Risk mailto:bb...@cornell.edu>>
Date: Tuesday, October 25, 2016 at 5:59 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: Timothy Coalson mailto:tsc...@mst.edu>>, "Harms, Michael"
mailto:mha...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@
Yes, you need "b-value 1" to be 0, in order to be able to select the Mosaic
output format. (Not sure why — seems to be a bug of some sort on Siemens part,
introduced in the VE11 line).
Then set “b-value 2” to be 3000. The b=1500 shell is then generated due to the
scaling the magnitude of the
Hi,
The current HCP structural pipeline was developed well before the forthcoming
FS version that will have improved support/processing of “hires” structurals.
In fact, parts of the HCP structural pipeline are there basically so that we
could refine the positioning of the surfaces to take full
Off the top of my head, no. Three comments though: (1) a 204 mm in-plane FOV
is rather tight; (2) 1.5 mm voxels is going to require a longer TE and echo
train, and/or the use of phase partial Fourier; (3) You’re going to be rather
SNR-starved at 1.5 mm isotropic at 3T.
cheers,
-MH
--
Michae
wustl.edu<mailto:glass...@wustl.edu>]
Sent: Monday, October 31, 2016 6:25 PM
To: Harms, Michael; Sebastien Hetu;
hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] FoV phase for fMRI
Indeed, why do you wish to scan at 1.5mm? Cortex is 1.6mm thick
Yes. What was the TR and voxel size of the images you showed for which the
ventricles were more prominent in the std maps? We don’t have much anatomical
contrast in the BOLD at TR=720 ms. Plus at 2 mm resolution we are thermal
noise dominated (so even if the ventricles have more “physiologic
The structural results (surfaces, thickness, myelin maps) are available on a
164k mesh because the structural data was acquired at a resolution (0.7 mm)
that supports such a fine grained mesh. The functional data were acquired at 2
mm resolution, which is approximately the average spacing in t
Hi,
Couple things:
1) That LSCMRR_3T_printout_2014.08.15.pdf protocol is a bit outdated. I’d
suggest that you see the following
http://protocols.humanconnectome.org/CCF/
where you can download a zip package with both an importable protocol (for
Siemens Prisma) and an updated protocol printout (PD
Isn’t it more like (data/4DMean*1), so that the percentage change relative
to the mean is preserved?
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
By “compress” do you mean merge into a single file? If so, you can use
wb_command -cifti-merge, or wb_shortcuts -cifti-concatenate. (The latter is a
wrapper that simplifies the merge call). And you can use FSL’s PALM to do a
permutation test.
If 164k is too dense a sampling, there are 32k v
6-11-22 14:14 GMT-05:00 nailin yao
mailto:ynai...@gmail.com>>:
Thank you MH!
Best,
Nailin
2016-11-22 13:30 GMT-05:00 Harms, Michael
mailto:mha...@wustl.edu>>:
By “compress” do you mean merge into a single file? If so, you can use
wb_command -cifti-merge, or wb_shortcuts -cifti-concatena
Hi,
In the context of FS, that is a pretty simple edit to the brainmask.mgz.
Unfortunately, the HCP Pipelines don’t easily support the common FS edits at
this time. It is on our “to-do” list however.
cheers,
-MH
--
Michael Harms, Ph.D.
Hi,
The TaskfMRIAnalysis Pipeline, as currently written, assumes two or more runs
of each task. You could comment out the last part of TaskfMRIAnalysis.v2.0.sh
where it calls TaskfMRILevel2.v2.0.sh, so that the TaskfMRIAnalysis.v2.0.sh
script would run without error.
cheers,
-MH
--
Michael H
ase you
actually do need to use the non-cifti files.
Tim
On Tue, Nov 22, 2016 at 2:57 PM, nailin yao
mailto:ynai...@gmail.com>> wrote:
where can I download wb_shortcuts command? Thanks!
Best,
Nailin
2016-11-22 15:28 GMT-05:00 Harms, Michael
mailto:mha...@wustl.edu>>:
Two things:
1)
ta: 59412
In file design.mat
How can I fix this?Thank you!
Best,
Nailin
2016-11-29 14:37 GMT-05:00 Harms, Michael
mailto:mha...@wustl.edu>>:
Hi,
Why do you think there is something wrong? 59412 is the expected number of
rows in the *MyelinMap.32k_fs_LR
e the two runs at a certain
point?
Thank you,
Yeun
On Tue, Nov 29, 2016 at 10:31 AM, Harms, Michael
mailto:mha...@wustl.edu>> wrote:
Hi,
The TaskfMRIAnalysis Pipeline, as currently written, assumes two or more runs
of each task. You could comment out the last part of
TaskfMRIAnalysis.v2.0.s
rg>>
Subject: Re: [HCP-Users] task fMRI analysis
Thanks for all the responses. Just to clarify, which is the latest version of
the HCP pipeline? 3.19 or 3.4?
Thank you again,
Yeun
On Tue, Nov 29, 2016 at 12:08 PM, Harms, Michael
mailto:mha...@wustl.edu>> wrote:
No, the fMRI preproc
it seems cannot be view by wb_view.
May I know how can I view the results properly? Thank you!
Best,
Nailin
2016-11-29 16:25 GMT-05:00 Dierker, Donna
mailto:do...@wustl.edu>>:
Try the -transposedata option.
> On Nov 29, 2016, at 1:49 PM, Harms, Michael
> mailto:mha...@wustl.edu>> wrote:
Note that the scenes we’ve assembled for “StructuralQC” include a check of
the FNIRT registration.
You can find the scripts necessary to generate those scenes here:
https://github.com/Washington-University/StructuralQC
cheers,
-MH
--
Michael Harms, Ph.D.
--
Hi,
Re (1): I believe you need a license to run in FREE mode. Do you have it?
Re (2): By how much was it clipped? You could try reducing the flip angles —
78/160 is what we’ve been using for HCP. Or, increase the duration of the
relevant pulse on the Sequence:Special tab.
Re (3): I see that y
Your Excite Pulse Duration on the Sequence:Special tab is much too low. We’ve
been using 6600 microsec for HCP.
Offline recon on a Skyra would require that you set up the “remote recon
server”. If that isn’t set up, you’ll need to use “Online” recon.
cheers,
-MH
--
Michael Harms, Ph.D.
BTW, Re (2): We are Excite/Refocus Pulse durations of 3840/7680 in our 1.5 mm
protocol currently.
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psych
Yes, all the HCP subjects scanned at 7T should have data at 3T as well.
Currently there are 73 subjects with 7T data (more to come with the final data
release). If you want to download or get a list of those subjects, select the
group “Subjects with 7T MR Session Data” from the “Explore Subje
Hi Yaroslav,
To reiterate something Mike Hodge mentioned, any given package only
contains files for one subject. When interacting with ConnectomDB, the
subjects to download, and the particular packages to download, are two
separate and distinct choices.
cheers,
-MH
--
Michael Harms, Ph.D.
r
>subject ID, modality, processing level, and smoothing level (for
>fMRI).
On Tue, 06 Dec 2016, Harms, Michael wrote:
> To reiterate something Mike Hodge mentioned, any given package only
> contains files for one subject. When interacting with ConnectomDB, the
> subjects to down
Hi,
It appears that you are trying to replicate the basics of one of our Lifespan
pilot protocols on a Skyra — i.e., 1.5 mm voxels with 20 total min of dMRI
scanning. But due to the longer TE and longer TR (resulting in fewer total
directions), you are definitely going to have worse overall SN
l.
Just wondering though on your or anyone else's suggestion on running BOLD with
MB>2.
Thanks
Regards
--VM
On Wed, Dec 7, 2016 at 10:50 AM, Harms, Michael
mailto:mha...@wustl.edu>> wrote:
Hi,
It appears that you are trying to replicate the basics of one of our Lifespan
pilot
it
gives us "Max amplitude overflow on gradient z axis" after MB factor exceeds 2.
It appears to me that then we have to sacrifice TR and only run with MB = 2.
We are using 32 channel head coil.
Thank you for any suggestions.
Regards
Virendra
On Wed, Dec 7, 2016 at 11:22 AM, Harms,
Aren’t those the sort of values that you’d expect when looking at p-values?
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 Sou
al...@gmail.com>>
Date: Thursday, December 8, 2016 at 4:56 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "Harms, Michael" mailto:mha...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnec
ailto:glass...@wustl.edu>> wrote:
What phase encoding directions are you using?
Peace,
Matt.
From: neuroimage analyst
mailto:neuroimage.anal...@gmail.com>>
Date: Thursday, December 8, 2016 at 1:37 PM
To: "Harms, Michael" mailto:mha...@wustl.edu>>
Cc: Ma
Hi,
Please check the PALM Wiki page examples again. They were just updated
yesterday. In particular, if you are using PALM without any spatial
statistics, you should be able to run directly using dscalar.nii files. You
can concatenate the dscalars into a single file using wb_shortcuts
-cift
e.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] group comparison
Hi,
I have successfully generated statistic result from palm, files are
results_dpv_tstat_mfwep_m1_c1.gii etc. But it seems cannot be view by wb_view.
May I know how can
gii:
/home/fas/glahn/ny87/scratch60/Connectivity_Study/S0039JRF/MNINonLinear/fsaverage_LR32k/S0039JRF.R.midthickness.32k_fs_LR.surf.gii
is not a valid NIfTI file
Thanks!
Best,
Nailin
2016-12-15 13:11 GMT-05:00 Harms, Michael
mailto:mha...@wustl.edu>>:
Do you mean for each individual sub
Yes, there is a giant nod of the head around frames 900-906 for the REST1_LR
run of 101107. The fMRI preprocessing pipeline is set up such that the final
brain mask requires that data be available in a given brain voxel for *every*
time point. If that isn’t the case, that voxel gets masked ou
complete brain coverage there. Yet
I also see how the responsibility could be left to the investigators who are
using the data, who should in all cases properly look at the images they are
using.
Thank you for all your work, and the sharing of this amazing resource.
- Julien
On Mon, Dec 19, 20
Hi,
Let’s step back. Why you want to convert the provided group z-stat maps
to p-values? Any such p-value map (converted simplistically from the
zstat map) will (1) not account for multiple comparisons over
grayordinates, and (2) will not account for the family structure
(dependence between subj
I believe that the DICOM field 0019,1018 (readout sample spacing) for Siemens
is units of nanoseconds. A value of 6500 sounds about right if your T1 scan
has a BW around 240 Hz/Px. For example, for the young adult HCP data,
collected with a BW of 210 Hz/Px, that value is 7400. You just need
Just to throw another variant into the mix, you can also compute a separate
network matrix for each run of each subject, Fisher transform those, and then
average those generate a representative network matrix for each subject, which
you can then average across subjects if you want a group avera
Hi,
There are differing opinions on the appropriateness of MGTR at the present time
(pending future alternatives). You may be interested in the following recent
paper from Murphy and Fox:
https://www.ncbi.nlm.nih.gov/pubmed/27888059
And, if you want to see some data on the effects of using it
Hi,
You can find that table in the "CCF Protocol Template” available here:
http://protocols.humanconnectome.org/CCF/
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School
For issues like this,
https://github.com/CMRR-C2P/MB/issues
may be an more appropriate venue to get assistance with your problem.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington Unive
Hi Leah,
Just an aside: If you are projecting FC maps (derived inherently in volume
space) to the surface for visualization you won’t have the benefits of a true
surface-based analysis.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center
if you want to see your subcortical parcellations, you’ll need to view them on
a volume (in the Volume tab of wb_view). All the png’s you showed were surface
views.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscienc
al I need to view the surface views?
Thank you so much,
Grace
Grace Shearrer, PhD
Post Doctoral Researcher
Neuropsychology of Ingestive Behavior Lab
University of North Carolina Chapel Hill
____
From: Harms, Michael mailto:mha...@wustl.edu>>
Sent: Wednesday, Januar
You might want to explicitly remove any mean that exists in Clean.dtseries.nii,
so that the mean of the final output is truly the same as the mean of the input
to FIX.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscie
ment of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
e...@wustl.edu<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>
From: Harms, Michael
Sent: Sunday, January 29, 2017 10:39 PM
To: Glass
uot;I can make the equivalent “cope1” file from the Level 3
‘flameo’ available via Box")
3rd) in the cope1 file, do (x-mean)/SD for every data point
Thank you very much,
Xavier.
From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>]
Just so you know, we also have a different (shorter) dMRI protocol (~22 min)
total that we used for our Lifespan Phase1b piloting, and which we intend to
use for the forthcoming launch of the HCP-Aging and HCP-Development projects.
That gradient table is the same as the one contained here:
ht
For the task group average maps in the S900 release, we used 787 subjects that
had 100% complete data on their resting data run and ALL tasks. A list of
those subjects is attached.
--
Michael Harms, Ph.D.
---
Conte Center for the Neurosci
Those 3 subjects only had behavior and structural data collected.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660
Those 3 subjects only had behavior and structural data collected.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660
That's susceptibility-based signal dropout in orbitofrontal cortex.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
66
There is no single "b-vector" table -- it will differ somewhat for every
subject due to the oblique nature of the acquisitions.
See my earlier post for details.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of M
s callosum only have the body part, both
>genu and splenium disappeared. I attached the reconstructed tract, could
>you tell me why this happens?
>
>Thank you very much,
>
>Su
>
>On Thu, 27 Jun 2013, Harms, Michael wrote:
>
>>
>> Hi Robert,
>> That is the grad
Hi Martin and Satra,
The HCP itself has not extensively evaluated a 1.5 mm multiband DWI
acquisition on the Trio platform, so we don't have anything concrete to
share at this time. Perhaps we should rephrase that sentence in the
Appendix I release guide, but it was included primarily to encourage
Hi Kelly,
I put some empirical task data comparing MB to no-MB acquisitions in the same subjects in a poster at the 2013 OHBM.
You are welcome to contact me off the list if you would like further details.
Best,
-MH
--
Michael Harms, Ph.D.
--
Hi Viviana,
We don’t supply traditional "phase" and "mag" images for distortion correction. Rather, the distortion correction is implemented using FSL's 'topup' and the SpinEchoFieldMap_{RL,LR} images that you'll find are included with the unprocessed packages. You
can see the Glasser et a
The impeding Q3 release will have a set of (approximately) 40 different
subjects of preprocessed dMRI data.
You probably should not mix these 40 (in analysis) with the previous set
of 40. We are in the process of "retro reconning" all the dMRI for the
subjects that won't be in the Q3 release, and
.
Tel: 314-747-6173
St. Louis, MO 63110
Email: mha...@wustl.edu
From: Timothy Verstynen <timot...@gmail.com>
Date: Sunday, September 8, 2013 8:06 PM
To: "Harms, Michael" <mha...@wustl.edu>, Fang-Cheng Yeh <frank@gmail.com>
Subject: Fwd: [HCP-Users] Only 40
uclid Ave.
Tel: 314-747-6173
St. Louis, MO 63110
Email: mha...@wustl.edu
From: Timothy Verstynen <timot...@gmail.com>
Date: Monday, September 9, 2013 7:38 AM
To: "Harms, Michael" <mha...@wustl.edu>
Cc: Fang-Cheng Yeh <frank@gmail.com>, "hcp-users@humanco
Hi Jo,
All the preprocessed fMRI data is in HCP-standard volume (MNI152) or
grayordinate space.
Those are contained in ${subj}/MNINonLinear/Results
The subject-specific FreeSurfer labels transferred to this space and at
the same surface mesh resolution are contained in
${subj}/MNINonLinear/fsaver
f Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110Email: mha...@wustl.edu
On 9/23/13 9:13 AM, "Harms, Michael" wrote:
>
>Hi Jo,
>All the preprocessed fMRI data is in HCP-standard volume (M
Just to follow-up on what Matt said, concatenating the two runs would NOT be the way that we would recommend to process/combine the two runs per task.
Best,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Me
glass...@wusm.wustl.edu>
Date: Tuesday, October 1, 2013 2:31 PM
To: "Harms, Michael" <mha...@wustl.edu>, "Yan, Shulin" <shu.ya...@imperial.ac.uk>, Elvis Dohmatob <gmd...@gmail.com>,
"HCP-Users@humanconnectome.org" <HCP-Users@humanconnectome.org>
Hi,
The legend is the same as used by FreeSurfer itself, which you can find (assuming you have FS locally installed) in $FREESURFER_HOME/FreeSurferColorLUT.txt
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neurosci
The label key is the same as that of $FREESURFER_HOME/FreeSurferColorLUT.txt
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Ps
Hi Benson,
How did you go about opening the csv file? When I open it directly into
Excel, all I get for Pallidum are columns for "L Pallidum Vol" and "R
Pallidum Vol". It sounds like your process for importing the data went
awry somehow.
Volumes wil be in mm^3. Surface areas in mm^2. Thicknes
If I recall correctly, the selection for SENSE reconstruction is one of the parameters on the Sequence:Special tab.
You will have to toggle one of the arrows on that tab to make the SENSE field the active one, at which point you can toggle the SENSE reconstruction on.
cheers,
-MH
--
Mi
From: Franck Lamberton <franck.lamber...@cermep.fr>
Organization: CERMEP-imagerie du vivant
Date: Monday, March 10, 2014 5:18 PM
To: "Harms, Michael" <mha...@wustl.edu>
Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users]
I don't think we've had any discussions about releasing the Freesurfer outputs in their "native" FS directory structure.
Indeed, it would be quite redundant to do so.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the N
Just to clarify: The full pipeline output that Donna was referencing
includes "internal" pipeline outputs that we don't include in our released
"package" outputs. As of now, I don't believe there is any plan to
release the FS results in the native FS directory structure.
cheers,
-MH
--
Michael
Just to add to the archives of this thread, I was able to load the rfMRI_REST1_RL.nii of 100307 using SPM's functions of 'spm_select', 'spm_vol', and 'spm_read_vols', but only using SPM12. It did not work with SPM8. (Both were tested using Matlab 2012b).
As an aside, it may be challengin
Hi,
You can get the behavior you desire by opening the Information Box and
then clicking "Volume ID".
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
De
Hi Mahshid,
We are not releasing the run-level (Level1) task processed data -- only the Level2 data, which effectively "averages" the two runs for each task and subject. To use the level1.fsf to generate the Level1 results on the grayordinate/CIFTI data involves
transforming the CIFTI into
You could do that if you just want a heuristic map of the "group activation". But I wouldn’t use that for anything that requires meaningful statistics. To compute "proper" Level 3 task maps what we do currently is convert the CIFTI copes/varcopes to
NIFTI, merge them into a 4D NIFTI file,
Hi Mahsa,
Yes, the volume data is already in MNI space.
When you posted on the SPM-list, I suggested that you review Glasser et al., 2014, and the HCP documentation, which together detail the processing steps performed. Have you done that already? If so, please provide more specific questi
ustl.edu
From: Mahsa Alizade shalchy <ma.shal...@yahoo.com>
Reply-To: Mahsa Alizade shalchy <ma.shal...@yahoo.com>
Date: Friday, August 8, 2014 10:55 AM
To: "Harms, Michael" <mha...@wustl.edu>, "HCP-Users@humanconnectome.org" <HCP-Users@humanconnect
Hi,
The 4D NIFTI files in MNI152 space are called rfMRI_REST{1,2}_{LR,RL}_hp2000_clean.nii.gz and are available as part of the "FIX Extended" packages.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of
Hello Ely,
If you want to run a "Level 3" group analysis, you already have everything you need if you downloaded the task "analysis" packages, which already contain the "Level 2" results (combining across runs) for each subject. The "prepare_level2_feat_analysis.sh"
is if you are trying to
Hi Romain,
Per Essa Yacoub at the CMRR, the HCP fMRI protocol (i.e., MB=8) recons in
real time on a Prisma. (I think that the Prisma comes with better default
GPU cards).
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuros
Hi Satra,
Can you be a little more specific about what you are asking for?
There are the /MNINonLinear/fsaverage_LR32k and /T1w/fsaverage_LR32k directories.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscienc
ajit Ghosh <sa...@mit.edu>
Date: Thursday, September 4, 2014 9:15 AM
To: "Harms, Michael" <mha...@wustl.edu>
Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] freesurfer directory structure for 32k average
hi michae
y, Box 8134
660 South Euclid Ave.
Tel: 314-747-6173
St. Louis, MO 63110
Email: mha...@wustl.edu
From: , Michael <mha...@wustl.edu>
Date: Thursday, September 4, 2014 9:23 AM
To: Satrajit Ghosh <sa...@mit.edu>, "Harms, Michael" <mha...@wustl.edu>
Cc:
Hi,
See the PostFreeSurfer scripts in the just released HCP Pipelines v3.4
https://github.com/Washington-University/Pipelines
https://github.com/Washington-University/Pipelines/releases
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center
Hi,
The omission of those 4 subjects from the 500 subject release was
intentional.
For the first 3 of those subjects, they didn't have gradient-echo
fieldmaps to accompany the structurals. The GE fieldmaps are not
mandatory for running the structurals through the HCP pipelines, but we
didn't get
Hi Estrid,
First, we highly recommend that users do not mix subjects between data
releases that were processed using different pipelines, which is the case
for the "500 Subject" and earlier "Q3" releases. Subject 727654 was not
included in the 500 Subject release for the reason that I outlined.
Also, I think that the script for launching workbench ('wb_view') is in a subdirectory of the higher level workbench folder.
i.e., you may need:
export PATH=$PATH:/home/TLA/Desktop/workbench/bin_rh_linux64
If you list the contents of the 'workbench' directory, it will become clear whether
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110Email: mha...@wustl.edu
On 9/3/14 11:54 AM, "Harms, Michael" wrote:
>
>Hi Romain,
>Per Essa Yacoub at the CMRR, the HCP fMRI protocol (i.e., MB=8) recons
Hi Frank,
Yes, the S/I labels for that subject are somehow incorrect in the "raw"
data, which corrupts the downstream processing. We noticed the issue
previously, but haven't captured this in our "Issues Tracker" wiki page
yet. We will get that information up on that page soon.
We will look into
There have been a lot of changes/additions from 3.4.0 to 3.21. If you are
starting a new study, it would be preferable for you to start with the latest
version.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of
All intermediate files are available via REST calls directly into the
database.
https://wiki.humanconnectome.org/display/PublicData/How+To+Access+Subject+D
ata+via+REST
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscie
Hi,
Let’s step back. Why can’t you use the group dense connectome that we’ve
already computed and provided?
As noted in our documentation
https://www.humanconnectome.org/documentation/S900/820_Group-average_rfMRI_Connectivity_December2015.pdf
computing the dense connectome optimally is not triv
esting-state
functional connectivity in a group including only the subjects who completed
all tasks (n=787). This is why I would like to generate a new dconn file.
Thank you,
Xavier.
________
From: Harms, Michael [mha...@wustl.edu<mailto:mha...@wustl.edu>]
Sent: Frid
As an aside, in the interest of methodological clarity, when reporting the
number of twins, you should distinguish between “self-report” and
“genetically-verified”. We intend to provide more guidance regarding this, as
relates to the variables in the database, in the near future.
--
Michael H
Hi,
Why can’t you use the ‘bvecs’ file that we’ve supplied?
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South
Note that the scanner gradient table does NOT account for the angulation of the
subject in the magnet, nor does it account for the (relatively minor) impact of
the imaging gradients on the effective diffusion sensitization — both of which
are accounted for in the ‘bvecs’ file supplied with each
Hi,
You’ll have to be more specific, as there are different “HCP Protocols” that
you could be referring to — e.g., what we used for Young Adults on the custom
Connectom scanner; what we used for the “Lifespan Piloting” on the custom
Connectom scanner; what we used for "Lifespan Piloting" on the
Hi,
Are you sure everything was installed successfully?
I would:
1) Re-install the latest (“R015”) version of the MB package.
2) Import the example “CCF protocol” available here:
http://protocols.humanconnectome.org/CCF/
If you are still having problems at that point, you can open a support requ
Hi,
If you specifically want FD, you can calculate it from the
Movement_Regressors.txt file provided with the minimally preprocessed data for
each task run. Or, use the FSL equivalent of “relative RMS” available in the
Movement_RelativeRMS.txt (time series) and Movement_RelativeRMS_mean.txt
(
201 - 300 of 538 matches
Mail list logo
