Re: [HCP-Users] creati cifti from nifti1

[Glasser, Matthew]

There have been a few recent posts on the list about this topic.  I believe we are still working on a detailed 7T HCP protocol document for the website. Peace, Matt. From: Marta Moreno <mmorenoort...@icloud.com> Date: Sunday, March 1, 2015 at 7:47 PM To: Matt Glasser <glass...@wusm.wustl.edu>, Timothy Coalson <tsc...@mst.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] creati cifti from nifti1 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" <glass...@wusm.wustl.edu> wrote: wb_command -volume-reorient Peace, Matt. From: Marta Moreno <mmorenoort...@icloud.com> Date: Sunday, March 1, 2015 at 7:14 PM To: Timothy Coalson <tsc...@mst.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>, Matt Glasser <glass...@wusm.wustl.edu> 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 <tsc...@mst.edu> 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" <mmorenoort...@icloud.com> 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" <glass...@wusm.wustl.edu> wrote: The medial wall ROIs are ${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.${Hemisphere}.atlasroi.32k_fs_LR.shape.gii. Peace, Matt. From: Timothy Coalson <tsc...@mst.edu> Date: Friday, February 27, 2015 at 6:44 PM To: Marta Moreno <mmorenoort...@icloud.com> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> 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 <mmorenoort...@icloud.com> 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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org 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. 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