Re: [HCP-Users] Subjects with less than 1200 time points

That just means that the scan did not complete for some reason. You can use them so long as your code does not assume all subjects have 1200 time points. Peace, Matt. From: > on behalf of Ruby Kong

Re: [HCP-Users] Distance between surface ROIs in MMP

the matrix. I don't think we have decided what the "best possible manner" is for dealing with the distance bias (or we would already have dealt with it). Regards, Karthik On Oct 6, 2017, at 7:32 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: We did it fo

Re: [HCP-Users] dtifit, bedpostx, voxel-wise correction of dMRI gradients

I believe both binaries will use the grad_dev to perform the correct described in the bvals and bvecs in a voxelwise manner. Peace, Matt. From: > on behalf of Athanasia Metoki

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

rfMRI_REST_Concat ${FSL_FIXDIR}/training_files/HCP_hp2000.RData I also tried to input the data as a list file, but the script didn’t work with error. It seems to get only one 4D rfMRI data set as input. That’s why I concatenated each run of rfMRI data set. Could you please confirm whether the above p

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

error. It seems to get only one 4D rfMRI data set as input. That’s why I concatenated each run of rfMRI data set. Could you please confirm whether the above procedures are correct or not? Thanks again. Sang-Young On Oct 6, 2017, at 3:57 PM, Glasser, Matthew <glass...@wustl.edu<mailto:gla

Re: [HCP-Users] Distance between surface ROIs in MMP

e to me. Do you have any suggestions on how I could best compute this proxy? Regards, Karthik On Oct 5, 2017, at 8:50 AM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Indeed I think we would need to know what you needed the distance for to know how best

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

rd one)? The third one should be processed with group ICA, right? What about the second one? This is processed with method 3 on above list? Thanks. Sang-Young On Oct 6, 2017, at 5:40 AM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: There is a beta version

Re: [HCP-Users] Distance between surface ROIs in MMP

the distance bias in tractography, so I want to use some proxy for actual connection distance between ROI pairs. Using tractography itself to account for its own bias against long-distance connections doesn’t make sense to me. Do you have any suggestions on how I could best compute this prox

Re: [HCP-Users] Distance between surface ROIs in MMP

rtices? If you can only get the distances in white matter voxels, or only the distances from the seed point, things could get challenging if you want to use different seeding strategies. Tim On Fri, Oct 6, 2017 at 6:24 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>&g

Re: [HCP-Users] Distance between surface ROIs in MMP

..@mst.edu<mailto:tsc...@mst.edu>> wrote: Right, I wasn't very precise in my wording. I was thinking of the "tractography distance bias" as the amount of the bias that is above and beyond the real biological distance relationship. Tim On Fri, Oct 6, 2017 at 4:36

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

There is a beta version of a multi-run ICA+FIX pipeline available in the HCP Pipeline’s repository. For 5 minute runs, I would expect combining across runs to be best. We haven’t tested combining across sessions yet, so you would have to check that that was working okay if you wanted to try

Re: [HCP-Users] Mean and variance normalization

Users FAQ. Would this be also your preference. Is there a reference or mathematical definitions for these functions (other than the obvious ones), so I can do a mathematical comparison between the two approaches? Heracles Panagiotides, PhD From: Harms, Michael Sent: Thursday, October 05, 2017 1

Re: [HCP-Users] Mean and variance normalization

MRI data files Does anyone know how the concatenation (see discussion below) of the ROI extracted time series needs to happen? Do I simply concatenate the time series as a temporal sequence, rfMRI_REST2_LR followed by rfMRI_REST2_RL ? Thanks again for the kind help. Heracles Panagiotides, PhD

Re: [HCP-Users] rfMRI data files

went into such detail.. Best wishes, Romuald -- Message: 2 Date: Tue, 3 Oct 2017 00:11:35 + From: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Subject: Re: [HCP-Users] rfMRI data files To: hercp <he...@uw.edu&

Re: [HCP-Users] Distance between surface ROIs in MMP

Indeed I think we would need to know what you needed the distance for to know how best to compute it. For things like MR artifacts, a 3D distance might be most appropriate. For something like smoothing, a geodesic distance would be appropriate. For something neurobiological, the tractography

Re: [HCP-Users] Surfaces, coordinates and beginner questions

Right we will recommend using the areal classifier to find these areas rather than the group parcellation once the areal classifier is available. Peace, Matt. From: > on behalf of Timothy Coalson

Re: [HCP-Users] rfMRI data files

Yes you ideally would analyze all of the resting state fMRI runs per subject. They have different phase encoding directions, so you should always analyze an equal amount of each. Be sure to demean and perhaps variance normalize prior to concatenating. Peace. Matt. From:

Re: [HCP-Users] Open files in wb_view via script

Add the files to a spec file and then open the spec file. Or perhaps it would be helpful to use quotes around your arguments. Peace, Matt. From: > on behalf of Keren Kotler

[HCP-Users] Method for Removing Global Noise While Retaining Global Signal in HCP fMRI Data

Dear HCP Users, A frequently discussed topic on the HCP-Users mailing list is how to clean HCP fMRI data above and beyond the recommended spatial ICA + FIX cleanup that has already been carried out. Several papers have noted that there is residual structured noise in HCP data and have

Re: [HCP-Users] DWI in CCF Prisma protocol

In general one wants to get as many gradient directions as possible. Perhaps Mike knows the answer to your other question. Matt. On 9/28/17, 2:59 AM, "hcp-users-boun...@humanconnectome.org on behalf of Jeffrey Spielberg"

Re: [HCP-Users] Update on vIdeo-watching data preprocessed

I¹d hope not more than another month or two. Peace, Matt. On 9/21/17, 1:11 PM, "hcp-users-boun...@humanconnectome.org on behalf of Nina de Lacy" wrote: >Hi there: > >I just wanted to check in and see if there was any

Re: [HCP-Users] Transformation matrices for tractography

Brain areas are not spheres. I don’t think this is a good approach. What is it that you are trying to do? Peace, Matt. From: > on behalf of Athanasia Metoki

Re: [HCP-Users] Cerebellum surface

This is built into the CIFTI format for the future, however we do not yet have an algorithm for making individual subject cerebellar surfaces. I believe a “Colin” individual surface is available somewhere and perhaps David knows the details. Peace, Matt. From:

Re: [HCP-Users] Correlation matrices

does it works to keep both cortical and subcortical gray matter? Thank you again, Carole Le 18 sept. 2017 à 17:08, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> a écrit : This should be possible with wb_command -cifti-cross-correlation. You would create a C

Re: [HCP-Users] CIFTI files do not contain volume data

Myelin maps are only for the cortex so you can omit the -volume-all data_sub.nii portion of the command. Peace, Matt. From: > on behalf of Sang-Young Kim > Date:

Re: [HCP-Users] Correlation matrices

This should be possible with wb_command -cifti-cross-correlation. You would create a CIFTI dense timeseries file of the subcortical region of interest and a CIFTI parcellated timeseries using the parcellation of your choice. You could then visualize the results in wb_view (depending on the

Re: [HCP-Users] Resampling freesurfer-HCP

I would ask on the FreeSurfer mailing list how to convert those file types to GIFTI as we are not familiar with them. Peace, Matt. From: > on behalf of Timothy Coalson >

Re: [HCP-Users] FIX error in fix_3_clean.m

addpath('${FSL_MATLAB_PATH}'); addpath('${FSL_FIX_CIFTIRW}');" to ML_PATHS="restoredefaultpath; addpath('${FSL_MATLAB_PATH}'); addpath('${FSL_FIX_CIFTIRW}');" -Keith On Mon, Sep 11, 2017 at 5:54 PM, Sang-Young Kim <sykim...@gmail.com<mailto:sykim...@gmail.com>> wrote: Yes, I’m

Re: [HCP-Users] FIX error in fix_3_clean.m

Are you using CIFTI data? Is this the compiled version of matlab or the interpreted version? Peace, Matt. On 9/11/17, 4:19 PM, "hcp-users-boun...@humanconnectome.org on behalf of Sang-Young Kim" wrote: >Dear HCP experts:

Re: [HCP-Users] rfMRI processing

e then, since the linear detrend has been already applied, right? Heracles Panagiotides, PhD From: Glasser, Matthew Sent: Friday, September 08, 2017 9:48 AM To: hercp ; HUMAN CONNECTOME Subject: Re: [HCP-Users] rfMRI processing We just use a linear detrend. Matt. From: hercp <he...@uw.edu

Re: [HCP-Users] rfMRI processing

are always very helpful. Would you recommend not using any temporal filter at all? Heracles Panagiotides, PhD From: Glasser, Matthew Sent: Thursday, September 07, 2017 7:53 PM To: NEUROSCIENCE tim ; hercp Cc: HUMAN CONNECTOME Subject: Re: [HCP-Users] rfMRI processing Also, I

Re: [HCP-Users] rfMRI processing

Also, I wouldn’t recommend doing that. There is plenty of BOLD signal outside those frequencies. Peace, Matt. From: > on behalf of Timothy Coalson > Date: Thursday,

Re: [HCP-Users] Table indicating location of clusters according to a dlabel file?

Right. Basically we are suspicious of defining areas based on statistical thresholds, as these are unlikely to reflect biological boundaries in the brain, but rather the vagaries of the statistical thresholding approach and the noise distribution. Peace, Matt. From:

Re: [HCP-Users] Slice-timing correction and latency structure of resting-state fMRI data

The TR=0.72s, but I think that is correct. Peace, Matt. From: > on behalf of "HINDRIKS, RIKKERT" > Date: Tuesday, September 5, 2017 at 8:48 AM To:

Re: [HCP-Users] clustering of subcortical structures - flipping and smoothing

have an "across parcels" option, that would be what "-volume-smoothing" is for. This option exists in cifti commands because cifti already contains the parcel ROIs, and we decided the default would be to treat them separately. Tim On Fri, Sep 1, 2017 at 2:11 PM, Glasser, M

Re: [HCP-Users] Error in the Diffusion analysis

Please use the latest version of the HCP pipelines and the latest version of FSL. Hopefully this user guide can be amended to suggest this, as it is from 2 years ago. Peace, Matt. From: > on behalf of

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

LR.surf.gii for a right-hemisphere ROI. Now these .gii files are the ones I provide to probtrackx. Regards, Karthik From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> Sent: Friday, September 1, 2017 4:30:31 PM To: Gopalakrishnan, Ka

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

The white matter surfaces used were: 100206.L.white_MSMAll.32k_fs_LR.surf.gii 100206.R.white_MSMAll.32k_fs_LR.surf.gii Thanks! Karthik From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> Sent: Friday, September 1, 2017 4:14:03 PM To

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

e-masks.txt and the file targets.txt contain newline-separated paths to each of the 360 ROIs (.gii files). Thanks! Karthik From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> Sent: Friday, September 1, 2017 4:06:15 PM To

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

-targetmasks=targets.txt --os2t --s2tastext Thanks! Karthik From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> Sent: Friday, September 1, 2017 8:16:51 AM To: Gopalakrishnan, Karthik; HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> Sub

Re: [HCP-Users] clustering of subcortical structures - flipping and smoothing

dy contains the parcel ROIs, and we decided the default would be to treat them separately. Tim On Fri, Sep 1, 2017 at 2:11 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: I guess I don’t know why one would want to smooth across the known boundaries, but th

Re: [HCP-Users] clustering of subcortical structures - flipping and smoothing

University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu<mailto:mha...@wustl.edu> From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-use

Re: [HCP-Users] clustering of subcortical structures - flipping and smoothing

1. That command for the surface is not quite what you are looking for. For the surface, the left and right hemisphere vertices are already in register (meaning that vertices with the same number will be in the anatomically corresponding location). You would need to translate between the

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

Can you post your probtrackx call? Peace, Matt. From: > on behalf of "Gopalakrishnan, Karthik" > Date: Thursday, August 31, 2017 at 9:27 PM To:

Re: [HCP-Users] fMRISurface Pipeline FinalfMRIResolution Variable

What kind of resolution are we talking about? The resolution parameters control the greyordinates space and the final volume space. Peace, Matt. From: > on behalf of Timothy Coalson

Re: [HCP-Users] failed running preprocessed dMRI data with FSL dtifit

ch provides a new way to me when I have FSL running problems in the future. Best regards, Xinyang At 2017-08-29 10:29:57, "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: If this is with FSL’s GUI, you might need to ask about it on the FSL list. Pea

Re: [HCP-Users] failed running preprocessed dMRI data with FSL dtifit

If this is with FSL’s GUI, you might need to ask about it on the FSL list. Peace, Matt. From: > on behalf of Xinyang Liu > Date: Monday, August 28, 2017 at

Re: [HCP-Users] Merging Annotation Files into Gifti Image

but I'd like to display the Yeo's atlas in its original form for the figure. As far as that registration goes, how would I go about doing so? On Fri, Aug 25, 2017 at 10:17 AM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: You might actually have to rema

Re: [HCP-Users] Merging Annotation Files into Gifti Image

You might actually have to remap that to the subject’s volume using the individual surfaces and then back to the merged surface. The reason is that by merging the surfaces you change the topology, and in such a way that we cannot use surface registration to handle things. Tim may have

Re: [HCP-Users] Tractography

Subject: Re: [HCP-Users] Tractography Thanks, Matt. Which files are the output of the Bedpostx process? I am currently looking at subject 116524. These are files I was able to download. [2017-08-24_9-36-36] Once again, thank you for your help. Heracles Panagiotides, PhD From: Glasser

Re: [HCP-Users] Tractography

Also as Steve has reminded me, you can download the Bedpostx outputs pre-computed. Peace, Matt. From: > on behalf of Matt Glasser > Date: Thursday, August 24,

Re: [HCP-Users] Tractography

That is the price one pays for really high spatial and angular resolution diffusion data. You can accelerate things quite a bit on CUDA capable GPUs. Peace, Matt. From: > on behalf of hercp

Re: [HCP-Users] residuals fmri

While that is true, what I suggested is the equivalent at least as far as measuring the smoothness of the unstructured noise goes. Matt. From: > on behalf of "Harms, Michael"

Re: [HCP-Users] residuals fmri

You could regress out the signal ICA components from the sICA+FIX cleaned volume timeseries and use the resulting residuals for this. Peace, Matt. From: > on behalf of Francesco

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

otiropou...@ndcn.ox.ac.uk>> wrote: 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

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

ocal/cuda is where you have installed CUDA, otherwise replace accordingly. Cheers Stam On 22 Aug 2017, at 20:01, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Actually that looks like a cuda library error and your pipeline setup looks fine. You might

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

="${RawDataDir}/${SubjectID}_3T_DWI_dir113_PA.nii.gz" EchoSpacing=0.77 PEdir=2 Gdcoeffs="${HCPPIPEDIR_Config}/coeff_AS82_Prisma.grad" ***** Thanks. Sang-Young On Aug 22, 2017, at 2:44 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: I mean the la

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

bal/scripts export HCPPIPEDIR_tfMRIAnalysis=${HCPPIPEDIR}/TaskfMRIAnalysis/scripts ********** Thanks. Sang-Young On Aug 22, 2017, at 2:38 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Need to know the variables in the laugh

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

ingBatch.sh > >I believe all environment variables are correctly set in >"SetUpHCPPipeline.sh". > >Thanks. > >Sang-Young > >> On Aug 22, 2017, at 2:28 PM, Glasser, Matthew <glass...@wustl.edu> >>wrote: >> >> How did you call the pipeline? &g

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

How did you call the pipeline? Peace, Matt. On 8/22/17, 10:57 AM, "hcp-users-boun...@humanconnectome.org on behalf of Kim, Sang-Young" wrote: >Dear HCP experts: > >We have diffusion MRI data acquired from Siemens Prisma 3 T

Re: [HCP-Users] Volumetric tfMRI data on ConnectomeDB

I suppose it would be reasonable to make unsmoothed individual subject volume data available, however that isn’t going to be high on the priority list given available resources. In my opinion the smoothed volume data shouldn’t have been made available in the first place, because they were

Re: [HCP-Users] Which T1 file for 7T Diffusion data?

All of the registration and distortion correction has already been done. All of the T1w images should be in the same mm space, but you may wish to use the file with 1.25 in the name for 3T diffusion and 1.05 in the name for 7T diffusion if you want to use a tool like FSLView that requires the

Re: [HCP-Users] Functional connectivity gradient map

wb_command -cifti-gradient and wb_command -cifti-correlation-gradient. There are also -metric-gradient for GIFTI files and -volume-gradient for NIFTI files. Peace, Matt. From: > on behalf of Sang-Yun Oh

Re: [HCP-Users] Gifti surface labels

For the 32k 2mm average spacing surfaces you can find the standard medial wall definitions here: https://github.com/Washington-University/Pipelines/blob/master/global/templ ates/91282_Greyordinates/L.atlasroi.32k_fs_LR.shape.gii

Re: [HCP-Users] help: extract MNI coordinates of tfMRI blobs from workbench

Nope, you can do the tractography directly from the surfaces using FSL: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#Using_surfaces Use the surfaces in ${StudyFolder}/${Subject}/T1w/fsaverage_LR32k. White surfaces are good for counting and pial surfaces are good for stopping. There

Re: [HCP-Users] BALSA dataset submission?

Hi Sean, We can discuss off list. Peace, Matt. On 8/14/17, 3:23 AM, "hcp-users-boun...@humanconnectome.org on behalf of Sean Tobyne" wrote: >Hello, > >Is it known when the option for user submissions to BALSA will be

Re: [HCP-Users] DTI on HCP data

It looks like you have the correct understanding of this. One cannot easily apply the gradient nonlinearity effects on the diffusion gradients to the images, as really you need to apply them to the bvals and bvecs. Peace, Matt. From:

Re: [HCP-Users] The best set of annotations for any MRI scan?

Subject: Re: [HCP-Users] The best set of annotations for any MRI scan? Hi Matt, Thanks for your response, I mean a set of human added labels that are associated with specific locations of the scan. Best, anita On Thu, Aug 10, 2017 at 9:52 AM, Glasser, Matthew <glass...@wustl.edu<mailto

Re: [HCP-Users] [SPAM] Brodmann area maps

Indeed the conversion from FreeSurfer annot format to GIFTI label format using FreeSurfer’s mris_convert does not preserve the probabilities (instead coloring every vertex with non-zero probability as a label). Really though, FreeSurfer only provides those labels on individual subjects as a

Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files?

It should work if you skip the last step and use the dlabel file. Peace, Matt. From: Xavier Guell Paradis > Date: Wednesday, August 9, 2017 at 9:43 AM To: Timothy Coalson >, Matt Glasser

Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files?

wb_command -cifti-create-dense-scalar and then wb_command -cifti-label-import with an appropriate label tabel. Alternatively, wb_command -volume-label-import and wb_command -cifti-create-label. Peace, Matt. From:

Re: [HCP-Users] about the HCP template

There is not enough information in this question to answer. I would need to know what files you are talking about and what you are trying to do. Peace, Matt. From: > on behalf of 罗

Re: [HCP-Users] Offline vs. online gradient nonlinearity correction

of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173<tel:(314)%20747-6173> St. Louis, MO 63110 Email: mha...@wustl.edu<mailto:mha...@wustl.edu>

Re: [HCP-Users] Offline vs. online gradient nonlinearity correction

1. Yes 2. We use dcm2nii. 3. Probably I would use offline so you are sure that all of your images are being corrected the same way and have control over how the resampling is being done (i.e. not adding blurring from trilinear interpolation). Peace, Matt. From:

Re: [HCP-Users] HCP dMRI quality control question

That means they didn¹t complete all of the scans. It is up to you whether you want to include such subjects in your study. Peace, Matt. On 8/3/17, 10:00 PM, "hcp-users-boun...@humanconnectome.org on behalf of Fang-Cheng Yeh"

Re: [HCP-Users] Follow-up to: Obtaining the MNI coordinates of cluster peaks in the melodic_IC.dscalar.nii ICA maps

ubject space using the MSMAll surfaces in the subject directory of the T1w folders. My result is data associated with those surfaces and I was planning on averaging the data across participants. Claude On 04.08.2017 00:28, Glasser, Matthew wrote: Tractography has quite strong folding-related bia

Re: [HCP-Users] Obtaining the MNI coordinates of cluster peaks in the melodic_IC.dscalar.nii ICA maps

They were run in the CIFTI greyordinates space. As it turns out, ICA results from well aligned data look different from those of poorly aligned data, as one gets many components representing misalignment if the data are not well aligned. Peace, Matt. From: James Morrow

Re: [HCP-Users] Obtaining the MNI coordinates of cluster peaks in the melodic_IC.dscalar.nii ICA maps

This is challenging for several reasons: Standard volumetric data don’t have good alignment of cortical areas, and cortical areas are complex patches on a convoluted surface not 3D points, so MNI coordinates are not especially meaningful as a way of determining if results are the same across

Re: [HCP-Users] Problems with the HCP Pipeline

es University of Reading ____________ From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> Sent: 28 July 2017 13:02:39 To: Nicolo Biagi; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>; Brown, Tim Subject: Re: [HCP-Users] Problems with the HCP Pipel

Re: [HCP-Users] Questions about parameters in CCF protocols

1. TI=1000 actually separates the CSF/Grey/White peaks of the the histogram more evenly than TI=900ms (CSF and Grey too close) or TI=1100 (Grey and White too close). I don’t understand why the FreeSurfer group has recommended TI=1100 as it wouldn’t seem to make things easier for their

Re: [HCP-Users] fslr32k or fsaverage parcellation as seeds for probtrackx2

t trickier. Do you have an example FSL command for a HCP subject? I can’t really figure out what I need to do, and what HCP has already done. For example, do any transforms need to be calculated? Do I just need the subject surface to fsaverage transform? Thanks again, Max On Aug 1, 2017, at 2

Re: [HCP-Users] fslr32k or fsaverage parcellation as seeds for probtrackx2

You can use wb_command -cifti-separate to get GIFTI label files out and then use https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#Using_surfaces Peace, Matt. From: > on behalf of Max Bertolero

Re: [HCP-Users] Reading Human Connectome Project (HCP) *.dtseries.* file in Python

below), but not in Python. I >can read cifti image in python. > >f=image.load_img(filename) > >But how do I get coordinates of the subcortical structures. I code >snippet would be appreciated. > >Thank you, >Best, >Anand > >___

Re: [HCP-Users] Reading Human Connectome Project (HCP) *.dtseries.* file in Python

For the volume structures these are in the CIFTI header, however for the surfaces there are no veridical xyz coordinates, it all depends on the surface model you are using. In general we recommend only using 3D coordinates of individual subject¹s midthickness surfaces (or in special circumstances

Re: [HCP-Users] Individual multi-modal parcellations

They aren¹t yet available however we hope to get them out soon when there is bandwidth available for the appropriate people. Peace, Matt. On 7/27/17, 2:39 PM, "hcp-users-boun...@humanconnectome.org on behalf of K. Wagstyl"

Re: [HCP-Users] Clarification regarding DWI datasets

1. Yes 2. Yes 3. Use the preprocessed data which has all files preprocessed and combined appropriately in ${StudyFolder}/${Subject}/T1w/Diffusion. If you are using your own diffusion model, be sure to take into account the gradient nonlinearity effects on the diffusion weighting and

Re: [HCP-Users] hcp_fix.for_fix1.06a

DIC can run on CIFTI files; temporal concatenation in MELODIC now defaults to using MIGP. Thank you, Yeun On Fri, Jul 21, 2017 at 1:19 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Hi Yeun, I think you should use multi-run ICA+FIX given the relatively short r

Re: [HCP-Users] Two questions about surfaces & template spaces | MSMall & FS

For tractography of HCP data you would use the surfaces in ${StudyFolder}/${Subject}/T1w/fsaverage_LR32k/ and the diffusion data in ${StudyFolder}/${Subject}/T1w/Diffusion, which have the same ACPC rigid registration to MNI space. If you want your tractography data to be aligned with MSMAll

Re: [HCP-Users] Two questions about surfaces & template spaces | MSMall & FS

It is also worth noting that the HCP Pipelines output MSMSulc and MSMAll surfaces only (FreeSurfer is worse at aligning function than MSMSulc with more distortion). Matt. From: > on behalf of Timothy Coalson

Re: [HCP-Users] hcp_fix.for_fix1.06a

: TR = 800ms, 488 volumes, voxel size 2mm^3, for 2 runs (one AP, one PA phase encoding). Total time when concatenating the two runs is about 13 minutes. Task fMRI runs are the same but shorter (300 volumes for CARIT; 338 vol x 2 runs for an in-house task). On Thu, Jul 20, 2017 at 5:38 PM, Glasser

Re: [HCP-Users] hcp_fix.for_fix1.06a

e fMRI scans (2 sets of rs-fMRIs and 2 sets of task-fMRIs). Should we use hcp_fix_multi_run? Thank you, Yeun On Wed, Jul 19, 2017 at 5:21 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: The latest of everything will work for most applications. Peace, M

Re: [HCP-Users] diffusion data merge pipeline

ne Don't recommend the parallel processing or the eddy_cuda? On Tue, Jul 18, 2017 at 2:13 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: We really don’t recommend you do that. I would ask about the eddy_cuda on the FSL or neurodebian lists. Peace, Matt

Re: [HCP-Users] hcp_fix.for_fix1.06a

Is the hcp_fix script in http://www.fmrib.ox.ac.uk/~steve/ftp/fix.tar.gz (the latest release - version 1.065) the correct one to use, then? On Wed, Jul 19, 2017 at 5:15 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: I wouldn’t worry about that. Those m

Re: [HCP-Users] hcp_fix.for_fix1.06a

# ${HOME}/pipeline_tools/fix1.06a/melodic -i $fmri -o ${fmri}.ica/filtered_func_data.ica -d -250 --nobet --report --Oall --tr=$tr --- Or should I be using the old melodic? On Wed, Jul 19, 2017 at 5:05 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: What is this in r

Re: [HCP-Users] hcp_fix.for_fix1.06a

What is this in reference to? Peace, Matt. From: > on behalf of Yeun Kim > Date: Wednesday, July 19, 2017 at 7:04 PM To:

Re: [HCP-Users] signal to noise ratio

What kind of resolution are you looking to do and for what purpose? Peace, Matt. From: > on behalf of Sebastien Hetu > Date: Wednesday, July 19, 2017 at 3:28 PM

Re: [HCP-Users] mapping HCP data into 7 functional networks (using Thomas Yeo parcellation)

ail). After that, we downsample them on the surface to the more sensible resolution. Tim On Mon, Jul 17, 2017 at 6:44 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: No that would be a massive oversampling of the data. The data are acquired at 2mm isot

Re: [HCP-Users] diffusion data merge pipeline

outh Euclid Ave.Tel: 314-747-6173<tel:(314)%20747-6173> St. Louis, MO 63110Email: mha...@wustl.edu<mailto:mha...@wustl.edu> From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Yeun Kim <yeun...@gmail.com<mailt

Re: [HCP-Users] mapping HCP data into 7 functional networks (using Thomas Yeo parcellation)

nal folding detail (even though 32k surfaces still have very good folding detail). After that, we downsample them on the surface to the more sensible resolution. Tim On Mon, Jul 17, 2017 at 6:44 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: No that

Re: [HCP-Users] CMRR vs MGH multiband/SMS sequences

What version of the software is this and what scanner? Also, what are the sequence parameters? Peace, Matt. From: > on behalf of A R > Date: Tuesday, July 18,

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