Thank you, Timothy I did the resampling with ANTs' WarpImageMultiTransform, as I thought the software used for this didn't matter. I have now done the same with wb_command as you suggested and the resulting ROIs are exactly the same.
I could not make FSL's applywarp work, so I cannot tell by now what would come out from that. Anyway I'm not sure I understand why would it fail. Is it something related to rounding coordinates or working directly in image space? Regards, Jaime El mar., 28 may. 2019 a las 20:46, Timothy Coalson (<[email protected]>) escribió: > 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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