Re: [HCP-Users] MATLAB libraries in Resting State Stats script

Hi, On Wed, Sep 19, 2018 at 8:13 PM, Glasser, Matthew wrote: > normalise is the custom function, not rms. I know - I was just hinting that maybe it would be worth dropping the requirement for the signal toolbox, by using that one-liner. Or maybe there are more signal toolbox functions you

Re: [HCP-Users] MATLAB libraries in Resting State Stats script

Hi, On Wed, Sep 19, 2018 at 7:52 PM, Glasser, Matthew wrote: > It is a custom function that I already pointed to. Am I right in thinking that the rms function boils down to: sqrt(mean(x .* conj(x), d)) where d is the dimension along which you want to operate (defaulting to 1)?

Re: [HCP-Users] MATLAB libraries in Resting State Stats script

normalise is the custom function, not rms. Matt. On 9/19/18, 4:10 PM, "Matthew Brett" wrote: >Hi, > >On Wed, Sep 19, 2018 at 7:52 PM, Glasser, Matthew >wrote: >> It is a custom function that I already pointed to. > >Am I right in thinking that the rms function boils down to: > >sqrt(mean(x .*

Re: [HCP-Users] MATLAB libraries in Resting State Stats script

Not sure, I think over all of the HCP and related pipelines the signal toolbox will have to remain a dependency. Matt. On 9/19/18, 4:16 PM, "Matthew Brett" wrote: >Hi, > >On Wed, Sep 19, 2018 at 8:13 PM, Glasser, Matthew >wrote: >> normalise is the custom function, not rms. > >I know - I was

Re: [HCP-Users] MATLAB libraries in Resting State Stats script

It is a custom function that I already pointed to. Matt. From: Timothy Coalson mailto:tsc...@mst.edu>> Date: Wednesday, September 19, 2018 at 3:27 PM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: Andrew Poppe mailto:poppe...@gmail.com>>,

Re: [HCP-Users] MATLAB libraries in Resting State Stats script

'rms' appears to be part of the signal toolbox. 'normalize' seems to be a built-in matlab function, but I have no idea about 'normalise'. Tim On Wed, Sep 19, 2018 at 11:15 AM, Glasser, Matthew wrote: > I believe rms is a matlab provided function. The custom functions are in > here:

Re: [HCP-Users] FIX denoised 3T task data release?

We do plan to release denoised 3T task data, but I don¹t have a time-table on that. We didn¹t specifically make a 59k version of the parcellation, but that is easy to create with wb_command -cifti-resample and the appropriate spheres + vertex area maps. Matt. On 9/19/18, 2:08 PM,

[HCP-Users] FIX denoised 3T task data release?

Hello, We were implementing the hcp_fix_multi_run script on the HCP 3T task data. Although the script is running, it is resource intensive. It seemed from a previous thread that FIX was implemented on the task data: https://www.mail-archive.com/hcp-users@humanconnectome.org/msg06605.html I

Re: [HCP-Users] SNR in WU-Minn HCP 1200 Subjects protocol

That number is something that may be useful when on the scanner fiddling with the protocols, but is otherwise irrelevant. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Jinxia Yao mailto:yao...@purdue.edu>> Date: Tuesday, September 18, 2018 at 6:41 PM To:

Re: [HCP-Users] An error when running AtlasRegistionToMNI152_FLIRTandFNIRT.sh

You didn’t set all of the required options: --ref= --refbrain= --refmask= --ref2mm= --ref2mmmask= Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "outlook_c843878f00767...@outlook.com"

[HCP-Users] SNR in WU-Minn HCP 1200 Subjects protocol

Dear Mr/Ms, First of all, let me thanks for your great work in HCP dataset. I am an graduate student from Purdue University in Biomedical Engineering department. Recently, I got a question about the SNR appears in protocol manual. I found all the detailed session scan protocol (e.g.

[HCP-Users] An error when running AtlasRegistionToMNI152_FLIRTandFNIRT.sh

Dear HCP experts Hi, I am Qunjun, A PhD student in China. I got an error when I ran PreFreeSurfer.sh. It came out when the program proceeded to AtlasRegistionToMNI152_FLIRTandFNIRT.sh. --- START: AtlasRegistration to MNI152 Unrecognised option /

Re: [HCP-Users] MATLAB libraries in Resting State Stats script

I believe rms is a matlab provided function. The custom functions are in here: https://github.com/Washington-University/HCPpipelines/tree/master/global/matlab Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Andrew Poppe mailto:poppe...@gmail.com>> Date: Wednesday,

[HCP-Users] MATLAB libraries in Resting State Stats script

Hello all, I've been working with the resting state stats batch script, and it seems to be running correctly on our data. I have it set to use the compiled "MCR" version of the RestingStateStats matlab script. However, I'd like to make a couple modifications to that script, most notably to save

Re: [HCP-Users] Can't use boto to download HCP subjects from AWS server anymore

Hi Matt, That wasn't it but I solved the problem, thanks for your help :-) Rutger On Wed, 19 Sep 2018 at 13:29, Glasser, Matthew wrote: > Are you using the temp server instead of the reactivated real server? > > Matt. > > From: on behalf of Rutger Fick < > fick.rut...@gmail.com> > Date:

Re: [HCP-Users] Can't use boto to download HCP subjects from AWS server anymore

Are you using the temp server instead of the reactivated real server? Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Rutger Fick mailto:fick.rut...@gmail.com>> Date: Wednesday, September 19, 2018 at 6:54 AM To:

[HCP-Users] Can't use boto to download HCP subjects from AWS server anymore

Hello, Until some time ago I have been able to download HCP subjects directly from the AWS server using the package "boto", using both my public and private AWS key. However, when do the same now (also after regenerating my AWS credentials) I receive the response "S3ResponseError: 403