Re: [HCP-Users] Boarder Information

Hi Rachel, Try this combination: wb_command -border-to-rois wb_command -metric-weighted-stats If this an individual's myelin map, then use -area-surface and the subject's midthickness surface to weight the stats. If this is a group map, then use -weight-metric with the group

Re: [HCP-Users] missing label in Composite Parcellation FRB08_OFP03_retinotopic map

I didn't solve this yesterday, but I confirmed that both the 164k and 32k versions of the parcellations_VGD11b.32k_fs_LR.dlabel.nii in Connectome Workbench v1.0 Tutorial dataset have unassigned vertices in the parcel encircled by the OFP03 13b border in the left hem. The right hem counterpart

Re: [HCP-Users] Generating a dlabel.nii file from a new parcellation

AFNI might have a way to convert a 1D file to GIFTI label file. Then you can use wb_command -cifti-create-label. On May 18, 2016, at 6:59 AM, Matthew George Liptrot wrote: > Thanks Matt! > But now how do I create a dscalar file from a text file of labels (one

Re: [HCP-Users] PALM and cifti

Hi Jarek, Using palm's -transposedata is worth trying, but I had to use wb_command -cifti-separate to peel off left and right hems (or subcortical nifti) before input to PALM. Maybe that is not needed anymore. Donna On Apr 20, 2016, at 4:37 AM, Jarek Rokicki wrote:

Re: [HCP-Users] Group analysis for Myelin Maps

Hi Catalina, It's been a while since I've used PALM on CIFTI data, so the support may have evolved since then, but last summer I was using wb_command's cifti-separate feature to export cortical left and right GIFTI and subcortical NIFTI for input into PALM. I used scripts like these, which

Re: [HCP-Users] Custom Parcellation Label Map

Each label has a pair of lines like this: Attached is an example exported from a yeo parcellation label.gii using wb_command -label-export-table. ___ HCP-Users mailing list HCP-Users@humanconnectome.org

Re: [HCP-Users] why hcp task analysed volume data has been removed?

If your groups have subjects who are related, PALM can model the family structure: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuide It is a very powerful tool. On Jan 24, 2016, at 11:59 AM, "Glasser, Matthew" wrote: > We’d recommend using FSL’s PALM, which supports

Re: [HCP-Users] about wb_command

Just a couple of links that pertain to Tim's reply: HCP course materials: https://www.humanconnectome.org/courses/2015/exploring-the-human-connectome.php I'd browse the PDF before downloading any datasets. Github Pipelines/global/templates

Re: [HCP-Users] How can I attach an image?

Hi Mahmoud, I see what you mean about the hcp-users archive not showing the image you attached: http://www.mail-archive.com/hcp-users@humanconnectome.org/msg02225.html But I can assure you that when you sent the message to hcp-users, it did come through. I'll attach it below in this reply.

Re: [HCP-Users] (no subject)

I don't know the name of the package, but it might be something like "structural extended" -- one of them has the subject's freesurfer directory in it. On Dec 27, 2015, at 7:08 PM, A-reum Min wrote: > hello > my name is areum. > i have some question to you. > a few days

Re: [HCP-Users] (no subject)

e HCP Reference Manual for the 900 > Subjects release, on the HCP wiki, and in various posts to the HCP-users > list (searchable in the archive). Links to these are all at > humanconnectome.org > > Best, > Jenn > > On Dec 28, 2015 10:06 AM, "Donna Dierker" <

Re: [HCP-Users] Pial surface

What version of Freesurfer are you using? There was a specific one for the pipelines, and the version did affect results in the medial temporal especially, but also the insula. On Dec 28, 2015, at 12:56 PM, Mahmoud wrote: > Hello Erin, > > Thank you for your response.

Re: [HCP-Users] Convert NIFTI to CIFTI

Yes, I have, like so: wb_command -cifti-convert -from-nifti ${NiftiIn} ${CiftiTemplate} ${CiftiOut} -reset-scalars But not in the context you describe. I was using randomise to generate group permuted t-maps and then bring them back to cifti before doing TFCE on the surface. (Now I use PALM

Re: [HCP-Users] Hcp Data with non-overlapping parcellations

as, the label:node > > mapping is fixed. > > It would also be great if we could compare against some MNI-based > > parcellation schemes, such as the Harvard-Oxford. (Other suggestions > > welcome!) > > > > So to my questions! :-) > > > > 1) What is t

Re: [HCP-Users] Hcp Data with non-overlapping parcellations

Hi Matthew, The aparc files Jenn meant are generated by Freesurfer, but we make them available in cifti (*dlabel.nii) and gifti (*.label.gii) formats: * 164k standard mesh Structural_preproc/MNINonLinear/994273.aparc.164k_fs_LR.dlabel.nii

Re: [HCP-Users] Cifti to gifti conversion

I use wb_command -cifti-separate for this purpose. On Nov 11, 2015, at 10:52 AM, LEVI SOLOMYAK wrote: > Dear All, > > I am working with a cifti dlabel.nii file. I'm attempting to use those labels > to create ROI's but i need those files to be in gifti. I have

Re: [HCP-Users] Running TRACULA on the HCP data

Hi Niklas, I found this note here: http://www.humanconnectome.org/documentation/ > IMPORTANT: Subjects 209733 and 528446 removed from ConnectomeDB. > > Second-level QC revealed two Q2 subjects, 209733 and 528446, with structural > brain abnormalities, specifically gray matter heterotopia, that

Re: [HCP-Users] help -cifti-smoothing

Hi Alessia, wb_command -cifti-smoothing needs both the -left-surface and -right-surface arguments in order to know each vertex's neighbor relationships. These are stored in the surf.gii files -- not the *dscalar.nii files. Try this: wb_command -cifti-smoothing

Re: [HCP-Users] NaNs after merging dconn files

entralLeft:706 voxels > DiencephalonVentralRight: 712 voxels > HippocampusLeft:764 voxels > HippocampusRight: 795 voxels > PallidumLeft: 297 voxels > PallidumRight: 260 voxels > PutamenLeft:

Re: [HCP-Users] Freesurfer parcellation - list of coordinates

01, 2015 12:51 PM To: 'Donna Dierker' Subject: RE: [HCP-Users] Freesurfer parcellation - list of coordinates Hi Donna Thanks! I will have a look right away. Yes, the idea is to compute center of gravity. But if all coordinates are available for each parcel then it's pretty easy (e.g

Re: [HCP-Users] accessing files directly via XNAT / Amazon S3 / boto

Hi Ben, See if this post sheds some light on your query: https://www.mail-archive.com/hcp-users@humanconnectome.org/msg01037.html Haven't had to do this myself yet, but it looks handy. Donna On Jun 13, 2015, at 3:20 AM, Ben Cipollini bcipo...@ucsd.edu wrote: For the first issue, I'm

Re: [HCP-Users] Tracking between two hemispheres using pial stop masks

Hi Longchuan, Currently, I'm having file system issues accessing the HCP archives to check this myself, but I suspect the HCP structural packages have files named like *.atlasroi.*shape.gii. These are standard mesh ROI files that exclude the medial wall and corpus callosum. I'm pretty sure

Re: [HCP-Users] Help understanding *_Atlas.dtseries.nii

Hi Philip, I don't know the python/matlab implementation specifics, but the CIFTI page may be helpful: http://www.nitrc.org/projects/cifti/ The format specification (http://www.nitrc.org/forum/attachment.php?attachid=341group_id=454forum_id=1955) may help. Donna On May 29, 2015, at 10:33

Re: [HCP-Users] rsfc preprocessing

Came across this recently in TaskfMRIAnalysis/scripts/TaskfMRILevel1.sh: AdditionalSigma=`echo $AdditionalSmoothingFWHM / ( 2 * ( sqrt ( 2 * l ( 2 ) ) ) ) | bc -l` So even more precise.;-) On Apr 13, 2015, at 8:59 AM, Harms, Michael mha...@wustl.edu wrote: Hi, Just wanted to mention, for

Re: [HCP-Users] 7 RSN Netoworks label file

I think you are just trying to get the label table. Try something like this on your label file: wb_command -file-information RSN-networks.32k_fs_LR.dlabel.nii On mine, RSN7 had these label keys/names: 38 7Networks_3 0.000 0.463 0.055

Re: [HCP-Users] failed to find header file for 'rfMRI_REST1_LR'

Yamur, It looks like you are feeding a command a directory name, rather than a file name. Note also that some files named like *..nii are CIFTI files, rather than NIFTI files. The ones named like *.nii.gz are typically NIFTI volumes. Donna On Jan 21, 2015, at 2:00 PM, Harms, Michael

Re: [HCP-Users] gifti labels to volume

As far as I know, caret5's multi-fiducial mapping is volume-surface rahter than surface-volume. The caret_command method works, but you'll need to convert HCP surf.gii - caret5 coord/topo (caret_command -file-convert -sc …). And your label.gii or func.gii will need to be converted, too

Re: [HCP-Users] activation region mask

Hi Lisa, While there is a -volume flag (e.g., for subcortical structures), it is not mandatory. This command works for me: wb_command -cifti-create-label $OUTPUT_DLABEL_1 \ -left-label $INPUT_LABEL_LH -right-label $INPUT_LABEL_RH I'm sorry I don't know how to extract the frames. Donna On

Re: [HCP-Users] subdivide parcellation

Hi basile, Note that I'm looking at the structure for the data that is about to come out, but I see the Freesurfer original directory structure here: T1w/106016 T1w/106016/label T1w/106016/mri T1w/106016/mri/orig T1w/106016/mri/transforms T1w/106016/scripts T1w/106016/stats T1w/106016/surf

Re: [HCP-Users] How to locate brain regions of HCP rfMRI data

Project Washington University School of Medicine Department of Anatomy and Neurobiology Email: burge...@pcg.wustl.edu On Mar 17, 2014, at 8:57 AM, Donna Dierker do...@brainvis.wustl.edu wrote: Explore these label goodies in each subject's structural directory: ./MNINonLinear/110411

Re: [HCP-Users] How to extract BAs from the BA.32k_fs_LR.label.gii file?

I'm not sure how to do this with workbench/wb_command, but it can be done with caret5: http://brainvis.wustl.edu/wiki/index.php/Caret:Download You would find the midthickness 32k surf.gii that corresponds to the label.gii and use commands like this: caret_command