates yet (at least as far as I know), but > there are severa

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 wrote: > Ok that is something I tried recently actually - to merge all the runs across > all the subjects and then do a correlati

Re: [HCP-Users] rfMRI_REST_fix

Hi - what is the *full* name of the file you're trying to open? It's possible that this is a CIFTI file, which you can see in HCP's wb_view viewer (previously called "workbench"), or else can open in matlab with the right toolkits. Cheers. On 14 Aug 2014, at 10:43, Michel Thiebaut de Schot

Re: [HCP-Users] rfMRI_REST_fix

> > Cheers > > michel > > > On 14 Aug 2014, at 10:55, Stephen Smith wrote: > >> Hi - what is the *full* name of the file you're trying to open? It's >> possible that this is a CIFTI file, which you can see in HCP's wb_view >

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

Hi On 1 Sep 2014, at 19:22, David Hofmann wrote: > Hello HCP-team, > > 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 a

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

ps - my email program "cleaned up" (!) a sentence missing here: The volumetric NIFTI files are: rfMRI_REST1_LR_hp2000_clean.nii.gz etc. On 2 Sep 2014, at 07:10, Stephen Smith wrote: > Hi > > On 1 Sep 2014, at 19:22, David Hofmann wrote: > >> Hello HCP-team, >

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

Hi On 2 Sep 2014, at 10:28, David Hofmann 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 and > > assume

Re: [HCP-Users] Dividing node timeseries

Hi On 3 Sep 2014, at 16:29, David Hofmann 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 of the individual

Re: [HCP-Users] Group-ICA maps

Hi That's correct: the 3D NIFTI ICA maps are released "primarily for display purposes" - as you say, the cortical parts of these live on the cortical surface and are projected onto the 3D volumes - meaning indeed tha the volumes aren't "filled out" volumetrically. So when viewed on the surface

Re: [HCP-Users] Group-ICA maps

Hi - that would be one way to do it - but slices_summary is simpler than that - it just thresholds the zstats at Z>6 Cheers On 15 Sep 2014, at 07:26, Bryan Paton wrote: > Hi Steve, > >> That's correct: the 3D NIFTI ICA maps are released "primarily for >> display purposes" - as you say, the

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 du

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 tes

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 analysis of rfMRI n

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 : > > The following links

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

ions” ? >> >> -- >> Michael Harms, Ph.D. >> --- >> Conte Center for the Neuroscience of Mental Disorders >> Washington University School of Medicine >> Department of Psychiatry, Box 8134 >> 660 South E

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 normalisati

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 the

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 second-

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 kee

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 them? > > Claude > > >

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 which conflicting info is to be found) spati

Re: [HCP-Users] Melodic ICA idle

Hi Will I'm not aware of any outstanding bugs in melodic that would cause it to silently hang. Are you sure it's not just that you've run out of RAM and are swapping? Yes it's better to do group-ICA on grayordinates. You can still dual-regress that (step one into subject CIFTI, step two back

Re: [HCP-Users] Melodic ICA idle

eers :) > > Will > > > From: Glasser, Matthew 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.org>; > Erin W. E. Dickie > Subject: Re

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 question about obtaining the d

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 FI

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] 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 Uni

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 http://