If you need to preserve the mm coordinates of the ROI, I would not trust FSL's resampling with an identity transform to get it right, because that will produce a different shift depending on what coordinates a particular corner voxel is at in each image (as I understand it, FSL's conventions come from originally handling ANALYZE format images). Instead, wb_command -volume-affine-resample, given an identity matrix (and NOT specifying -flirt) will do the resampling via nifti mm coordinates, with no guesswork.
Tim On Tue, May 28, 2019 at 8:08 AM Jaime Caballero <[email protected]> wrote: > Thank you so much! > > It worked fine, and the resulting ROIs are were they are suposed to be. > > Regards, > Jaime > > El lun., 27 may. 2019 22:20, Glasser, Matthew <[email protected]> > escribió: > >> That file does exist in the structural package then. >> >> >> >> Matt. >> >> >> >> *From: *Jaime Caballero <[email protected]> >> *Date: *Monday, May 27, 2019 at 3:20 PM >> *To: *"Glasser, Matthew" <[email protected]> >> *Cc: *"[email protected]" <[email protected]> >> *Subject: *Re: [HCP-Users] Convert nifti-ROIs to cifti format >> (subcortical) >> >> >> >> 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 <[email protected]> >> escribió: >> >> I thought you said you were using a locally collected sample you ran the >> HCP Pipelines on? >> >> Matt. >> >> >> >> *From: *Jaime Caballero <[email protected]> >> *Date: *Monday, May 27, 2019 at 3:10 PM >> *To: *"Glasser, Matthew" <[email protected]> >> *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 (<[email protected]>) >> 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 <[email protected]> >> *Date: *Monday, May 27, 2019 at 12:56 PM >> *To: *"Glasser, Matthew" <[email protected]> >> *Cc: *"[email protected]" <[email protected]> >> *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 (<[email protected]>) >> escribió: >> >> What do you plan to do with the file? >> >> >> >> Matt. >> >> >> >> *From: *Jaime Caballero <[email protected]> >> *Date: *Monday, May 27, 2019 at 12:08 PM >> *To: *"Glasser, Matthew" <[email protected]> >> *Cc: *"[email protected]" <[email protected]> >> *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 (<[email protected]>) >> escribió: >> >> Are you wanting a .dlabel.nii output or a .dscalar.nii output? >> >> >> >> Matt. >> >> >> >> *From: *<[email protected]> on behalf of Jaime >> Caballero <[email protected]> >> *Date: *Monday, May 27, 2019 at 10:37 AM >> *To: *"[email protected]" <[email protected]> >> *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 >> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> >> ------------------------------ >> >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. 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