Re: [HCP-Users] Shared Library Error

We are in the process of updating the codebase that uses matlab to hopefully make it easier for folks to use compiled matlab. Until that is completed, I would recommend using interpreted matlab if you can. Peace, Matt. From:

Re: [HCP-Users] Additional topup run for LR-RL rest files?

Distortion correction occurs in the first Pipeline that fMRI data encounters, the fMRIVolumePipeline. The order of pipelines for fMRI data is (assuming structural pipelines have already been run): fMRIVolume ‹> fMRISurface ‹> ICA+FIX ‹> MSMAll+Resample ‹> Analysis Peace, Matt. On 4/25/17,

Re: [HCP-Users] Using multiple cores while running Structural Pipelines

PreFreeSurfer uses mostly single threaded tools. Some of FreeSurfer is multi-threaded (and importantly one binary has some issues with oversubscribed cores leading to much longer execution times). PostFreeSurfer is largely multi-threaded. In all cases, the pipelines use multiple threads by

Re: [HCP-Users] prescan normalize

We didn¹t use pre scan normalize with fMRI or diffusion data and also kept it off for structural data. We deal with the bias field in the HCP pipelines. That said, one could turn it on for T1w and T2w if one wanted and everything would work fine (so long as it was on for BOTH T1w and T2w). As

Re: [HCP-Users] Using fsl 5.0.9 and freesurfer v. 6.0

You can use the latest FSL. FreeSurfer needs to be kept at version 5.3 at this time. Peace, Matt. From: > on behalf of Lisa Kramarenko > Date:

Re: [HCP-Users] change dimensions in a cifti file

[HCP-Users] change dimensions in a cifti file Dear Matt, I have used wb_command -cifti-reduce STDEV to assess dense timeseries data and there are NANs. Please advise. Thank you very much, -L From: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Date: Tu

Re: [HCP-Users] about the Glasser_et_al_2016_HCP_MMP1.0_5_StudyDataset.scene

Have a look at this new page: https://balsa.wustl.edu/help/fileTypes Did you not see it before? Peace, Matt. From: > on behalf of 罗 <963619...@qq.com> Date: Tuesday, April 18, 2017

Re: [HCP-Users] change dimensions in a cifti file

fti file Yes, there are NANs. What should I do next? Thanks again, -L From: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Date: Tuesday, April 18, 2017 at 7:58 AM To: Leah Moreno <mmorenoort...@icloud.com<mailto:mmorenoort...@icloud.com>&g

Re: [HCP-Users] change dimensions in a cifti file

ot get an error running the HCP pipeline in any step, and the dtseries.nii looks fine to me using wb_view. Please advise. Thanks a lot, -L From: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Date: Monday, April 17, 2017 at 10:06 PM To: Leah Moren

Re: [HCP-Users] Subcortical surface sampling outside borders of CIFTI

I would map from volume to surface from the regular volume data without smoothing and then do the smoothing on the surface (which is what we do for the cerebral cortex). What structures do you have surfaces of subcortically? It might make the most sense to use the ICA+FIX cleaned data for

Re: [HCP-Users] [SPAM] 答复: PhaseEncodinglist

Subject: [SPAM] 答复: [HCP-Users] PhaseEncodinglist Hi, It’s in GenericfMRIVolumeProcessingPipelineBatch.sh. Thanks. 发件人: Glasser, Matthew [mailto:glass...@wustl.edu] 发送时间: 2017年4月17日 21:37 收件人: wtj <1257735...@qq.com<mailto:1257735...@qq.com>>; hcp-users@humanconnectome.org<mailto:hcp-

Re: [HCP-Users] PhaseEncodinglist

Which pipeline are you asking about? Peace, Matt. From: > on behalf of wtj <1257735...@qq.com> Date: Monday, April 17, 2017 at 6:29 AM To:

Re: [HCP-Users] change dimensions in a cifti file

This is what the ciftisavereset function is for (which should be available in the same place you found ciftiopen and ciftisave. Peace, Matt. From: > on behalf of Leah Moreno

Re: [HCP-Users] 答复: [SPAM] 回复： [SPAM] 回复：[SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: myelin maps

-Dense Scalar, what does “Connectivity” mean? Thanks. 发件人: Glasser, Matthew [mailto:glass...@wustl.edu] 发送时间: 2017年4月16日 21:19 收件人: stargazy pie <1257735...@qq.com<mailto:1257735...@qq.com>>; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> 主题: Re: [SPAM] 回复： [SPAM]

Re: [HCP-Users] 答复: [SPAM] 回复：[SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: myelin maps

] myelin maps Hi, https://www.mail-archive.com/hcp-users@humanconnectome.org/msg03582.html If you are still confused, my question is just like what Timothy Hendrickson said. The most important thing is, objectively, can I get a subject’s myelin value of different brain regions? Thanks. 发件人: Glasse

Re: [HCP-Users] [SPAM] 回复： [SPAM] 回复：[SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: myelin maps

-- 原始邮件 ---------- 发件人: "Glasser, Matthew";<glass...@wustl.edu<mailto:glass...@wustl.edu>>; 发送时间: 2017年4月16日(星期天) 中午12:03 收件人: "stargazy pie"<1257735...@qq.com<mailto:1257735...@qq.com>>; "hcp-users@humanconnectome

Re: [HCP-Users] [SPAM] 回复：[SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: myelin maps

AM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [HCP-Users] myelin maps Hi, It is just a float number following the -cifti-stats command. I don't know, but, will there be other output file anywhere else? Thanks. ---原始邮件--- 发件人: "Glasser, Matthew"<glass...@wustl.edu<mailto:glass...@w

Re: [HCP-Users] [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: myelin maps

AM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [HCP-Users] myelin maps Hi, What I mean is, every region of brain have different average thickness, at the same time, they should also have different myelin values. This is what I want. Sorry to bother you so late… Thanks. 发件人: Glasser, Matthew [mailto:

Re: [HCP-Users] [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: myelin maps

nii -roi /home/Tianjie/connectome_workbench/workbench/bin_rh_linux64/mycommandlabeltoroi.dscalar.nii -reduce MEAN The result is still just a number. Maybe , I sould use a file of only one ROI at a time? Thanks. 发件人: Glasser, Matthew [mailto:glass...@wustl.edu] 发送时间: 2017年4月16日 9:53 收件人: wtj <1257735...@qq.c

Re: [HCP-Users] [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: myelin maps

asser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Subject: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [HCP-Users] myelin maps Hi, Do you mean that I used wrong ROI file, or ROI file is not produced yet? Thanks. 发件人: Glasser, Matthew [mailto:glass...@wustl.edu] 发送时间: 2017年4月16日 9:11 收件人

Re: [HCP-Users] [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: myelin maps

;> Subject: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [HCP-Users] myelin maps Hi, What does –reduce flag mean in wb_command –cifti-stats? When I used –reduce MEAN, it only outputed one number. I need myelin values of every ROI. What should I do? Thanks. 发件人: Glasser, Matthew [mailto:glass...@wustl.edu] 发

Re: [HCP-Users] [SPAM] 答复: [SPAM] 答复: myelin maps

home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/fsaverage_LR32k/LS2001.aparc.32k_fs_LR.dlabel.nii ERROR: you must use exactly one of –spatial-weights or –cifti-weights. If I use the latter, what will the weights file’s name be like? Where can I find it? Thanks. 发件人: Glasse

Re: [HCP-Users] [SPAM] 答复: myelin maps

P-Users] myelin maps Hi, There is another error when I exchanged the position of –roi flag and the myelin map file. ERROR: roi-cifti is missing(No more parameters). Should I add something else? Thanks. 发件人: Glasser, Matthew [mailto:glass...@wustl.edu] 发送时间: 2017年4月15日 22:25 收件人: wtj <12577

Re: [HCP-Users] myelin maps

You have put the myelin map where the ROI should go. Peace, Matt. From: > on behalf of wtj <1257735...@qq.com> Date: Saturday, April 15, 2017 at 9:22 AM To:

Re: [HCP-Users] how to convert the connectome matrix to CIFTI dense connectomes

You need to use a GIFTI .func.gii fie for this rather than the surface file. That .func.gii file should have a one in every location that your surface ROI has a one. Peace, Matt. From: > on behalf of

Re: [HCP-Users] Fwd: Help with the group comparison of seed-based FC

clarify, after I run -cifti-average-roi–correlation on each participant, do I then merge all the .dscalar.nii files for the members of the respective group before comparing the groups with PALM? Do I do it with -cifti -concatenate? thanks for all your help. best, Lisa On 7 April 2017 at 22:07

Re: [HCP-Users] problems in understanding the FIX denoised data downloaded from HCP1200

There are four rfMRI runs per subject. LR vs RL refers to the phase encoding direction and 1 and 2 refers to the session each run was acquired in. You should use balanced amounts of RL and LR data ideally, as the phase encoding direction does create some asymmetry in the data. You want to

Re: [HCP-Users] Fwd: Help with the group comparison of seed-based FC

ts? I want to do group-level comparison so at some step I need to create group maps. Or am I misunderstanding something? Sorry for such basic confused questions and thanks a lot! Lisa On 5 April 2017 at 21:05, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wro

Re: [HCP-Users] hcp_fix and correlation maps

ent from my mobile phone On Apr 6, 2017, at 5:58 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: If you want to explore the functional connectivity, you can do that by loading the dtseries into Connectome Workbench and selecting the dyconn layer and clickin

Re: [HCP-Users] hcp_fix and correlation maps

est way for us to display the connectivity map (after running wb_command correlation) for single patient and using different seeding locations. It's preferred to have dynamic seed placement that yields specific connectivity pattern to that specific seed. All the best. Osama _

Re: [HCP-Users] Error during Field Map Preprocessing and Gradient Unwarping in the Functional Volume Pipeline

fsl_prepare_fieldmap is an unmodified FSL script that is called by the HCP Pipelines. I would ask on the FSL mailing list about that. You could try testing that script outside of the HCP Pipelines by using these commands line on the files: ${FSLDIR}/bin/fslmaths ${MagnitudeInputName} -Tmean

Re: [HCP-Users] hcp_fix and correlation maps

Unfortunately not all of the errors of ICA+FIX are reported to the main stderr. You’ll need to look in the log files inside the directory created by ICA+FIX to see what the error was (in matlab or R). There isn’t usually any need to add additional files to the spec file (this simply causes

Re: [HCP-Users] lifespan pilot data

I don’t know if SPM requires uncompressed NIFTI or not. As for the additional files, some are gradient corrected versions of a given file, or auxiliary files to be used in processing that file with the HCP Pipelines (e.g. for a structural image there are two phase reversed spin echo images

Re: [HCP-Users] most typical subject for FA registration?

formed recommendation about which subject to choose for the first registration step. On 1 April 2017 at 15:13, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: That does seem like a lot of computations. Why not pick a random individual, register

Re: [HCP-Users] most typical subject for FA registration?

That does seem like a lot of computations. Why not pick a random individual, register to that and then remove the group average effect of registration, retaining the improved alignment across subjects while eliminating the bias caused by the initial subject? Peace, Matt. From:

Re: [HCP-Users] [fMRIVolumeProcessingPipeline]cannot find eye.dat

The order of running the pipelines is: PreFreeSurfer —> FreeSurfer —> PostFreeSurfer —> fMRIVolume —> fMRISurface —> ICA+FIX —> MSMAll PostFreeSurfer —> DiffusionPreprocessing —> BedpostX Peace, Matt. From: >

Re: [HCP-Users] wb_view : Unable to load labels through features tab

to:hcp-users@humanconnectome.org>>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] wb_view : Unable to load labels through features tab Dear Sir, is there any way that i can suggest the colors for each subfield, instead of so

Re: [HCP-Users] wb_view : Unable to load labels through features tab

Then do as Tim suggests. Matt. From: > on behalf of Dev vasu > Date: Thursday, March 30, 2017 at 7:59 PM To: Timothy Coalson

Re: [HCP-Users] freesurferpipeline

I don’t see that in the GitRepo, so perhaps you need to update to the latest version of the HCP Pipelines from the GitRepo. Peace, Matt. From: > on behalf of wtj <1257735...@qq.com>

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

o you think? Incorporate the exact vertex locations for each subject anyway, or ignore them and (somehow) just use the fact that vertex n has the same neuroanatomical meaning in every subject? Thanks again, Nicola On 03/29/2017 04:02 PM, Glasser, Matthew wrote: We don¹t recommend using the ft_ t

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

We don¹t recommend using the ft_ tools with MRI data. Instead use ciftiopen/ciftisave/ciftisavereset: https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ item 2B As for your other question, the vertex indices have neuroanatomical correspondence across subjects, but that often does

Re: [HCP-Users] ICA failure with volumetric ICA-FIX denoised files

this up? Thanks for your help! Jenny On Tue, Mar 7, 2017 at 3:48 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Hi Jenny, Indeed you can use wb_command -cifti-convert -to-nifti to convert the files to NIFTI, run melodic, do dual regression, etc, an

Re: [HCP-Users] 答复: 答复: 答复: 答复: brainmask.mgz

eed to change number 0.7 to 0.8 in T1wTemplate, T1wTemplateBrain, T2wTemplate, T2wTemplateBrain and TemplateMask, right? Second, to change the value of T1wSampleSpacing and T2wSampleSpacing(Is this what you mean?) according to my data, where should I find proper value of them? Thanks. 发件人: Glasse

Re: [HCP-Users] 答复: 答复: 答复: brainmask.mgz

t it need provided by prefreesurfer part. So, why not just create the new folder and files? Why it stopped? Thanks. 发件人: Glasser, Matthew [mailto:glass...@wustl.edu] 发送时间: 2017年3月28日 17:29 收件人: wtj <1257735...@qq.com<mailto:1257735...@qq.com>>; HCP-Users@humanconnectome.org<mailto:

Re: [HCP-Users] 答复: 答复: brainmask.mgz

freesurfer part have all inputs that it need provided by prefreesurfer part. So, why not just create the new folder and files? Why it stopped? Thanks. 发件人: Glasser, Matthew [mailto:glass...@wustl.edu] 发送时间: 2017年3月28日 17:29 收件人: wtj <1257735...@qq.com<mailto:1257735...@qq.com>>; HCP-

Re: [HCP-Users] 答复: brainmask.mgz

Users] brainmask.mgz Hi， There are 69.5GB left in my studyfolder directory at present. Isn’t that enough? My freesurfer version is 5.3.0-HCP. There are 27 donors’ data. Each of them occupies about 2.5GB space, how much more space is needed before freesurfer part of pipeline? Thanks. 发件人: Glasse

Re: [HCP-Users] incomplete display of activations on the inflated cortex

image (say ch2bet.nii.gz) as reference to map it onto surface? Best, Bingjiang On Sun, Mar 26, 2017 at 11:41 AM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: I really don’t recommend using inflated surfaces for volume to surface mapping… Peace, Matt. From: &l

Re: [HCP-Users] incomplete display of activations on the inflated cortex

I really don’t recommend using inflated surfaces for volume to surface mapping… Peace, Matt. From: > on behalf of Bingjiang Lyu > Date: Saturday, March

Re: [HCP-Users] incomplete display of activations on the inflated cortex

1) It is not recommended that you try to map group average volume data to group average surfaces as there is poor cortical alignment across subjects in group average volume data and group average surfaces do not match group average volumes because of incompatibility of folding patterns and

Re: [HCP-Users] Single Subject Pipelines

Not yet. There are still several things ahead of them in the queue. Peace, Matt. From: > on behalf of Nicolo Biagi > Date: Friday, March 24, 2017

Re: [HCP-Users] OneStepResample fails b/c of missing BiasField image

gative="NONE" SpinEchoPhaseEncodePositive="NONE" DwellTime="NONE" SEUnwarpDir="NONE" TopupConfig="NONE" GEB0InputName="${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR1/${Subject}_3T_GradientEchoFieldMap.nii.gz"

Re: [HCP-Users] OneStepResample fails b/c of missing BiasField image

Hi Michael, That indeed sounds like a bug, though I’m a bit puzzled as to how it occurs. Can you post the contents of ${StudyFolder}/${Subject}/T1w and ${StudyFolder}/${Subject}/MNINonLinear? ${StudyFolder}/${Subject}/MNINonLinear/BiasField.nii.gz should be produced by PreFreeSurfer and

Re: [HCP-Users] Contents of processed dtseries files

You can use our CIFTI Matlab tools to read the matrix into matlab (2B on this website): https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ It will be 91282 Grayordinates X 1200 time points. For more information on the CIFTI file format and Grayordinates, please see this

Re: [HCP-Users] hcp_fix bug

Please include the error message, I don’t know what you are referring to else. Peace, Matt. From: > on behalf of Timothy Hendrickson > Date: Wednesday, March 22, 2017

Re: [HCP-Users] film_gls surface mode error Newmat: incompatible dimensions

Matt You were right. The values on the medial wall are all zeros and the time series are constant. Do you perhaps have a reliable solution to this? Many thanks in advance!! Best, Blazej On 21 March 2017 at 21:51, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:

Re: [HCP-Users] film_gls surface mode error Newmat: incompatible dimensions

or even when no input2 ("--in2") is specified, while I believe it should say "file missing". Best, Blazej On 21 March 2017 at 18:03, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: I wouldn’t recommend smoothing with the inflated surface, but r

Re: [HCP-Users] film_gls surface mode error Newmat: incompatible dimensions

runs smoothly: film_gls --in=test.lh.func.gii --in2=lh.inflated.surf.gii --mode=surface --rn=SURF_STATS --con=design.con --pd=design.mat --noest Thanks!! Blazej On 21 March 2017 at 14:50, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Please post your film_gls command lin

Re: [HCP-Users] film_gls surface mode error Newmat: incompatible dimensions

Please post your film_gls command line. Peace, Matt. From: > on behalf of Blazej Baczkowski > Date: Tuesday, March 21, 2017 at 8:33 AM To:

Re: [HCP-Users] Questions regarding coordinates infomation of vertex

In individual subjects, you can use the midthickness surface coordinates as the 3D coordinates. Peace, Matt. From: > on behalf of Irisqql0922 > Date: Monday,

Re: [HCP-Users] Questions regarding values in .dscalar.nii file

Yes. In the future that will be more explicitly labeled in the file name. Peace, Matt. From: > on behalf of Irisqql0922 > Date: Monday, March 20, 2017 at 4:09

Re: [HCP-Users] reference surface file for probtrackx2

The appropriate image to use is: ${StudyFolder}/${Subject}/T1w/T1w_acpc_dc_restore_1.25.nii.gz. Peace, Matt. On 3/19/17, 10:53 AM, "hcp-users-boun...@humanconnectome.org on behalf of Govinda Surampudi"

Re: [HCP-Users] extracting hemispheres from dconn files

You should be able to use external binary format with the GIFTI toolbox as well. Peace, Matt. From: > on behalf of Estrid Jakobsen > Date: Friday, March 17,

Re: [HCP-Users] about scanning stability of CMRR_MB Sequences

about scanning stability of CMRR_MB Sequences something like: Preparation of Image Reconstruction System failed. Best wishes！ -- Meizhen Han PhD Candidate Center for MRI Research Peking University Beijing, China -----原始邮件----- 发件人:"Glasser, Matthew" <glass...@wustl.edu<mailto:gl

Re: [HCP-Users] about scanning stability of CMRR_MB Sequences

What is the scanner error message? Peace, Matt. From: > on behalf of 韩美贞 > Date: Wednesday, March 15, 2017 at 7:22 AM To: hcp-users

Re: [HCP-Users] how to perform registration from MNI152 to native space

The appropriate transforms are provided: ${StudyFolder}/${Subject}/MNINonLinear/xfms/acpc_dc2standard.nii.gz — Native to MNI ${StudyFolder}/${Subject}/MNINonLinear/xfms/standard2acpc_dc.nii.gz — MNI to Native But what is it that you are trying to do? Peace, Matt. From:

Re: [HCP-Users] GIFTI read and save in Matlab

he gifti file in the terminal. Is this what you're referring to? On Tue, Mar 14, 2017 at 7:09 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Dims of the gifti you read in. Peace, Matt. From: Rita Elena Loiotile <rloiot...@gmail.com<mailto:rloiot.

Re: [HCP-Users] GIFTI read and save in Matlab

umanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] GIFTI read and save in Matlab both the gifti.cdata and the matrix have dimensions 32492 by 209. On Tue, Mar 14, 20

Re: [HCP-Users] GIFTI read and save in Matlab

It seems like the newest version of GIFTI (according to artefact) is 1.6. Please let me know if there's a newer one that I'm missing. I've attached screenshots of the info, in case there is really something obvious that I'm doing incorrectly. Thanks again, Rita On Tue, Mar 14, 2017 at 7:43 AM

Re: [HCP-Users] why didn't choose the minimal TR for DWI sequence?

Another consideration is the amount of T1 recovery. If you allow too little TR you end up losing SNR for that reason. Peace, Matt. From: > on behalf of 韩美贞

Re: [HCP-Users] GIFTI read and save in Matlab

through every possible index of the matrix M and assign each value separately. However, I'd very much like to avoid this if possible, since it's quite slow. Please let me know if this works for you, and/or if I am missing something obvious. Thank you again, Rita On Mon, Mar 13, 2017 a

Re: [HCP-Users] about the PostFreeSurferPipeline

t the HCP fMRI data, what you afford in cifti format is 96854×1200 dimension, which means too many for me, and what I want is about 600～1000×1200 demension. Best wishes! Yours -- Original -- From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>

Re: [HCP-Users] about the PostFreeSurferPipeline

3619...@qq.com>> wrote: Thanks for you reply. As far as I know, the 32k vertices template is based on the fsaverage in FreeSurfer which also contains fsaverage3, fsaverage4, fsaverage5 and fsaverage6, what should I do if I want to make a template based on fsaverage3? Thanks Yours 发自我的iP

Re: [HCP-Users] GIFTI read and save in Matlab

I find it better to reuse the GIFTI object one read into matlab in the first place: gnew=g; gnew.cdata=M; save(gnew,’saveName.gii’); Peace, Matt. From: > on behalf of Rita Elena Loiotile

Re: [HCP-Users] about the PostFreeSurferPipeline

That is really low. What spacing do you think would be reasonable on the cortical surface? 32k is 2mm on average. Peace, Matt. From: > on behalf of 罗 <963619...@qq.com> Date:

Re: [HCP-Users] about surface corrdinate

By 2D coordinate are you asking about latitude and longitude, or do you just want the positions of the vertices in 3D space? Peace, Matt. From: > on behalf of 罗 <963619...@qq.com>

Re: [HCP-Users] ICA failure with volumetric ICA-FIX denoised files

I think there is a bug in melodic, which I also encountered. I would report this to the FSL list, but it is likely the issue will be fixed in the next FSL release. Also, if you are running melodic in the volume and combining across subjects, this is not recommended because much of the brain

Re: [HCP-Users] HCP Pipelines v3.19.0 pre-reqs?

I will add that you can run the HCP pipelines with the latest version of FSL. The question Tim was responding to was how to get exactly what was run within ConnectomeDB. Peace, Matt. From: > on behalf of

Re: [HCP-Users] Subcortical region-average time series

I agree that is odd. It is true that the subcortical SNR is not as high as the cortical SNR, but since you are parcellating that should mitigate that to some degree. Have you found this issue consistently across subjects? Peace, Matt. On 3/1/17, 9:38 AM, "hcp-users-boun...@humanconnectome.org

Re: [HCP-Users] Memory required for -cifti-correlation of 700 subjects?

It is also worth noting that data takes the same amount of space on disk and in RAM if it wasn’t compressed on disk. Peace, Matt. From: > on behalf of "Harms, Michael"

Re: [HCP-Users] HCP script for freesurfer

What kind of error? Peace, Matt. From: > on behalf of Juhyoung Ryu > Date: Tuesday, February 21, 2017 at 11:55 PM To:

Re: [HCP-Users] dMRI after eddy but before acpc-T1W

We don’t distribute the diffusion space data. Peace, Matt. From: > on behalf of Szabolcs David > Date: Wednesday, February 22, 2017 at 6:46 AM To:

Re: [HCP-Users] mean intensity for FIX-denoised 7T data

Ugg, I thought we fixed that. You can take the mean image from the uncleaned data and add it to the cleaned data to have the mean present if you need it for some reason. Remember if you are concatenating across scans you will need to have the data demeaned. Peace, Matt. From:

Re: [HCP-Users] Variation in HCP Minimal Preprocessing Pipeline Differences Across Releases

pipelines associated with the fMRI and DTI data smart enough to overwrite data files or do I have to totally delete files and start over? -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) On Tue, Feb 21, 2017 a

Re: [HCP-Users] Variation in HCP Minimal Preprocessing Pipeline Differences Across Releases

I had a look over this and there are some important changes for fMRIVolume (change in the way bias field correction is done) and potentially also some changes in the diffusion pipeline. While it would probably work fine, I would recommend rerunning if it isn’t too painful. Peace, Matt.

Re: [HCP-Users] Variation in HCP Minimal Preprocessing Pipeline Differences Across Releases

I’ll respond to this when I have a bit more info. Peace, Matt. From: > on behalf of Timothy Hendrickson > Date: Tuesday, February 21, 2017 at 11:07 AM To: "Harms,

Re: [HCP-Users] Expected date of 1,200 subjects release?

It will happen when it happens… Peace, Matt. From: > on behalf of "Gopalakrishnan, Karthik" > Date: Monday, February 20, 2017 at 1:33 PM To: "Elam, Jennifer"

Re: [HCP-Users] Comparing ICA-FIX results to results without ICA-FIX

We have found that ICA+FIX does improve the HCP taskfMRI data. It reduces false positives/false negatives in the beta maps and increases Z statistics. For short tfMRI runs, I would recommend combining across runs so that ICA+FIX can better separate signal and noise and so that the clean up

Re: [HCP-Users] how to register the DTI T1 to the structure T1

Run the diffusion preprocessing pipeline. Peace, Matt. From: > on behalf of *signal > Date: Monday, February 20, 2017 at 8:45 AM To: hcp-users

Re: [HCP-Users] Reading gifti into matlab

If what you want to do is read the CIFTI into matlab, you can use the ciftiopen tool for this (2B): https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ Peace, Matt. From: > on behalf of Lauren

Re: [HCP-Users] HCP 180 parcel atlas - Canonical networks?

Hi Mike, This is something we are looking into. Best, Matt. From: > on behalf of "Stevens, Michael" > Date: Monday, February 6, 2017 at

Re: [HCP-Users] Downloading HCP data to a shared computing cluster

If it is anything more than a small amount of data, you might consider Connectome in a Box. Peace, Matt. From: > on behalf of Xavier Guell Paradis > Date: Friday,

Re: [HCP-Users] How to know cluster size (number of voxels) after -cifti-find-clusters

That would only be needed if we had surface-based cerebellar data. This is unfortunately not currently obtainable. Peace, Matt. From: > on behalf of Xavier Guell Paradis

Re: [HCP-Users] T1 divided by T2 in MNI space

It is probably best to divide after resampling, as division isn't linear, though I don't know that it matters much. Keep in mind that the cerebral cortex is not well aligned in MNI space. Peace, Matt. From:

Re: [HCP-Users] How many voxels in the cerebellum?

LTASKS_level3_zstat1_hp200_s2_MSMAll.dscalar Thanks, Xavier. ____ From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Thursday, February 02, 2017 11:28 AM To: Xavier Guell Paradis; hcp-users@humanconnectome.org<mailto:hcp-users@

Re: [HCP-Users] How many voxels in the cerebellum?

What file? Peace, Matt. From: > on behalf of Xavier Guell Paradis > Date: Thursday, February 2, 2017 at 10:26 AM To:

Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance?

file from the Level 3 ‘flameo’ available via Box" 2nd) For each data point of the group cope1 file, calculate (x-mean)/SD. This gives a Cohen's d map. Is this correct? Thank you, Xavier. From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.ed

Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance?

e1 files? Thanks, Xavier. ____ From: Harms, Michael [mha...@wustl.edu<mailto:mha...@wustl.edu>] Sent: Monday, January 30, 2017 12:30 PM To: Elam, Jennifer; Glasser, Matthew; Xavier Guell Paradis; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome

Re: [HCP-Users] Problem using FIX clean data in parcellated stats pipeline

ect 1 1 -repeat Is this correct? Is there a better way to do it? Thanks, Andrew Poppe, Ph.D. Postdoctoral Fellow Olin Neuropsychiatry Research Center Institute of Living Hartford Hospital On Fri, Jan 27, 2017 at 4:03 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu&

Re: [HCP-Users] Problem using FIX clean data in parcellated stats pipeline

chiatry Research Center Institute of Living Hartford Hospital On Fri, Jan 27, 2017 at 3:00 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: It is correct that the taskfMRI pipeline requires the data to not be demeaned and by default currently the ICA+FIX pipe

Re: [HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance?

terms of statistical significance? Thank you again for the reply. Is there a way to access data that was produced but not packaged up? Thank you for your help, Xavier. ____ From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Friday, Jan

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