Re: [HCP-Users] MSMAll Failure Following hcp-fix_multi-run

ject: [HCP-Users] MSMAll Failure Following hcp-fix_multi-run Hello, I am having issues running MSMAll following hcp-fix_multi-run for a study that I am doing processing for. The particular study that I am processing data for has 6 fMRI scans totalling 2950 timepoints per scanning session. I am

[HCP-Users] MSMAll Failure Following hcp-fix_multi-run

Hello, I am having issues running MSMAll following hcp-fix_multi-run for a study that I am doing processing for. The particular study that I am processing data for has 6 fMRI scans totalling 2950 timepoints per scanning session. I am certainly aware of the large amount of memory that

Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

;Harms, Michael" , Steve Smith Cc: HCP 讨论组 Subject: RE: [HCP-Users] MSMAll vs. MSMSulc reliability in our data Thank you for all of the insightful comments, this has been a huge help. I think we’ll stick with MSMSulc measures until we have a clearer idea of what data we’d need to confi

Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

. Best, Maria From: Glasser, Matthew Sent: Thursday, May 9, 2019 9:22:51 PM To: Harms, Michael; Maria Sison; Steve Smith Cc: HCP 讨论组 Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data This issue of what kind of data and how much is something we plan

Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: on behalf of "Glasser, Matthew" Date: Thursday, May 9, 2019 at 4:23 PM To: Maria Sison , Stephen Smith Cc: HCP 讨论组 Subject: Re: [HCP-Users] MSMAll vs. M

Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

Email: mha...@wustl.edu From: on behalf of "Glasser, Matthew" Date: Thursday, May 9, 2019 at 4:23 PM To: Maria Sison , Stephen Smith Cc: HCP 讨论组 Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data Not running sICA+FIX might well

Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

will more tend to correlate with MSMAll. Matt. From: on behalf of Maria Sison Date: Thursday, May 9, 2019 at 3:40 PM To: Steve Smith Cc: HCP 讨论组 Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data Thank you so much, this is very helpful and interesting to think about. We

Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

requirement for MSMALL would be. Best, Maria From: Steve Smith Sent: Thursday, May 9, 2019 4:19:24 PM To: Maria Sison Cc: HCP 讨论组 Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data Hi - probably the single primary thing is number of timepoints

Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

Total > scan length is 496 s. > > Out of curiosity, which parameters would be most important for MSMAll? > > Thank you, > Maria > > From: Steve Smith mailto:st...@fmrib.ox.ac.uk>> > Sent: Thursday, May 9, 2019 3:56:49 PM > To: Maria Sison > Cc: HCP 讨论组 > Subj

Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

From: Steve Smith Sent: Thursday, May 9, 2019 3:56:49 PM To: Maria Sison Cc: HCP 讨论组 Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data Hi - what is your rfMRI protocol? It might be that you're right that the difference is in the preprop - but my first guess might

Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

Hi - what is your rfMRI protocol? It might be that you're right that the difference is in the preprop - but my first guess might be that - if the rfMRI data is not as high quality as HCP rfMRI data - it might not be good enough to reliably drive MSMALL? Cheers. > On 9 May 2019, at 14:45,

[HCP-Users] MSMAll vs. MSMSulc reliability in our data

Dear experts, We have run the HCP minimal preprocessing pipelines on our data (1 mm isotropic T1w and FLAIR + rest and 4 tasks) and compared test-retest reliability for MSMSulc and MSMAll in 20 subjects. Specifically, we looked at intraclass correlations for parcellated cortical thickness and

Re: [HCP-Users] MSMAll, missing _vn file

This issue will be resolved in the upcoming MR+FIX release. There is no simple workaround. Matt. Sent from my Verizon, Samsung Galaxy smartphone Original message From: Marta Moreno Date: 3/4/19 10:30 AM (GMT-06:00) To: HCP Users Subject: [HCP-Users] MSMAll, missing _vn

[HCP-Users] MSMAll, missing _vn file

Dear experts, I am running MSMAllPipelineBatch.sh after hcp_fix on a 10min run (rsfMRI) and getting an error saying that the file: "RS_fMRI_1_Atlas_hp2000_clean_vn_tempcompute.dscalar.nii" does not exist. I am using fsl 5.0.11 and fix 1.067. Any help? Thanks, Leah

Re: [HCP-Users] MSMAll

cp-users@humanconnectome.org>> Subject: [HCP-Users] MSMAll Dear HCP users, I am using Movie Task fMRI 2mm/32k FIX-Denoised (Compact), and I found MSMALL in one file's name, but not found fs_LR in any file's name. I wonder whether can I simply understand MSMALL file as registered to fs_LR mesh? Or

[HCP-Users] MSMAll

Dear HCP users, I am using *Movie Task fMRI 2mm/32k FIX-Denoised (Compact), *and I found MSMALL in one file's name, but not found fs_LR in any file's name. I wonder whether can I simply understand MSMALL file as registered to fs_LR mesh? Or still in individual space? Can I just project the

Re: [HCP-Users] MSMall Question

p-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] MSMall Question Hello, I have a question about MSMall, as I am trying to better understand how it is performing the alignment in the HCP Pipelines. My under

[HCP-Users] MSMall Question

Hello, I have a question about MSMall, as I am trying to better understand how it is performing the alignment in the HCP Pipelines. My understanding is that MSMall uses areal features that include myelin maps and resting state network maps for alignment. MSM uses a discrete optimization

Re: [HCP-Users] MSMAll for MultiRunICAFIX

Watch this space for an update on MSMAll with MultiRunFIX. The pipelines in the current master aren¹t all working together and we are working on fixing that. Matt. On 10/9/18, 9:58 AM, "hcp-users-boun...@humanconnectome.org on behalf of Sang-Young Kim" wrote: >Dear Experts: > >I have a

[HCP-Users] MSMAll for MultiRunICAFIX

Dear Experts: I have a question for MSMAll alignment for MultiRunICAFIX cleaned data. Once I run the MultiRunICAFIX pipeline, I get the output like "${fMRIConcatName}_Atlas_hp2000_clean.dtseries.nii". But I want to align the data (e.g., ${fMRIConcatName}_Atlas_hp2000_clean.dtseries.nii)

Re: [HCP-Users] MSMAll

There are a couple of things that we need to sort out to make MSMAll work with the new multi-run FIX code. We will be working on that next week. Matt. On 10/5/18, 3:05 PM, "hcp-users-boun...@humanconnectome.org on behalf of Shankar Tumati" wrote: >Hello, > >After running the

[HCP-Users] MSMAll

Hello, After running the hcp_fix_multi_run.sh script on the task data, a folder for concatenated files is created and a .ica folder is created in each task folder. However, MSMAllPipeline.sh script tries to find /filtered_func_data.ica/melodic_mix, which is present only in the Concat folder.

[HCP-Users] MSMAll

Hello, After running the hcp_fix_multi_run.sh script on the task data, a folder for concatenated files is created and a .ica folder is created in each task folder. However, MSMAllPipeline.sh script tries to find /filtered_func_data.ica/melodic_mix, which is present only in the Concat folder.

Re: [HCP-Users] MSMAll

: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:HCP-Users@humanconnectome.org>> Subject: Re: [HCP-Users] MSMAll I noticed on the FSL FIX FAQ page the following: Can I use FIX to clean task fMRI data? * Yes, although you will probably need to create a stu

Re: [HCP-Users] MSMAll

t; > On Tue, Jul 24, 2018 at 3:21 PM, Glasser, Matthew > wrote: > >> The MR+FIX pipeline automatically breaks the runs back up at the end. >> >> Matt. >> >> From: Timothy Hendrickson >> Date: Tuesday, July 24, 2018 at 3:17 PM >> >> To: M

Re: [HCP-Users] MSMAll

, Jul 24, 2018 at 3:21 PM, Glasser, Matthew wrote: > The MR+FIX pipeline automatically breaks the runs back up at the end. > > Matt. > > From: Timothy Hendrickson > Date: Tuesday, July 24, 2018 at 3:17 PM > > To: Matt Glasser > Cc: "hcp-users@humanconnectome.org&quo

Re: [HCP-Users] MSMAll

@humanconnectome.org>" mailto:HCP-Users@humanconnectome.org>> Subject: Re: [HCP-Users] MSMAll So once I finish with the multiICAFIX pipeline I wold have to manually separate the concatenated cleaned nifti file and then run MSMAll on those scans. Is that right? Timothy Hendrickson Ne

Re: [HCP-Users] MSMAll

> From: Timothy Hendrickson > Date: Monday, July 23, 2018 at 1:26 PM > > To: Matt Glasser > Cc: "hcp-users@humanconnectome.org" > Subject: Re: [HCP-Users] MSMAll > > I handle processing for several studies, an upward bound for the studies I > handle would b

Re: [HCP-Users] MSMAll

: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:HCP-Users@humanconnectome.org>> Subject: Re: [HCP-Users] MSMAll I handle processing for several studies, an upward bound for the studies I handle would be approximately 3000 frames. Timothy Hendrickson Ne

Re: [HCP-Users] MSMAll

some bugs. How many frames are you > wanting to do? > > Peace, > > Matt. > > From: Timothy Hendrickson > Date: Monday, July 23, 2018 at 1:02 PM > To: Matt Glasser > Cc: "hcp-users@humanconnectome.org" > Subject: Re: [HCP-Users] MSMAll > > T

Re: [HCP-Users] MSMAll

...@umn.edu>> Date: Monday, July 23, 2018 at 1:02 PM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:HCP-Users@humanconnectome.org>> Subject: Re: [HCP-Users] MSMAll Thanks Matt. With the

Re: [HCP-Users] MSMAll

gt; From: on behalf of Timothy > Hendrickson > Date: Thursday, July 19, 2018 at 6:24 PM > To: "hcp-users@humanconnectome.org" > Subject: [HCP-Users] MSMAll > > Hello, > > From the HCP course material I noticed that that suggested format to use > MSMAll is to do so i

Re: [HCP-Users] MSMAll

2018 at 6:24 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:HCP-Users@humanconnectome.org>> Subject: [HCP-Users] MSMAll Hello, >From the HCP course material I noticed that that suggested format to use >MSMAll is to do so immediately

[HCP-Users] MSMAll

Hello, >From the HCP course material I noticed that that suggested format to use MSMAll is to do so immediately after the Minimal Pre-Processing stream and immediately before subsequent tfMRI and rfMRI processing. As MSMAll expects the data inputted to be run through ICA-FIX I am curious what I

Re: [HCP-Users] MSMAll data in HCP_1200 set

nday, January 22, 2018 at 1:51 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re

Re: [HCP-Users] MSMAll data in HCP_1200 set

: "Glasser, Matthew" <glass...@wustl.edu> Date: Monday, January 22, 2018 at 2:19 PM To: "Ho, Wilson Christopher" <w...@mgh.harvard.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] MSMAll data in HCP_1200

Re: [HCP-Users] MSMAll data in HCP_1200 set

"Ho, Wilson Christopher" <w...@mgh.harvard.edu<mailto:w...@mgh.harvard.edu>> Date: Monday, January 22, 2018 at 1:16 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectom

[HCP-Users] MSMAll data in HCP_1200 set

Hello HCP experts, I have a question about the MSMAll data. I know it’s advised to use the MSMAll variants of maps and surfaces for group analyses but some subjects are missing these (from what I’ve attempted to pull from the Amazon S3 database ). Take for example subject 168038, which has:

Re: [HCP-Users] MSMALL and areal classifier

s-boun...@humanconnectome.org>> on behalf of 杨国元 <yangguoy...@pku.edu.cn<mailto:yangguoy...@pku.edu.cn>> Date: Saturday, November 18, 2017 at 5:37 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@hum

[HCP-Users] MSMALL and areal classifier

Hi, We want to use the multi-modal parcellation to produce a Chinese brain parcellation. We have already made the minimal preprocessing pipeline. Now we need the MSMALL and areal classifier to make the brain parcellation. So, where can I get these methods' source code? Any suggestions?

Re: [HCP-Users] MSMALL atlas usage

gt;> -- >>> Michael Harms, Ph.D. >>> --- >>> Conte Center for the Neuroscience of Mental Disorders >>> Washington University School of Medicine >>> Department of Psychiatry, Box 8134 >>&g

Re: [HCP-Users] MSMALL atlas usage

t. Louis, MO 63110 Email: mha...@wustl.edu >> >> From: <hcp-users-boun...@humanconnectome.org> on behalf of A Nunes < >> adonay.s.nu...@gmail.com> >> Date: Tuesday, August 9, 2016 at 4:13 PM >> To: "HCP-Users@humanconnectome.org" <HCP-

Re: [HCP-Users] MSMALL atlas usage

See entries 1 and 2 at https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ . Tim On Tue, Aug 9, 2016 at 4:13 PM, A Nunes wrote: > Hi, > > I would like to use this new MSMall atlas. For that I need to open it in > a toolbox or matlab, however I am not

[HCP-Users] MSMALL atlas usage

Hi, I would like to use this new MSMall atlas. For that I need to open it in a toolbox or matlab, however I am not able to open it using either freesurfer, caret, FSlviwer, fieldtrip, only through the workbench. So lets say I want to load this nii file in matlab using freesurfer MRIread: