Sorry for the confusion.
Locally acquired data wasn't processed using the HCP pipelines, it is in a
different resolution and it was processed in volume space, no problem there.
I want to use Choi's parcellation with HCP data. All the process I
described is mi workaround to adapt Choi files to HCP files.
Jaime
El lun., 27 may. 2019 22:12, Glasser, Matthew <glass...@wustl.edu> escribió:
> I thought you said you were using a locally collected sample you ran the
> HCP Pipelines on?
>
> Matt.
>
>
>
> *From: *Jaime Caballero <jcabai...@gmail.com>
> *Date: *Monday, May 27, 2019 at 3:10 PM
> *To: *"Glasser, Matthew" <glass...@wustl.edu>
> *Subject: *Re: [HCP-Users] Convert nifti-ROIs to cifti format
> (subcortical)
>
>
>
> Ok, thank you! I will try that.
>
>
>
> I asume the reference image
> ${StudyFolder}/${Subject}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz is to be
> downloaded with the structural package?
>
>
>
> Regards,
>
> Jaime
>
>
>
> El lun., 27 may. 2019 a las 21:00, Glasser, Matthew (<glass...@wustl.edu>)
> escribió:
>
> 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>)
> escribió:
>
> What do you plan to do with the file?
>
>
>
> Matt.
>
>
>
> *From: *Jaime Caballero <jcabai...@gmail.com>
> *Date: *Monday, May 27, 2019 at 12:08 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)
>
>
>
> 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>)
> escribió:
>
> Are you wanting a .dlabel.nii output or a .dscalar.nii output?
>
>
>
> Matt.
>
>
>
> *From: *<hcp-users-boun...@humanconnectome.org> on behalf of Jaime
> Caballero <jcabai...@gmail.com>
> *Date: *Monday, May 27, 2019 at 10:37 AM
> *To: *"hcp-users@humanconnectome.org" <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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> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
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> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
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