I will look at recent posts and document/info in website, 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
On Mar 1, 2015, at 8:50 PM, "Glasser, Matthew" <[email protected]> wrote: > 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 <[email protected]> > Date: Sunday, March 1, 2015 at 7:47 PM > To: Matt Glasser <[email protected]>, Timothy Coalson <[email protected]> > Cc: "[email protected]" <[email protected]> > 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" <[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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