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. 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. > > > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
