Re: [HCP-Users] PostFreeSurfer Pipeline

Have a look at the example script: https://github.com/Washington-University/HCPpipelines/blob/master/Examples/Scripts/PostFreeSurferPipelineBatch.sh I have just fixed it to default to MSMSulc in the latest master. As for 0.9mm T1w and T2w data, you could make 0.9mm templates of the various

[HCP-Users] Re:   HCP pipeline for Lifespan Pilot Data

to use fsl_sub to queue or run ${HCPPIPEDIR}/PreFreeSurfer/PreFreeSurferPipeline.sh" queuing_command="${FSLDIR}/bin/fsl_sub ${QUEUE}" fi # Run (or submit to be run) the PreFreeSurferPipeline.sh script # with all the specified parameter values ${queuing_command} ${HCPPIPEDIR}/PreFreeSurfer/PreF

[HCP-Users] Re:   HCP pipeline for Lifespan Pilot Data

_MPR1/LS2001_3T_FieldMap_Magnitude for reading! Shujiro 2018年8月27日 08:02、"Glasser, Matthew" mailto:glass...@wustl.edu>>さんのメッセージ： What about your pipeline call? Matt. From: 南 修司郎 mailto:shujiromin...@me.com>> Date: Sunday, August 26, 2018 at 6:00 PM To: Matt Glasser mailto

[HCP-Users] Re:   HCP pipeline for Lifespan Pilot Data

_3T_SpinEchoFieldMap_RL_gdc.nii.gz LS2001_3T_T1w_MPR1.nii.gz Shujiro 2018年8月27日 07:48、"Glasser, Matthew" mailto:glass...@wustl.edu>>さんのメッセージ： List your pipeline call and the files you have available, as I don’t recall what was distributed in the pilot data. Matt. From: mailto:hcp-users

Re: [HCP-Users] HCP pipeline for Lifespan Pilot Data

List your pipeline call and the files you have available, as I don’t recall what was distributed in the pilot data. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of 南 修司郎 mailto:shujiromin...@me.com>> Date: Sunday, August 26, 2018 at 5:45 PM To:

Re: [HCP-Users] two maximum points using -metric-extrema

27, 48. So I am quite confusing about what happened here. Best regards, Xinyang At 2018-08-26 13:03:42, "Glasser, Matthew" mailto:glass...@wustl.edu>> wrote: How about posting some screen captures so we know what is happening? Matt. From: Xinyang Liu mailto:xinyang_ie...@163.

Re: [HCP-Users] two maximum points using -metric-extrema

two drawings instead of two separate ones? Because the problem is that, when I count the total vertex number for each created ROI using -metric-stats, a few results showed two values for one ROI. I am wondering why this happen and how to deal with that. Best regards, Xinyang At

Re: [HCP-Users] two maximum points using -metric-extrema

ng why this happen and how to deal with that. Best regards, Xinyang At 2018-08-24 19:14:56, "Glasser, Matthew" mailto:glass...@wustl.edu>> wrote: I believe there is a configurable setting that sets the minimum distance between extrema. It is a local min/max that is found. M

Re: [HCP-Users] two maximum points using -metric-extrema

I believe there is a configurable setting that sets the minimum distance between extrema. It is a local min/max that is found. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Xinyang Liu mailto:xinyang_ie...@163.com>> Date: Friday, August 24, 2018 at 4:21 AM To: HCP

[HCP-Users] FW: FSL FIX no memory with hcp_fix_multi_run

t University of Minnesota Informatics Institute University of Minnesota Bioinformatics M.S. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay) On Tue, Aug 21, 2018 at 4:36 PM, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: You might need to configure swap space or increase

Re: [HCP-Users] FSL FIX no memory with hcp_fix_multi_run

on too large for Octave's index type The limit appears to be 2 billion elements total (signed 32-bit). Tim On Fri, Aug 17, 2018 at 4:42 PM, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: Is everything 64bit? Do you have swap space? Matt. From: Timothy Hendrickson mailto:hendr...@u

Re: [HCP-Users] A 2D T2-scan for HCP Pipelines?

@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] A 2D T2-scan for HCP Pipelines? Thanks for the quick reply Matt! Just to be sure, by resolution, do you mean voxel size, i.e. at least 1mm, and preferably smaller? On Tue, Aug 21, 2018 at 1:11

Re: [HCP-Users] PreFreeSurfer and FreeSurfer pipelines questions

CP. are there any other version-specific elements that are influenced by the use of a more updated version? what do you think is best to do in this case? Hope to hear from you, Shachar On Mon, 20 Aug 2018 at 21:26, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: I think you need to ask tha

Re: [HCP-Users] A 2D T2-scan for HCP Pipelines?

Really what matters is the resolution of the scan. If the slice resolution is low, it probably won’t work well. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Darko Komnenić mailto:komnen...@gmail.com>> Date: Tuesday, August 21, 2018 at 4:42 AM To:

Re: [HCP-Users] PreFreeSurfer and FreeSurfer pipelines questions

lib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib thanks again Sahchar On Mon, 20 Aug 2018 at 18:38, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: 1. You can get

Re: [HCP-Users] PreFreeSurfer and FreeSurfer pipelines questions

1. You can get the gradient distortion coefficients from your scanner. NONE can be set and for some scanners it does not make much difference (e.g. Trio). 2. recon_all_seed is a random number seed. Presumably this is an optional argument, but you could set 12345. 3. Need to look at the

Re: [HCP-Users] FSL FIX no memory with hcp_fix_multi_run

kson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University of Minnesota Bioinformatics M.S. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay) On Fri, Aug 17, 2018 at 2:04 PM, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: I have

Re: [HCP-Users] FSL FIX no memory with hcp_fix_multi_run

I have attached an updated version of read_avw_img.m that forces matlab to retain the same precision as the input file rather than converting everything to doubles. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Hendrickson mailto:hendr...@umn.edu>> Date:

Re: [HCP-Users] Locating a seed for functional connectivity

Note that MNI space is difficult to accurately relate to surface-based data for a variety of reasons related to the limitations of volume-based analyses that are detailed in these papers: https://www.nature.com/articles/nn.4361 http://www.pnas.org/content/early/2018/06/19/1801582115.short

Re: [HCP-Users] FSL melodic gives hex format ICs

as using FSL 5.0.6 Are there updated installation guidelines for the latest release ? Thanks Paul 2018-08-13 2:28 GMT+02:00 Glasser, Matthew mailto:glass...@wustl.edu>>: Please use the latest version of the HCP Pipelines. Also can you tell us where this instruction to use FSL 5.0.6 is so tha

Re: [HCP-Users] FSL melodic gives hex format ICs

Please use the latest version of the HCP Pipelines. Also can you tell us where this instruction to use FSL 5.0.6 is so that we can remove it? It is out of date. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Paul Triebkorn mailto:paul.triebk...@googlemail.com>>

Re: [HCP-Users] HCP_MMP1.0 parcellation of the Resting State fMRI FIX-Denoised (Compact) data using workbench.exe

That seems reasonable, however I would use the matlab CIFTI tools to wrap the CIFTI to GIFTI conversion and loading into matlab all in one step: https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB? Matt. From:

Re: [HCP-Users] Error writing .ptseries file in Matlab

The ft CIFTI functions are unsupported. Please use the functions located here: https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB? Peace, Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Leonardo Tozzi

Re: [HCP-Users] Finding a significant difference only in one hemisphere

ail=g>. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu<mailto:mha...@wustl.edu> From: Darko Komnenić mailto:komnen...@gmail.com>> Date: Wednesday, August 8, 2018 at 2:08 PM To: "Glasser, Matthew" mailto:g

Re: [HCP-Users] Finding a significant difference only in one hemisphere

went wrong along the pipeline… You can also open the residuals and see if there are large outliers with a lot of spatial spread. These are just suggestions… hope they could help anyway… All the best, Anderson From: "Glasser, Matthew" mailto:glass...@wustl.edu>> Date: Wednesday,

Re: [HCP-Users] Using Glasser parcellation for task activations

1. Just cortical areas. As far as I know, there isn’t a multi-modal subcortical parcellation available a this time unfortunately. Some folks have integrated the FreeSurfer subcortical parcels in, but e.g. for the cerebellum it includes a lot of different areas in the same parcel. 2. I

Re: [HCP-Users] Finding a significant difference only in one hemisphere

Email: mha...@wustl.edu<mailto:mha...@wustl.edu> From: Darko Komnenić mailto:komnen...@gmail.com>> Date: Wednesday, August 8, 2018 at 2:08 PM To: "Glasser, Matthew" mailto:glass...@wustl.edu>> Cc: "Harms, Michael" mailto:mha...@wustl.edu>>, &quo

Re: [HCP-Users] Finding a significant difference only in one hemisphere

ity School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave<https://maps.google.com/?q=660+South+Euclid+Ave=gmail=g>. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu<mailto:mha...@wustl.edu> From: mailto

Re: [HCP-Users] Finding a significant difference only in one hemisphere

, Darko On Thu, Aug 2, 2018 at 10:01 PM, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: How about posting some pics. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Darko Komnenić mailto:komnen...@gmail.com>> Date: Thursday, August 2, 2018 at 9

Re: [HCP-Users] Finding a significant difference only in one hemisphere

How about posting some pics. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Darko Komnenić mailto:komnen...@gmail.com>> Date: Thursday, August 2, 2018 at 9:16 AM To: "hcp-users@humanconnectome.org"

Re: [HCP-Users] Index error in diffusion preprocessing

I would post this on the FSL list because Jesper would need to tell you what to do with your data. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Leonardo Tozzi mailto:lto...@stanford.edu>> Date: Wednesday, August 1, 2018 at 5:19 PM To:

Re: [HCP-Users] Using ICA-FIXed HCP-pipeline data in FSL Feat

This is really a question about FEAT for the FSL list. I would recommend using the CIFTI data output by the HCP Pipelines with other tools (such as connectome workbench) for doing seed-based functional connectivity with HCP Pipelines processed data. Matt. From:

Re: [HCP-Users] Number of "good" vs "bad" independent components classified by FIX

Number of components depends on a large number of things including length of run, TR, voxel resolution, brain state, and amount of motion. In general as scans improve/have more information in them you will get more total components. Also as you have more motion in a scan, this will increase

Re: [HCP-Users] gradunwarp error

Do you have the latest version of gradunwarp? Matt. On 7/31/18, 11:32 PM, "hcp-users-boun...@humanconnectome.org on behalf of Marc Dubin" wrote: >Hello All, When I run PreFreeSurferPipelineBatch.sh I get the following >error. I tried installing Python 2.7, but I still get the same error. >

Re: [HCP-Users] Seed-based tractography group analysis

You might cross-post this on the FSL list as well. The approach seemed okay, though I’m not sure I would do that if I was trying to do something similar. Not sure what I would do. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Amin Dadashi

Re: [HCP-Users] question about wb_command

You need to open a terminal and then use wb_command from inside of that. It isn’t something you double click on and run. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "shalo...@gmail.com" mailto:shalo...@gmail.com>> Date: Saturday, July

Re: [HCP-Users] The coordinates of surface time-series of Resting State fMRI FIX-Denoised (Compact)

is stage, we can apply our mask to this data. Thank you in advance for your time and consideration. Best regards, Aslan On Thu, Jul 19, 2018 at 1:15 AM Timothy Coalson mailto:tsc...@mst.edu>> wrote: As an additional note, if you do use the non-MSMAll data, you should not use an MSMAll surface wi

Re: [HCP-Users] HCPpipelines Task Analysis Level 2 design error

I think this is tricky because the fsf format is somewhat opaque. What we did to make the original FSFs for the HCP was to run the volume analyses in FEAT for one subject and then modify the FSFs (minimally) for CIFTI. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of

Re: [HCP-Users] MSMAll

nnesota Informatics Institute University of Minnesota Bioinformatics M.S. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay) On Tue, Jul 24, 2018 at 3:21 PM, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: The MR+FIX pipeline automatically breaks the runs back up at the end.

Re: [HCP-Users] wb_command error

Hi Mohana, Is this the latest Connectome Workbench? Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Mohana Ramaratnam mailto:mohanakann...@gmail.com>> Date: Friday, July 27, 2018 at 12:44 PM To: "HCP-Users@humanconnectome.org"

Re: [HCP-Users] gradient_unwarp.py error

<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] gradient_unwarp.py error Thanks! Do you know how I would install gradient_unwarp.py ? On 25 Jul 2018, at 21:39, Glasser, Matthew wrote: That error suggests the tool is not insta

Re: [HCP-Users] gradient_unwarp.py error

That error suggests the tool is not installed or not installed correctly so it is available on the path. Peace, Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marc Dubin mailto:mrd9...@med.cornell.edu>> Date: Wednesday, July 25, 2018 at 8:37 PM To:

Re: [HCP-Users] Where to find warp field from standard to original resting state fMRI data

be appreciated. > >Best, > >Sang-Young > > > >> On Jul 24, 2018, at 3:03 PM, Glasser, Matthew >>wrote: >> >> There is no need to go to original fMRI space in most cases. If you >>want >> data in the native physical space of the subject y

Re: [HCP-Users] MSMAll

uroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University of Minnesota Bioinformatics M.S. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay) On Mon, Jul 23, 2018 at 1:31 PM, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: Give it a try, but you may

Re: [HCP-Users] Where to find warp field from standard to original resting state fMRI data

There is no need to go to original fMRI space in most cases. If you want data in the native physical space of the subject you can use ${StudyFolder}/${Subject}/MNINonLinear/xfms/standard2acpc_dc.nii.gz to warp the data to structural space (and can use a 2mm reference volume in that space if you

Re: [HCP-Users] HCP pipeline working directory documentation

I am not aware of such a document. I am happy to review it when you are ready for accuracy. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Theis, Nicholas" mailto:the...@upmc.edu>> Date: Tuesday, July 24, 2018 at 9:54 AM To:

Re: [HCP-Users] Recon-all errors when calculating Talaraich coordinates

Find this file (orig_nu.log) and post it. Also important to always make sure to include the prior e-mails in your post. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Jayasekera, Dinal" mailto:dinal.jayasek...@wustl.edu>> Date: Monday, July 23, 2018 at 2:47 PM To:

Re: [HCP-Users] Recon-all errors when calculating Talaraich coordinates

Also post that MNI tool’s log file from the e-mail I forwarded you. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Jayasekera, Dinal" mailto:dinal.jayasek...@wustl.edu>> Date: Monday, July 23, 2018 at 2:31 PM To:

Re: [HCP-Users] Issues implementing ICA FIX Multi Run

Please get the latest gitrepo and the comment issue should be fixed. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Theis, Nicholas" mailto:the...@upmc.edu>> Date: Monday, July 23, 2018 at 1:32 PM To: Timothy Coalson mailto:tsc...@mst.edu>> Cc:

Re: [HCP-Users] MSMAll

uroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University of Minnesota Bioinformatics M.S. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay) On Mon, Jul 23, 2018 at 1:12 PM, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: FSL 6.0 h

Re: [HCP-Users] MSMAll

-0783 Mobile: 507-259-3434 (texts okay) On Thu, Jul 19, 2018 at 6:26 PM, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: There is a new Multi-run FIX pipeline currently available in the Git repository that you can use. I would consider it beta a this time. Matt. From: mailto:hcp-user

Re: [HCP-Users] WM and CSF signal extraction

it. Again, this is not crucial by any means… It’s just if I’m going to do something that I already know is a bit sub-optimal, I’d like it to be “the least sub-optimal” I can possibly do in the timeframe I have available. In this case, I just have a couple of days to assemble some nice preliminary r

Re: [HCP-Users] WM and CSF signal extraction

Hi Michael, WM and CSF aren’t saved in CIFTI. Also I don’t think that you gain much by regressing those out and might even lose some. sICA+FIX will deal with movement effects but does not handle global physiological noise (which WM and CSF don’t do a good job with either). You can use

Re: [HCP-Users] Generating Field Maps for PreFreeSurferPipelineBatch.sh input

.cornell.edu>> Date: Saturday, July 21, 2018 at 10:28 PM To: "Harms, Michael" mailto:mha...@wustl.edu>> Cc: "Glasser, Matthew" mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@human

Re: [HCP-Users] Issues implementing ICA FIX Multi Run

Sorry about that I have fixed this in the latest master. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson mailto:tsc...@mst.edu>> Date: Friday, July 20, 2018 at 3:49 PM To: "Theis, Nicholas" mailto:the...@upmc.edu>> Cc:

Re: [HCP-Users] Generating Field Maps for PreFreeSurferPipelineBatch.sh input

he Matlab DICOM viewer and got BWPPPE as a private field, but did not see a field for ReconMatrixPE (is the latter a field in the DICOM header or computed from fields?) Thanks again! On 19 Jul 2018, at 22:36, Glasser, Matthew wrote: I would just pull the numbers directly from the i

Re: [HCP-Users] MSMAll

There is a new Multi-run FIX pipeline currently available in the Git repository that you can use. I would consider it beta a this time. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Hendrickson mailto:hendr...@umn.edu>> Date: Thursday, July 19, 2018 at 6:24

Re: [HCP-Users] The coordinates of surface time-series of Resting State fMRI FIX-Denoised (Compact)

the rsfMRI data, what can we do without having the coordinates of surface time-series? I mean, how we can infer the map from mask to the rsfMRI data. Best regards, Aslan On Wed, Jul 18, 2018 at 5:46 PM Glasser, Matthew mailto:glass...@wustl.edu>> wrote: 1. rfMRI_REST1_LR_Atla

Re: [HCP-Users] The coordinates of surface time-series of Resting State fMRI FIX-Denoised (Compact)

1. rfMRI_REST1_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii 2-3. 100307.L.midthickness_MSMAll.32k_fs_LR.surf.gii Note that the surface coordinates or only valid for single individuals. There is no “standard space” (like MNI space) that properly lines up the cortical areas, instead surface

Re: [HCP-Users] Generating Field Maps for PreFreeSurferPipelineBatch.sh input

You need to follow the instructions in the file to find the appropriate DICOM fields. SEUnwarpDir will be the phase encoding direction of your SE Fieldmaps (e.g. y). Peaces, Matt. On 7/17/18, 11:48 PM, "hcp-users-boun...@humanconnectome.org on behalf of Marc Dubin" wrote: >Hi Michael, >

Re: [HCP-Users] Generating Field Maps for PreFreeSurferPipelineBatch.sh input

You need to follow the instructions listed to find those DICOM fields and put in the values. b02b0.cnf is fine. Peace, Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marc Dubin mailto:mrd9...@med.cornell.edu>> Date: Tuesday, July 17, 2018 at 11:29 PM To: "Harms,

Re: [HCP-Users] GradientDistortionUnwarp error help.

--t1="$T1wInputImages" \ --t2="$T2wInputImages" \ --t1template="$T1wTemplate" \ --t1templatebrain="$T1wTemplateBrain" \ --t1template2mm="$T1wTemplate2mm" \ --t2template="$T2wTemplate" \

Re: [HCP-Users] The coordinates of surface time-series of Resting State fMRI FIX-Denoised (Compact)

For any given subject, the coordinates of the surfaces are given in the surface file, e.g. ${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.${Hemisphere}.midthickness_MSMAll.32k_fs_LR.surf.gii. Note that you should be using the MSMAll FIX cleaned data. Peace, Matt. From:

Re: [HCP-Users] GradientDistortionUnwarp error help.

Hi Ammar, Please post your .bat call to the pipeline script. Most likely you need to set somethings to NONE Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Steve Smith mailto:st...@fmrib.ox.ac.uk>> Date: Tuesday, July 17, 2018 at 11:23 AM To: "Hawasli, Ammar"

Re: [HCP-Users] A question HCP FIX-denoised resting-state data

Yes, that is one of the reasons we don’t recommend lowpass filtering of the data. Peace, Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Aaron C mailto:aaroncr...@outlook.com>> Date: Monday, July 16, 2018 at 1:12 AM To:

Re: [HCP-Users] Recon-all ERRORS in Freesurfer HCP Pipeline

I think this was on the mailing list a while back so you might search for that solution. In any case, those logs don’t show the error so you might need to find the log from the MNI tool itself. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Boukhdhir Amal

Re: [HCP-Users] HCP Atlas

The HCP’s multi-modal parcellation was released when the paper was published and is available here: https://balsa.wustl.edu/file/show/3VLx Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Rachel Hanson mailto:rachel.wood...@york.ac.uk>> Date: Friday, July 13, 2018 at

Re: [HCP-Users] Core Dump ${MSMBINDIR}/msm

You should run the specific command that generates the .rot. file in PostFreeSurfer to get that file. Starting with FreeSurfer for MSMAll is definitely not recommended as that will make the problem harder for MSMAll (having to try to undo the bad FreeSurfer distortions), and it might be better

Re: [HCP-Users] Brainstem to cortex baseline r-value

There is more unstructured noise in HCP data because of small voxel size and fast TR. Basically that means the ratio between the neural signal and the random noise is lower and that leads to lower correlation coefficients. Peace, Matt. From: mailto:hcp-users-boun...@humanconnectome.org>>

Re: [HCP-Users] question about dlabel.nii

Use the “features toolbox” on the right hand side of Workbench and the labels tab of that to uncheck things you don’t want shown. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Yu Sun Chung mailto:yusu...@gmail.com>> Date: Thursday, July 5, 2018 at 3:15 PM To:

Re: [HCP-Users] Comment on the paper by Righart et al. from 2017?

I think I had seen this paper before. Their post-mortem T1w/T2w myelin maps don’t really look like our in vivo ones, so its hard to know exactly what happened. Perhaps the issue is with MR contrast changing with post-mortem MRI imaging. Peace, Matt. From:

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] 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] how to map DTI data to CIFTI space and do network analysis by MMP parcellation ?

Do you want to do tractography? Peace, Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "baixi...@gmail.com" mailto:baixi...@gmail.com>> Date: Thursday, June 28, 2018 at 8:53 AM To: hcp-users mailto:hcp-users@humanconnectome.org>> Subject:

Re: [HCP-Users] Gambling task phase encoding

The Gambling contrast itself (reward-punish) didn¹t work very well. Matt. On 6/28/18, 3:48 AM, "hcp-users-boun...@humanconnectome.org on behalf of Filip Grill" wrote: >Dear HCP users, > >I am interested in using the fMRI data from the gambling task for my >project. Ultimately I will use the

Re: [HCP-Users] list of significant parcels

wb_command -file-information might be able to help with this. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Aaron R mailto:aaro...@gmail.com>> Date: Wednesday, June 27, 2018 at 8:19 AM To: "hcp-users@humanconnectome.org"

Re: [HCP-Users] DiffusionToStructural issue with epi_reg_dof

That is okay. FSL BBR is only used to initialize FreeSurfer BBR anyway. Peace, Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Parvathaneni, Prasanna" mailto:prasanna.parvathan...@vanderbilt.edu>> Date: Thursday, June 21, 2018 at 12:59 AM To:

Re: [HCP-Users] a question about *.dconn.nii files

No. Probably best to load the dtseries and then only compute one row of the matrix. Peace, Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Aaron C mailto:aaroncr...@outlook.com>> Date: Friday, June 15, 2018 at 5:24 AM To:

Re: [HCP-Users] HCP MMP (Glasser et al Atlas) on native surfaces?

You can find the parcellation on the 32k_fs_LR mesh here: https://balsa.wustl.edu/file/show/3VLx You can resample the parcellation to a given subjects native mesh by using the reverse of the process used to bring data from the native mesh to the standard mesh (i.e. reversing the spheres).

Re: [HCP-Users] wb_command -metric-rois-from-extrema

On a standard mesh anatomical surface the vertex spacing is non-uniform across the surface. If you used the spheres you could get a uniform number of vertices (though now the patches would cover different total areas). Probably the uniform in mm approach (on the midthickness with appropriate

Re: [HCP-Users] MNI coordinates

Please have a look at these publications for why we don’t recommend use of MNI coordinates for anything: https://www.nature.com/articles/nn.4361 https://www.biorxiv.org/content/early/2018/04/23/255620 Peace, Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Dongjun Rew

Re: [HCP-Users] CIFTI resample

What is the wb_command -file-information -no-map-info output of the two CIFTI files you are trying to resample. Also what is your wb_command -cifti-resample command line? Peace, Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Amin Dadashi

Re: [HCP-Users] error running hcp_fix

mbia.edu<mailto:mmor...@nyspi.columbia.edu> On Jun 5, 2018, at 1:32 PM, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: What do you have on line 94 of the FIX settings.sh? Matt. From: Marta Moreno mailto:mmorenoort...@icloud.com>> Date: Tuesday, June 5, 2018 at 12:

Re: [HCP-Users] error running hcp_fix

sity Medical Center 1051 Riverside Drive, Unit 21 New York, NY 10032 phone: (914) 218-7311 email: mm4...@cumc.columbia.edu<mailto:mm4...@cumc.columbia.edu> email: mmor...@nyspi.columbia.edu<mailto:mmor...@nyspi.columbia.edu> On May 27, 2018, at 4:24 PM, Glasser, Matthew mailto:glass...@

Re: [HCP-Users] Variation in aparc ROIs between subjects in 32k_fs_LR space

un 4, 2018 at 5:41 PM, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: Hi Tom, Why not use the multi-modal parcellation? https://balsa.wustl.edu/file/show/3VLx Matt. From: Thomas Nichols mailto:thomas.nich...@bdi.ox.ac.uk>> Date: Monday, June 4, 2018 at 11:37 AM To: Matt Glasser ma

Re: [HCP-Users] Variation in aparc ROIs between subjects in 32k_fs_LR space

4, 2018 at 4:29 PM, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: Hi Tom, This is because FreeSurfer “fits” the aparc to each subject. There is probably an atlas aparc somewhere inside FreeSurfer that wouldn’t have this property. That does raise the question of why you are us

Re: [HCP-Users] Variation in aparc ROIs between subjects in 32k_fs_LR space

Hi Tom, This is because FreeSurfer “fits” the aparc to each subject. There is probably an atlas aparc somewhere inside FreeSurfer that wouldn’t have this property. That does raise the question of why you are using aparc instead of one of the more functionally relevant parcellations available

Re: [HCP-Users] Conte69 164k and 32k mesh

bet? Thanks, Joe -- Joseph M. Orr, Ph.D. Assistant Professor Department of Psychological and Brain Sciences Texas A Institute for Neuroscience Texas A University College Station, TX On Fri, Jun 1, 2018 at 7:12 PM, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: I would note that we don’t

Re: [HCP-Users] Conte69 164k and 32k mesh

I would note that we don’t recommend mapping group average volume data to group average surfaces. It is a much better idea to map the data onto the individuals' surfaces and register it on the surface (and also avoid smoothing in the volume or even better avoid smoothing entirely): See this

Re: [HCP-Users] Trouble reproducing groupPCA -> groupICA

Instead what probably happened was that the CIFTI file was converted to a fake NIFTI file with wb_command -cifti-convert and run on melodic without the --CIFTI switch. You might report this on the FSL list as I’m not sure if melodic is supposed to do mixture modeling of CIFTI data or not. Peace,

Re: [HCP-Users] Mapping NIFTI to CIFTI

$Caret7_Command -cifti-create-dense-scalar $ciftiOut -volume $volumeData $labelVolume -left-metric $lMetric -roi-left $lRoiMetric -right-metric $rMetric -roi-right $rRoiMetric rm ${lMetric} ${rMetric} done rm ${volumeData} Matt. From: Seyedehrezvan Farahibozorg mailto:rezvan.far

Re: [HCP-Users] Mapping NIFTI to CIFTI

That process does not replicate how the timeseries data were gotten on the surface to begin with. What is it that you are trying to accomplish with this? Peace, Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Seyedehrezvan Farahibozorg

Re: [HCP-Users] Additional smoothing of FIX extended resting state data?

Indeed that is one of the major fallacies in brain imaging. Have a look at this paper in press at PNAS: https://www.biorxiv.org/content/early/2018/04/23/255620 Peace, Matt. From: David Hofmann mailto:davidhofma...@gmail.com>> Date: Wednesday, May 30, 2018 at 5:14 AM To: Timothy Coalson

Re: [HCP-Users] Additional smoothing of FIX extended resting state data?

Why do you need smoothing if you are using ROIs? If you smooth in the volume you will be mixing in CSF, white matter, and cortex from the opposite banks of gyri and sulci. Even smoothing on the surface will mix signal between different cortical areas and isn’t needed if you are doing an ROI

Re: [HCP-Users] question about using wb_command -cifti-average command

ries.pconn.nii DEC_RL_..parcel.ptseries.pconn.nii but still got error saying unexpected parameter of output name.. Am I still missing some command? - Yu Sun On Tue, May 29, 2018 at 1:36 PM, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: You are not calling a specific function with wb_command there.

Re: [HCP-Users] error running hcp_fix

training file: /usr/local/fix1.065/training_files/HCP_hp2000.RData and threshold 10 FIX Applying cleanup using cleanup file: RS_fMRI_1_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and motion cleanup set to 1 Please advice. Thanks! -L On May 26, 2018, at 2:52 PM, Glasser, Matthew <glass..

Re: [HCP-Users] error running hcp_fix

Perhaps you are running out of memory. Peace, Matt. From: > on behalf of Marta Moreno > Date: Saturday, May 26, 2018 at 1:50 PM To: HCP Users

Re: [HCP-Users] Guidelines for preparing HCP-processed data for graph theory based analysis

Once you have a parcellated timeseries I would expect things to be pretty similar and just a matter of getting the data in the expected format for the software program. I don’t have any experience with brain connectivity toolkit, but you can use wb_command -cifti-parcellate to generate

Re: [HCP-Users] CSF and WM masks

That is correct. We don’t recommend WM and CSF regression necessarily, as it doesn’t do much (when the masks are eroded by 2 2mm voxels from the greymatter as these are). If they are not eroded they behave more like global signal regression, which is controversial for removing a portion of

Re: [HCP-Users] question about noise components in PTN release

I don’t think these were the same components. There are probably a couple of noise components in the PTN release but I don’t know if anyone went through and numbered them. Peace, Matt. From: > on behalf of

<    1   2   3   4   5   6   7   8   9   10   >