Thank you both! I have already created my fc-cifti file and looks great! I would like to use hcp for 7-T and to acquire my data to make it comparable to yours. Any information, please?
Thanks a lot! 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 On Mar 1, 2015, at 8:16 PM, "Glasser, Matthew" <[email protected]> wrote: > wb_command -volume-reorient > > Peace, > > Matt. > > From: Marta Moreno <[email protected]> > Date: Sunday, March 1, 2015 at 7:14 PM > To: Timothy Coalson <[email protected]> > Cc: "[email protected]" <[email protected]>, Matt > Glasser <[email protected]> > Subject: Re: [HCP-Users] creati cifti from nifti1 > > 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 > > > > > On Mar 1, 2015, at 6:54 PM, Timothy Coalson <[email protected]> wrote: > >> 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 >>> >>> >>> >>> >>> On Feb 27, 2015, at 7:49 PM, "Glasser, Matthew" <[email protected]> >>> wrote: >>> >>>> The medial wall ROIs are >>>> ${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.${Hemisphere}.atlasroi.32k_fs_LR.shape.gii. >>>> >>>> Peace, >>>> >>>> Matt. >>>> >>>> From: Timothy Coalson <[email protected]> >>>> Date: Friday, February 27, 2015 at 6:44 PM >>>> To: Marta Moreno <[email protected]> >>>> Cc: "[email protected]" <[email protected]> >>>> Subject: Re: [HCP-Users] creati cifti from nifti1 >>>> >>>> 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 >>>> >>>> >>>> On Fri, Feb 27, 2015 at 5:53 PM, Marta Moreno <[email protected]> >>>> wrote: >>>>> Hi users, >>>>> >>>>> I am working on 7 T data doing some testing for fc analyses and would >>>>> like to to create a cifti file from nifti1 (my nifti1 fc t-map was >>>>> created with SPM). >>>>> >>>>> I am using wb_command -volume-to-surface-mapping and wb_command >>>>> -cifti-create-dense-scalar to have my cifti file but when loading into >>>>> workbench my subcortical data is not separated from my surface t-map. >>>>> What am I doing wrong? >>>>> >>>>> Thanks, >>>>> >>>>> 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 >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> HCP-Users mailing list >>>>> [email protected] >>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>> >>>> _______________________________________________ >>>> 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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