Re: [HCP-Users] Rest fMRI pipeline

The FIX cleaned data have a very gentle high pass filter that mainly removes linear trends, 24 motion parameters regressed, and noise ICA components (classified by FIX) regressed.  The minimally preprocessed data do not have any of these. Peace, Matt. From: Mahsa Alizade shalchy

Re: [HCP-Users] Rest fMRI pipeline

ned data". Best, Mahsa On Wednesday, October 1, 2014 6:13 PM, "Glasser, Matthew" <glass...@wusm.wustl.edu> wrote: The FIX cleaned data have a very gentle high pass filter that mainly removes linear trends, 24 motion parameters regressed, and noise ICA components (classifi

Re: [HCP-Users] deleting unnecessary files

Once you are satisfied with a run having completed successfully and registered properly, you can delete the ${StudyFolder}/${Subject}/${fMRIName} folder which contains only intermediate files.   Peace, Matt. From: , Gregory Date: Wednesday, October 8, 2014 at

Re: [HCP-Users] Reg. DPARSF

I wouldn’t recommend trying to redo the preprocessing, as getting that right is complicated.  Why not use the FIX cleaned data and focus on whatever analysis you are interested in doing? Peace, Matt. From: Ranga Deshpande Date: Wednesday, October 8, 2014 at 6:48 PM T

Re: [HCP-Users] Zeros found in the surface space resting-state fMRI data.

What is it that you are trying to do?  I’m not sure why the -cifti-separate and -cifti-create-dense-timeseries commands are in there, but you won’t have zeros if you simply run -cifti-smoothing on the cleaned dense timeseries. Peace, Matt. From: Long Date: Friday,

Re: [HCP-Users] Reg. DPARSF

_ Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Anatomy and Neurobiology Phone: 314-362-7864 Email: burge...@pcg.wustl.edu On Oct 8, 2014, at 6:53 PM, Glasser,

[HCP-Users] FW: Converting/analysing preprocessed rfMRI grayordinates

On 9/9/14, 2:48 PM, "Glasser, Matthew" wrote: >I¹d recommend option ii. > >You can use the surfaces and label data in the >${StudyFolder}/${SubjectID}/MNINonLinear/fsaverage_LR32k folder together >with the dense timeseries data. To load the data into matlab, you can u

Re: [HCP-Users] Zeros found in the surface space resting-state fMRI data.

See the e-mail I just forwarded to the list. Peace, Matt. From: Long Date: Saturday, October 11, 2014 at 7:36 AM To: Timothy Coalson Cc: Matt Glasser , "hcp-users@humanconnectome.org" Subjec

Re: [HCP-Users] How to do network analysis from resting-state fMRI data?

See the e-mail I forwarded to the list entitled: [HCP-Users] FW: Converting/analysing preprocessed rfMRI grayordinates for reading in .pconn.nii files into matlab. Peace, Matt. From: 木村一皓 Date: Monday, October 13, 2014 at 2:11 AM To: "hcp-users@humanconnectome.org

Re: [HCP-Users] FW: HCP Scripts

Please use the launcher scripts in ${GitRepo}/Examples and don’t modify the pipelines themselves unless you know what you are doing (i.e. have read and understood the code).  Only the code in examples is intended for you to modify.   Peace, Matt. From: Jennifer Elam

Re: [HCP-Users] gradient unwarp in preFS script

As for the error message, you might not have the HCP customized gradient correction code installed (which will output different files from the original code).  Make sure you have this version installed: https://github.com/Washington-University/gradunwarp I agree with Mike that turning gradie

Re: [HCP-Users] How to do network analysis from resting-state fMRI data?

e 93) s = struct(... Error in gifti (line 71)     this = read_gifti_file_standalone(varargin{1},giftistruct); Error in ciftiopen (line 16) cifti = gifti([tmpname '.gii']); Do you  have any idea what's going on and what should I do? Best, Ikko 2014-10-14 2:11 GMT+09:00 Glasser, Matthew &

Re: [HCP-Users] Metric gradient giving only zeros

You should not be using the inflated surface (rather the midthickness surface would be more appropriate). It is possible that the command does not work correctly without a little pre-smoothing but Tim will need to comment on that. Peace, Matt. On 10/17/14, 5:29 AM, "K. Wagstyl" wrote: >Hi HCP

Re: [HCP-Users] EchoSpacing

It looks like that pipeline takes the echo spacing in ms instead of the rest of HCP pipelines which take the value in seconds.  What were the raw values you entered into the equation there? Peace, Matt. From: Micah Chambers Date: Tuesday, October 21, 2014 at 7:46 PM To

Re: [HCP-Users] EchoSpacing

58 AM, Micah Chambers <mica...@ucla.edu> wrote: I have 10.352 for Dwelltime and 140 for number of phase encoding samples, which comes out to 0.00069.  On Tue, Oct 21, 2014 at 5:53 PM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: It looks like that pipeline takes the echo spacing in

Re: [HCP-Users] freesurfer errors

Is that image you initially sent one of the down sampled FreeSurfer images? It seems a lot blurrier than your raw images. Do you use fatsat in your T1w images? Peace, Matt. On 10/24/14, 1:49 PM, "Gaurav Patel" wrote: >ok thanks...I was wondering how you guys handle errors like these? Or >ar

Re: [HCP-Users] freesurfer errors

cond set of >unprocessed data screen shots came from fslview). As for fatsat, I'm not >sure but I'll check with our sequence programmer. Do you? > >__ > gaurav patel > gauravpa...@gmail.com > www.neurofreak.net > > > > >> O

Re: [HCP-Users] Extracting individual task maps from group-average data

What kind of analysis do you have in mind? There is a new ³native² matlab CIFTI reader/writer written by Robert Oostenveld that you could give a try: https://github.com/oostenveld/cifti, which I think reads in the header info. If you have issues, you¹ll need to ask him about them, as I¹ve not yet

Re: [HCP-Users] T1UnwarpDir

That note in the pipeline example code was put there because I don¹t know how to tell what readout direction was used from the DICOMs and z seems to be the Siemens default. If someone else does, I¹d be interested in what field(s) they used. Gordon, I¹d be a bit surprised here if the shim mattered

Re: [HCP-Users] GenericfMRIVolumeProcessingPipelineBatch motion correction

What is the resolution of this fMRI data? I seem to recall someone else had trouble with the motion correction pipeline on lower resolution data. It may be that we need to allow an option for mcflirt in the pipelines if the default method doesn¹t work for someone. Peace, Matt. On 10/28/14, 7:45

Re: [HCP-Users] T1UnwarpDir

to assume that there should be no difference between a locally generated T1w_acpc_dc.nii.gz file and the one from ConnectomeDB? -Micah On Sun, Oct 26, 2014 at 7:56 PM, Xu, Junqian <junqian...@mssm.edu> wrote: On Oct 26, 2014, at 9:21 AM, Glasser, Matthew <glass...@wusm

Re: [HCP-Users] MNINonLinear ROIs

The files with “Atlas_” are the same across all individuals, whereas the ones without are individual specific. Peace, Matt. From: Linden Parkes Date: Monday, November 3, 2014 at 1:08 AM To: "hcp-users@humanconnectome.org" Subject

Re: [HCP-Users] MNINonLinear ROIs

 |  0402 516 574 E: linden.par...@monash.edu W: www.med.monash.edu.au/psych/mcin/ B7AE8BF0-4F0C-4F0B-9BDE-B582B9331FA1 From: Glasser, Matthew Reply: Glasser, Matthew > Date: 4 November 2014 at 1:11:15 am To: Linden Parkes >, hcp-users@humanconnectome.org> Subject:  Re: [HCP-Users] MNINonL

Re: [HCP-Users] MNINonLinear ROIs

las_ variant to generate ROIs for tractography mean that for each participant the ROIs are going to include some of the surrounding white matter?  Does using the xfms transforms account for this? On 4 November 2014 10:07, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: Yes, that would allow th

Re: [HCP-Users] How to limit the number of cores when wb_command is running?

Perhaps you should have one job at a time requesting all cores (and allow it to use more RAM)?  That will likely be more efficient than running multiple jobs in parallel. Peace, Matt. From: Oscar Miranda Dominguez Date: Tuesday, November 11, 2014 at 12:15 PM To: "hcp-

Re: [HCP-Users] How to limit the number of cores when wb_command is running?

me.org] On Behalf Of Oscar Miranda Dominguez Sent: Tuesday, November 11, 2014 12:25 PM To: Glasser, Matthew Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] How to limit the number of cores when wb_command is running?   Ok. I’ll try that.   I’ll also give another try to the // submission se

Re: [HCP-Users] missing fullWarp_abs

Please install the HCP version of the gradient distortion correction code: https://github.com/Washington-University/gradunwarp Tim, this error probably should be added to the FAQ as it is coming up a lot.  Also, perhaps the pipelines could be tweaked to produce a more descriptive error messa

Re: [HCP-Users] Projecting from Grayordinates to Nifti / Analyze voxels and vice versa

You would need to map the ROIs onto the surface for the surface portion and into subcortical parcels for the subcortical portion.  You can use wb_command -volume-to-surface-mapping to map ROIs onto the surface and then you can use wb_command -cifti-create-dense-scalar -volume <${StudyFolder}/

Re: [HCP-Users] Distances between vertices in the cortical surface

Vertex areas are used in resampling from the native mesh to the 32k registered mesh (this process occurs on the sphere and aside from the vertex areas which are calculated on the subjects native mesh and 32k registered mesh midthicknesses the midthicknesses are not involved). The small amount of s

Re: [HCP-Users] About data processing

Can you post a picture of what you are talking about? Peace, Matt. From: liaoxuhong Date: Friday, November 14, 2014 at 8:36 PM To: hcp-users Subject: [HCP-Users] About data processing Hi:     I'm currently working with minimall

Re: [HCP-Users] Questions about preprocesssing of dMRI data

Have a look at the HCP diffusion pipeline: https://github.com/Washington-University/Pipelines/tree/master/DiffusionPreprocessing In particular scripts/eddy_postproc.sh Peace, Matt. From: 木村一皓 Date: Saturday, November 22, 2014 at 3:25 AM To: "hcp-users@humancon

Re: [HCP-Users] About data processing

bilateral inferior temporal gyrus. I hope above statement is clear, if not please contact with me.       Thanks again!   Best regards,   Xuhong Liao   -- 已转发邮件 ------ From: "Glasser, Matthew" <glass...@wusm.wustl.edu> To: liaoxuhong <liaoxuh...@gmail.com>, hcp-

Re: [HCP-Users] Q) Is there any way to color-label overlapping regions when two images are overlaid?

Perhaps play with the opacity settings which are visible in your screenshot?  Let us know if you cannot accomplish what you want to do with those. Peace, Matt. From: "Yune S. Lee" Date: Monday, November 24, 2014 at 9:54 AM To: "hcp-users@humanconnectome.org"

Re: [HCP-Users] PreFreeSurferPipeline

I would probably try to upsample rather than downsample to take advantage of your 0.9mm T1w (we’ve not tried 0.9mm before, but given how much better 0.8mm is than 1mm, it would probably be worth it).  You could see if things run smoothly if you just use the 0.8mm template, or otherwise could

Re: [HCP-Users] 7T pipelines and protocols

Hi Jenn, I’m almost certain the Ugurbil citation will not be sufficient for documenting the main HCP 7T data acquisition protocol, since that was finalized after that paper was published.   Matt. From: Jennifer Elam Date: Wednesday, December 3, 2014 at 11:05 AM To:

Re: [HCP-Users] White matter mask availability in HCP

For whitematter/greymatter interface, it sounds like you need a surface (the white matter surface).   This will be much more exact than a volume mask (e.g. if you are doing tractography, you can get quite misleading results if you use masks vs surfaces for cortex).   As for a white matter mas

Re: [HCP-Users] error when setting SpinEchoPhaseEncodeNegative="NONE"

What is it that you are trying to do? Peace, Matt. From: , Gregory Date: Monday, December 8, 2014 at 10:33 AM To: "hcp-users@humanconnectome.org" Subject: [HCP-Users] error when setting SpinEchoPhaseEncodeNegative="NONE"

Re: [HCP-Users] error when setting SpinEchoPhaseEncodeNegative="NONE"

d to process them using the fieldmaps instead. I’ve setup the PreFS/FS/PostFS using the fieldmaps, and then I run the GenericfMRIBatch script on the output of the freesurfer scripts. -G   From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu] Sent: Monday, December 08, 2014 12:30 PM To: Book, Gregory;

Re: [HCP-Users] error when setting SpinEchoPhaseEncodeNegative="NONE"

EncodePositive \   --fmapmag=$MagnitudeInputName \   --fmapphase=$PhaseInputName \   --echospacing=$DwellTime \   --echodiff=$DeltaTE \   --unwarpdir=$UnwarpDir \   --fmrires=$FinalFMRIResolution \   --dcmethod=$DistortionCorrection \   --gdcoeffs=$GradientDistort

Re: [HCP-Users] error when setting SpinEchoPhaseEncodeNegative="NONE"

oPhaseEncodeNegative \   --SEPhasePos=$SpinEchoPhaseEncodePositive \   --fmapmag=$MagnitudeInputName \   --fmapphase=$PhaseInputName \   --echospacing=$DwellTime \   --echodiff=$DeltaTE \   --unwarpdir=$UnwarpDir \   --fmrires=$FinalFMRIResolution \   --dcmethod=$DistortionCorrection

Re: [HCP-Users] error when setting SpinEchoPhaseEncodeNegative="NONE"

n purposes. Besides, if you are going to offer a NONE option anyway, it makes sense to have the option actually work. -Micah On Mon, Dec 8, 2014 at 11:35 AM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: Hi Micah, This sort of thing is not recommended, as you cannot get an accurate r

Re: [HCP-Users] error when processing more than 2 tasks with GenericfMRIVolume script

Can you post the text of your launcher script?  Only one task is run at a time inside the pipeline, so the issue will be there. Peace, Matt. From: , Gregory Date: Tuesday, December 9, 2014 at 12:29 PM To: "hcp-users@humanconnectome.org"

Re: [HCP-Users] error when processing more than 2 tasks with GenericfMRIVolume script

ldMap_LR.nii.gz   Dec 9, 2014 15:52:11    rwxr-xr-x    1,119,399 /analysis/unprocessed/3T/domino3/analysis_3T_SpinEchoFieldMap_RL.nii.gz   Dec 9, 2014 15:52:12    rwxr-xr-x    1,127,080 /analysis/unprocessed/3T/domino3/analysis_3T_domino3.nii.gz  Dec 9, 201

Re: [HCP-Users] error when processing more than 2 tasks with GenericfMRIVolume script

the spin echos? Does it assume the positive image is the same encoding direction as the EPI and the negative image is the opposite direction?   From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu] Sent: Tuesday, December 09, 2014 3:33 PM To: Book, Gregory; hcp-users@humanconnectome.org Cc: Br

Re: [HCP-Users] error when processing more than 2 tasks with GenericfMRIVolume script

=(y y- y y-) > >nTasklist=${#Tasklist[@]} >nPhaseEncodinglist=${#PhaseEncodinglist[@]} > >if [ $nTasklist -ne $nPhaseEncodinglist ]; then > >fi > > >Gordon > >> On Dec 9, 2014, at 3:33 PM, Glasser, Matthew >>wrote: >> >> You need to expan

Re: [HCP-Users] White matter mask availability in HCP

lexus, RightLateralVentricle, RightInfLatVent, RightChoroidPlexus     wmparc_del_structures = [4, 5, 14, 15, 24, 31, 43, 44, 63]     #LeftCaudate RightCaudate       wmparc_del_structures2 = [11, 50] Thx again!  Best regards, Eleftherios On Fri, Dec 5, 2014 at 2:54 AM, Glasser, Matthew <

Re: [HCP-Users] error while writing cifti with Matlab

I’m not sure the wb_command -cifti-convert -reset options work with a dconn as the input header file.  Do you have some other dscalar or dtseries file you can load into matlab and use as the header?   Then it should work fine.  Also I have a new version of ciftisavereset that I could distribut

Re: [HCP-Users] error while writing cifti with Matlab

Let’s hear a confirmation from Tim Coalson that a dconn header would actually be properly reset, I’m not sure that is true. Matt. From: , Michael Date: Wednesday, December 10, 2014 at 3:38 PM To: Julien Dubois , "hcp-users@humanconnectome.org"

Re: [HCP-Users] tfMRI masking, lateralization

Why wouldn’t you do this in CIFTI space? Peace, Matt. From: Aaron R Date: Thursday, December 11, 2014 at 3:12 PM To: "hcp-users@humanconnectome.org" Subject: [HCP-Users] tfMRI masking, lateralization Dear HCP users, I'd like to

Re: [HCP-Users] GenericfMRIVolumeProcessingPipelineBatch motion correction

Hi Julien, You are not the first to report this for lower resolution fMRI data. We¹re not completely sure why the performance is different in these cases, however we would definitely be interested in a patch for the fMRIVolume pipeline that allowed choosing to use mcflirt instead of mcflirt_acc fo

Re: [HCP-Users] spin echo phase encoding direction

If your phase encoding directions are inverted, I would recommend swapping the SpinEchoPositive and NegativeImage values.  This would make the computed field map have the same sign as a typical field map and then the PhaseEncodeList would not have to change. Peace, Matt. From: , Gregory

Re: [HCP-Users] Integration of FIX cleanup with the minimal preprocessing pipeline

Hi Julien, We simply ran melodic + FIX on the MNI space volume results of each resting state run (i.e. the outputs of the minimal preprocessing pipelines).  The cleanup was then applied to both the volume timeseries and the CIFTI timeseries.  Look in the FIX distribution for a shell script hc

Re: [HCP-Users] spin echo phase encoding direction

I’m slightly more confused now. So, using the CMRR sequences, if I set the phase encoding direction on my spin echo to A>>P, and “Invert RO/PE Polarity” option is checked… a) what is the actual phase direction of the data b) what is recorded in the DICOM header in the *.dInPlaneRot f

[HCP-Users] FW: GenericfMRIVolumeProcessingPipelineBatch motion correction

h like you describe, I'll probably whip one up for my purposes so I'll keep you in the loop. - Julien > On Dec 14, 2014, at 12:45 PM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: > > Hi Julien, > > You are not the first to report this for low

Re: [HCP-Users] GenericfMRIVolumeProcessingPipelineBatch motion correction

l Scholar California Institute of Technology, Pasadena, CA http://www.emotion.caltech.edu/~jdubois On Tue, Dec 16, 2014 at 10:06 AM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: Hi Julien, Thanks for sending this in.  Why do you think the mid volume is b

Re: [HCP-Users] GenericfMRIVolumeProcessingPipelineBatch motion correction

t;  > If no one else is working on a patch like you describe, I'll probably > whip one up for my purposes so I'll keep you in the loop. >  > - Julien >  >  >  >  >  > > On Dec 14, 2014, at 12:45 PM, Glasser, Matthew > > <glass...@wusm.wu

Re: [HCP-Users] fieldmap processing error

Probably the easiest thing to do would be to fix the outlying image dimension by editing the NIFTI header.  What program are you using to convert from scanner format to NIFTI?  We use dcm2nii in the HCP. Peace, Matt. From: , Gregory Date: Thursday, January 8,

Re: [HCP-Users] fieldmap processing error

24ZVW/2/HCPfMRI-MID/pipeline/step48.log-Fix this (probably in reconstruction stage) before re-running this script   From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu] Sent: Thursday, January 08, 2015 2:07 PM To: Book, Gregory; hcp-users@humanconnectome.org Subject: Re: [HCP-User

Re: [HCP-Users] fieldmap processing error

l of Medicine >Department of Anatomy and Neurobiology >Phone: 314-362-7864 >Email: gburg...@wustl.edu > >> On Jan 9, 2015, at 1:59 PM, Glasser, Matthew >>wrote: >> >> Can you check that the headers of these files look okay: >> >> >>${StudyFolder}/${Sub

Re: [HCP-Users] -cifti-separate

Please post your wb_command -cifti-separate command line. Peace, Matt. From: Marta Moreno Date: Monday, January 12, 2015 at 9:52 PM To: "hcp-users@humanconnectome.org" Subject: [HCP-Users] -cifti-separate Hi users, I am us

Re: [HCP-Users] -cifti-separate

low Division of Experimental Therapeutics New York State Psychiatric Institute Department of Psychiatry Columbia University College of Physicians and Surgeons On Jan 12, 2015, at 10:54 PM, "Glasser, Matthew" <glass...@wusm.wustl.edu> wrote: Please post your wb_command -cifti-sepa

Re: [HCP-Users] -cifti-separate

e of Physicians and Surgeons On Jan 12, 2015, at 11:01 PM, "Glasser, Matthew" <glass...@wusm.wustl.edu> wrote: I didn’t read your question closely enough.  You cannot make a surface from -cifti-separate (you can make data that you can display and analyze on a surface howev

Re: [HCP-Users] -cifti-separate

d Surgeons On Jan 12, 2015, at 11:09 PM, "Glasser, Matthew" <glass...@wusm.wustl.edu> wrote: Is this HCP data or your own data? Matt. From: Marta Moreno <mmorenoort...@icloud.com> Date: Monday, January 12, 2015 at 10:06 PM To: Matt Glasser <glass...@wusm.wust

Re: [HCP-Users] Abnormality in Healthy Control from Connectome

Our radiologist noted that it is a midline calcification and read the brain as normal. Peace, Matt. From: , "Samantha [F] (NIH/NIAAA)" Date: Thursday, January 15, 2015 at 3:59 PM To: "supp...@humanconnectome.org" , "hcp-users@hum

Re: [HCP-Users] numpy error running PreFreeSurferPipeline.bat

It looks like you need to install the python package numpy. Peace, Matt. On 1/16/15, 8:49 AM, "Juan Sanchez" wrote: >Dear All, >I am using Centos 6.5 >with FSL 5.0.6 >Free Surfer 5.3 >Python 2.7.6 >numpy-1.4.1-9.el6.x86_64 > >I am trying to troubleshoot the following error When running >PreFr

Re: [HCP-Users] numpy error running PreFreeSurferPipeline.bat

already installed and latest version >Nothing to do > >____________ >From: Glasser, Matthew [glass...@wusm.wustl.edu] >Sent: Friday, January 16, 2015 9:52 AM >To: Juan Sanchez; hcp-users@humanconnectome.org >Subject: Re: [HCP-Users] numpy error runni

Re: [HCP-Users] 4D to 3D conversion

fslsplit will do this, but why is it that you want to do this and why would a DICOM to NIFTI converter be a part of the process when the data are already in NIFTI format? Peace, Matt. From: yamur osmanova Date: Saturday, January 17, 2015 at 2:16 PM To: "hcp

Re: [HCP-Users] Number of diffusion directions inconsistent in some subjects preprocessed dMRI data

The most likely explanation is that the subject did not complete the diffusion acquisition session or that something was later found to be wrong with one or more of their diffusion runs.  You can filter subjects to only get complete datasets in ConnectomeDB. Peace, Matt. From: Michael

Re: [HCP-Users] grey matter volume

That should be in ${StudyFolder}/${Subject}/T1w/${Subject}/stats Peace, Matt. From: Marta Moreno Date: Tuesday, January 20, 2015 at 7:59 PM To: "hcp-users@humanconnectome.org" Subject: [HCP-Users] grey matter volume Hi users

Re: [HCP-Users] grey matter volume

ersity College of Physicians and Surgeons On Jan 20, 2015, at 9:21 PM, "Glasser, Matthew" <glass...@wusm.wustl.edu> wrote: That should be in ${StudyFolder}/${Subject}/T1w/${Subject}/stats Peace, Matt. From: Marta Moreno <mmorenoort...@icloud.com> Date: T

Re: [HCP-Users] 7 RSN Netoworks label file

You can also use the map number if that is the issue. Else perhaps we need more info on what you are trying to do. Peace, Matt. On 1/22/15, 9:20 PM, "Marta Moreno" wrote: >Hi users, > >I am trying to get the labels from 7 RSN Networks but "map" on export >table command is not recognized and I

Re: [HCP-Users] Phase Encoding Direction

How much RAM do you have? The CIFTI files use far less RAM than the volume files, but contain all the grey matter information represented in a way that makes combining across subjects more accurate. If you don¹t use all the data your estimates of the subject¹s functional connectivity will be nois

Re: [HCP-Users] Phase Encoding Direction

. Is this ok? > >Many thanks! >Chao > >> On 23 Jan 2015, at 13:57, Glasser, Matthew >>wrote: >> >> How much RAM do you have? The CIFTI files use far less RAM than the >> volume files, but contain all the grey matter information represented >>in a >

Re: [HCP-Users] mris_make_surfaces: undefined symbol ncerr in FreesurferPipelineBatch.sh

Fellow > Division of Experimental Therapeutics > New York State Psychiatric Institute > Department of Psychiatry > Columbia University College of Physicians and Surgeons > > > > > On Jan 23, 2015, at 12:03 AM, "Glasser, Matthew" <glass...@wusm.wustl.edu> >

Re: [HCP-Users] mris_make_surfaces: undefined symbol ncerr in FreesurferPipelineBatch.sh

Regards Devakumar Sent from Windows Mail From: Glasser, Matthew Sent: Thursday, January 29, 2015 11:58 AM To: Devakumar gmail, hcp-users@humanconnectome.org Cc: Brown, Tim What OS is this?  It’s probably too old.   Peace, Matt. From: "dkumar.in...@gmail.com" <dkuma

Re: [HCP-Users] Group ICA with Melodic on 20 or more subjects

If you update to the latest version of FSL the MIGP algorithm may be in there and is designed to help with this.  The main limitation with melodic has been that it was single threaded.  I don’t know if that has been addressed yet. Peace, Matt. From: Micah Chambers D

Re: [HCP-Users] Group ICA with Melodic on 20 or more subjects

t is a good bit more than 8GB now, unless the PCA is performed per subject. Has anyone done Group ICA on datasets this size? -Micah On Thu, Jan 29, 2015 at 6:40 PM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: If you update to the latest version of FSL the MIGP algorithm may be in

Re: [HCP-Users] Group ICA with Melodic on 20 or more subjects

CA is performed per subject. Has anyone done Group ICA on datasets this size? -Micah On Thu, Jan 29, 2015 at 6:40 PM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: If you update to the latest version of FSL the MIGP algorithm may be in there and is designed to help with this.  The

Re: [HCP-Users] Group ICA with Melodic on 20 or more subjects

hambers <micahc...@gmail.com> wrote: Well the resting state data provided through the HCP around 1GB each so I'm guessing the memory requirement is a good bit more than 8GB now, unless the PCA is performed per subject. Has anyone done Group ICA on datasets this size? -Micah On

Re: [HCP-Users] Phase Encoding Direction

session. As I understood, only using 1200 volumes which is only one phase encoding direction, seems to be problematic. What do you guys think? Is it ok to do it this way? greetings David 2015-01-23 16:54 GMT+01:00 Glasser, Matthew <glass...@wusm.wustl.edu>: The function

Re: [HCP-Users] requirements for HCP pipeline?

You also need a T2w scan unless you want to do major hacking on the pipelines. Peace, Matt. From: Jennifer Elam Date: Tuesday, February 3, 2015 at 11:25 AM To: "Harms, Michael" , 'Marta Moreno' , "hcp-users@humanconnectome

Re: [HCP-Users] probably obvious question, but . . .

You’ll want to make sure you’re using the latest version of the main HCP public release, rather than tutorial data.  You can run wb_command -cifti-correlate to compute functional connectivity from the dense timeseries data.  If you want to combine across runs, you should demean the data first u

Re: [HCP-Users] probably obvious question, but . . .

issue of global signal, and agree with you . . .  Your point about not needing to do WM or CSF time series regression after ICA FIX is quite helpful.   Thanks, Matt From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu] Sent: Thursday, February 05, 2015 10:55 AM To: Hoptman, Matthew; 'hc

Re: [HCP-Users] probably obvious question, but . . .

ctome.org> Cc: "Elam, Jennifer" <el...@pcg.wustl.edu> Subject: RE: [HCP-Users] probably obvious question, but . . . Fair enough.  And the movement signal regression?   From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu] Sent: Thursday, February 05, 2015 11:31 AM To: Hopt

Re: [HCP-Users] PBS vs fsl_sub in CHPC cluster

This might be a better question for the mailing list of this specific cluster, but I believe the version of fsl_sub on the Wash U cluster still works with PBS (I helped modify it to do this some years ago). Peace, Matt. On 2/5/15, 11:48 AM, "Ramirez San Martin, Carolina" wrote: >Hi, > >I¹m sta

Re: [HCP-Users] Fwd: Regarding: No FieldMap_Magnitude in lifespan dataset

In ${GitRepo}/Examples/Scripts/PreFreeSurferPipelineBatch.sh change these variables to use spin echo field maps to correct T1w and T2w scans for readout distortion in the HCP LifeSpan scans: AvgrdcSTRING="SiemensFieldMap" To AvgrdcSTRING=“TOPUP" MagnitudeInputName="${StudyFol

Re: [HCP-Users] manual AC-PC realignment

How do you define failure and what kind of subjects are these?  This is only intended to be a rough alignment that gets the rest of the pipeline into a “funnel” by which the alignment continues to be refined.  For us, failure of the AC/PC registration means that subsequent steps cannot work pro

Re: [HCP-Users] Regarding: No T2w_reg_fast_pve_2 for reading

Your e-mail got some attachments stripped out, but it looked like you might have exceeded a queue limit on a cluster or something like that, as the first error was a processing being killed. Peace, Matt. On 2/12/15, 12:52 AM, "Dr Sampada Sinha" wrote: >WARNING: This e-mail has been altered by

Re: [HCP-Users] Preprocessing questions

The code for that derivation (written by Mark Jenkinson) is posted online: https://github.com/Washington-University/Pipelines/blob/master/global/scripts/aff2rigid.py Yes *_restore means the bias field has been removed. Why do you want to see fMRI data with and without distortion correction

Re: [HCP-Users] Preprocessing questions

e effect of distortion correction (b0 field). - Anders Den 12 feb 2015 18:14 skrev "Glasser, Matthew" <glass...@wusm.wustl.edu>: The code for that derivation (written by Mark Jenkinson) is posted online: https://github.com/Washington-University/Pipelines/blob/master/global/sc

Re: [HCP-Users] Duplicate names in "${HCPPIPEDIR_Config}/FreeSurferAllLut.txt" ?

Hi Alex, Those were translated directly from FreeSurfer’s master LUT file, so you’ll have to ask them… :) Peace, Matt. From: Alex Cohen Reply-To: "alexco...@gmail.com" Date: Thursday, February 12, 2015 at 11:17 PM To: "hcp-users@humanconnecto

Re: [HCP-Users] Duplicate names in "${HCPPIPEDIR_Config}/FreeSurferAllLut.txt" ?

dolescent Neurology E-mail: cohen.alexan...@mayo.edu (Medical/Science Email) E-mail: alexco...@gmail.com (Lifetime Email) Mayo Clinic 200 First Street SW Rochester, MN 55905 mayoclinic.org ------------ On Thu, Feb 12, 2015 at 11:19

Re: [HCP-Users] Using MarsBar on HCP data

What is MarsBar?  That sounds like a type of candy…  Peace, Matt. From: Mary Meacham Date: Friday, February 13, 2015 at 1:41 PM To: "hcp-users@humanconnectome.org" Subject: [HCP-Users] Using MarsBar on HCP data Hi there!

Re: [HCP-Users] Using MarsBar on HCP data

Fri, Feb 13, 2015 at 1:43 PM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: What is MarsBar?  That sounds like a type of candy…  Peace, Matt. From: Mary Meacham <mary.kate.meac...@gmail.com> Date: Friday, February 13, 2015 at 1:41 PM To: "hcp-users@humanconnectome

Re: [HCP-Users] Using MarsBar on HCP data

rve me the same way? --Mary Kate On Feb 13, 2015, at 1:48 PM, "Glasser, Matthew" <glass...@wusm.wustl.edu> wrote: Hopefully someone out there uses SPM with HCP data and can comment, as most of us use FSL/Connectome Workbench. Peace, Matt. From: Mary Meacham <mary.ka

Re: [HCP-Users] Projecting Label into White Matter

We recommend you run tractography directly from the surfaces using probtrackx2.  You can use these surfaces if you want your other volume (i.e. non-cortical) ROIs in native subject space: ${StudyFolder}/${Subject}/T1w/fsaverage_LR32k/${Subject}.${Hemisphere}.white.32k_fs_LR.surf.gii Or these

Re: [HCP-Users] Projecting Label into White Matter

ri_label2vol assumes that the labels derived from the annot files are defined for the ?h.white surface, but I wanted to see if this is actually the case. Should I use, e.g., ?h.white.hires instead? John On Fri, Feb 13, 2015 at 2:31 PM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote

Re: [HCP-Users] Incorporating physiological monitoring data

Note that a major reason we didn’t use these physiological confound regressors was they don’t exist for every subject, so be sure to select a subset of subjects that have them.  We’d also be interested to know if you found they were helpful. Peace, Matt. From: Stephen Smith

Re: [HCP-Users] Processing Diffusion MRI Data

Why do you need to use FLIRT/FNIRT with already registered data?  As for the others and aside from the flags you already mention, I think the recommendation for bedpostX will include these flags: -n 3 (for 3 fibers)  --cnonlinear --rician --model=3 Not all of this may yet be available in the

Re: [HCP-Users] Incorporating physiological monitoring data

Also to Steve: if these are used after ICA+FIX, don’t they need to have the 24 motion parameters and noise ICA component timeseries confounds regressed out as well, before being used on the cleaned data? Peace, Matt. From: , Michael Date: Monday, February 16, 2015 at 1

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