Re: [HCP-Users] Fw:

of FSL options. Do > you know if there is anyone who might be able to help with this? > > Thanks again, > -hp > > *From:* Timothy Coalson > *Sent:* Friday, March 16, 2018 2:15 PM > *To:* Glasser, Matthew > *Cc:* HERACLES PANAGIOTIDES ; hcp-users@humanconnectome.org > *Subject:*

Re: [HCP-Users] PALM Viewing results

we can do both; an effect size map and then .95-1 in the corr p map? > > > On Mar 16, 2018, at 4:59 PM, Timothy Coalson <tsc...@mst.edu> wrote: > > Since the extent that passes significance tests is dependent on number of > subjects and other statistical power considerations, we

Re: [HCP-Users] Fw:

Load both of the volumes into wb_view (high-res mask and low-res fMRI - you may want to separate out a single frame from the fMRI to keep memory usage down) and see if they align with each other (if they don't display correctly, turn on oblique volume drawing mode). If they do align, the answer

Re: [HCP-Users] PALM Viewing results

Since the extent that passes significance tests is dependent on number of subjects and other statistical power considerations, we instead recommend viewing the effect size (beta) map. You can overlay outlines of what passed the significance threshold by making that into a label file with

Re: [HCP-Users] ERROR: Unexpected parameter: -local-affine-method in PostFreeSurferPipeLineBatch.sh

Yes, the newest pipelines used an option that isn't in the 1.2.3 release. Grab the "dev_latest" zip file that matches your OS from here: http://brainvis.wustl.edu/workbench/ Tim On Mon, Mar 12, 2018 at 5:57 PM, Viessmann, Olivia M. < oviessm...@mgh.harvard.edu> wrote: > Hello, > > > I am

Re: [HCP-Users] Concatenating resting state runs

When we compute parcellated connectivity, we first compute the average timeseries within the parcels, and then correlate those, as it vastly reduces the impact of noise. If we first computed the correlations, and then averaged them within parcels, we would be losing a huge amount of power. The

Re: [HCP-Users] HCP-Users Digest, Vol 64, Issue 2

ease edit your Subject line so it is more specific > than "Re: Contents of HCP-Users digest..." > > > Today's Topics: > > 1. Re: Best Approach for using old volumetric data to pick > parcels-of-interest (Stevens, Michael) > 2. Movement regressor missing (Linnman

Re: [HCP-Users] ROI cluster centers to surface grayordinates

Unfortunately, it is worse than that - even ignoring the individual variability issue (which should not be ignored), a small change in MNI coordinate can jump from one bank of a sulcus to the other, so having only the center coordinate of a cluster makes this a badly posed problem (and thus

Re: [HCP-Users] Best Approach for using old volumetric data to pick parcels-of-interest

me-to-surface > mapping you describe? I’ll whip up a quick script to loop through about > 120 datasets from this R01 project and let you know how well it works. > > > > Mike > > > > > > *From:* Timothy Coalson [mailto:tsc...@mst.edu] > *Sent:* Friday, February 23

Re: [HCP-Users] wbsparse

t know if I can run > probtrackx using it. > > Regards, > Kamal > > From: Timothy Coalson <tsc...@mst.edu> > Date: Wednesday, February 28, 2018 at 6:56 PM > To: "Glasser, Matthew" <glass...@wustl.edu> > Cc: "Shadi, Kamal" <kamal.shad...@g

Re: [HCP-Users] Neighbors of a vertex

Workbench does this internally, but it doesn't currently have a command to output it (the number of neighbors varies per vertex, so it could be hard to make efficient use of in something like matlab). The .surf.gii file has this information in it, in the triangles array, so if you load it, you

Re: [HCP-Users] wbsparse

Also beware, since one of the dimensions is white matter voxels, the dconn from -convert-matrix4-to-matrix2 will be larger than a standard 91k dconn (78GB based on the information you posted, versus ~30GB for a 91k dconn). Surface-to-surface tractography would normally be done with a different

Re: [HCP-Users] path to bbregister .dat file for REST call

The 6dof transform using the MNI template is only to get the orientation of the structural images to be more predictable - we actually refer to the result of this transform as "native volume space", because it is somewhat more useful for our purposes than the scanner coordinates. It is based only

Re: [HCP-Users] border file

The weights are to be able to place the border point somewhere other than at a vertex. The three vertices are one of the triangles in the surface file, and the weights represent where to place the point on that triangle. If you want a border point at a vertex, the weight for that vertex should

Re: [HCP-Users] Best Approach for using old volumetric data to pick parcels-of-interest

Surface-based methods may boost your statistical power enough (by better alignment, exclusion of irrelevant tissue, and smoothing that doesn't cross sulcal banks, if you decide you need smoothing) that you may not need to rely as much on existing ROIs. Parcel-based statistics have a lot of power,

Re: [HCP-Users] An error in Post-FreeSurfer Pipeline

The error message appears to be from syntax in a bash script, so it should be possible to track it down. If you put "set -x" at the top of the script it fails in and rerun it, it will tell you each command before executing it, which should help narrow down which line is the problem. If the line

Re: [HCP-Users] about interpreting EVs and .dtseries.nii files

On the technical end, cifti dtseries are arranges such that a row is a timecourse - you will need to select columns rather than rows. wb_command -cifti-merge can do this. On the math side, I don't know the details needed to sync the EV files with the dtseries (whether the 0s from the EVs match

Re: [HCP-Users] Extracting Thalamus Brainordinates

pfields but cannot seem to > find them could you point me in the right direction/directory? > > Cheers, > > Claude > > On il-Ħamis, 22 ta Fra, 2018 01:07 , Timothy Coalson wrote: > > It may be better to use the individual subject's "native space" > definitions. The

Re: [HCP-Users] Extracting Thalamus Brainordinates

It may be better to use the individual subject's "native space" definitions. The files in the T1w folder are in what we refer to as native volume space (it is actually rigidly-aligned MNI space, but rigid alignment preserves shape, so it can be used as if it were distortion-corrected scanner

Re: [HCP-Users] gif surface to obj

It appears that .obj is a fairly simple text format ( https://en.wikipedia.org/wiki/Wavefront_.obj_file), so you could hack it together in shell, if nothing else. You can use wb_command -gifti-convert to convert to ASCII encoding, and that would allow you to get the coordinate and triangle

Re: [HCP-Users] A question about workbench command

orkbench? I didn't > find it on the HCP website. Thank you. > > > Aaron > -- > *From:* Timothy Coalson <tsc...@mst.edu> > *Sent:* Wednesday, February 14, 2018 4:53:54 PM > *To:* Aaron C > *Cc:* hcp-users@humanconnectome.org > *Subject:* Re: [HCP-

Re: [HCP-Users] A question about workbench command

Not currently, no, though it could be added. It is undefined between left and right hemispheres, so the obvious format would be a metric file, rather than cifti grayordinates. Our uses of geodesic distance are generally limited to a short distance, we haven't really found it useful to know the

Re: [HCP-Users] Restrict dscalar to only CORTEX_LEFT+CORTEX_RIGHT

Once you have done it once (or if you already have another cifti file that has the correct setup), you can use -cifti-create-dense-from-template to do this to another file in one step. Tim On Thu, Feb 8, 2018 at 7:53 PM, Glasser, Matthew wrote: > You need to export the

Re: [HCP-Users] Software to convert ANTs warps to FSL format

Something that just bit me: you should probably specify "--rel" on convertwarp and applywarp, because wb_command doesn't currently understand the absolute warpfield convention that seems to be the default. Tim On Fri, Feb 2, 2018 at 10:07 PM, Timothy Coalson <tsc...@mst.edu>

Re: [HCP-Users] Software to convert ANTs warps to FSL format

z < mois...@fmrib.ox.ac.uk> wrote: > I had the same problem in the past... try: > *c3d_affine_tool -itk ANTSmat.txt -ref myref -src mysrc -ras2fsl -o > FSLmat.txt * > > However, as Tim said, this tool only converts the affine, not the warp. > > Moises. > > > > On 2

Re: [HCP-Users] Software to convert ANTs warps to FSL format

I haven't finished figuring this out, but it appears that the affine file's "Parameters" array contains the 12 affine components you'd find in a normal affine file. The warpfield does not seem to include the affine, so you need to convert and use both of them, which may be why what you did looked

Re: [HCP-Users] Workbench: save images using the command line

No, scene files are highly GUI-centric, taking captures of what is in a scene is somewhat secondary. The number of display options for files (and when we add new display features) would make it very cumbersome to make and maintain a command to do the equivalent without the GUI. You can set up a

Re: [HCP-Users] Convert dlabel to dscalar

Inline comments. Tim On Mon, Jan 29, 2018 at 9:51 AM, Xavier Guell Paradis wrote: > Dear HCP experts, > I have a dlabel file that labels a particular nucleus of the left thalamus > (thalamusnucleus.dlabel.nii). I would like to convert this dlabel file to a > whole-brain

Re: [HCP-Users] E-prime log

For specifically wb_command, there is online documentation, though it is just another representation of the various help information you can get from running wb_command: https://www.humanconnectome.org/software/workbench-command If you are referring to the HCP Course, trying to cover all of the

Re: [HCP-Users] Dear HCP users,

If the CIFTI XML specifies that it is "Version=1", then that is expected, though in some sense it was an error. The CIFTI-1 specification unfortunately specified that the nifti header must be used incorrectly. This was changed in the CIFTI-2 specification. Tim On Fri, Jan 19, 2018 at 5:09 PM,

Re: [HCP-Users] Create a dtseries file with only cerebral cortical surface data

It is possible, first you need a cortical-only cifti file to use as a template, if you don't have one, you can make one from the original ROI files. The files are in the pipelines repo: https://github.com/Washington-University/Pipelines/tree/master/global/templates/91282_Greyordinates Use this

Re: [HCP-Users] volume to average surface with Nearest Neighbour interpolation

ditional effort. > I managed to get the Nearest-Neighbour-like mapping I wanted done in > Matlab. When I display this on the group average surfaces, it also looks > pretty good. I just want to check that the workbench steps I have taken are > correct. > > Best wishe

Re: [HCP-Users] workbench command error from 3_22 Pipelines

Get the "dev_latest" zip file that says "mac64" from here: http://brainvis.wustl.edu/workbench/ Tim On Fri, Jan 12, 2018 at 1:41 PM, Glasser, Matthew wrote: > You need the development version of Connectome Workbench, which Tim can > point you to. We will soon be getting

Re: [HCP-Users] Resting State processing

To further explain: "latest master" means you should *not* go to the "releases" page on github. Instead, go to the main page, https://github.com/Washington-University/Pipelines , and click the green "clone or download" button on the upper right above the file list. Tim On Tue, Jan 9, 2018 at

Re: [HCP-Users] A question about the geodesic distance

To clarify further, until a surface registration is done, there is no obvious relationship between the vertices of one subject and another (and the surfaces even have different numbers of vertices). After registration and resampling to a standard mesh (MSMAll and fs_LR 32k are options for these

Re: [HCP-Users] Smoothing, discarding volumes

To expand on the smoothing issue a bit, even 4mm FWHM spatial smoothing in the volume causes substantial signal mixing between areas on opposite sides of sulci, which sounds like a particularly bad idea for ICA. As I understand it, group ICA shouldn't care much about spatial noise, especially

Re: [HCP-Users] volume to average surface with Nearest Neighbour interpolation

The fs_LR 32k spheres use a resolution (vertex spacing) that is suitable for 2mm fMRI data, but it sounds like you are using structural-resolution voxels. As Matt says, I would put the fs_LR surface into your volume space, and do only a single mapping, because nearest neighbor or enclosing voxel

Re: [HCP-Users] ft_write_cifti with multiple columns

You can set map names on data files with wb_command -set-map-names. However, as Matt says, we would rather support the ciftiread/ciftiwrite functions for fMRI data. Tim On Mon, Dec 18, 2017 at 2:56 PM, A Nunes wrote: > Hi HCP community, > > I have some parcellations

Re: [HCP-Users] Volumetric Data to Surface Data Question

.surf.gii files only store geometry of cortex, they do not store activation data. We generally suggest .func.gii rather than .shape.gii, even though those two formats are the same, and with fMRI data, .func.gii is more appropriate. To get data from the volume onto the surface, you need to have

Re: [HCP-Users] Glasser atalas version in volumetric space - good enough for tractography?

Since tractography is done on individual subject data, you don't want a version of the parcellation that was mapped to the volume with the group average surfaces (like the one you linked to). You can do per-subject mapping yourself with wb_command -label-to-volume-mapping, using either the group

Re: [HCP-Users] wb_shortcuts: global_temporary_files: unbound variable

This was a bug in the code. Please use the version from here instead: https://github.com/Washington-University/wb_shortcuts Tim On Mon, Dec 11, 2017 at 7:50 AM, Dev vasu < vasudevamurthy.devulapa...@gmail.com> wrote: > Dear Sir, > > When i am using wb_shortcuts for my analysis , i am

Re: [HCP-Users] label list file from dlabel

For cifti files, you need to use -cifti-* commands, so you want to use -cifti-label-import instead. Most wb_command operations require a very specific file format for input. You can run it without a label-list-file (as the help info says, use a pair of quotes instead of a filename: ""), which

Re: [HCP-Users] RGBA files in connectome workbench

enough to be a problem. Tim On Wed, Dec 6, 2017 at 4:55 PM, Timothy Coalson <tsc...@mst.edu> wrote: > Another possibility for a quick and dirty approximation to what you want, > you may be able to use transparency of layers to blend together coloring > from the different componen

Re: [HCP-Users] RGBA files in connectome workbench

Another possibility for a quick and dirty approximation to what you want, you may be able to use transparency of layers to blend together coloring from the different components, rather than manually mixing them beforehand. However, you would need to play with the palettes, and it couldn't be used

Re: [HCP-Users] Show outline of dscalar map at a given threshold?

First, use -cifti-math to do the thresholding you want (if you have negative p-values for deactivations, you could add something like " + 2 * ((x < 0) && (x > -0.05))"): $ wb_command -cifti-math '(x > 0) && (x < 0.05)' above_thresh.dscalar.nii -var x Then, import it as a label file (this basic

Re: [HCP-Users] wb_shortcuts dyld: lazy symbol binding error

The wb_shortcuts command is actually just a bash script. However, it calls other utilities, and that function specifically calls both "mris_convert" and "wb_command". Since it is complaining about "libgomp" which is involved in parallelization, it may in fact be an issue with wb_command, as I

Re: [HCP-Users] Subcortical atlas of S900_AverageT1w_restore.nii.gz?

Using -cifti-separate will get you the 2mm definitions of these structures, in particular using "-volume-all -label ", but the same information is already available in the pipellines repository:

Re: [HCP-Users] A question about brain registration matrix

"How much deformation" is a tricky subject, and we may very well mean something different than you do when you say it. The short version: surface registration does not cause anatomical deformation. Any registered, resampled anatomical surface will still line up perfectly with the volume it

Re: [HCP-Users] MEG Surface Parcellation

You can resample cifti data to a different resolution without splitting it up first, use wb_command -cifti-resample . You will need to specify both -left-spheres and -right-spheres. Tim On Fri, Nov 3, 2017 at 1:26 PM, Jan Mathijs Schoffelen < jm.schoffe...@gmail.com> wrote: > Dear Julia, > >

Re: [HCP-Users] Regarding the multi-modal parcellation of the cortex

Volume-based alignment of cortex is significantly worse than surface-based cortical alignment, so we have not released a volume-based version of the parcellation (because it can't be equivalent to using MSMAll), see this previous thread:

Re: [HCP-Users] exporting borders to freesurfer annot / pySurfer

The -*-label-import commands do not convert from separate ROIs to single-map label format, because ROIs could overlap while labels are not allowed to. You need to first create a file with a single map of different integers for each ROI, before using these commands. First, you need to ensure that

Re: [HCP-Users] Merging a gifti file

For a quick introduction to CIFTI, see FAQ #1: https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ You may also want to read wb_command -cifti-help, while some of it is redundant with the FAQ, it also explains things you need to know about when using cifti commands in wb_command:

Re: [HCP-Users] (no subject)

rfMRI_REST1_LR_hp2000_clean.nii.gz is a volume file, not a cifti file. Cifti files end in things like .dtseries.nii. See wb_command -cifti-help: https://www.humanconnectome.org/software/workbench-command/-cifti-help Tim On Mon, Oct 23, 2017 at 4:17 PM, hercp wrote: > I am

Re: [HCP-Users] Extraction of mean myelination values from a custom roi

I just want to see what the mean myelination in these exact areas that > turned out to be significant is in the groups I compared. Hope it makes > sense. > > Thanks again! > > Lisa > > On 18 October 2017 at 01:12, Timothy Coalson <tsc...@mst.edu> wrote: > >> T

Re: [HCP-Users] Extraction of mean myelination values from a custom roi

The -cifti-parcellate command is currently the easier way to do this, if your ROIs don't overlap. The -roi option to -cifti-stats currently uses only the first map, and only tests for whether the value is greater than 0, so probably the first map in your roi input is actually all positive. Also

Re: [HCP-Users] surf2surf

oud...@tcd.ie> wrote: > Hi Tim, > > Was there a response to the question about sumsDB requesting login > information? I also ran into that problem a couple of days ago. > > Best wishes, > > Sean > > Sean Froudist-Walsh > Postdoc > New York University > > O

Re: [HCP-Users] surf2surf

The s...@brainvis.wustl.edu address is still active, but it is a manual process. As David gave you the information, I don't plan on redundantly responding to the email to sums@brainvis. Tim On Mon, Oct 16, 2017 at 11:40 AM, Mars, R.B. (Rogier) wrote: > Hi David, > >

Re: [HCP-Users] CIFTI tools in the Python

Nibabel should support cifti files now, though it may be fairly basic: https://github.com/nipy/nibabel I don't know of other projects for cifti in python. Tim On Wed, Oct 11, 2017 at 11:18 PM, Aaron Crank wrote: > Dear HCP experts, > > > I have a question about

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

It was probably killed because it ran out of memory. The best solution is to use a machine with more memory. A workaround, but one that will take a LOT more time to run on each subject (unless you happen to already have fast SSDs), is to add swap space to your system, which will allow it to

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

That looks like a generic matlab error related to the amount of memory the computer has. The memory requirements for some of these scripts are fairly high (the machines we often use have 64GB of memory). Tim On Mon, Oct 9, 2017 at 9:58 AM, Sang-Young Kim wrote: > Dear

Re: [HCP-Users] How to transform all subcortical values to 0 in a dscalar?

he rows that did not belong to cortical vertices, and then did the math > operations. > Thank you very much, > Xavier. > ---------- > *From:* Timothy Coalson [tsc...@mst.edu] > *Sent:* Wednesday, October 04, 2017 4:09 PM > *To:* Xavier Guell Paradis > *Cc:*

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

erenced. > > Peace, > > Matt. > > From: Timothy Coalson <tsc...@mst.edu> > Date: Friday, October 6, 2017 at 5:30 PM > To: "Gopalakrishnan, Karthik" <gkart...@gatech.edu> > Cc: Matt Glasser <glass...@wustl.edu>, "hcp-users@humanconnecto

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

want to use different seeding strategies. Tim On Fri, Oct 6, 2017 at 6:24 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > --ompl option in probtrackx2. > > Peace, > > Matt. > > From: "Gopalakrishnan, Karthik" <gkart...@gatech.edu> > Date: Friday, Oc

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

appropriate. > > Peace, > > Matt. > > From: <hcp-users-boun...@humanconnectome.org> on behalf of Timothy > Coalson <tsc...@mst.edu> > Date: Tuesday, October 3, 2017 at 6:30 PM > To: "Gopalakrishnan, Karthik" <gkart...@gatech.edu> > Cc: &q

Re: [HCP-Users] Unable to Capture image using Wb_view

One of the methods to capture images (render pixmap) is not supported well by intel GPUs. We use nvidia GPUs in the linux computers we run workbench on, and they generally work well for us. One workaround is to switch the image capture method in wb_view -> Preferences -> OpenGL to "Grab Frame

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

nformation in the MMP paper: https://www.ncbi.nlm.nih.gov/pubmed/27437579 Tim On Wed, Oct 4, 2017 at 1:38 PM, Romuald Janik <romuald.ja...@gmail.com> wrote: > Thanks for the detailed explanations! > > I have just one follow up question regarding this point: > > On Tue, Oct 3, 20

Re: [HCP-Users] ERROR: Unexpected parameter: -local-affine-method

That is a new option that is not yet in a released version of workbench, and was probably not intended to be pushed to the pipelines repository. You can use github to find the version before that line was added, and use that instead. Alternatively, you can probably just comment out that line and

Re: [HCP-Users] How to transform all subcortical values to 0 in a dscalar?

You can use -cifti-replace-structure with the -volume-all option and a volume file of zeroes. If you have a lot of maps (or you want to do something similar to a long dtseries), you can make a cifti file with 1's in the surfaces and 0's in voxels, and use -cifti-math to multiply them together.

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

Since ROIs are not points, distance between them becomes a trickier question. Since areas are connected through white matter rather than gray matter, that also implies that the easy ways to calculate distance may not be all that biologically relevant. This would point to using tractography to

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

Inline comments. On Tue, Oct 3, 2017 at 12:49 PM, Romuald Janik wrote: > Hi, > > I have recently started to look at the HCP single subject rfMRI data and I > have a couple of beginner questions: > > 1) What is the difference between the various files (I downloaded just

Re: [HCP-Users] about surface template and writing matrix to.dlabel cifti file

We do have a version of the 7 networks labels as the first map in this file: https://balsa.wustl.edu/file/show/Q2xn It currently does not use a medial wall mask, so extra steps may be needed for using it with HCP data. I don't know if either current matlab method of cifti file IO has much

Re: [HCP-Users] Correlation matrices

The -cifti-create-dense-* commands are indeed involved in manually making cifti versions of your data, though you would also need things like -volume-to-surface-mapping, as well as FreeSurfer to generate the subject surfaces - the HCP pipelines are designed for automating these steps for HCP and

Re: [HCP-Users] Resampling freesurfer-HCP

I am not familiar with the .w format, but it sounds like mris_convert is not actually converting it to gifti format. The second error from the .mgh method sounds like it has the surface geometry in the file, which must be removed - workbench requires geometry files (.surf.gii) and data files

Re: [HCP-Users] Restricting workbench thread usage

Workbench uses OpenMP for parallelization, and is therefore controlled via its environment variables. OMP_NUM_THREADS is probably the one you are looking for. We will add this information to the help info of wb_command in a future release. Tim On Fri, Sep 8, 2017 at 2:47 PM, Reinder Vos de

Re: [HCP-Users] rfMRI processing

We do not apply that kind of narrow temporal filtering (we basically only do a detrend), you will need to do such things yourself. Tim On Thu, Sep 7, 2017 at 9:27 PM, hercp wrote: > I am looking at rfMRI data. Are there files that are already > time-filtered between .01 and .08

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

The commands in wb_command are designed for scripting flexibility, they each do a small, low-level operation, to be chained together to achieve various tasks. However, they mainly output data files, there isn't much for text output currently. You could use -cifti-parcellate to parcellate your

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

Technically, what should matter more is what frequencies dominate the correlation in the data of interest - if they are lower enough in frequency than your sample rate (and therefore slice timing spread), then each latency should produce reasonable maps. However, this also means that when you

Re: [HCP-Users] Creating Custom dlabel File

Creating a label file from ROIs is a bit more complicated than a single command (label files automatically have a guarantee that the areas don't overlap, but arbitrary ROIs can overlap). >From what you currently have, one way to get to a new dlabel file is to concatenate the ROIs you want to use

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

d smoothing to get > things up to 3mm FWHM. > > Matt. > > From: Timothy Coalson <tsc...@mst.edu> > Date: Friday, September 1, 2017 at 3:02 PM > To: Matt Glasser <glass...@wustl.edu> > Cc: "Harms, Michael" <mha...@wustl.edu>, Daria Jensen <

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

Using that transform that flips X around the origin should put left on right and right on left, yes. Note, however, that the left and right parcel ROIs are not the same, so you will have to figure out how to handle the mismatched edges. I would not suggest -volume-parcel-resampling. If you want

Re: [HCP-Users] fMRISurface Pipeline FinalfMRIResolution Variable

I believe the pipelines generally expect isotropic resolution, yes. I don't think there is currently a way to use that variable to represent a non-isotropic resolution. However, there may be few (or no) steps that actually interpret that variable as a number and generate a new volume space using

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

In workbench, we do not do things this way at all. Putting both surfaces into a single file is neither necessary nor recommended, even for visualization. wb_view will happily display both left and right surfaces in a single tab, just load the surfaces as separate left and right gifti files.

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

*Cc:* hcp-users@humanconnectome.org > *Subject:* 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 <xavie...@mit.edu

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

I'm assuming you want them to match a standard grayordinate space, so that they can be compared across subjects. The simple way that doesn't account for residual subject differences in subcortical locations is to first resample the data to the appropriate resolution/orientation MNI space (222 for

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

colin are the best we can do at present for displaying the cerebellum as a surface. > Regards, > Claude > > On 03.08.2017 02:05, Timothy Coalson wrote: > > On Wed, Aug 2, 2017 at 6:02 PM, James Morrow <james.mor...@monash.edu> > wrote: > >> Thanks Tim and Matt fo

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

oss gifti surfaces to create a > so-called "average surface" > > Can I ask then, is averaging the data associated with vertices from > individual subjects and plotting the result on a template surface (eg colin > or a just using an individual as a template) also problematic?

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

School of Psychological Sciences > Monash University > c/o MBI, 770 Blackburn Road > Clayton VIC 3800 > Australia > > T: 03 9902 9768 > E: james.mor...@monash.edu <amy.al...@monash.edu> > www.med.monash.edu.au/psych/bmh/ > > <http://www.med.monash.edu.au/psy

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

I don't have a code snippet for you, but there is a separate "brain model" for each subcortical structure, which contains voxel indices. The "index map" that contains that brain model has the volume space information to turn them into coordinates in mm. Note that for the cortex, the CIFTI files

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

Hold on, you have gone past the point. CIFTI files *DO NOT CONTAIN* coordinates for surface vertices. Do not look for them in the header, they are not there. They are in gifti surface files (.surf.gii) that we provide alongside the cifti files. What Anand has done is use the fieldtrip matlab

Re: [HCP-Users] Clarification regarding DWI datasets

As some additional explanation, the reason there are multiple files in the unprocessed data is that we did not acquire all the directions in a single scan (that would have been excessively long). Instead, they are split across several scans, which are separate files before preprocessing. The

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

we do not take these coordinates through a volume warpfield twice - using the coordinates from the existing native mesh surfaces already in that volume space is much simpler. > The question is: > >- Is this now a correct interpretation? > > Regards, > > Claude > > On 24.07.

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

On Mon, Jul 24, 2017 at 8:40 AM, Claude Bajada wrote: > Dear all, > > I have a two questions about the surfaces that live in the HCP data > folders: > >1. MNINonLinear/fsaverage/ >2. T1w/fsaverageLR32k/ > > I assume you mean the fsaverage_LR32k folder within each

Re: [HCP-Users] Statistical comparison of whole brain (surface "voxels" + subcortical / cerebellar voxels) connectivity between two explicitly defined voxels

On Mon, Jul 17, 2017 at 6:21 PM, Regner, Michael < michael.reg...@ucdenver.edu> wrote: > Hello Matt and HCP Community, > > > > Thank you for the helpful e-mail and words of encouragement. We are very > encouraged by the data / results we can view in the Connectome Workbench; > however,

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

> on behalf of David Hartman < > dhartman1...@gmail.com> > Date: Monday, July 17, 2017 at 6:24 PM > To: Timothy Coalson <tsc...@mst.edu> > Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] mapping HCP data int

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

as the first map: https://balsa.wustl.edu/file/show/Q2xn Tim On Fri, Jul 14, 2017 at 2:42 PM, Timothy Coalson <tsc...@mst.edu> wrote: > We have a version of the 17-network Yeo parcellation here: > > https://balsa.wustl.edu/W8wK > > 163842 sounds like a freesurfer resolution

Re: [HCP-Users] saving one of the .dconn maps as a separate cifti?

The -cifti-separate command is for getting sections of a cifti file as gifti (single hemisphere) or nifti (volume) files, and it is generally not a good idea to run it on dconns. The -cifti-merge command is how you would do this on the command line, and you would give it the row index (though if

Re: [HCP-Users] Statistical comparison of whole brain (surface "voxels" + subcortical / cerebellar voxels) connectivity between two explicitly defined voxels

Connectome Workbench currently does not have tools designed for doing statistical inference. PALM is what we recommend, and it has support for CIFTI files. You can also use wb_command -cifti-convert -to-nifti to feed CIFTI data into FSL tools, if they don't use spatial information. Note that

Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found

Symbolic links don't require the folders to be on the same filesystem. The 'operation not supported' error seems unusual for making a symbolic link. Aside from the usual things to check (folder write permissions, whether there is already something there with that name), also know that windows and

Re: [HCP-Users] values from ROIs

You can combine the ROIs into a single map (with a different integer for each) with -cifti-reduce using INDEXMAX. You should then also mask out the areas that aren't in any ROI by using -cifti-reduce MAX on your ROIs file, and then using -cifti-math with 'index * (mask > 0)'. Finally, you need

Re: [HCP-Users] Custom visualisation help

Then when I'm trying to visualise it, I'm just loading it in and trying to > display over the atlas I'm using. > > Not sure if there's more info I can give. > > Thanks again for the help. > > Best wishes, > > Sean > > > On 21 June 2017 at 11:42, Timothy Coalson <t

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