>
> I hope this helps. Note, I didn’t include the file Tim mentioned that you
> would already in your download folders.
>
> Regards,
>
> Mike
>
> *From:* hcp-users-boun...@humanconnectome.org [mailto:hcp-users-bounces@
> humanconnectome.org <hcp-users-boun...@humanconnect
-MH
>>
>>
>>
>> --
>>
>> Michael Harms, Ph.D.
>>
>> ---
>>
>> Associate Professor of Psychiatry
>>
>> Washington University School of Medicine
>>
>> Department
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
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
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
>
> On Sat, Mar 17, 2018 at 8:22 PM, HERACLES PANAGIOTIDES <he...@uw.edu>
> wrote:
>
>> Tim,
>>
>> Thank you very much for taking the time to reply. I am hoping to be able
>> to resolve this issue with FSL. I have no experience with the Workbench
>
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:*
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
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
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
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
You can export the data from the parcellated cifti file with wb_command
-cifti-convert -to-text, but that doesn't contain the parcel names. The
-file-information command will tell you the parcel names, in the order they
are in the file, giving you the missing piece.
Tim
On Thu, Jun 28, 2018,
Also note that for viewing purposes, wb_view can generate the correlation
maps on the fly, rather than needing the large dconn file generated in
advance - the dconn is generally only needed if you want to do further
processing on the correlations.
Tim
On Thu, Sep 27, 2018 at 3:32 PM, Zhuochen
That implies that when launched by matlab, it is either not finding QT
libraries at all, or finding a version it doesn't work with.
Are you using linux? Are you using a zip distribution downloaded from the
website (as opposed to neurodebian or the older default version the
distribution may
There are two steps you need to do, and you can do them in either order:
put the label names into the data file in the way workbench expects, and go
from volume to cifti format. I would probably do it as making a
workbench-style label volume file first:
1) wb_command -volume-label-import
2)
The cifti format doesn't support that, because it is designed to allow use
without loading the entire file into memory - there is no obvious file
organization that would allow efficient loading of a full row from a single
triangular file, when seek times are nontrivial (rotating disks). I don't
, Mike
wrote:
> Yep, using the version in bin_linux64 from the zip fixes things.
>
>
>
> Thanks
>
>
>
> -Mike
>
>
>
> *From:* hcp-users-boun...@humanconnectome.org humanconnectome.org> *On Behalf Of *Angstadt, Mike
> *Sent:* Wednesday, October 24, 201
That looks correct, though it uses more file space than needed. I don't
know that we have tested asymmetric dconns thoroughly, this may be a bug in
wb_view - you are supposed to be able to click on hippocampus, same as in
step 4, and see the result in another tab set to surface, montage, or all,
The structures to specify to the -label option are CORTEX_LEFT and
CORTEX_RIGHT (use the -label option twice).
Tim
On Tue, Oct 30, 2018 at 6:35 PM, Glasser, Matthew
wrote:
> Also use the label ones to make GIFTI label files.
>
> Matt.
>
> From: Leonardo Tozzi
> Date: Tuesday, October 30,
If your swap space isn't on an SSD, then it will be extremely slow to do
anything on it.
Tim
On Wed, Oct 24, 2018 at 7:19 PM, Glasser, Matthew
wrote:
> Use swap space.
>
> Matt.
>
> From: on behalf of Timothy
> Coalson
> Date: Wednesday, October 24, 2018 at 4:57 PM
>
y so long as they are the same resolution everything
> should work. We have tested on 0.8mm human data and 0.5mm monkey data.
>
> Matt.
>
> From: Timothy Coalson
> Date: Friday, November 9, 2018 at 3:53 PM
> To: "Jayasekera, Dinal" , Matt Glasser <
> glass...@
t; *To: *Leonardo Tozzi , NEUROSCIENCE tim <
> tsc...@mst.edu>
> *Cc: *Stamatios Sotiropoulos ,
> hcp-users
>
> *Subject: *Re: [HCP-Users] Diffusion connectivity matrix with cortical
> and subcortical parcellation
>
>
>
> I think that --omatrix1 always outp
GrayOrdinates.txt ?
>
>
>
> Thank you very much,
>
>
>
>
>
> Leonardo Tozzi, MD, PhD
>
> Williams PanLab | Postdoctoral Fellow
>
> Stanford University | 401 Quarry Rd
> <https://maps.google.com/?q=401+Quarry+Rd=gmail=g>
>
> lto...@stanford.edu
atrix by taking
> the upper triangle. I think it should track from all my ROIs to all my
> ROIs.
>
> Concerning wb_command -probtrackx-dot-convert, it requires a few inputs
> but I am not sure what files to use.
>
> I hope this adds more information, thank you very much,
>
>
>
>
>
There is wb_command -probtrackx-dot-convert which should be able to convert
the fdt_matrix1.dot file, which should allow a better visualization of the
results. I'm not entirely clear on the arguments to your probtrackx
command, or what the actual ROIs you used are, but it looks like they were
rtment of Biomedical Engineering | Washington University in St. Louis
>
> --
> *From:* Timothy Coalson
> *Sent:* Thursday, November 8, 2018 6:03:10 PM
> *To:* Jayasekera, Dinal
> *Cc:* Dierker, Donna; hcp-users@humanconnectome.org
>
> *Subject:* Re: [HCP-
es definitely not. I also upgraded my R packages.
> >
> >
> > Kind regards,
> > Dinal Jayasekera
> >
> > PhD Candidate | InSITE Fellow
> > Ammar Hawasli Lab
> > Department of Biomedical Engineering | Washington University in St. Louis
> >
>
Hawasli Lab
> Department of Biomedical Engineering | Washington University in St. Louis
>
> --
> *From:* Timothy Coalson
> *Sent:* Monday, November 12, 2018 4:04:33 PM
> *To:* Jayasekera, Dinal
> *Cc:* Glasser, Matthew; Dierker, Donna
*To:* NEUROSCIENCE tim
> *Cc:* Jayasekera, Dinal; Dierker, Donna; hcp-users@humanconnectome.org
>
> *Subject:* Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh
>
> We should change that line to use this file:
>
> ${StudyFolder}/${Subject}/MNINonLinear/brainmask_fs.nii.gz
>
If by "convenient" you mean "not cifti", then wb_command -cifti-separate
will allow you to get gifti surface label files. If you mean "binary
ROIs", use wb_command -cifti-all-labels-to-rois (and then -cifti-separate
if you want them in gifti format).
If you mean "volume files", we do not
-cifti-convert does not do this, it only dumps the matrix into different
file formats as-is, the spatial relationships are not accessible from its
output.
If you are only interested in subcortical/cerebellum data, that is trivial
to extract from cifti as a volumetric nifti using -cifti-separate
- are these the tfMRI timeseries data already
> converted to 91282 greyordinate space (ie could I use these files in lieu
> of trying to convert the tfMRI_MOTOR_LR.nii files from 91x109x91 space to
> greyordinate space)?
>
> Best,
> Cathy
>
> Am Di., 2. Okt. 2018
You need to update workbench to the latest release, that option is a recent
addition to the command that is failing.
Tim
On Tue, Oct 9, 2018 at 6:08 PM, ARMAN PRAFUL KULKARNI
wrote:
> Hi,
>
> I have been running the HCP Pipeline (v 3.27.0) on one subject's
> unprocessed data from the HCP-1200
If you mean the fact that the HCP MMP v1.0 doesn't include any subcortical
indices, you can use "wb_command -cifti-create-dense-from-template" to
expand it to the standard 91282 grayordinates. However, the
-cifti-parcellate command will allow you to use it on standard 91282
grayordinate data
quick reply. I'm not quite sure I understand what your
> recommended course of action. I've attached the affine for one of the
> patients I ran the pipeline on. Based on the .mat file I've attached, what
> would you recommend to be my next best course of action?
> ---------
If the volume files are per-individual results, then mapping them to that
individual's own MSMAll surfaces will result in them being accurately
registered through multimodal surface matching, yes. I am not clear on the
"SubjID=300" line, though.
To be clear, group average "subjects" do not count
s still mostly spherical.
Tim
On Fri, Sep 28, 2018 at 1:49 PM, Timothy Coalson wrote:
> That warning message does not prevent the command from generating its
> output. It is generated by wb_command -surface-modify-sphere. I am not
> sure why it would be tripped during PostFreeSurfer,
That warning message does not prevent the command from generating its
output. It is generated by wb_command -surface-modify-sphere. I am not
sure why it would be tripped during PostFreeSurfer, though, as the main
thing that might trip it is dedrifting (which should be done only when
making a new
The surfaces are fine, we generally recommend very_inflated for viewing
data. To expand on what Matt said, the data in the map you are displaying
in that image appears to have an unusual distribution, with most values
near the minimum value, and a few spots with higher values (or perhaps the
To clarify the phrasing: the existing release doesn't have a way to change
the size of these symbols. We will consider making the size controllable
in the next release, but that may be a while off.
Tim
On Wed, Oct 10, 2018 at 12:15 PM, Harwell, John wrote:
> When drawing a border, I am able
I'd probably need to see the dlabel file being used. -cifti-parcellate
doesn't seem to have changed much recently. Can you do -file-information
on the dlabel file and paste the result?
Tim
On Mon, Oct 1, 2018 at 6:59 PM, Keith Jamison wrote:
> Whenever I try to run wb_command
here (
> https://wiki.humanconnectome.org/display/PublicData/HCP+
> Users+FAQ#HCPUsersFAQ-16.Ca) to get the resting-state data back into
> native volume space.
>
> Thanks again!
> Jacob
>
> On Mon, Oct 1, 2018 at 1:29 PM Timothy Coalson wrote:
>
>> As a fina
You are not intended to double click wb_command or wb_import, they are
utilities that are used from a terminal or script (generally, after adding
their location to your $PATH, per the install instructions in README.txt).
Double clicking them from a folder window is expected to make a window that
You should generally only need the number from the label file when
manipulating files with tools other than workbench (or when altering a
label file). You can get the list of all labels, keys, and colors from a
dlabel file with wb_command -cifti-label-export-table .
Tim
On Mon, Oct 8, 2018 at
I would also question what you hope to accomplish by using the native
freesurfer mesh - the fMRI data doesn't have that kind of resolution, and
the result of resampling to it means you can't compare across subjects
without resampling again later. Surface resampling is also unlike volume
of this data), this effect should be
small.
Tim
On Mon, Oct 1, 2018 at 3:22 PM, Timothy Coalson wrote:
> I would also question what you hope to accomplish by using the native
> freesurfer mesh - the fMRI data doesn't have that kind of resolution, and
> the result of resampling to it
Yes, that is the problem. Somehow, the ROI cifti file was created without
a cortical mask that excludes the medial wall. The quick way to solve this
is to use -cifti-create-dense-from-template, which ensures its output
matches the indices of the template file (but can take many different types
th TFCE for cortical surfaces:#*
>
> palm -i Y_left.func.gii -i Y_right.func.gii -d ../design.mat -t
> ../design.con -o results_dense_cortical -n 500 -corrcon -corrmod -C 2.3
> -Cstat "extent" -fdr -logp -accel tail -T -tfce2D -s
> L_midthickness.sur
-cifti-cross-correlation is for when you want to correlate between two
different files. If you want roi-to-roi correlations, it is not the best
way to get them.
The easy way to get roi-to-roi correlations is to use -cifti-parcellate and
then -cifti-correlation. However, you first need to
'rms' appears to be part of the signal toolbox. 'normalize' seems to be a
built-in matlab function, but I have no idea about 'normalise'.
Tim
On Wed, Sep 19, 2018 at 11:15 AM, Glasser, Matthew
wrote:
> I believe rms is a matlab provided function. The custom functions are in
> here:
The purpose of the surface ROIs in -cifti-create-label is to prevent the
cifti file from needing to represent data inside the medial wall (where it
would generally be nonsensical). Since you haven't converted the data to
any kind of label format yet, it is not the command you want - putting the
e other supporting program?
>
>
> Kind regards,
> *Dinal Jayasekera*
>
> PhD Candidate | InSITE Fellow
> Ammar Hawasli Lab
> Department of Biomedical Engineering | Washington University in St. Louis
>
> --
> *From:* Timothy Coalson
> *Sen
The easiest to use (especially if your goal is to match other cifti files)
is generally -cifti-create-dense-from-template. It will even turn a 59k
surface-only cifti into a standard 91282 cifti (or vice versa, if you are
so inclined).
Yes, -cifti-export-dense-mapping will give you the cifti
To expand on Jenn's answer, one way to see what wb_command does on windows
is to open "command prompt", cd to the "bin_windows64" folder where you
unzipped workbench, and then type "wb_command" and press enter.
If you do as the README.txt suggests and add that folder onto your PATH
environment
Scene files are not a vector format internally, they store the entire GUI
state of wb_view (loaded files, window sizes, tab types and order, order of
layers in tabs, palette settings), and when they are displayed (or captured
via wb_command), the data files are loaded and all the display logic in
The strongest directional information in the diffusion data is in the white
matter, so I assume you are computing some measure from the scans and
specifically want to study its value only in gray matter?
The main command for this purpose is wb_command -volume-to-surface-mapping,
and we recommend
BALSA was designed to support data use terms, not only does it have the HCP
data use terms available for easy selection when submitting a study, it
also allows entering other data use terms (so it can support non-HCP
datasets that require agreement to terms).
The HCP data use terms may not
Cifti files are defined not only by their resolution, but also by ROIs that
exclude uninteresting or redundant locations, in particular the medial wall
vertices and white matter voxels for fMRI. This is the reason that
-cifti-resample needs a template, to define what is included/excluded.
I'm
As for your second question, the transform between MNINonLinear and
"Native" space (actually, undistorted, rigid registered) is a nonlinear
warpfield, not a 4x4 matrix (affine). As I recall, we ignore the 4x4
matrices in gifti surface files (.surf.gii), as they have caused more
trouble than good.
Try doing:
system('/wb_command');
Except using the exact string you are providing to ciftiopen's second
argument. You should get the usage information for wb_command if the path
is correct and things are working.
Tim
On Thu, Jan 17, 2019 at 4:38 PM Anita Sinha wrote:
> Matt/Michael,
>
>
>
If you save those vectors of values as .func.gii files (maybe this is how
you made the .func.gii files you have?), you can use wb_command
-metric-label-import to turn them into .label.gii files:
https://www.humanconnectome.org/software/workbench-command/-metric-label-import
To get them onto HCP
; I set the second parameter as null and the color was created as default.
> Is there an example of the text file of the label-list file. I used the
> file as attachment but failed. Is there any problems with this file?
>
> Thank you so much.
>
> Best wishes
> -
> Zaixu
>
>
&
enley, Jeanette
> *Cc:* hcp-users; Kaplan, Sydney
> *Subject:* Re: [HCP-Users] average dconn from individual dconns
>
> To be more specific: In the HCP we use a technique called MIGP to make
> group fMRI data and generate dense connectomes from that. Concatenated
> dense ti
t; But there are 10 more vertices in right hemisphere than left hemisphere
>>> ...
>>>
>>>
>>> On Tue, Nov 20, 2018 at 2:50 PM Glasser, Matthew
>>> wrote:
>>>
>>>> Left and right are registered.
>>>>
>>>>
The HCP MMP v1.0 parcellation is defined on MSMAll-registered surfaces. I
am not familiar with FSFAST, but if it gives you surface-based data, you
should be able to resample the data or parcellation so that they are on the
same mesh, following these instructions:
ifti file should also include the subcortical regions, right?
> Do I need to combine the left and right surface and subcortcial volume into
> one cifti file? Sorry for the very basic questions. Thank you very much.
>
> Best wishes,
>
> Zhi Li
>
> On Tue, 27 Nov 2018 at 16:09, Timothy
The HCP pipelines deliberately resample the subcortical data in such a way
that the subcortical voxels used in each subject are the same, this is how
we handle the problem you are having.
If you concatenate your timeseries across subjects before correlation, you
don't need to generate a dconn for
> apparently this is not the case! Any reason for this?
>
>
> On Fri, Nov 16, 2018 at 11:58 PM Timothy Coalson wrote:
>
>> The easiest to use (especially if your goal is to match other cifti
>> files) is generally -cifti-create-dense-from-template. It will even tur
gt; would be nice if HCP developers, in future, consider a version of CIFTI
> with medial wall included.
>
>
> On Mon, Nov 19, 2018 at 11:53 PM Timothy Coalson wrote:
>
>> The left and right hemisphere are intended to be in register, though I
>> don't recall
For display, another possibility is to put the analysis results for all
areas into a parcellated cifti file, which will show each area in a color
representing the value for that area.
Tim
On Thu, Jan 10, 2019 at 6:17 AM Glasser, Matthew wrote:
>
>
>1. These would not be with the HCP's
e resolution
> would be 1.25mm as the volumes are created from the diffusion image. (I'm
> working with the HCP test retest data)
>
> In other words, is there any command that can generate a CIFTI file with a
> different volume resolution?
>
> On Sat, 5 Jan 2019 a
On Thu, Jan 3, 2019 at 10:47 AM Glasser, Matthew wrote:
> 1) FSL does not respect Workbench’s header info, so the labels get
> removed. You might need to use wb_command -volume-resample or copy over
> the header info.
>
Yes, use wb_command -volume-warpfield-resample and the enclosing voxel
It is possible, though it makes comparisons to the existing 2mm cifti data
more challenging. For instance, we have a 1.6mm space for our 7T data, the
files defining it are here:
https://github.com/Washington-University/HCPpipelines/tree/master/global/templates/170494_Greyordinates
Making yet
If you mean you just want to combine the magnitudes (the main output of
-cifti-gradient) across timepoints, that isn't hard. There isn't a built
in option to do it, but you can do it afterwards by -cifti-math to square
everything, -cifti-reduce to sum across time, and then -cifti-math to
square
On Thu, Jan 3, 2019 at 6:32 PM Glasser, Matthew wrote:
> I believe that FSL convertwarp converts between relative and absolute
> conventions, though the FSL coordinates issue might prevent that from being
> helpful.
>
> Matt.
>
> From: Timothy Coalson
> Date: Thursday, Ja
Label commands take pains to avoid making collisions between labels with
different names, or altering label key values when not necessary. They
also generally don't remove labels simply for not being used in the output,
because that could introduce problems when a small, hard to find area is
Workbench doesn't have that kind of visualization - it can be displayed as
a matrix, or interactively selecting a "seed" parcel and coloring the other
parcels. The FSLNets stuff has something related to what you want, but is
based on networks, and doesn't really spatially organize them:
We generally do use timeseries for single-subject analysis. The only
involvement of ICA there is in cleaning up things like artifacts - think of
it as using ICA to identify nuisance regressors. The end result is still a
timeseries, but with greatly reduced artifacts.
You can use wb_command
Surface data is different - we don't actually put surface coordinates into
dscalar, or any other cifti files (or metric files). In our data, the
surface coordinates are only contained in .surf.gii files. Getting the
surface data into "Native" volume space is as simple as using the surfaces
in
r
>
> On Tue, Apr 2, 2019 at 2:23 PM Timothy Coalson wrote:
>
>> The HCP MMP 1.0 parcellation could not have been made without using
>> surface-based methods, due to their increased accuracy in aligning
>> functional areas over existing volume-based registrations. Vo
The HCP MMP 1.0 parcellation could not have been made without using
surface-based methods, due to their increased accuracy in aligning
functional areas over existing volume-based registrations. Volume-based
group data generally cannot have the cortical precision that the HCP MMP
1.0 implies. See
The labels are used in the order of their keys, which is also how the
exported label table is ordered. If your dlabel file has more label names
than there ended up being parcels, you can first use
-cifti-parcel-mapping-to-label to get a minimal dlabel file that exactly
matches the parcels
No, since the subcortical data needed to be in MNI space, we chose to use
MNI space surfaces for each subject so that we only needed to generate a
single motion-corrected volume timeseries. Because the per-subject
processing uses the individual surfaces and the same warpfield for surface
and
The 1.0 and 3.0 versions on github are nearly identical, that was just a
naming issue.
The version in FSL may be based on version 2, and is missing a library
needed for HOCR, so some options in v3 aren't available. You should be
able to use the fsl versions of the executables other than msm (so,
The files themselves are in the pipelines repository, if that helps:
https://github.com/Washington-University/HCPpipelines/tree/master/global/templates
It is visually obvious that they are not left/right symmetric, assuming
that is what you were asking.
Tim
On Fri, Apr 5, 2019 at 4:54 PM
You could use the group average MNI surfaces from connectomedb for
visualization. If you need a single coordinate per parcel, you can use
wb_command -surface-coordinates-to-metric on the surfaces, combine those
metric files into a cifti file with -cifti-create-dense-from-template, and
use
That looks like you cut off some brain tissue. I'm not really sure what
your goal is here, but if you have images with different voxel sizes, what
you may actually need to do is to resample an image (flirt, applywarp, or
wb_command -volume-*-resample), and not crop it.
Tim
On Sun, Mar 24, 2019
Parcellated files contain only one value per parcel (per map), so it isn't
a good idea to try to reconstitute them into a spatial map before
analysis. I think the correct thing to do is to put them through PALM in a
way that doesn't use spatial information (no tfce, no smoothing, etc).
Tim
On
A medial wall mask is used to mask out data for at least cifti files. It
is hard to say for sure (the volume to surface mapping is more involved
than the closest vertex logic used in the GUI to identify a vertex), but I
would guess that both get masked out by the medial wall currently. Future
There isn't a dedicated command to get the parcel names, but they are in
the output of wb_command -file-information on the parcellated file, or you
can take them from -cifti-label-export-table on the dlabel file.
Tim
On Mon, Mar 4, 2019 at 1:55 AM Tali Weiss wrote:
> i did
> wb_command
00307.L.sphere.164k_fs_LR.surf.gii \
> BARYCENTRIC \
> 100307/T1w/100307.L.sphere.164k_fs_LR.surf.gii
>
> Many thanks for your help!
>
>
>
> Le mer. 20 févr. 2019 à 20:34, Timothy Coalson a écrit :
>
>> Sorry, the recommended sphere for resampling any subject will of
Sorry, the recommended sphere for resampling any subject will of course be
that subject's version of that file, not specifically subject 100307's
sphere.
Tim
On Wed, Feb 20, 2019 at 1:31 PM Timothy Coalson wrote:
> On Wed, Feb 20, 2019 at 8:03 AM CHAUMON Maximilien <
> maximilien.ch
On Wed, Feb 20, 2019 at 8:03 AM CHAUMON Maximilien <
maximilien.chau...@icm-institute.org> wrote:
> Hello,
>
> I'm looking at fine changes in MEG forward leadfields and would like to
> use the 164k meshes in each subject (I know 164k vertices are overkill, but
> I need this high res rendering for
In that gifti file, the label table indicates that ??? is label 0, as is
recommended (it means things that haven't been labeled, such as the medial
wall). The matlab gifti library must be shifting these values, possibly
because they are taken as indices into another matlab array (matlab doesn't
That is saying that you don't have the matlab gifti library installed (or
it isn't on your matlab path).
Tim
On Tue, Feb 26, 2019 at 6:09 PM Leonardo Tozzi wrote:
> Dear Michael,
>
>
>
> Thank you very much for all the consideration on the use of FIX for the
> task data.
>
> I have tried the
The command wb_command -surface-vertex-areas will give you the area of each
vertex. For vertex volume, you should use wb_command -surface-wedge-volume.
When comparing these kinds of measures, it is usually better to measure
them in an anatomically faithful space (such as the T1w space of each
I have occasionally seen the volume slice outline show something like that
before, but as far as I could tell, the surface was actually okay. It may
just be a display bug in wb_view, but we haven't pinned it down.
Tim
On Mon, Mar 18, 2019 at 8:44 AM Aaron C wrote:
> Dear HCP experts,
>
> I
First, you'll need to export the label table of the original file (the
name, key value, and color values for each label, see -cifti-label-import),
with wb_command -cifti-label-export-table. You'll need to either figure
out a key value (first number in each row of numbers) that hasn't been used
Inline replies.
Tim
On Fri, Mar 22, 2019 at 10:17 AM Claude Bajada
wrote:
> Dear experts,
>
> Could I just confirm that the data that is found in:
>
>
> ${SubjectFolder}/MNINinLinear/Results/rfMRI_REST?_LR/rfMRI_REST?_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii
>
> Is the resting state data
If your data is organized as a value per parcel/network, you should be able
to turn it into parcellated cifti files, which can be displayed in wb_view
(and therefore in scenes) as a matrix and/or as colored regions on the
surfaces and in the volume.
See wb_command -cifti-parcellate (to make a
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