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

[Glasser, Matthew]

Myelin maps are only for the cortex so you can omit the -volume-all 
data_sub.nii portion of the command.

Peace,

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Sang-Young Kim mailto:sykim...@gmail.com>>
Date: Monday, September 18, 2017 at 3:13 PM
To: "HCP-Users@humanconnectome.org" 
mailto:HCP-Users@humanconnectome.org>>
Subject: [HCP-Users] CIFTI files do not contain volume data

Dear HCP experts:

I’m trying to compare myelin map between two groups using FSL Palm. I generated 
each subject’s myelin map using the HCP pipelines scripts (e.g., PreFreeSurfer, 
FreeSurfer, and PostFreeSurfer pipeline). Before running FSL Palm, I have 
merged each subject myelin map using following command: wb_command -cifti-merge.

Then, to separate a CIFTI file into GIFTI and NIFTI, I ran the following 
command:
wb_command -cifti-separate data.dscalar.nii COLUMN -volume-all data_sub.nii 
-metric CORTEX_LEFT data_L.func.gii -metric CORTEX_RIGHT data_R.func.gii

When I run above command, I get error message as below:
ERROR: specified file and direction does not contain any volume data

So I checked the information of both merged myelin map data and each subject 
data using wb_command -file-information.
I found that the CIFTI file really does not contain any volume data (Please see 
below).

Name: data.dscalar.nii
Type: Connectivity - Dense Scalar
Structure:CortexLeft CortexRight
Data Size:4.28 Megabytes
Maps to Surface:  true
Maps to Volume:   false
Maps with LabelTable: false
Maps with Palette:true
All Map Palettes Equal:   true
Map Interval Units:   NIFTI_UNITS_UNKNOWN
Number of Maps:   18
Number of Rows:   59412
Number of Columns:18
Volume Dim[0]:0
Volume Dim[1]:0
Volume Dim[2]:0
Palette Type: Map (Unique for each map)
CIFTI Dim[0]: 18
CIFTI Dim[1]: 59412
ALONG_ROW map type:   SCALARS
ALONG_COLUMN map type:BRAIN_MODELS
Has Volume Data:  false
CortexLeft:   29696 out of 32492 vertices
CortexRight:  29716 out of 32492 vertices

Could anyone please explain what’s wrong with data processing?
Since I didn't see any error messages when I ran the HCP pipeline, I have no 
idea why CIFTI file does not contain volume data.

Thanks in advance.

Sang-Young Kim

Postdoctoral Research Fellow
Department of Radiology, University of Pittsburgh






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

[Sang-Young Kim]

Dear HCP experts:

I’m trying to compare myelin map between two groups using FSL Palm. I generated 
each subject’s myelin map using the HCP pipelines scripts (e.g., PreFreeSurfer, 
FreeSurfer, and PostFreeSurfer pipeline). Before running FSL Palm, I have 
merged each subject myelin map using following command: wb_command 
-cifti-merge. 

Then, to separate a CIFTI file into GIFTI and NIFTI, I ran the following 
command:
wb_command -cifti-separate data.dscalar.nii COLUMN -volume-all data_sub.nii 
-metric CORTEX_LEFT data_L.func.gii -metric CORTEX_RIGHT data_R.func.gii

When I run above command, I get error message as below:
ERROR: specified file and direction does not contain any volume data

So I checked the information of both merged myelin map data and each subject 
data using wb_command -file-information. 
I found that the CIFTI file really does not contain any volume data (Please see 
below).

Name: data.dscalar.nii
Type: Connectivity - Dense Scalar
Structure:CortexLeft CortexRight 
Data Size:4.28 Megabytes
Maps to Surface:  true
Maps to Volume:   false
Maps with LabelTable: false
Maps with Palette:true
All Map Palettes Equal:   true
Map Interval Units:   NIFTI_UNITS_UNKNOWN
Number of Maps:   18
Number of Rows:   59412
Number of Columns:18
Volume Dim[0]:0
Volume Dim[1]:0
Volume Dim[2]:0
Palette Type: Map (Unique for each map)
CIFTI Dim[0]: 18
CIFTI Dim[1]: 59412
ALONG_ROW map type:   SCALARS
ALONG_COLUMN map type:BRAIN_MODELS
Has Volume Data:  false
CortexLeft:   29696 out of 32492 vertices
CortexRight:  29716 out of 32492 vertices

Could anyone please explain what’s wrong with data processing?
Since I didn't see any error messages when I ran the HCP pipeline, I have no 
idea why CIFTI file does not contain volume data. 

Thanks in advance. 

Sang-Young Kim

Postdoctoral Research Fellow
Department of Radiology, University of Pittsburgh 
  





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Re: [HCP-Users] Correlation matrices

[Glasser, Matthew]

This should be possible with wb_command -cifti-cross-correlation.  You would 
create a CIFTI dense timeseries file of the subcortical region of interest and 
a CIFTI parcellated timeseries using the parcellation of your choice.  You 
could then visualize the results in wb_view (depending on the order in which 
you specify the arguments, either you can visualize the connectivity in the 
space of the subcortical ROI or as parcellation.  You would click in the other 
space to see the results.

Peace,

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Carole Guedj mailto:carole.gu...@unige.ch>>
Date: Monday, September 18, 2017 at 3:58 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Correlation matrices

Dear HCP experts,

I’m using HCP resting-state fMRI data for functional connectivity analyses. I 
have actually two question about that:

1/ After preprocessed the data, I would like to compute a functional 
connectivity matrix between all voxels of a defined subcortical 
region-of-interest with the rest of the brain (using a GM mask) to obtain an 
NxM correlation matrix. Could I do that with wb_command?

2/ To reduce the size of this correlation matrix, is it possible to resample 
the M dimension using an atlas?

Thanks in advance for any help!

Carole


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[HCP-Users] Correlation matrices

[Carole Guedj]

Dear HCP experts,

I’m using HCP resting-state fMRI data for functional connectivity analyses. I 
have actually two question about that:

1/ After preprocessed the data, I would like to compute a functional 
connectivity matrix between all voxels of a defined subcortical 
region-of-interest with the rest of the brain (using a GM mask) to obtain an 
NxM correlation matrix. Could I do that with wb_command?

2/ To reduce the size of this correlation matrix, is it possible to resample 
the M dimension using an atlas?

Thanks in advance for any help!

Carole


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