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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