To make the .dscalar.nii file, you seem to be on the right track. If the Choi
ROIs are properly in MNI space, hopefully you could simply use applywarp
--interp=nn -i <ROIs.nii.gz> -r
${StudyFolder}/${Subject}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz -o <ROIs.2.nii>
and then the wb_command -cifti-create-dense-from-template you mention.
Matt.
From: Jaime Caballero <jcabai...@gmail.com>
Date: Monday, May 27, 2019 at 12:56 PM
To: "Glasser, Matthew" <glass...@wustl.edu>
Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
The objective is to extract functional connectivity between cortical and
striatal ROIs, and ALFF and ReHo from both cortical and striatal ROIs.
Up to this point I have imported each subject's dtseries.nii file into MATLAB,
and also the previously defined ROIs in an HCP-compatible format. For the
dtseries I have a 96854x1200 matrix, and for the ROI a 96854x1 matrix
containing a mask, which I use to extract the time series I'm interested in for
further processing.
Jaime
El lun., 27 may. 2019 a las 19:14, Glasser, Matthew
(<glass...@wustl.edu<mailto:glass...@wustl.edu>>) escribió:
What do you plan to do with the file?
Matt.
From: Jaime Caballero <jcabai...@gmail.com<mailto:jcabai...@gmail.com>>
Date: Monday, May 27, 2019 at 12:08 PM
To: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
A .dscalar.nii output, I think. Basically I want an equivalent of the nifti
ROI, but in cifti: for each voxel/vertex, value 1 if inside the ROI, 0 if
outside. Would a dlabel file be better for this application?
El lun., 27 may. 2019 a las 19:03, Glasser, Matthew
(<glass...@wustl.edu<mailto:glass...@wustl.edu>>) escribió:
Are you wanting a .dlabel.nii output or a .dscalar.nii output?
Matt.
From:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Jaime Caballero <jcabai...@gmail.com<mailto:jcabai...@gmail.com>>
Date: Monday, May 27, 2019 at 10:37 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)
Dear experts
In my center we are studying cortico-striatal functional connectivity, and
cortical/striatal local measures (ALFF, ReHo) on a locally acquired sample. For
that we are using Choi's functional parcellation, distributed as a volumetric
NIFTI file, in MNI152 space. We want to validate our measures with a subset of
the S1200 release (resting state, 3T). Specifically I have used the ICA-FIX
cleaned and MSM-all registered files, i.e.:
<subject_dir>/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii
The thing is I have doubts on the way to convert nifti ROIs to cifti format in
this case.
My first approach:
1. Load a cifti template file and the NIFTI ROI file in MATLAB. The roi file is
a volume containing 0s and 1s.
2. Use the inverse of the NIFTI's transformation matrix to convert the XYZ
coordinates in MNI space from each grayordinate to XYZ coordinates in the
NIFTI'S volume space. (The matrix is corrected to account for MATLAB's 1-based
matrix indexing)
3. The values of the NIFTI volume for the obtained coordinates define the ROI
in the output cifti.
4. Keep only the grayordinates that are set to one by my method and that are
labeled as striatum (i.e. caudate, putamen or accumbens) in the cifti files.
This aproach is rather hand-made, and I wonder if I am missing something
important. Conceptually it looks correct to me, but the ROIs appear slightly
displaced to the right, which might affect the results.
To load the CIFTIs I use fieltdrip's ft_cifti_read( ), which for this purpose
works well (it reads the grayordinate positions and labels), and to load the
NIFTIs I use Freesurfer's load_nifti( ).
Is this method correct, or is there something important I'm not taking into
account?
Now I'm trying to do the same with wb_command to compare, but I cannot get it
working. The procedure I use is:
# Resample the ROI file to 2x2x2 resolution with ANTs:
ResampleImage 3 "$NiftiFileIn" "$NiftiFileResampled" 2x2x2 0
# Convert the obtained nifti to cifti:
wb_command -cifti-create-dense-from-template "$CiftiDscalarTemplateFile"
"$CiftiOut" -volume-all "$NiftiFileResampled"
Which outputs the error: -volume-all specifies a volume file that doesn't match
the volume space of the template cifti file
Is there anything wrong with my way of doing this procedure?
Thanks in advance,
Best regards,
Jaime Caballero-Insaurriaga
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