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wb_command -volume-reorient
Peace,
Matt.
Tim,
You are right: Atlas_ROIs.2.nii is Right-to-Left oriented while rspmT_0001.nii is Left-to-Right. Is there a way to reorient in workbench?
Thank you!!
Leah
_______________
Marta Moreno-Ortega, Ph.D.
Postdoctoral Research Fellow
Division of Experimental Therapeutics
New York State Psychiatric Institute
Department of Psychiatry
Columbia University College of Physicians and Surgeons
In workbench, "volume space" also refers to the spacing, origin, and orientation information. Check the files using fslhd or or wb_command -nifti-information -print-header, and look at the sform and qform information.
Tim
On Mar 1, 2015 3:06 AM, "Marta Moreno" < [email protected]> wrote:
Hi,
Thank you very much for your help.
I have done detailed steps in order to create the cifti file from my fc file at 7 T (spmT_001.nii) but I am getting an error in -volume step: "label volume has a different volume space than data volume"; but the fact is that I resized my spmT_001.nii file
in Matlab in order to have same dimensions as Atlas_ROIs.2.nii (rspmT_001.nii).
I am coping here what I am doing to be clear: What is wrong?
1)wb_command -volume-to-surface-mapping (I created
spmT_0001_L.func.gii and spmT_0001_R.func.gii)
2)wb_command -cifti-create-dense-scalar spmT_0001_definitive.dscalar.nii -volume rspmT_0001.nii Atlas_ROIs.2.nii -left-metric spmT_0001_L.func.gii -roi-left MSTECT_6427_s001_140602.L.atlasroi.32k_fs_LR.shape.gii -right-metric
spmT_0001_R.func.gii -roi-right MSTECT_6427_s001_140602.R.atlasroi.32k_fs_LR.shape.gii
Also would like to know if the hcp pipeline for 7 T will be available soon and what would be the requisites for acquisition.
Thank you,
Leah
pd.: Here you have the dimensions to verify same volume space:
fslinfo rspmT_0001.nii
data_type FLOAT32
dim1 91
dim2 109
dim3 91
dim4 1
datatype 16
pixdim1 2.000000
pixdim2 2.000000
pixdim3 2.000000
pixdim4 0.000000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
fslinfo Atlas_ROIs.2.nii
data_type FLOAT32
dim1 91
dim2 109
dim3 91
dim4 1
datatype 16
pixdim1 2.000000
pixdim2 2.000000
pixdim3 2.000000
pixdim4 1.000000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
_______________
Marta Moreno-Ortega, Ph.D.
Postdoctoral Research Fellow
Division of Experimental Therapeutics
New York State Psychiatric Institute
Department of Psychiatry
Columbia University College of Physicians and Surgeons
The medial wall ROIs are ${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.${Hemisphere}.atlasroi.32k_fs_LR.shape.gii.
Peace,
Matt.
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 data (and -roi-left and -roi-right options to exclude the medial wall), and -volume with a label volume that has only the subcortical labels of interest in it, that is, it should
not have CORTEX_LEFT and CORTEX_RIGHT labels (unless you want the cortex data to be represented as voxels also).
If you want to do comparisons between it and the HCP released data, you'll likely want to use the medial wall rois and label volume that we use for our grayordinate space, rather than files derived from the subject. The surface ROIs can be retrieved from
an existing HCP cifti file with -cifti-separate using the -metric and -roi options. The volume label file exists in HCP subject directories (I don't know if it exists somewhere else also), here:
${StudyFolder}/${SubjectID}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz
Tim
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