[HCP-Users] 13-volume mismatch between rsfMRI volumes and trigger file?

Dear HCP Staff, I have been looking at the trigger logs (column 1 of the *Physio_log.txt files) in rsfMRI data (both sessions) for the 100 unrelated subjects. While the total temporal length of the physio logs matches the total length of the fMRI data (1200 * TR), in all physio logs I

Re: [HCP-Users] Unresolved: 13-volume mismatch between rsfMRI volumes and trigger file?

Washington University School of Medicine Department of Anatomy and Neurobiology Email: burge...@pcg.wustl.edu mailto:burge...@pcg.wustl.edu On May 15, 2015, at 3:46 PM, Nicola Toschi tos...@med.uniroma2.it mailto:tos...@med.uniroma2.it wrote: Dear List, I have not yet been able to find

Re: [HCP-Users] Exact Meaning of ICA maps in 800 subjects release

for that is... Cheers. On 6 Jul 2016, at 07:26, Nicola Toschi <tos...@med.uniroma2.it <mailto:tos...@med.uniroma2.it>> wrote: Hi, The volumetric version! Thanks in advance, Nicola Original message From: Stephen Smith <st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>

Re: [HCP-Users] Exact Meaning of ICA maps in 800 subjects release

Great, thanks a lot,  Nicola  Original message From: Stephen Smith <st...@fmrib.ox.ac.uk> Date: 06/07/2016 10:09 AM (GMT+01:00) To: Nicola Toschi <tos...@med.uniroma2.it> Cc: hcp-users <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Exact M

Re: [HCP-Users] Exact Meaning of ICA maps in 800 subjects release

Hi,  The volumetric version! Thanks in advance,  Nicola Original message From: Stephen Smith <st...@fmrib.ox.ac.uk> Date: 04/07/2016 12:37 PM (GMT+01:00) To: Nicola Toschi <tos...@med.uniroma2.it> Cc: hcp-users <hcp-users@humanconnectome.org> Subje

[HCP-Users] Exact Meaning of ICA maps in 800 subjects release

Hi list,  This may be more of a MELODIC question, but I would be grateful for any input: In the ICA release on 800+ subjects, what is the exact mathematical meaning / definition of the (non-binary) intensities of the different component volumes? Are they easily relatable to a statistical map (I

[HCP-Users] Regions "missing" in grayordinate space?

(85GB) <https://db.humanconnectome.org/app/action/ChooseDownloadResources?project=HCP_Resources=GroupAvg=HCP_S900_PTNmaps_d300.zip> Thanks! On 14 Jul 2016, at 06:49, Nicola Toschi <tos...@med.uniroma2.it <mailto:tos...@med.uniroma2.it>> wrote: Dear Prof. Smith, Dear List, one more qu

Re: [HCP-Users] Regions "missing" in grayordinate space?

sh_atlases/Avgwmparc.nii.gz Thanks, Matt. From: Nicola Toschi <tos...@med.uniroma2.it <mailto:tos...@med.uniroma2.it>> Date: Sunday, November 27, 2016 at 11:18 AM To: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>>, hcp-users <hcp-users@h

[HCP-Users] Atlas-based localizations in workbench space

ng state connectivity) to give better > cross-subject alignment than traditional volume-based alignment approaches > to MNI space. > > Peace, > > Matt. > > On 11/18/16, 5:06 AM, "hcp-users-boun...@humanconnectome.org on behalf of > Nicola Toschi" <hcp-users-b

Re: [HCP-Users] Atlas-based localizations in workbench space

.pscalar.nii) and you could simply report > the connectivity values of each area to your ROI. > > Peace, > > Matt. > > On 11/19/16, 4:42 AM, "Nicola Toschi" <tos...@med.uniroma2.it> wrote: > >> Dear Matt, dear List, >> >> after extracting seed-based conne

[HCP-Users] Dense Connectome: extracting seed-based connectivity

Hi List, we are working with the R820 dense connectome (in connectome workbench) and have a few (basic?) questions which we are struggling with: 1) What is the recommended sequence of commands to extract a seed-based connectome from the 33GB dense connectome file (e.g. all nodes which are

[HCP-Users] Position of vertices in myelin maps and 164k sphere

Dear List, I am trying to do some postprocessing on myelin and thickness maps (164k versions) contained in the MNINonLinear Directory of the Structural dataset (e.g. ${subject}.corrThickness_MSMAll.164k_fs_LR.dscalar.nii and ${subject}.MyelinMap_BC_MSMAll.164k_fs_LR.dscalar.nii). I thought

Re: [HCP-Users] Position of vertices in myelin maps and 164k sphere

, but that often does not equate to having the same 3D coordinates (as volumetric registration is not able to align cortical areas across subjects). Peace, Matt. On 3/29/17, 8:41 AM, "hcp-users-boun...@humanconnectome.org on behalf of Nicola Toschi" <hcp-users-boun...@humanconnectome.org on

Re: [HCP-Users] Position of vertices in myelin maps and 164k sphere

to step out of the Workbench. Thanks! Nicola On 03/29/2017 04:18 PM, Glasser, Matthew wrote: What operations beyond smoothing do you need? There is wb_command -cifti-smoothing. Peace, Matt. From: Nicola Toschi <tos...@med.uniroma2.it <mailto:tos...@med.uniroma2.it>> Date: Wedn

Re: [HCP-Users] Position of vertices in myelin maps and 164k sphere

12:57 AM, Timothy Coalson wrote: On Wed, Mar 29, 2017 at 3:47 PM, Nicola Toschi <tos...@med.uniroma2.it <mailto:tos...@med.uniroma2.it>> wrote: Dear Donna and Tim, thank you very much for your replies and insights. Yes, flatmaps is exactly what I was looking for!

Re: [HCP-Users] Position of vertices in myelin maps and 164k sphere

s into matlab, which contain vertex neighbor >> information, by using the gifti toolbox >> (https://www.artefact.tk/software/matlab/gifti/). The easiest way to get >> vertex correspondence to the data in matlab is currently to use wb_command >> -cifti-separate to convert the su

Re: [HCP-Users] Discrepancy in files downloaded from the web interface w.r.t CREST

100206.R.sphere.MSMAll.native.surf.gii The md5sum from the file I’m retrieving via CREST/curl matches what I get from the package. Thanks, Mike *From:* hcp-users-boun...@humanconnectome.org [mailto:hcp-users-boun...@humanconnectome.org] *On Behalf Of *Nicola Toschi *Sent:* Tuesday, October 31, 2017 10

Re: [HCP-Users] Discrepancy in files downloaded from the web interface w.r.t CREST

of allowed sessions.  Then your output might just contain an error message rather than the actual file contents.  Performance should also be a bit better if each call isn’t generating a new session. Regards, Mike *From:*Hodge, Michael *Sent:* Thursday, November 2, 2017 12:11 PM *To:* 'Nicola To

Re: [HCP-Users] Discrepancy in files downloaded from the web interface w.r.t CREST

oh wait - I have and extra 'archive' in the path... is this what the problem is? On 11/02/2017 06:00 PM, Nicola Toschi wrote: Hi Michael, I am using: sub=100206 h=R curl -u USER:PASS -O https://db.humanconnectome.org/data/archive/projects/HCP_1200/subjects/${sub}/experiments/${sub}_CREST

Re: [HCP-Users] Discrepancy in files downloaded from the web interface w.r.t CREST

curl command, and worked as-is once I removed the duplicate slash. Regards, Mike *From:*hcp-users-boun...@humanconnectome.org [mailto:hcp-users-boun...@humanconnectome.org] *On Behalf Of *Nicola Toschi *Sent:* Thursday, November 2, 2017 12:02 PM *To:* Hodge, Michael <hod...@wustl.edu>

Re: [HCP-Users] Discrepancy in files downloaded from the web interface w.r.t CREST

100206.R.sphere.MSMAll.native.surf.gii The md5sum from the file I’m retrieving via CREST/curl matches what I get from the package. Thanks, Mike *From:* hcp-users-boun...@humanconnectome.org [mailto:hcp-users-boun...@humanconnectome.org] *On Behalf Of *Nicola Toschi *Sent:* Tuesday, October 31, 2017 10

[HCP-Users] Discrepancy in files downloaded from the web interface w.r.t CREST

Hi list, though a processing error I noticed the following strange behaviour: 1) When i download the complete structural package using the Aspera plugin and extract the file I am interested in, I get (for example):

[HCP-Users] Glasser atalas version in volumetric space - good enough for tractography?

Hello List and Lello Matthew, I found a few versions of your new atlas in volumetric space. (e.g. https://figshare.com/articles/HCP-MMP1_0_projected_on_MNI2009a_GM_volumetric_in_NIfTI_format/3501911)

[HCP-Users] Discrepancy in files downloaded from the web interface w.r.t CREST

Hi list, though a processing error I noticed the following strange behaviour: 1) When i download the complete structural package using the Aspera plugin and extract the file I am interested in, I get (for example):

[HCP-Users] Diffusion Times (Delta and delta) for HCP 1200 release?

Dear List, I was looking for the data mentioned in the subject line (specific about the monopolar sequence used in diffusion scanning, i.e. the diffusion times bigdelta and smalldelta). I could not find them in the manual ro appendix (forgive me if this is an oversight). Could someone please

Re: [HCP-Users] NEO-FFI Agreeableness scoring

. Louis, MO 63110 314-362-9387 e...@wustl.edu<mailto:e...@wustl.edu> www.humanconnectome.org<http://www.humanconnectome.org/> ---- *From:* Nicola Toschi <tos...@med.uniroma2.it> *Sent:* Friday, March 9, 2018 11:3

Re: [HCP-Users] NEO-FFI Agreeableness scoring

Hi Jenn, Hi List, I was wondering if this issue with the Agreeableness scoring had been a) confirmed and b) addressed in the current data available for download. It would be great if you could post an update on this. Thanks!!! Nicola On 10/04/2017 05:16 PM, Elam, Jennifer wrote: Hi Josh,

Re: [HCP-Users] Fiber tracking starting from PTM volumetric labels

ike that with the MSMAll CIFTI data. > > Matt. > > On 10/23/18, 6:49 PM, "hcp-users-boun...@humanconnectome.org on behalf of > Nicola Toschi" tos...@med.uniroma2.it> wrote: > >> Hello List, >> >> I would like to ask the experts an opinion about an

Re: [HCP-Users] Convert subject-specific ICA node maps to volumetric space?

bundle them in the PTN release. You can easily get them though by regressing node timeseries into 4D FIX-cleaned data. Cheers. On 13 Nov 2018, at 16:09, Nicola Toschi <mailto:tos...@med.uniroma2.it>> wrote: Dear HCP list and experts, I was wondering if the subject-specific node

[HCP-Users] Convert subject-specific ICA node maps to volumetric space?

Dear HCP list and experts, I was wondering if the subject-specific node maps from the latest PTN release (which are available in CIFTI format) are also available in volumetric space (which would aid the specific analysis we are running). Or if not, maybe a pointer on how to convert them?

Re: [HCP-Users] Convert subject-specific ICA node maps to volumetric space?

-convert will allow you to feed the data through virtually any tool that doesn't use spatial neighborhood information. Tim On Tue, Nov 13, 2018 at 10:45 AM, Nicola Toschi mailto:tos...@med.uniroma2.it>> wrote: Thank you Steve, I was hoping to get them out of the CIFTI versions

[HCP-Users] Time-of-day when scans where performed?

Dear List, I am running inference on a hypothesis that is influenced by circadian rhythms and was wondering what the easiest way would be to retrieve, for any particular scan, at what time of day it was performed. Is this possible without access to the DICOM files? Guidance much appreciated!

[HCP-Users] Intermediate freesurfer files not available through CREST?

Hello List, I am trying to retrieve the files present in the 'surf' directory of the freesurfer reconstruction via CREST. However, when trying to retrieve (e.g) lh.white I always end up with a file containing only error messages. I would be grateful for any pointers. below is an example of my

Re: [HCP-Users] Intermediate freesurfer files not available through CREST?

Tel: 314-747-6173 > > St. Louis, MO 63110 Email: mha...@wustl.edu > > On 9/24/18, 6:25 PM, "hcp-users-boun...@humanconnectome.org on behalf of > Nicola Toschi" tos...@med.uniroma2.it> wrote: > > Hello List, > > I am trying to retriev

[HCP-Users] Number of Scanners used in S1200 release

Dear List, a basic piece of info which I would like to put in paper: how many scanners exactly were used in the S1200 release? Could anyone point me to thin information? Thanks a lot in advance, Nicola --- This email has been checked for viruses by Avast antivirus software.

Re: [HCP-Users] AWS S3 maximum number of attempts (at first attempt)

bucket from the command line? Are you able to access from the command-line? > Have you tried regenerating and replacing your access keys? > > Regards, > > Mike > > -----Original Message- > From: Nicola Toschi > Sent: Monday, February 4, 2019 4:46 PM > To: Hodge, Michael

Re: [HCP-Users] AWS S3 maximum number of attempts (at first attempt)

s3://hcp-openaccess-temp, which has since been removed. Our current bucket > is s3://hcp-openaccess. I'm able to access that one fine. > > Regards, > > Mike > > -Original Message- > From: hcp-users-boun...@humanconnectome.org > On Behalf Of Nicola Toschi >

[HCP-Users] AWS S3 maximum number of attempts (at first attempt)

Dear List, this may be trivial, but I keep running into the below error (I seem to be maxing out on login attempts) when using the ASW S3 browser under windows. I have managed to login twice in total (in 2-3 days) but no luck since. Thank you very much in advance, Nicola [I] [2/4/2019

[HCP-Users] Eye tracking data for 3T scans?

-- _ Prof. Nicola Toschi Associate Professor of Medical Physics Medical Physics Section - Department of Biomedicine and Prevention University of Rome "Tor Vergata" Via Montpellier 1 - 00133 Rome (IT) tos...@med.uniroma2.it Research Staff,

Re: [HCP-Users] Eye tracking data for 3T scans?

ctome.org/> *From:* hcp-users-boun...@humanconnectome.org on behalf of Nicola Toschi *Sent:* Friday, April 19, 2019 4:03:20 AM *To:* hcp-users@humanconnectome.org >> hcp-users *Subject:* [HCP-Users] Eye tracking data for 3T scans? Dear List, from what I understand fro