Re: [HCP-Users] Custom parcellation for HCP data

FreeSurfer might do it if you simply specify the correct extension, but if not, mris_convert will do the conversion. Peace, Matt. From: > on behalf of Timothy Coalson >

Re: [HCP-Users] eddy_parameters file

I don't think they are in the packages, but they ought to be for folks interested in the same question you are. Perhaps someone from the OT-7 group can explain how you could extract the files via the REST command line interface. Peace, Matt. From:

Re: [HCP-Users] eddy_parameters file

I don't know about that, but it was an oversight to leave this file out, as I had intended for it to be available. From Glasser et al 2013 Pipelines paper: "All these distortions are corrected in a single resampling step using the "eddy" tool in FSL5 (Andersson et al., 2012; Sotiropoulos it et

Re: [HCP-Users] wb_view and freesurfer surfaces/volumes

This is because FreeSurfer uses a more complicated coordinate system than Connectome Workbench. The next version of FreeSurfer will have some options in mris_convert to fix this, but for now you can do the following: #Find c_ras offset between FreeSurfer surface and volume and generate matrix to

Re: [HCP-Users] Cluster-extent thresholding of CIFTI data

se formats, run the test, then convert back to CIFTI using the Workbench tools. PALM has the ability to take into account the family structure of the HCP data, and one of the reasons why it was developed was precisely so that we could use permutation tests with HCP. All the best, Anderson On

Re: [HCP-Users] Use of spin-echo EPI scans for distortion correction of fMRI data

1 and 2 performed similarly when we compared them. 3 is not a good idea, as GRE images have signal dropout that is asymmetric and will mess up the registration that underlies the reversed phase encoding direction method. Matt. From:

Re: [HCP-Users] 4D CIFTI file for PALM random-effects analysis

wb_command -cifti-merge is the right command and you want to create a dscalar that has the dimensions 91282 grayordinates x 45 maps. It sounds like you have a simple issue of a matrix transpose not being right when the data makes it into PALM. Is it possible that you aren’t using a recent

Re: [HCP-Users] help

Perhaps it is the transformation matrix that is stored in GIFTI files. Matt. From: > on behalf of Timothy Coalson > Date: Thursday, September 24, 2015 at 3:52 PM To:

Re: [HCP-Users] Mapping grayordinate vertices to atlas labels

He undoubtably means the difference between FreeSurfer registration (used to generate the individual subject labels) and MSMSulc registration used to align subjects in the HCP. Matt. From: > on behalf of

Re: [HCP-Users] help -cifti-smoothing

Except that you¹ll want to use 32k surfaces. Peace, Matt. On 9/11/15, 1:08 PM, "hcp-users-boun...@humanconnectome.org on behalf of Donna Dierker" wrote: >Hi Alessia, > >wb_command -cifti-smoothing needs both the

Re: [HCP-Users] Structural masks on Diffusion data

No registration is necessary, you can simply resample with an identity transformation as the data are already aligned (they just have differing resolutions). This could be done with wb_command -volume-affine-resample Input Masks eye.mat

Re: [HCP-Users] failure to replicate dual regression 1 results (PTN nodetimeseries)

them directly. Thanks, Cherry On Fri, Jul 31, 2015 at 11:58 AM, Glasser, Matthew glass...@wusm.wustl.edu wrote: Did you demean the timeseries (remove the mean image) before concatenating? Peace, Matt. From: hcp-users-boun...@humanconnectome.org on behalf of Yizhou Ma maxxx...@umn.edu

Re: [HCP-Users] FIRST on HCP strucs

Hopefully Mark or someone else at Oxford who uses FIRST a lot can help with this (not sure if Mark reads this list or not). Thanks, Matt. From: hcp-users-boun...@humanconnectome.org on behalf of Joseph Orr joseph@tamu.edu Date: Wednesday, July 29, 2015 at 11:21 AM To: HCP Users

Re: [HCP-Users] volume to surface mapping

that would let me proceed with what I have. If I do proceed that way, is the t1w_restore the nifti to which functional data should be registered? Thanks, PB On Mon, Jul 27, 2015 at 3:29 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote: Did you try running your raw functional data through

Re: [HCP-Users] Tractography and brainordinates

file to do the conversion as the number of brainordinates is different. Any further suggestions? -M p.s. I changed the subject as this thread got lost in the list somewhere. On Thu, Jul 23, 2015 at 12:25 AM, Glasser, Matthew glass...@wusm.wustl.edu wrote: I would try switching row

Re: [HCP-Users] tractography

-row-cifti 91282_Greyordinates.dscalar.nii COLUMN -transpose On Mon, Jul 20, 2015 at 5:54 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote: No I meant the dot convert. Matt. From: Maarten Vaessen m.vaes...@gmail.com Date: Monday, July 20, 2015 at 3:29 AM To: Matt Glasser glass

Re: [HCP-Users] ft_read_cifti too many grayordinates

Some of us dont think that code should do that. You can manually remove the NaNs, or use alternative software (option B): https://wiki.humanconnectome.org/display/PublicData/HCPUsersFAQ Peace, Matt. From: hcp-users-boun...@humanconnectome.org on behalf of Janine Bijsterbosch

Re: [HCP-Users] tractography

=L.STS.func.gii Is this what you were referring to? -Maarten On Sun, Jul 19, 2015 at 10:20 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote: The--onewaycondition flag doesn’t seem sensible with matrix3. AlsoI don’t know what your command was for doing the conversion. Here is the probtrackx2

Re: [HCP-Users] tractography

strange: only connectivity to what appears to be the right inferior posterior cortex. Could this be an issue with the seed-space to dti-space parameters? -M On Sun, Jul 19, 2015 at 5:31 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote: What is it that you are trying to achieve? Usually one uses

[HCP-Users] FW: tractography

of all, they appear at column indices which are probably somewhere in the right hemisphere (seed is in the left). Thanks, -Maarten On Wed, Jul 15, 2015 at 6:20 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote: You should be able to use this file: https://github.com/Washington-University

Re: [HCP-Users] automating figure creation with wb_command

Thats how I would do it, except that you dont need to do step 1, just make the scene file as you see fit. Peace, Matt. From: hcp-users-boun...@humanconnectome.org on behalf of Alexandra Walton Weston walto...@ohsu.edu Date: Saturday, July 18, 2015 at 8:47 PM To:

Re: [HCP-Users] tractography

You should be able to use this file: https://github.com/Washington-University/Pipelines/blob/master/global/templates/91282_Greyordinates/91282_Greyordinates.dscalar.nii Peace, Matt. From: hcp-users-boun...@humanconnectome.org on behalf of Maarten Vaessen m.vaes...@gmail.com Date:

Re: [HCP-Users] probtrackx2 surface tracking in matrix2 mode

That error suggests that that particular flag is not ready for surfaces yet and is looking for a NIFTI volume. Do you have the latest version of FSL? Perhaps Stam can comment on whether --target2 will be able to handle surfaces in the future. Peace, Matt. From:

Re: [HCP-Users] T1w/wmparc_1mm

...@cumc.columbia.edu On Jun 26, 2015, at 8:22 AM, Glasser, Matthew glass...@wusm.wustl.edu wrote: It sounds like the FreeSurfer pipeline might not have finished okay. Does the ${StudyFolder}/${Subject}/T1w/${Subject}/mri/wmparc.mgz file exist? Peace, Matt. On 6/25/15, 9:14 PM

Re: [HCP-Users] T1w/wmparc_1mm

It sounds like the FreeSurfer pipeline might not have finished okay. Does the ${StudyFolder}/${Subject}/T1w/${Subject}/mri/wmparc.mgz file exist? Peace, Matt. On 6/25/15, 9:14 PM, hcp-users-boun...@humanconnectome.org on behalf of Marta Moreno hcp-users-boun...@humanconnectome.org on behalf of

Re: [HCP-Users] Status of MSMsulc ( MSMall) binaries?

The hope is to have the MSM binary ready for the next FSL release. Peace, Matt. From: hcp-users-boun...@humanconnectome.org on behalf of Julien Dubois jcrdub...@gmail.com Date: Friday, June 26, 2015 at 12:39 PM To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject:

Re: [HCP-Users] CIFTI files for testing CIFTI support

Also, you could download the single subject dataset from the HCP for more real life examples:https://db.humanconnectome.org/ Thanks for working on CIFTI for nipy! Matt. From: hcp-users-boun...@humanconnectome.org on behalf of Timothy Coalson tsc...@mst.edu Date: Thursday, June 25, 2015

Re: [HCP-Users] Myelin mapping with FLAIR

For the moment one just treats the FLAIR as a T2w scan for the purposes of the pipelines. Peace, Matt. From: hcp-users-boun...@humanconnectome.org on behalf of Michael Dwyer mgdw...@bnac.net Date: Sunday, June 21, 2015 at 8:24 PM To: Gaurav Patel gauravpa...@gmail.com Cc: HCP Users

Re: [HCP-Users] Myelin mapping with FLAIR

, Glasser, Matthew glass...@wusm.wustl.edu wrote: For the moment one just treats the FLAIR as a T2w scan for the purposes of the pipelines. Peace, Matt. From: hcp-users-boun...@humanconnectome.org on behalf of Michael Dwyer mgdw...@bnac.net Date: Sunday, June 21, 2015 at 8:24 PM To: Gaurav

Re: [HCP-Users] Diffusion Preprocessing Error

That would probably help. It is important that the names of the files match what the script is expecting. Peace, Matt. From: levi solomyak lsolom...@gmail.com Date: Friday, June 19, 2015 at 12:34 PM To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: [HCP-Users]

Re: [HCP-Users] User-provided colormaps for wb_view?

Not yet. What color map are you wanting to use? Peace, Matt. From: Oscar Miranda Dominguez miran...@ohsu.edu Date: Friday, June 12, 2015 at 10:13 AM To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: [HCP-Users] User-provided colormaps for wb_view? Hey I

Re: [HCP-Users] User-provided colormaps for wb_view?

a specific color to a set of rois or grayordinates that share the same value. Providing my own-color map would avoid making a dlabel file, I guess. May be there ways with existing tools to deal with those 2 scenarios Thank you! From: Glasser, Matthew [glass...@wusm.wustl.edu] Sent: Friday

[HCP-Users] FW: Error Running Probtrackx

you will see what options are supported. Cheers Stam On 4 Jun 2015, at 15:32, Glasser, Matthew glass...@wusm.wustl.edu wrote: Thats a question for Stam, but if you want 3 fibers, you would need to run --nf=3. Peace, Matt. From: Archer, Derek B arche...@ad.ufl.edu Date: Thursday

Re: [HCP-Users] Error Running Probtrackx

: RE: [HCP-Users] Error Running Probtrackx Hi Matt, Sorry, I was mistaken on this. However, what I did do is run model=3 instead of model=2. I remember from a previous post that this is released in FSL yet. Should this have given an error within bedpostx? Thanks, Derek From: Glasser

Re: [HCP-Users] Resting fMRI Cortex Vertices Indices

to get a set of consistently labelled points in subcortical structures, or can this only be done at the level of subcortical structures (20 or so, rather than 30K, per subject)? -dh From: hcp-users-boun...@humanconnectome.org hcp-users-boun...@humanconnectome.org on behalf of Glasser, Matthew glass

Re: [HCP-Users] Help understanding *_Atlas.dtseries.nii

Here is a page that should be helpful to getting started: https://wiki.humanconnectome.org/display/PublicData/HCPUsersFAQ Peace, Matt. From: Philip Henningsen philip.henning...@gmail.com Date: Friday, May 29, 2015 at 7:29 AM To: hcp-users@humanconnectome.org Users

Re: [HCP-Users] SBref Distortion Correction

...@humanconnectome.org You can reach the person managing the list at hcp-users-ow...@humanconnectome.org When replying, please edit your Subject line so it is more specific than Re: Contents of HCP-Users digest... Today's Topics: 1. Re: SBref Distortion Correction (Glasser, Matthew) 2

Re: [HCP-Users] L-R or R-L phase encoding?

We use all four resting state runs and we use the CIFTI ${fMRIName}_Atlas_hp2000_clean.dtseries.nii data which has been cleaned with ICAFIX. When using runs with a different phase encoding direction, it is important to remove the mean image first. We then temporally concatenate multiple runs.

Re: [HCP-Users] SBref Distortion Correction

procedure is failing. Any help would be appreciated. Thanks! _ gaurav patel gauravpa...@gmail.com www.neurofreak.net On May 22, 2015, at 3:00 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote: It helps to reply to the previous e-mail chain so that all of the info

Re: [HCP-Users] where are the head shape file for MEG

models to the helmet space ... Best, Denis 2015-05-18 18:42 GMT02:00 Glasser, Matthew glass...@wusm.wustl.edu: Can someone explain why it is important to use original FreeSurfer surfaces? These have a much higher density that is needed for most applications, are very irregular, and do

Re: [HCP-Users] Minimal Preprocessing Pipelines

Probably need to specify your probtrackx2 command lines, but both rigid alignment to MNI space and nonlinear alignment are available in the ${StudyFolder}/${Subject}/T1w and ${StudyFolder}/${Subject}/MNINonLinear locations respectively. Peace, Matt. From: Archer, Derek B

Re: [HCP-Users] Minimal Preprocessing Pipelines

, So to get the diffusion data into the standard space, which files are relevant under the MNINonLinear folder? Sorry for the confusion. Derek From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu] Sent: Monday, May 18, 2015 3:15 PM To: Archer,Derek B; hcp-users@humanconnectome.org Subject: Re

Re: [HCP-Users] Minimal Preprocessing Pipelines

? Thanks, Derek From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu] Sent: Monday, May 18, 2015 1:57 PM To: Archer,Derek B; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Minimal Preprocessing Pipelines Probably need to specify your probtrackx2 command lines, but both rigid

Re: [HCP-Users] Epi-T1 co-registration using TOPUP

I would check that your SE field map has the same geometry and echo spacing as your SBRef. Also I would post some examples of what looks wrong to you in your processing. Peace, Matt. From: Juan Sanchez sanch...@nyspi.columbia.edu Date: Monday, May 18, 2015 at 3:21 PM To:

Re: [HCP-Users] Downsample 32k surface into fsaverage4

There was a post to the mailing list about this very recently, so have a quick search. Peace, Matt. From: Manousos Klados mkla...@gmail.com Date: Friday, May 15, 2015 at 3:19 PM To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: [HCP-Users] Downsample 32k surface

Re: [HCP-Users] Slice Timing Correction

I wouldnt do it for HCP data. Really it seems like if you were to do something like this, youd want to do it at the same time as motion correction and distortion corrections in one single giant interpolation. A better idea for many reasons is to just image fast enough so that it doesnt matter.

Re: [HCP-Users] Myelin Mapping

for myelin mapping. Best wishes and thanks for your help. Barbara Anne On 05/05/2015 23:00, Glasser, Matthew wrote: (1) Use the 1mm templates. (2) You can do this, but it’s important to note that the myelin/iron relationship, which is very close in cortex, may deviate more in subcortical white

Re: [HCP-Users] Myelin Mapping

to look out for? As I notice some differences in my acquisition parameters when comparing to other papers. Also, we did not apply FAT saturation, I read somewhere this would be beneficial for myelin mapping. Best wishes and thanks for your help. Barbara Anne On 05/05/2015 23:00, Glasser, Matthew

Re: [HCP-Users] Downsampled grayordinate data?

I don¹t recommend using data with large amounts of spatial smoothing (downsampling is actually a more forthright acknowledgement of what you are doing to the data and saves space and computational time). Also, it¹s worth thinking if your use case would be better served by using a brain

Re: [HCP-Users] Help with dtifit on participants

I would write it like this: Subjlist=YOUR LIST OF SUBJECT IDS SEPARATED BY SPACES StudyFolder=YOUR_STUDYFOLDER_THAT_CONTAINS_SUBJECT_FOLDERS_HERE for Subject in ${Subjlist} ; do #Loop over subject IDs DIR=`pwd` #Save the current directory cd ${StudyFolder}/${Subject}/T1w/Diffusion #cd

Re: [HCP-Users] Help with dtifit on participants

:51 PM To: Glasser, Matthew; mha...@wustl.edu; hcp-users@humanconnectome.org Subject: RE: [HCP-Users] Help with dtifit on participants Hi, Thanks for the help. I'm going to go with Matt's script first before consulting IT. I have reason to believe it isn't an issue that can be solved

Re: [HCP-Users] MNI atlas registration in volume space for task fMRI grayordinates datasets?

@humanconnectome.org/msg01323.html http://www.mail-archive.com/hcp-users@humanconnectome.org/msg01234.html http://www.mail-archive.com/hcp-users@humanconnectome.org/msg00356.html thanks again Matt and Tim, Jo On 4/24/2015 11:56 AM, Glasser, Matthew wrote: I don’t really want to recapitulate my more detailed

Re: [HCP-Users] Creating a parcellated connectome from a label file

wb_command -cifti-parcellate is indeed the first step. The next step you could load the resulting .ptseries.nii file into matlab or use wb_command -nifti-information with the -print-matrix option to output the terminal window, which you could redirect to a text file. I dont know if this is in

Re: [HCP-Users] MNI atlas registration in volume space for task fMRI grayordinates datasets?

Yes that¹s how it works. Peace, Matt. On 4/24/15, 9:56 AM, J.A. Etzel jet...@artsci.wustl.edu wrote: I have a question about the preprocessing for the task-fMRI grayordinates datasets, specifically the images from the Level 2 fixed-effects analysis. For clarity, the images I'm asking about are

Re: [HCP-Users] MNI atlas registration in volume space for task fMRI grayordinates datasets?

registration is preferable? thanks again, Jo On 4/24/2015 9:59 AM, Glasser, Matthew wrote: Yes that¹s how it works. Peace, Matt. On 4/24/15, 9:56 AM, J.A. Etzel jet...@artsci.wustl.edu wrote: I have a question about the preprocessing for the task-fMRI grayordinates datasets

Re: [HCP-Users] MNI atlas registration in volume space for task fMRI grayordinates datasets?

registration to atlas space described in Anticevic et al., 2008? thanks, Jo On 4/24/2015 11:24 AM, Glasser, Matthew wrote: There were a few threads on this in the past. The volume and surface registration are pretty much independent. The cortical data are aligned with surface registration

Re: [HCP-Users] help for identifying MNI atlas in the fMRI pipeline

What we use is based on FSL¹s nonlinear MNI templates, but was made using Conte69 data registered to these templates. Peace, Matt. On 4/23/15, 8:34 AM, Alpay Özcan al...@vt.edu wrote: Hello, I would appreciate if anyone can help me identify the atlas used in fMRI pipeline. I believe

Re: [HCP-Users] stat output of pipeline

What FSL version? I dont think that error is important and is related to whether the variablePOSIXLY_CORRECT is set or not (have a google search about it in relation to FreeSurfer and being queued by the fsl_sub command). As for the stats differences, FreeSurfer isnt expected to give

Re: [HCP-Users] cifti-correlation-gradient settings and surface-based math?

Hi Alex, For group data I usually use a gradient pre-smoothing of 1mm sigma, though for some modalities like myelin maps, even this reduces some detail (you might try both ways…). For seed exclusion I use 2mm (the acquisition resolution), basically the goal is to exclude the central spike in

Re: [HCP-Users] cifti-correlation-gradient settings and surface-based math?

, Glasser, Matthew glass...@wusm.wustl.edu wrote: Hi Alex, For group data I usually use a gradient pre-smoothing of 1mm sigma, though for some modalities like myelin maps, even this reduces some detail (you might try both ways…). For seed exclusion I use 2mm (the acquisition resolution), basically

Re: [HCP-Users] Minimal Preprocessing Pipeline (on my own data): Flipped EPI (AP)

Can you give us more details on the data you are feeding into the pipelines and how you called fMRIVolume? We have not experienced this issue with HCP data or the non-HCP data we have tried the pipelines with. Peace, Matt. From: Julien Dubois jcrdub...@gmail.com Date: Friday, April 17,

Re: [HCP-Users] missing _Atlas.dtseries.nii

Did you run the fMRISurface pipeline yet? That file gets generated by that pipeline. Peace, Matt. From: Book, Gregory gregory.b...@hhchealth.org Date: Thursday, April 16, 2015 at 9:30 AM To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: [HCP-Users] missing

Re: [HCP-Users] missing _Atlas.dtseries.nii

of the fMRISurface pipeline error? Thanks, -G From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu] Sent: Thursday, April 16, 2015 12:20 PM To: Book, Gregory; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] missing _Atlas.dtseries.nii Did you run the fMRISurface pipeline yet? That file gets

Re: [HCP-Users] Regarding: fsl version 5.0.6

and saved me a lot of time to go through each process separately otherwise). If I have questions ,I would send email to you again.Thank you so much again! Kind regards! Sampada On Sun, Apr 12, 2015 at 12:22 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote: Hi Tim, I thought

Re: [HCP-Users] rsfMRI at 7 Tesla

The assertion that more data doesn¹t improve reproducibility is based on what? Investigators inside the HCP have shown that reproducibility of resting state functional connectivity asymptotes at around 80 minutes (vs many hundreds of minutes collected over many days). The slope is very steep up

Re: [HCP-Users] rsfc preprocessing

That seems like a good reason -- can you refer me somewhere for the better alternatives? We're on a bit of a timeline so I am hesitant to wait for the HCP version. Thanks again for all the help! On Mon, Apr 13, 2015 at 12:34 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote: Well, I

Re: [HCP-Users] rsfc preprocessing

? The reason I ask is that we are looking to replicate voxel by voxelcommunity detection results with a different type of factoranalysis. I will check out fslnets, that seems really perfect. Thanks again! Kim On Sunday, April 12, 2015, Glasser, Matthew glass...@wusm.wustl.edu wrote: Unfortunately

Re: [HCP-Users] Regarding: fsl version 5.0.6

/Pipelines/wiki/v3.4.0-Release-Notes,-Installation,-and-Usage#task-analysis Best Regards, Tim On Sat, Apr 11, 2015, at 12:57, Glasser, Matthew wrote: We do need to get a version of this code compatible with current FSL out, but it is true that the code won’t run properly with FSL version greater

Re: [HCP-Users] Regarding: fsl version 5.0.6

We do need to get a version of this code compatible with current FSL out, but it is true that the code won’t run properly with FSL version greater than 5.0.6. All of this copying of files seems concerning, as it should not be necessary. You should simply be able to run the script if you have

Re: [HCP-Users] FreesurferPipelineBatch

pipeline 3.4.1, pipeline 3.5.0 and pipeline 3.6.0-GEFM? Which one to use? Best, Peka On Sat, Apr 4, 2015 at 7:51 AM, Peka Savayan savay...@umn.edu wrote: Thank you. Best, Peka On Fri, Apr 3, 2015 at 11:34 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote: I would delete your attempted

Re: [HCP-Users] FreesurferPipelineBatch

I would delete your attempted preprocessing and start over from the raw data. Then, confirm that FreeSurfer ran successfully and don’t try to run it multiple times on the same data. Peace, Matt. From: Peka Savayan savay...@umn.edu Date: Friday, April 3, 2015 at 11:25 PM To:

[HCP-Users] Brain Imaging, Built Better: The HCP Course in Hawaii

To advance the field of brain imaging, the HCP was given the unusual NIH mandate to devote its first two years to rethinking data acquisition and analysis methods prior to collecting its core dataset.The HCP course provides an excellent opportunity for brain imagers to profit from this

Re: [HCP-Users] netmats in HCP

Hi Steve, What about the correction for temporal autocorrelation? Matt. From: Stephen Smith st...@fmrib.ox.ac.uk Date: Monday, March 30, 2015 at 12:15 PM To: Yizhou Ma maxxx...@umn.edu Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] netmats in

Re: [HCP-Users] definition of grayordinates

The whole point of grayordinates is not to work in MNI volume space, but to work in a combined cortical surface and subcortical volume space with better grayordiante-wise correspondence across subjects. The improvements gained with grayordinates are simply not possible to achieve in MNI volume

Re: [HCP-Users] definition of grayordinates

of surface coordinates? Was the surface generated by the anatomical images in the MNI space or the native space? Zhongming Sent from my iPhone On Mar 27, 2015, at 2:23 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote: So we had a thread about this a few weeks back. Surface registration

Re: [HCP-Users] definition of grayordinates

your NeuroImage_2013 paper, it looks like that 2) is being done in the HCP pipeline. Zhongming On Mar 27, 2015, at 12:44 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote: That will depend on the surface you choose to use, as the cortical grayordinates are particular surface vertices

Re: [HCP-Users] rsfMRI at 7 Tesla

We used ipat=2 MB=5 for 1.6mm isotropic data with TR=1s (for reasons of improving temporal cleanup, I might be inclined to do 2mm and shorten the TR further like the 3T HCP data, but there are still active investigations into whether the 1.6mm data allow us to see finer details). The main

Re: [HCP-Users] rsfMRI at 7 Tesla

? I am using SPM now. Thank you very much for this communication!! Best wishes always, Leah Sent from my iPhone On Mar 24, 2015, at 6:53 AM, Glasser, Matthew glass...@wusm.wustl.edu wrote: We used ipat=2 MB=5 for 1.6mm isotropic data with TR=1s (for reasons of improving temporal cleanup

Re: [HCP-Users] rsfMRI at 7 Tesla

, Glasser, Matthew glass...@wusm.wustl.edu wrote: I would get at least 30 min of resting state if not more so that your estimates are more stable. The faster your TR, the better you will be able to clean your data and the more robust multivariate statistics like ICA will be. I would recommend

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

did do intensity correction on the MPRAGEs prior to passing them to the pipeline, would it have a negative effect? -Greg -Original Message- From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu] Sent: Tuesday, March 03, 2015 1:09 PM To: Book, Gregory Subject: Re: [HCP-Users] manual AC-PC

Re: [HCP-Users] Probabilistic structural dense connectome

It’s coming. We’ve (mostly the Oxford diffusion group) put a large amount of effort into getting the neurobiologically most reasonable tractography results we can from our data and that has taken time. We're sorry for the delay, but usually the HCP has taken the approach to only release stuff

Re: [HCP-Users] calculating surface areas

Hi Tim, Could you explain how you want users to compute surface areas of ROIs now that the previous command that did that seems deprecated? The example usage for doing this should probably be in the command’s usage as well, since this will be a common task. Thanks, Matt. From:

Re: [HCP-Users] Fwd: Difficulties reading cifti into matlab with ft_read_cifti or ciftiopen

that it can no longer be read by ciftiopen. Best, Cherry On Sun, Mar 8, 2015 at 12:18 AM, Glasser, Matthew glass...@wusm.wustl.edu wrote: I’m puzzled by that as well, unless you don’t have write permission to the location which can mess things up. Peace, Matt. From: Yizhou Ma

Re: [HCP-Users] Difficulties reading cifti into matlab with ft_read_cifti or ciftiopen

Are you not including the directory path to the file? Peace, Matt. From: Yizhou Ma maxxx...@umn.edu Date: Saturday, March 7, 2015 at 10:47 PM To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: [HCP-Users] Difficulties reading cifti into matlab with ft_read_cifti or

Re: [HCP-Users] Fwd: Difficulties reading cifti into matlab with ft_read_cifti or ciftiopen

purposes. But I don't think I could have done any significant change to a cifti file in wb_view, to the point that it can no longer be read by ciftiopen. Best, Cherry On Sun, Mar 8, 2015 at 12:18 AM, Glasser, Matthew glass...@wusm.wustl.edu wrote: I’m puzzled by that as well, unless you

Re: [HCP-Users] Fwd: Difficulties reading cifti into matlab with ft_read_cifti or ciftiopen

: Difficulties reading cifti into matlab with ft_read_cifti or ciftiopen -- Forwarded message -- From: Yizhou Ma maxxx...@umn.edu Date: Sun, Mar 8, 2015 at 12:07 AM Subject: Re: [HCP-Users] Difficulties reading cifti into matlab with ft_read_cifti or ciftiopen To: Glasser, Matthew

Re: [HCP-Users] projecting from volume to R440 template (subcortical and cerebellum)

in the volumetric space. Although this may not be accurate, it'll offer us some insight into the HCP maps. On Sun, Mar 1, 2015 at 10:09 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote: I would recommend mapping your individual subject data onto individual subject surfaces and then registering

Re: [HCP-Users] The minimal preprocessing pipelines for HCP

This is a good point and something we thought about at the time. The reason we did it this way was to avoid having to generate two separate volume timeseries files (making these is by far the most time-consuming part of the fMRIVolume pipeline). We would have had to make one that was fully

Re: [HCP-Users] creati cifti from nifti1

The medial wall ROIs are ${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.${Hemisphere}.atlasroi.32k_fs_LR.shape.gii. Peace, Matt. From: Timothy Coalson tsc...@mst.edu Date: Friday, February 27, 2015 at 6:44 PM To: Marta Moreno mmorenoort...@icloud.com Cc:

Re: [HCP-Users] 7 tesla MRI

I’d get the best spatial resolution you can (e.g. 2mm-1.6mm) while keeping the TR under 1 second (with multi-band EPI). Peace, Matt. From: Marta Moreno mmorenoort...@icloud.com Date: Sunday, February 22, 2015 at 7:26 PM To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org

Re: [HCP-Users] Myelin Mapping

Please use the HCP Minimal Preprocessing Pipelines to create T1w/T2w myelin maps with the latest code/methods (including bias correction and normalization): https://github.com/Washington-University/Pipelines You will need a T1w and a T2w images acquired in the same scanning session with the

Re: [HCP-Users] Myelin Mapping

@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Myelin Mapping after the talk? On 20 February 2015 at 13:42, Glasser, Matthew glass...@wusm.wustl.edu wrote: If I recall correctly, they withdrew their SFN 2014 presentation. I don’t know the reason for that. Peace, Matt

Re: [HCP-Users] Spatial smoothing of RS data

A very minimal 2mm FWHM constrained to the grayordinates space (as a part of resampling to the grayordinates space). See this paper: http://www.sciencedirect.com/science/article/pii/S1053811913005053 I don’t recommend people apply any substantial spatial smoothing to HCP data because it

Re: [HCP-Users] Regarding: (standard_in) 2: Error: comparison in expressionSourcing AFNI to run my resting state python script

The killed part is unrelated to the first error (which has no impact on the FreeSurfer outputs as far as I know). Killed means your job was killed externally by something or someone. If you are running your job on a cluster that has time limits on particular queues, that might be what got

Re: [HCP-Users] Processing Diffusion MRI Data

be causing the issue. Thanks, Derek From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu] Sent: Tuesday, February 17, 2015 12:47 PM To: Archer,Derek B; Stamatios Sotiropoulos; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Processing Diffusion MRI Data How about posting

Re: [HCP-Users] Regarding: FreeSurfer: recon-all: command not found

What are your environment variables immediately before calling the main FreeSurfer.sh pipeline script? Peace, Matt. On 2/17/15, 11:47 AM, Donna Dierker do...@brainvis.wustl.edu wrote: Sounds like it can't find the freesurfer executables. This page might help:

Re: [HCP-Users] Incorporating physiological monitoring data

Also to Steve: if these are used after ICAFIX, 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: Harms, Michael mha...@wustl.edu Date: Monday, February 16, 2015

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] Using MarsBar on HCP data

@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Using MarsBar on HCP data It is a region of interest (ROI) toolbox for SPM. http://marsbar.sourceforge.net/ Is there another toolbox or method that you would suggest I use? Best, Mary Kate On Fri, Feb 13, 2015 at 1:43 PM, Glasser

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

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.kate.meac...@gmail.com Date: Friday, February 13, 2015 at 1:45 PM

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