Re: [HCP-Users] Subcortical atlas of S900_AverageT1w_restore.nii.gz?

Using -cifti-separate will get you the 2mm definitions of these structures, in particular using "-volume-all -label ", but the same information is already available in the pipellines repository:

Re: [HCP-Users] FreeSurfer brain volume question

Thanks, Jennifer and Michael. Best, Chao On Wed, Nov 22, 2017 at 3:38 PM, Harms, Michael wrote: > > > Hi, > > In FS, “Intracranial volume”, renamed to “EstimatedTotalIntraCranialVol” > (aka “eTIV”) in more recent FS versions, is solely based on the determinant > of a

Re: [HCP-Users] FreeSurfer brain volume question

Hi, In FS, “Intracranial volume”, renamed to “EstimatedTotalIntraCranialVol” (aka “eTIV”) in more recent FS versions, is solely based on the determinant of a talairach transform that is internal to FS. That particular transform does not necessarily need to be accurate for FS to generate

Re: [HCP-Users] FreeSurfer brain volume question

Hi Chao, See this earlier list thread: https://www.mail-archive.com/hcp-users@humanconnectome.org/msg05148.html As is stated in that thread, we don't recommend using the the IntraCranial volume estimate. Best, Jenn Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project

[HCP-Users] FreeSurfer brain volume question

Hi We were checking the FS brain volumes and found that out of the 1113 subjects for 14 subjects the FS_BrainSeg_Vol is larger than the FS_IntraCranial_Vol (so that the column FS_BrainSegVol_eTIV_Ratio is larger than 1). We wonder if this is due to some error in calculating either of the two

Re: [HCP-Users] R: MEG resting state

Hi Georgios and Francesco Thanks for your help and the script! My doubts are solved. Cheers, Adoney On Mon, Nov 20, 2017 at 10:22 AM, Georgios Michalareas wrote: > Hi Adoney (and Francesco), > > Francesco is right. The ICA was done independently per session. But this > should

Re: [HCP-Users] Accessing full SSAGA HCP-Wu-Min1200 data

Hi James, We used a version of SSAGA for HCP in which some items were omitted. We did ask about medications used for anxiety and depression, and drugs used in combination with alcohol or illicit drugs, but the other categories were omitted. In order to get access to the HCP SSAGA data as

[HCP-Users] Accessing full SSAGA HCP-Wu-Min1200 data

Hi, I'm a researcher from Australia hoping to use the HCP-Wu-Min n1200 data. 1. How can I access full SSAGA (semi-structured assessment for the genetics of alcoholism) data? Exploring the connectomedb site, can only get CSV column stating SSAGA is complete, rather than the details within it. 2.

Re: [HCP-Users] How does the HCP calculate the Cohen d effect in S1200 GroupAvg results?

Hi, It’s a standard Cohen’s d calculation -- mean of the individual subject (lev2) copes, divided by the std of the individual subject copes In terms of FSL code, if $mergedcope is the 4D file containing all the individual subject cope estimates, the code is just: fslmaths $mergedcope

Re: [HCP-Users] A question about brain registration matrix

You can compute the displacement of vertices on the spherical surface by comparing the registered spheres to the original or MSMSulc spheres. Peace, Matt. From: Timothy Coalson > Date: Tuesday, November 21, 2017 at 11:17 PM To: Aaron C

Re: [HCP-Users] Subcortical atlas of S900_AverageT1w_restore.nii.gz?

Dear Michael and Matt, Thank you very much for your reply. As for Michael's question - yes, I am looking for a dlabel file that includes volumes such as caudate and putamen as separate structures. Perhaps there is a workbench command that would allow to isolate these structures in a random