Re: [HCP-Users] Blank p-value maps after running PALM on CIFTI files

Hi, If you are just testing the mean activation, then you need to use the -ise option to allow sign flipping. Otherwise, by default, PALM does permutations, but permutations of your model will always generate the exact same mean, which explains your results. Cheers, -MH -- Michael Harms,

Re: [HCP-Users] vertex ordering with wb_command -cifti-convert -to-nifti (or -to-text) and gifti

-cifti-separate and -cifti-convert have very different purposes. -cifti-separate is there to make usable volume and metric files from the information in cifti files. -cifti-convert is there only to get data values into other tools that can't read cifti, without any respect for spatial

[HCP-Users] vertex ordering with wb_command -cifti-convert -to-nifti (or -to-text) and gifti

Is there a way to determine (or specify) the correspondence between the vertices when a cifti is converted to a "fake nifti" vs. separated to giftis? For example, wb_command -cifti-separate Parcels_LR.dtseries.nii COLUMN -metric CORTEX_LEFT out.func.gii produces a gifti with 32492 vertices,

[HCP-Users] Data

Dear experts,  I have a question about MNI coordinates. I am trying to find/make sets of MNI coordinates for my consumer research. However it is difficult for me to dig into the coordinates of all behaviors for each subject from HCP images. So is there any way or suggestion for me to get a set

Re: [HCP-Users] Blank p-value maps after running PALM on CIFTI files

Hi Tim, Thanks for the clarification. Here are the calls to palm for the separated subcortical and cortical files: palm -i data_sub.nii -d ${StudyFolder}Level3/L3Setup.mat -t ${StudyFolder}Level3/L3Setup.con -o mbmfResults${contrast}_vol -T -logp palm -i data_L.func.gii -d

Re: [HCP-Users] Blank p-value maps after running PALM on CIFTI files

As you have found, the outputs from PALM contain only 0s, therefore using a different wb_command operation to convert them will not help with your current issue. If you can post the PALM call you used, it might help others who know PALM figure out what your problem might be. Tim On Mon, Jul 2,

Re: [HCP-Users] Blank p-value maps after running PALM on CIFTI files

Hi Tim, Thank you for your quick reply. I renamed the maps and confirmed that there are no values in the maps (I pasted the output of wb_command -file-information for the left hemisphere output below in case that is useful). Regarding -cifti-create-dense-from-template: I used this command in

Re: [HCP-Users] Blank p-value maps after running PALM on CIFTI files

Please name your tstat and p-value outputs ending in .func.gii, not simply .gii . This will allow you to open them in wb_view directly, allowing you to do sanity checks with fewer intervening steps. However, from what you have said, I am fairly certain they are entirely 0s (you can use

[HCP-Users] Blank p-value maps after running PALM on CIFTI files

Hi, I am trying to run PALM with TFCE on dense timeseries CIFTI files created through an HCP-style protocol, and preprocessed using the HCP pipeline (version 3.22). I am running these analyses on an HPC using SLURM. It seems that I successfully ran PALM (there were no warnings or errors). When

[HCP-Users] HCP AWS data moving to temporary bucket location on July 5th, 2018

Attention all users of HCP Data in our Amazon Web Services (AWS) S3 Bucket: Recent changes in the AWS Public Dataset Program have required migration of HCP data stored in AWS S3 to a new account. As part of this transition, we must temporarily disable access to the current s3://hcp-openaccess/

Re: [HCP-Users] Communities for MMP atlas?

Mike is correct - we did this in the following paper, in collaboration with our colleague Mike Cole: https://www.biorxiv.org/content/early/2018/01/12/206292 This paper provides a grayordinate wide partition (cortex and subcortex). We plan to make thenetwork scheme public via BALSA shortly

[HCP-Users] Mapping DTI to surface

Dear all, I was emailing today to ask a specific question about some of the specifics of mapping volumetric data to the surface with CIFTI files. I would like to use the HCP diffusion data to generate FA and MD maps using the DTIFIT command. Following this, I would like to map these to the

Re: [HCP-Users] A few specific questions about the HCP data | MNI space dedrifting & file structure

On Mon, Jul 2, 2018 at 12:26 PM, Bajada, Claude Julien < c.baj...@fz-juelich.de> wrote: > Thanks Matt and Mike, I'll await to hear from Tim re: his thoughts on > drifting. > > Mike, thanks for confirming that all structural quantities are measured in > real (native) space. Just a quick follow-up

Re: [HCP-Users] A few specific questions about the HCP data | MNI space dedrifting & file structure

On Mon, Jul 2, 2018 at 7:13 AM, Claude Bajada wrote: > > 2) from what I understand, structural qualities such as cortical > thickness etc are measured in the individual's real space. However then, > what I do not understand is the file structure of the HCP data. The > structural measures such as

Re: [HCP-Users] Communities for MMP atlas?

Here is another effort: https://www.biorxiv.org/content/early/2018/06/23/350462 Peace, Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Harms, Michael" mailto:mha...@wustl.edu>> Date: Monday, July 2, 2018 at 12:30 PM To: Benjamin Risk mailto:bb...@cornell.edu>>,

Re: [HCP-Users] Communities for MMP atlas?

Hi, There is something in the works: https://www.biorxiv.org/content/early/2018/01/12/206292 cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box

Re: [HCP-Users] A few specific questions about the HCP data | MNI space dedrifting & file structure

We previously looked at the MNI drift, and found that it is almost entirely an affine, even for the nonlinear template. We have a suspicion that this means that it was originally caused by the early MNI linear template, and that the issue was known by the time MNI nonlinear templates were

Re: [HCP-Users] A few specific questions about the HCP data | MNI space dedrifting & file structure

Thanks Matt and Mike, I'll await to hear from Tim re: his thoughts on drifting. Mike, thanks for confirming that all structural quantities are measured in real (native) space. Just a quick follow-up question / comment to ensure my understanding. Am I correct in assuming that the quantities have

[HCP-Users] Communities for MMP atlas?

Hi all, Are there any community definitions based on the MMP atlas, preferably based on functional connectivity? I saw there are 22 regions in Fig 1 in https://media.nature.com/full/nature-assets/nature/journal/v536/n7615/extref/nature18933-s3.pdf. I am looking for something aligning more with 7

Re: [HCP-Users] A few specific questions about the HCP data | MNI space dedrifting & file structure

Tim Coalson can explain how to dedrift MNI space (which as Mike says is no longer true MNI space). Peace, Matt. On 7/2/18, 10:10 AM, "hcp-users-boun...@humanconnectome.org on behalf of Harms, Michael" wrote: > >Hi, >Re (1): >If you want to work with streamlines in MNI space then you have to

Re: [HCP-Users] A few specific questions about the HCP data | MNI space dedrifting & file structure

Hi, Re (1): If you want to work with streamlines in MNI space then you have to accept the "drift" (volume expansion) that is part of MNI space itself. Re (2): Maps may be resampled to surfaces in MNI space. But all the FreeSurfer structural quantities that we provide in the

[HCP-Users] A few specific questions about the HCP data | MNI space dedrifting & file structure

Dear experts, I have a few questions: 1) I am currently working on a project using tractography and the HCP data. I have used the HCP provided FNIRT based MNI registration in order to register individual streamlines from "native" or diffusion space (as per post HCP minimal processing pipeline)