ves - I see they're SATA drives, and since they're 8TB,
> I figure they're 3.5"?
>
> Thanks again.
>
> -M
>
> On Tue, Apr 26, 2016 at 10:46 PM, Timothy Coalson wrote:
>
>> Correction: The connectome in a box does not contain the data in zip
>>
"Out of memory."
Use a machine with more memory, install more memory in that machine, or
increase your swap space and expect it to take a while to run.
Tim
On Tue, May 17, 2016 at 6:58 AM, Dev vasu <
vasudevamurthy.devulapa...@gmail.com> wrote:
> Dear Sir,
>
> I am encountering a conversion er
;ciftisavereset" or "ciftisave".
> Would you please give me some hints how to fix this problem? Thank you very
> much! From: glass...@wustl.edu To: tsc...@mst.edu; aaroncr...@outlook.com
> CC: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Some questions
> about t
n
>
>
> --
> *From:* Timothy B. Brown
> *Sent:* Monday, May 16, 2016 2:13:34 PM
> *To:* Gengyan Zhao; Timothy Coalson
> *Cc:* hcp-users@humanconnectome.org; glass...@wustl.edu
>
> *Subject:* Re: [HCP-Users] How to monitor Pipeline's running
Some guesses: have you set the queue name in your modified
...PipelineBatch.sh script(s) to one that exists on your system? Does the
subject list contain more than one subject? If not, then queue submission
won't do much, as it isn't about multithreading on single subjects, and
running it with an
Inline replies.
Tim
On Fri, May 13, 2016 at 1:20 PM, Aaron C wrote:
> Dear HCP experts,
>
> I have some questions about the usage of CIFTI files.
>
> 1. I checked the number of grayordinates of the following files using the
> command “wb_command -file-information”, and I noticed some of them h
To get the center of gravity, use -gifti-label-to-roi,
-surface-coordinates-to-metric, and then -metric-weighted-stats (with both
-roi and -area-surface or -weight-metric with average vertex areas,
depending on if it is individual or atlas data). Be aware that this
coordinate is unlikely to lie ex
may take a bit more scripting logic to deal
with the separate filesystems.
Tim
On Tue, Apr 26, 2016 at 9:03 PM, Timothy Coalson wrote:
> Yes, they should work in a jbod unit, and the only way to mount them is as
> individual volumes, each disk simply has an ext3 filesystem on it.
>
&
Yes, they should work in a jbod unit, and the only way to mount them is as
individual volumes, each disk simply has an ext3 filesystem on it.
The data arrangement is as a set of "packages" for each subject, that is,
zip files each containing a set of related data files (structural, rfMRI,
etc).
I
; pipeline repository, I wonder if it would make sense for me to first
> upsample from fs_LR_32k using
> fsaverage.L_LR.spherical_std.164k_fs_LR.surf.gii and then downsample to
> fsaverage5 from there?
>
> Thanks again!
>
> Estrid
>
> On Mon, Apr 18, 2016 at 11:25 PM, Timothy
The -surface-sphere-project-unproject command is used for concatenating
registrations, and since you want to go from fs_LR to fsaverage, which is a
registration that we compute, concatenating registrations isn't the way to
get there.
However, I don't know if we release the fsaverage registrations
Matlab is known to do some strange things to dynamic linking at least on
linux for things run with system() or similar. It might be appropriate to
write a workaround passthrough script for binaries/shell scripts to
set/clear LD_LIBRARY_PATH and related, specifically to deal with matlab's
strangene
I'm not sure why nobody else has responded to this, but the cifti-average
URL basically points to a precomputed file, and it may not be feasible for
us to compute this kind of result for arbitrary filters on the list of
subjects. I'm not sure where the group PCA methods are documented, or
whether/
It looks you you may have an incomplete download. Please do the following
in the terminal:
ls -l HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.zip
md5sum HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.zip
unzip -v | head
Here is what I get:
$ ls -l HCP_S900_820_rfMRI_MSMAll_groupPCA_d4
NiFTI-1.1 does in fact support both signed and unsigned int16:
#define DT_INT16 4
...
#define DT_UINT16512 /* unsigned short (16 bits) */
I don't know if this was the case in NiFTI-1.0, but NiFTI-1.1 has been
around so long it would be strange if tools di
That looks like the same kind of error - an unset variable that is supposed
to point to the location of the pipeline scripts.
Tim
On Mon, Feb 8, 2016 at 5:52 PM, Dev vasu <
vasudevamurthy.devulapa...@gmail.com> wrote:
> Dear Professor :
>
> I have resolved this issue on my own, but i still coul
Notice that the first row of the -nifti-information -print-matrix output is
labeled with a 0, and that the count of the output rows is 59412. It is
zero-indexed. For extracting the data in a file in text form, you may also
want to look at -cifti-convert -to-text.
I believe the data in the medial
So, the output of the command is actually a CIFTI file, so it needs similar
volume structure information as is used in making other cifti files - in
this case, though, you want white matter, and probably from the
individual's segmentation, rather than the atlas structures used in the
grayordinate s
That was meant to say "take the part of your measures that is in grey
matter".
Tim
On Feb 1, 2016 7:45 AM, "Timothy Coalson" wrote:
> So, you can make cifti files that contain white matter, but they won't
> match up to our grey matter cifti files. If you
So, you can make cifti files that contain white matter, but they won't
match up to our grey matter cifti files. If you want to take the past of
your measures that is in grey matter and put that into cifti, you first
need to use -volume-to-surface-mapping for both hemispheres, then you can
use -cif
Take a look at wb_command -metric-label-import , it will take that data
saved as .func.gii and make it into a .label.gii .
Tim
On Jan 29, 2016 12:36 AM, "Kristian M. Eschenburg" wrote:
> Hi All
>
> I'm interested in generating a custom parcellation for the low-resolution
> (32k) cortical mesh.
/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 wrote:
> I'm not sure what could have gone wrong in the script, but as you may have
> gu
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
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 invo
16, 2015 at 12:41 PM, Timothy Coalson 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
> &quo
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 manua
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
"disk" to shrink and start at a different offset). Hardware raid
controllers are u
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
> 10
To get the total volume of a volume ROI (ones in ROI, zeros elsewhere), use
wb_command -volume-weighted-stats with -sum, as this uses voxel volume as
the weights.
I suppose you could get gray matter volume per voxel by using -volume-math
to multiply a gray matter mask by the cube of the voxel reso
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
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
en
Areal distortion is a measure of how much stretching/compression was done
during a surface registration, and that filename suggests it is for the
freesurfer registration. I don't think we store per-voxel gray matter
volume in any file.
Tim
On Tue, Dec 1, 2015 at 11:05 PM, peipei_xiao wrote:
>
t; nifti and work with that? I presume at that point I wouldn't need the
> spatial info (actually Im not actually sure what kind of spatial info this
> is?)
>
> Thanks,
> Joelle
>
> On Wed, Nov 25, 2015 at 5:21 PM, Timothy Coalson wrote:
>
>> Because the surface
r 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 wrote:
>
>> The -label-to-border command requires gifti label files, as it does one
>> surface at a time - there i
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:
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
wa
e
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO 63110 Email: mha...@wustl.edu
>
> From: Joelle Zimmermann
> Date: Wednesday, November 25, 2015 2:40 PM
> To: Timothy Coalson
> Cc: "hcp-users@humanconnectome.org"
>
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 wh
nks for the help
> David
>
>
>
> 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 wrote:
>>
>>> To get a dconn loaded in matlab,
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
m
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 yo
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 resemble
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 wrote:
> Inline r
Inline replies.
On Wed, Nov 18, 2015 at 8:47 AM, Matthew George Liptrot <
matthew.lipt...@di.ku.dk> wrote:
> Hi,
>
> Thanks both of you.
>
> On 17/11/15 21:32 , "Timothy Coalson" wrote:
>
> So, cifti is not a 1:1 mapping to surface vertices. If what you p
So, cifti is not a 1:1 mapping to surface vertices. If what you plan to
use can read gifti, the less error-prone route is probably to use
-cifti-separate to get a nifti volume and gifti files that do have a 1:1
mapping to vertices.
Otherwise, have a look at -cifti-label-export-table, -cifti-conve
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 comm
-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 tur
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
-cifti-create-
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
register
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 l
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:
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
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
wou
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 t
h for the help!
>
>
>
> I have one final question:
>
>
> I assume that this ROI is from the freesurfer subcortical segmentation?
>
>
>
>
>
>
>
> --
> *From:* Timothy Coalson
> *Sent:* Tuesday, September 1, 2015 9:20 PM
>
s 30_min.dtseries.nii -reduce MEAN -roi
> roi_left_amygdala.dscalar.nii
>
>
>
>
> Thanks for your patience on this Tim -
>
>
>
> --
> *From:* Timothy Coalson
> *Sent:* Tuesday, September 1, 2015 8:12 PM
>
> *To:* Nomi, Jason
> *Cc:*
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
>
>
>
>
&g
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 -
>
>
> Jason
>
&g
-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 AMYGDALA_LEF
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
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 MEAN mean.dscalar.nii"
and then do -file-information on that? If that shows NaNs, I suggest also
running it on
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,
${StudyFolder}/${Subject}/MN
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
significa
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 mode
on
them, perhaps we should.
Tim
On Thu, Jun 25, 2015 at 3:47 PM, Matthew Brett
wrote:
> Hi,
>
> On Thu, Jun 25, 2015 at 1:22 PM, Timothy Coalson wrote:
> > We have some example files here that cover each mapping type at least
> once:
> >
> > http://www.nitrc.or
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:
https://github.com/nipy/nib
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.
As
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 wrote:
> Hi, HCP users
>
> Could someone tell me how I can display more than three layers of
> functional activations in workbenc
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,
di
The CIFTI indices don't refer to a different surface, but they do exclude
the vertices that fall inside the medial wall, for a modest reduction in
file size. Similarly, voxels that are not inside a subcortical gray matter
structure are also not represented in the file, which is a more significant
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 wrote:
> Hi HCP Users,
>
> There appear to be commands within PostFreeSurferPipelineBatch that use
> multi-threading, because my call to this script was just
Essentially, yes, but don't call a cifti index a vertex, and note that it
is specifically the left cortex vertex 68. You may also want to look at
the -cifti-export-dense-mapping command:
http://www.humanconnectome.org/software/workbench-command.php?function=-cifti-export-dense-mapping
There is a
; file for the -volume and options. How can I
> create a volume label file for only the left hemisphere subcortical ROIs?
>
> Thanks!
>
> kristian
>
> On Wed, May 27, 2015 at 6:13 PM, Timothy Coalson wrote:
>
>> First off, this part:
>>
>> -row-surface
File->Preferences, Volume tab, "Volume Axes Crosshairs".
Tim
On Thu, May 28, 2015 at 7:08 PM, miao wei wrote:
> Dear all,
> I am working on using workbench to visualize my data. How can I remove the
> red and green crosshair? when trying to capture the result image, the
> crosshair is always
First off, this part:
-row-surface fdt_paths_surface.func.nii -col-surface
fdt_paths_surface.func.nii
Those files should be named .func.gii, they are GIFTI metric files, not
NIfTI volumes.
Second, you appear to be doing tractography to subcortex and left
hemisphere (only?) at once. In order to
ible re-map the resampled
> 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 :
>
>> Back on this other question, wb_command indeed does not do decimation of
>> t
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
On Tue, May 12, 2015 at 4:34 AM, Estrid Jakobsen
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 (header file
Doing things with the nifti output of -cifti-convert is not what we mean by
"volume-based analysis". What we mean by volume-based analysis is relying
on volume-based registration to align the cortex, and combining same-index
voxels across subjects in an attempt to get statistics or other results f
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
th
You can't do surface registration before you have data on the surface to
register with, which is what the volume to surface mapping does. We do use
surface registration, and we highly recommend its use to everyone, but
volume registration is still an important preceding step - they are not
mutuall
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.
I would suspect an orientation problem between the current and new parcel
volumes, one volume being LPI and the other being RPI, or similar. Do
-file-information on all the input files, and look at the orientation
fields (or -nifti-information -print-header and compare the sforms).
It has been a
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
A quick possibility: if you have pasted in the formula you used, I see an
order of operations problem: .5*ln(1+r)-ln(1-r) means (.5*ln(1+r))-ln(1-r),
where the usual formula is .5*ln((1+r)/(1-r)), which after some log
identities becomes .5*(ln(1+r)-ln(1-r)).
Tim
On Mon, Mar 30, 2015 at 11:02 AM,
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
wrote:
> Thanks!
>
>
> I should be able to use
>
>
> > wb_co
It is not deprecated in the current release. In the next release
-metric-vertex-sum will be deprecated by -metric-stats and
-metric-weighted-stats. The -metric-vertex-sum command will still work for
several releases, but the new commands are more flexible, and will be the
recommended commands to
I'm a bit late on this, but the error messages in the original post are
consistent with an incorrect header on the file being opened, please try a
different cifti file and see if that works.
Tim
On Sun, Mar 8, 2015 at 4:01 AM, jan-mathijs schoffelen <
jm.schoffe...@gmail.com> wrote:
>
> Hi Cher
rs away in 2D from the correct location on the folded cortical
>>> sheet. Also, group average surfaces are very blurry in many cortical
>>> regions because different people have different folding patterns that
>>> cannot be registered (e.g. some people can have two gyri wh
tics
> New York State Psychiatric Institute
> Department of Psychiatry
> Columbia University College of Physicians and Surgeons
>
>
>
>
> On Feb 27, 2015, at 7:49 PM, "Glasser, Matthew"
> wrote:
>
> The medial wall ROIs are
> ${StudyFolder}/${Subject}/MN
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
surfac
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 wi
anconnectome.org/software/workbench-command.php?function=-cifti-separate
Tim
On Wed, Feb 18, 2015 at 8:17 PM, Peka Savayan wrote:
> Hi Timothy Coalson,
>
>
> Thank you for your response to my question.
>
>
> Can you please give me examples, along with the specific Workbench
&g
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
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 d
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 t
I believe the needed label file to match our grayordinate space is here,
and should be just a copy of the same file in each subject:
${StudyFolder}/${SubjectID}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz
We don't use cerebellum surfaces for much yet (they are not in the 91k
grayordinate space, instead
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 and
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
O
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> Anyway, the count of vertices per parcellated r
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