Re: [HCP-Users] Fwd: Nifti2 extensions - are they converted correctly?

We appear to be padding to 8 bytes rather than 16, not sure how that happened. It should not affect us to change that (workbench doesn't care what the alignment is on reading), so I will make it pad to a multiple of 16 bytes. Tim On Mon, Aug 19, 2013 at 10:44 AM, Matthew Brett

Re: [HCP-Users] tfMRI in native space?

Surface adjacency information is only available through gifti surface files, as a list of triangles that make up the surface (each triangle has three vertex indices). You can use wb_command -cifti-separate to get the timeseries for full surfaces as a gifti metric file, which is easier to match to

Re: [HCP-Users] Q3 rfMRI

Sorry I didn't notice your comment about reverse engineering cifti, it is intended to be an open format, we do have documentation here: http://www.nitrc.org/projects/cifti/ In particular, http://www.nitrc.org/plugins/mwiki/index.php/cifti:ConnectivityMatrixFileFormatsdetails how things work in

Re: [HCP-Users] Questions about parcellated time series (ptseries)

You may be running into an unfortunate design problem in CIFTI-1, if NiBabel expects them to be standard NIfTI-2 - the dimensions are backwards in the header, so non-square matrices will have their elements rearranged. You may be able to get matlab to fix them via a reshape with the dimensions

Re: [HCP-Users] nibabel gifti files with workbench

From the .dtd on https://www.nitrc.org/projects/gifti/, I see this: Endian (BigEndian | LittleEndian) #REQUIRED From GIFTI_Surface_Format.pdf on the same site (which also echos the above on page 7), it looks like line breaks are also implicitly forbidden: The

[HCP-Users] Initial release of CIFTI-2 XML code

The initial release of the CIFTI-2 XML parsing/manipulating/writing code is available on the NITRC download page, http://www.nitrc.org/frs/?group_id=454. It additionally supports CIFTI-1 XML, but note that supporting CIFTI-1 requires dealing with reversed dimensions in the NIfTI-2 header (CIFTI-2

Re: [HCP-Users] nibabel gifti files with workbench

To finally follow up on this, we have not made source code available yet, but plan to with the next release (which will support CIFTI-2). Sorry about the delay (both source code and reply). Tim On Tue, Mar 4, 2014 at 9:47 AM, Glasser, Matthew glass...@wusm.wustl.eduwrote: I think we can

Re: [HCP-Users] Grayordinate data

As to your first question, it may currently be easier to use wb_command -cifti-separate to get the different hemispheres and voxels (either by structure or all in a single file) as separate GIFTI/NIFTI files. The GIFTI files made this way have direct correspondence to vertices in the relevant

Re: [HCP-Users] Grayordinate data

You could try using wb_command -surface-geodesic-rois, it will draw circular ROIs around vertices, as separate maps in a metric file. If you want them all in one map, the -overlap-logic option to that command, and the commands -metric-reduce, -metric-math and -metric-label-import may come in

Re: [HCP-Users] 0.85 is coming!!! Was: Workbench suddenly closes itself

As per the announcement, yes, it does include the source (on github, https://github.com/Washington-University/workbench, see releases for the code matching the released binaries), with some basic instructions for building (src/README - short version, we use cmake), a few tests of some simple

Re: [HCP-Users] activation region mask

If you have only one ROI, you could also look at the -cifti-average-dense-roi command: http://www.humanconnectome.org/software/workbench-command.php Tim On Tue, Apr 29, 2014 at 10:11 AM, Glasser, Matthew glass...@wusm.wustl.eduwrote: To convert the output of -cifti-math to a label file, use

Re: [HCP-Users] activation region mask

Sorry, didn't get the URL right: http://www.humanconnectome.org/software/workbench-command.php?function=-cifti-average-dense-roi Tim On Tue, Apr 29, 2014 at 1:18 PM, Timothy Coalson tsc...@mst.edu wrote: If you have only one ROI, you could also look at the -cifti-average-dense-roi command

Re: [HCP-Users] activation region mask

Date: Wednesday, April 30, 2014 at 3:15 AM To: Matt Glasser glass...@wusm.wustl.edu, Timothy Coalson tsc...@mst.edu Cc: Donna Dierker do...@brainvis.wustl.edu, hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: RE: [HCP-Users] activation region mask Thanks all for your

Re: [HCP-Users] activation region mask

to it for it to be usable in this case I think (and I think it should be added). Matt. From: Timothy Coalson tsc...@mst.edu Date: Tuesday, April 29, 2014 at 1:19 PM To: Matt Glasser glass...@wusm.wustl.edu Cc: Donna Dierker do...@brainvis.wustl.edu, Luo,Yishan lys84...@hotmail.com, hcp-users

Re: [HCP-Users] multiple versions of workbench

As some expansion on the preferences location, the organization we used is brainvis.wustl.edu, on linux the file is here: ~/.config/brainvis.wustl.edu/Caret7.conf Tim On Tue, May 6, 2014 at 5:51 PM, Timothy Coalson tsc...@mst.edu wrote: We use qt's preferences system, this describes where

Re: [HCP-Users] Probtrackx connectivity matrices

I don't think we currently have a command to warp the fiber orientations into a different space. It is possible in theory, and the matrix4 wouldn't need to be regenerated, but the fiber drawing locations won't line up with voxel centers anymore (this is cosmetic more than anything, but it bothers

Re: [HCP-Users] Probtrackx connectivity matrices

time. Tim On Fri, May 9, 2014 at 5:31 PM, Glasser, Matthew glass...@wusm.wustl.eduwrote: How would one then average across subjects (if that is why they wanted data in standard space)? Matt. From: Timothy Coalson tsc...@mst.edu Date: Friday, May 9, 2014 at 3:12 PM To: Matt Glasser

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

(and then z-transform and average the connectomes across subjects). There will be a better way in the future. Peace, Matt. From: Timothy Coalson tsc...@mst.edu Date: Monday, May 19, 2014 at 10:48 PM To: Ausaf Bari aus...@gmail.com Cc: hcp-users@humanconnectome.org hcp-users

Re: [HCP-Users] gifti labels to volume

Workbench currently doesn't have a way to do that. caret5 has a way to do this (caret_command -surface-to-volume, and there is another method called multi-fiducial mapping, though I'm not sure how to invoke it), though you may need to do some file conversion. On a side note, FSL's probtrackx

Re: [HCP-Users] Brain Connectivity Matrices

I believe we don't include those in the releases, because dense connectome files are very large (~30GB each). You should be able to generate them by running wb_command -cifti-correlate on a subject's rfMRI dtseries file. Tim On Tue, Jun 3, 2014 at 5:55 PM, Ommen, Jurgen omme0...@stthomas.edu

Re: [HCP-Users] Brain Connectivity Matrices

could use to get the network. Is there maybe a Matlab library available which is able to read .dconn.nii files? Thanks again for your help, Jürgen *From:* Timothy Coalson [mailto:tsc...@mst.edu] *Sent:* Wednesday, June 04, 2014 7:42 PM *To:* Ommen, Jurgen *Cc:* hcp-users

Re: [HCP-Users] Brain Connectivity Matrices

. Many thanks again for your help, Jürgen *From:* Timothy Coalson [mailto:tsc...@mst.edu] *Sent:* Friday, June 06, 2014 6:41 PM *To:* Ommen, Jurgen *Cc:* hcp-users@humanconnectome.org *Subject:* Re: [HCP-Users] Brain Connectivity Matrices First, a slight correction to my previous reply

Re: [HCP-Users] merge traj files

To finally answer this, no, -wbsparse-merge-dense does not have any sparse summation logic, it is meant only for the dense (brain models) dimension, for concatenation. We don't currently have a command to do such a summation, trajectory support is somewhat a work in progress. I don't know why

Re: [HCP-Users] Map index of dense connectome matrix to name of brain region

To expand on the wb_command part, the released versions don't have a friendly way to find that information, but that will be improved somewhat in the next release - the -file-information command will print some information from the XML in cifti files, including parcel names in cifti index order

Re: [HCP-Users] projecting functional MRI to gii surfaces

The inner and outer surfaces should be the white and pial surfaces to map all of cortex (of the same vertex count as the midthickness, so not the native surfaces). I believe we generally also use a volume mask to exclude things like CSF and noisy voxels, but I'm not sure exactly what it masks out

Re: [HCP-Users] question about connectome workbench

It isn't just a format conversion, it is a volume to surface mapping you need to do. See the -volume-to-surface-mapping command for the ways that wb_command can do this: http://www.humanconnectome.org/software/workbench-command.php?function=-volume-to-surface-mapping Tim On Thu, Jul 31, 2014

Re: [HCP-Users] Converting/analysing preprocessed rfMRI grayordinates

-cifti-separate is probably what you want, if you want to use spatial and/or surface neighbor information (because the indices in the metric files will line up with the relevant surface files). Also, with the v1.0 release, the -file-information command will give you a quick summary of the

Re: [HCP-Users] Inter-subject vertex:voxel correspondence

On Thu, Sep 25, 2014 at 9:00 AM, Matthew George Liptrot matthew.lipt...@di.ku.dk wrote: Hi, I am a novice at handling surfaces, and at using the Connectome Workbench/commandline, so apologies if the following is obvious. We want to be able to perform connectivity analysis of subjects

Re: [HCP-Users] Metric gradient giving only zeros

editing the HCP general pipeline but am getting stuck with naming convention issues. Is there a script somewhere else that I might have missed? Thanks, Konrad On 17 Oct 2014, at 21:07, Timothy Coalson tsc...@mst.edu wrote: The command should (and for me, does) work without telling

Re: [HCP-Users] Using Connectome Workbench Commands

Inline replies. Tim On Mon, Oct 27, 2014 at 10:26 AM, Nomi, Jason jxn...@miami.edu wrote: Dear Experts, I am trying to use the workbench commands but cannot get them to work. After opening the “wb_command” file in my linux terminal, I get the message printed below. Linux terminal? The

Re: [HCP-Users] Using Connectome Workbench Commands

, Ph.D. Post-Doctoral Researcher (BCCL Lab) Department of Psychology University of Miami 5151 San Amaro Drive: Room 114A Website: http://www.psy.miami.edu/bccl/ Email: jxn...@miami.edu -- *From:* Timothy Coalson tsc...@mst.edu *Sent:* Monday, October 27, 2014 5:38

Re: [HCP-Users] Distances between vertices in the cortical surface

and areas of the vertices are the same for all subjects? Thanks again! Ben On Thu, Nov 20, 2014 at 6:12 PM, Timothy Coalson tsc...@mst.edu wrote: No, we do not have a precomputed file of geodesic distances, we compute them on the fly in any operation that needs them. Using

Re: [HCP-Users] tfMRI masking, lateralization

You can do this on the surface for the cortex, you will probably want to use -cifti-separate to get the left/right pieces as separate files, then you can use -metric-math for difference/thresholding/masking/etc, and then -metric-vertex-sum with an -integrate option to get an answer in terms of

Re: [HCP-Users] Duplicate names in ${HCPPIPEDIR_Config}/FreeSurferAllLut.txt ?

Correct, it still produces a valid label file, even if it does sound rather annoyed. Side note, if it would have to go past _99 to resolve a name collision, it instead gives up and throws an error. I figured, if your label names collide that often, you must have done something you didn't mean to

Re: [HCP-Users] roi grayordinates time series

?function=-cifti-separate Tim On Wed, Feb 18, 2015 at 8:17 PM, Peka Savayan savay...@umn.edu wrote: Hi Timothy Coalson, Thank you for your response to my question. Can you please give me examples, along with the specific Workbench commands? I would like to get unaveraged time series

Re: [HCP-Users] 7 RSN Netoworks label file

The map name/number is not a label name, it is the map index or name that you select in the overlays toolbox in the gui, use 1 and it will probably give you what you want. A single map usually has multiple labels, specifically all the ones that get displayed at the same time in the gui. Tim On

Re: [HCP-Users] List of grayordinates belonging to each ROI-cifti parcellate

203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 Anyway, the count of vertices per parcellated roi is good enough for my purposes! Thank you very much and best regards OMD *From:* Timothy Coalson

Re: [HCP-Users] List of grayordinates belonging to each ROI-cifti parcellate

. --- Conte Center for the Neuroscience of Mental Disorders Washington 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 From: Timothy Coalson tsc...@mst.edu Date

Re: [HCP-Users] List of grayordinates belonging to each ROI-cifti parcellate

In the dlabel.nii file, this information is in the data matrix, not the header. One way to get this information is from the header of a ptseries.nii file (or other parcellated file type) resulting from parcellating with it. The -file-information command should report the counts of vertices

Re: [HCP-Users] roi grayordinates time series

Those pieces of information reside in separate files. The mapping of what area each vertex/voxel belongs to exists in the data of this cifti dlabel file: ${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.aparc.a2009s.32k_fs_LR.dlabel.nii The various fMRI timeseries are in cifti

Re: [HCP-Users] Using MarsBar on HCP data

You can get cifti data into matlab fairly easily (I mention matlab because you mentioned SPM, which uses matlab), see this FAQ entry: https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB? Depending on how your ROIs are specified, you may

Re: [HCP-Users] roi grayordinates time series

As in my previous answer, the best way to get them into matlab is to pick an option from this FAQ entry: https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB? In either case, you will need to install some toolboxes into matlab, and you

Re: [HCP-Users] Group average rfRMI - demean, variance normalize, concatenate OR demean, concatenate, then variance normalize?

fsl doesn't support CIFTI files yet. What you want for those is wb_command -cifti-merge: http://www.humanconnectome.org/software/workbench-command.php?function=-cifti-merge Tim On Tue, Mar 24, 2015 at 4:18 PM, Farrant, Kristafor kxf...@miami.edu wrote: Thanks! I should be able to use

Re: [HCP-Users] projecting from volume to R440 template (subcortical and cerebellum)

with CIFTI. Peace, Matt. From: Yizhou Ma maxxx...@umn.edu Date: Sunday, March 1, 2015 at 9:27 PM To: Timothy Coalson tsc...@mst.edu Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] projecting from volume to R440 template (subcortical

Re: [HCP-Users] creati cifti from nifti1

We are going to need a bit more information than that, I don't know what you mean by subcortical data is not separated from the surface, do you mean that the cortex data is represented in voxels in the cifti file also? You should be using the -left-metric and -right-metric options for the surface

Re: [HCP-Users] Plot analysis results on HCP resting state fMRI data

We need to know what format your data is currently in to give a definitive answer, but I'm going to guess matlab, as we have provided code for it to load cifti files, which you appear to have done. The matlab code we provide also allows for saving data back out into cifti files, latest version

Re: [HCP-Users] Problem with wb_command -volume-parcel-resampling? dimension mismatch?

Your data is RPI, but both label volumes are LPI. The -generic version doesn't accept that either, the current labels must be in the same volume space as the data. Maybe when you pulled the first volume off the data, it changed something? Use -volume-reorient to get them to match, and it works.

Re: [HCP-Users] from volume to gifti file to cifti roi

You can always get help for an individual command by running it without any arguments, and you can list the commands and only a short description with -list-commands. You can also browse the commands here: http://www.humanconnectome.org/software/workbench-command.php In this case, you will want

Re: [HCP-Users] Downsampled grayordinate data?

An additional note on downsampling: when using the ADAP_BARY_AREA surface resampling, you do not need to smooth before downsampling (it will not lose data that falls between the sampling points). However, with downsampling volume data, the available methods do require some presmoothing to avoid

Re: [HCP-Users] Converting new group average connectome

On Tue, May 12, 2015 at 4:34 AM, Estrid Jakobsen ejakob...@cbs.mpg.de wrote: Dear all, I've just downloaded the newly released corrected 468 group average connectome file, HCP_S500_R468_MIGPd4500ROW.dconn.nii, and I have two questions: 1. I would like to convert this file to a binary gifti

Re: [HCP-Users] where are the head shape file for MEG

Back on this other question, wb_command indeed does not do decimation of the remove vertices from existing topology variety. The usual way to do surface downsampling with wb_command is to generate a new sphere with the desired number of vertices (and highly regular topology/spacing), and then

Re: [HCP-Users] where are the head shape file for MEG

topologies to the original ones or not? If it is possible, how could it be achieved? Cheers, Denis 2015-05-19 0:57 GMT+02:00 Timothy Coalson tsc...@mst.edu: Back on this other question, wb_command indeed does not do decimation of the remove vertices from existing topology variety

Re: [HCP-Users] Multithreading in wb_command?

Setting the OMP_NUM_THREADS environment variable to 1 will make it use only 1 core. Tim On Sat, Jun 6, 2015 at 4:43 AM, Daniel P. Bliss dbl...@berkeley.edu wrote: Hi HCP Users, There appear to be commands within PostFreeSurferPipelineBatch that use multi-threading, because my call to this

Re: [HCP-Users] how to manage compute threads?

Some operations in wb_command automatically use OpenMP without being enabled by an argument, using however many cores it can find. You can change the number it uses by setting the environment variable OMP_NUM_THREADS. I'm not as sure about multithreading in other software used in the scripts.

Re: [HCP-Users] CIFTI files for testing CIFTI support

We have some example files here that cover each mapping type at least once: http://www.nitrc.org/frs/?group_id=454 If this is the pull request you are starting from, the cifti files from it appear to already be in it, search for ones and you will see 5 binary files:

Re: [HCP-Users] CIFTI files for testing CIFTI support

on them, perhaps we should. Tim On Thu, Jun 25, 2015 at 3:47 PM, Matthew Brett matthew.br...@gmail.com wrote: Hi, On Thu, Jun 25, 2015 at 1:22 PM, Timothy Coalson tsc...@mst.edu wrote: We have some example files here that cover each mapping type at least once: http://www.nitrc.org/frs

Re: [HCP-Users] displaying more than three layers of activations

On one of the layers, click the yellow construction button, and choose add overlay above or add overlay below. Tim On Sun, Jun 14, 2015 at 2:07 PM, Longchuan Li leonad...@yahoo.com wrote: Hi, HCP users Could someone tell me how I can display more than three layers of functional activations

Re: [HCP-Users] User-provided colormaps for wb_view?

For data to be displayed on a logarithmic scale, we have had a small amount of discussion of doing the log transform on the fly, though considering that -*-math will do this easily with the main drawback being filesystem use, it hasn't been a priority. As for faking it with a log-scale palette,

Re: [HCP-Users] Extracting motor cortex ROI from the tfmri data

We recommend analyzing cortical data on surface representations, and this is reflected in the formats we use for our released data, so files ending in .nii.gz will generally not contain useful ROIs for this purpose, as they are volume files. We have cifti label files,

Re: [HCP-Users] Freesurfer parcellation - list of coordinates

I would agree that center of gravity doesn't seem all that useful a measure of a parcel, which is why parcellated cifti files contain the information of the entire ROI of each parcel. Note that the center of gravity may lie significantly outside the surface if the ROI is large and covers

Re: [HCP-Users] downsample

That command is meant for that purpose, yes, but you will first need to use one of the -cifti-create-* commands to make a template cifti in the downsampled space (you can use things like -surface-vertex-areas, -volume-create, and -volume-affine-resample to get the needed inputs for a

Re: [HCP-Users] Converting the huge dense connectome to a csv

The only thing -cifti-convert generally tries to preserve is the data matrix, all the header info is not retained, and to convert it back, most formats require a template cifti file that has the appropriate header info. You can get the relevant header info with the -cifti-export-dense-mapping

Re: [HCP-Users] Cifti to gifti conversion

-cifti-convert is not intended to make files that will work nicely as single-surface files, it is more of a hack for software that can't read cifti yet: -cifti-convertDUMP CIFTI MATRIX INTO OTHER FORMATS The -cifti-separate command is how you take a structure from a cifti file and

Re: [HCP-Users] Custom parcellation for HCP data

Additionally, if you generate a cortex-only parcellation, you shouldn't need to put it into a volume to use it with the HCP CIFTI data. However, I'm not sure how to get freesurfer to write GIFTI label files, and unless you generate it on the fs_LR 32k mesh, you'll need to resample it (via

Re: [HCP-Users] workbench plugin development

As further information, the example in that directory is very out of date, as CiftiXMLReader is an older implementation (which doesn't support cifti-2) that we haven't entirely replaced yet. Take a look at CiftiFile instead for a more convenient interface that does support cifti-2. You can also

Re: [HCP-Users] visualisation via WB

The MEG data uses a different surface resolution than the MRI data, so the MRI spec file and data cannot be visualized in the same instance of workbench. You were on the right track with what you did first, opening the *.surf.gii and related MEG data files. You may need to switch the viewing

Re: [HCP-Users] Acquire text file with averaged volume time series for subcortical structures from cifti file

-cifti-separate can't do any averaging, that isn't its purpose. Instead, you can use -cifti-stats and the roi of the amygdala to do such an average: #what you already did, for the purpose of getting the ROI wb_command -cifti-separate tfMRI_EMOTION_LR_Atlas.dtseries.nii COLUMN -volume

Re: [HCP-Users] Acquire text file with averaged volume time series for subcortical structures from cifti file

then I figure that would get me the averaged time > series. > > > If that is not possible, I am unclear where the file in the second step, > "tfMRI_EMOTION_LR_Atlas.dtseries.nii > roi_left_amygdala.dscalar.nii", comes from. > > > Thanks for the help - >

Re: [HCP-Users] Acquire text file with averaged volume time series for subcortical structures from cifti file

; > Thanks so much for the help! > > > > I have one final question: > > > I assume that this ROI is from the freesurfer subcortical segmentation? > > > > > > > > -- > *From:* Timothy Coalson <tsc...@mst.edu> > *Sen

Re: [HCP-Users] Acquire text file with averaged volume time series for subcortical structures from cifti file

> > wb_command -cifti-stats 30_min.dtseries.nii -reduce MEAN -roi > roi_left_amygdala.dscalar.nii > > > > > Thanks for your patience on this Tim - > > > > -- > *From:* Timothy Coalson <tsc...@mst.edu> > *Sent:* Tuesday, September 1, 2015

Re: [HCP-Users] Acquire text file with averaged volume time series for subcortical structures from cifti file

The code I am using for the second step: > > wb_command -cifti-create-dense-from-template 30_min.dtseries.nii > roi_left_amygdala.dscalar.nii -volume AMYGDALA_LEFT > roi_left_amygdala.nii.gz -from-cropped > > > > Any advice on what is happening? > > Jason > > >

Re: [HCP-Users] NaNs after merging dconn files

I don't suppose you're seeing NaNs specifically in matlab after using ft_read_cifti? I don't know of anything else that is expected to add NaNs. Could you do wb_command -cifti-reduce your dconn MEAN mean.dscalar.nii and then do -file-information on that? If that shows NaNs, I suggest also

Re: [HCP-Users] How to extract time course for a volume voxel with MNI coordinate

So, 2/3 of the spatial locations in HCP CIFTI files are not voxels, only the cerebellum and subcortical structures are represented as voxels. I'm not all that familiar with the structure that ft_read_cifti returns, but it should have the information needed to translate between data matrix indices

Re: [HCP-Users] HCP_S500_R468_MIGPd4500ROW.dconn.nii

I'm not clear on what you actually want to do. Timeseries are in the .dtseries.nii file, not in the .dconn.nii file. How to use an ROI as a mask depends on what you want to do with it, but you can use it to average contained rows together with -cifti-roi-average. You can get the closest vertex

Re: [HCP-Users] 4D CIFTI file for PALM random-effects analysis

wb_command -cifti-merge takes the output filename first, then you repeat "-cifti " for each input file (which is why in the help the -cifti option is marked as repeatable), in the order you want them concatenated. The help information for -cifti-merge includes this example and explanation:

Re: [HCP-Users] help

I don't know what the mat attribute is, as it doesn't seem to correspond to anything that exists in a normal gifti surface file. The other two arrays are the floating point coordinates of each vertex, and the sets of three integer vertex indices that make the triangles between the vertices. I

Re: [HCP-Users] help

CIFTI files store data on a combination of surface and volume representations, so first you need to know (roughly) what structure the thing you are looking for is on. Currently, the options are left cortex, right cortex, and everything else is represented as voxels. If all you have to start with

Re: [HCP-Users] How to use TransformationMatrixVoxelIndicesIJKtoXYZ

As you said, the voxels in cifti files are stored by their integer indices as if they were in a volume file, so to get their location in space, you need a transformation matrix, similar to the nifti sform. This is exactly what the TransformationMatrixVoxelIndicesIJKtoXYZ element is. The simple

Re: [HCP-Users] create borders based on .dlabel files

The -label-to-border command requires gifti label files, as it does one surface at a time - there is not a cifti version of this command (because border files are surface only and single hemisphere, and there is no equivalent volume operation). So, first -cifti-separate to get gifti label files:

Re: [HCP-Users] How to draw points on the brain surface

Consider this command: http://www.humanconnectome.org/software/workbench-command.php?function=-surface-closest-vertex You can draw ROIs around the identified vertices on the surface with this command: http://www.humanconnectome.org/software/workbench-command.php?function=-surface-geodesic-rois

Re: [HCP-Users] mapping correlations on a template

If your .csv file matches a particular .dlabel.nii file, what you could do is use -cifti-parcellate to generate a template parcellated cifti file, and then use -cifti-convert -from-text to put the data into that format (you will need to strip off the labels first, leaving only the numbers, after

Re: [HCP-Users] Having problems with installing aspera, upgrade chromium, download data for doing tutorials with workbench....

With a .sh file, you don't use "apt-get install", it is a script that you run directly in a terminal: tim@timsdev:~/Downloads$ ./aspera-connect-3.6.0.106805-linux-64.sh Installing Aspera Connect Deploying Aspera Connect (/home/tim/.aspera/connect) for the current user only. Restart firefox

Re: [HCP-Users] connectome in a box disk configurations

:41 PM, Timothy Coalson <tsc...@mst.edu> wrote: > Creating any kind of raid array on a disk nearly always involves labeling > the disk with the raid configuration, which probably overwrote the > partition table (and is hidden from the exposed raid-0 "disk", causing the >

Re: [HCP-Users] Hcp Data with non-overlapping parcellations

rned about is not so much the labels for > Key=0, but that some of the other vertices have different labels – see > lines 22-27 below: > A B > 10 10 > 29 29 > 24 24 > 28 28 > 11 11 > 31 31 > 27 27 > 0 -1 > 13 13 > 15 15 > 35 35 > 35 35

Re: [HCP-Users] ERROR: surface exceeds the bounding box of the warpfield

I'm not sure what could have gone wrong in the script, but as you may have guessed, that error means the input surface to -surface-apply-warpfield is too large for the specified warpfield volume, and thus some vertices would have undefined coordinates if it proceeded with the transformation. Tim

Re: [HCP-Users] ERROR: surface exceeds the bounding box of the warpfield

/standard2acpc_dc.nii.gz Pipelines_ExampleData/C10/T1w/T1w_acpc_dc_restore.nii.gz And upload them here: http://brainvis.wustl.edu/cgi-bin/upload.cgi Tim On Wed, Jan 6, 2016 at 4:04 PM, Timothy Coalson <tsc...@mst.edu> wrote: > I'm not sure what could have gone wrong in the script, but as you

Re: [HCP-Users] error in loading spec file

As a short-term fix, you could add an additional "../" to the start of those paths, and it would likely find it (because the main thing that appears wrong with the path is that "data" shows up twice). We have identified a few troublesome aspects of spec file relative path handling (especially

Re: [HCP-Users] CIFTI and NIFTI -parcellating rfMRI

The .nii.gz files are nifti-1 volumes, while the .dtseries.nii files are Cifti files. If you need spatial information, converting Cifti to nifti-1 is not the way to go about it, instead you could use wb_command -cifti-separate into metric (.func.gii, one per hemisphere) and volume files, or use

Re: [HCP-Users] Trying to read HCP_S500_R468_MIGPd4500ROW.dconn.nii

gt; On Mon, Nov 23, 2015 at 9:14 PM, Rose Tharail John < > mailboxofr...@gmail.com> wrote: > >> Thank you! >> >> On Mon, Nov 23, 2015 at 3:03 PM, Timothy Coalson <tsc...@mst.edu> wrote: >> >>> To get a dconn loaded in matlab, you of course n

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

If you are using -cifti-correlation, there is a -mem-limit option for this purpose, so there isn't a required minimum memory to do it (even in matlab where everything has to be in memory, the 90k x 4.8k timeseries input pales in comparison to the 90k x 90k output). If you are doing everything in

Re: [HCP-Users] Convert NIFTI to CIFTI

The -cift-convert command is only files that are organized the way cifti is - the data in question has to have already been in cifti space before using the command will do anything for you. The nifti files written and accepted by the command are "fake" nifti files, they only superficially

Re: [HCP-Users] Trying to read HCP_S500_R468_MIGPd4500ROW.dconn.nii

To get a dconn loaded in matlab, you of course need to have a large amount of available memory. Freezing is what I would expect if you don't have enough memory, and start using a lot of swap space (some ways of loading might initially load it as double precision, and need twice the memory). As

Re: [HCP-Users] CIFTI and NIFTI -parcellating rfMRI

ine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: mha...@wustl.edu > > From: Joelle Zimmermann <joelle.t.zimmerm...@gmail.com> > Date: Wednesday, November 25, 2015 2:40 PM > To: Timothy Coalson <tsc...@

Re: [HCP-Users] create borders based on .dlabel files

to get the color table. Is there a way I can > save a border file with my own color table? > > Thanks, > Cherry > > On Mon, Nov 30, 2015 at 4:01 PM, Timothy Coalson <tsc...@mst.edu> wrote: > >> The -label-to-border command requires gifti label files, as it d

Re: [HCP-Users] Hcp Data with non-overlapping parcellations

Sorry, the -*-label-export-table commands don't put the unlabeled key in the text file. Use -file-information on them instead to check what key value the "???" label is (it means the unlabled value). Tim On Wed, Nov 18, 2015 at 12:54 PM, Timothy Coalson <tsc...@mst.edu>

Re: [HCP-Users] Location of CIFTI vertices in standard space

On Thu, Jun 9, 2016 at 5:49 AM, Thomas Nichols wrote: > Hi Tim, > > Thanks for taking the time to delve into this. > > wb_command does have surface to volume mapping now. >> > > Just to be clear, which command are talking about? Using the output of > wb_command

Re: [HCP-Users] Location of CIFTI vertices in standard space

Yeah, that command should have the structure strings in the help info, I'll add that. However, I would not say that brainordinates inherently have an "exact location" in terms of XYZ coordinates, they have different coordinates in each subject. We try to register them so that the brainordinates

Re: [HCP-Users] geodesic-distance

It is possible to get a center of gravity of a surface ROI, but it is more involved (and doesn't result in a vertex). We don't really use ROI centers, as the entire ROI is generally more informative. See: https://www.mail-archive.com/hcp-users%40humanconnectome.org/msg02495.html With the

Re: [HCP-Users] Questions about Run Diffusion Preprocessing Parallelly

Many of the executables and operations in the pipelines do not use parallelization across cores within a single subject. You may be better off setting up a queue with fewer cores available per slot, and submitting many subjects at once to the queue. Make sure you set the queue name correctly in

Re: [HCP-Users] The grayordinates adjacent to the medial wall

We do have -metric-erode now (and volume, label, cifti). You can also do this more generally for any cifti file (for instance a custom grayordinate space) by using the -roi options in -cifti-separate. Tim On Tue, Jun 21, 2016 at 1:56 PM, Glasser, Matthew wrote: > You

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