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
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 gradient table as specified on the Connectome Skyra scanner
for acquisition, but you should not use it for analyzing
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
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 preprocessed diffusion data in Q2 and Q1 reproc?
Dear Michael,
Thanks
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. Thicknesses
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
--
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] details about a sequence parameter for DWI
Many thanks for your
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
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, and
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
South Euclid Ave.
Tel: 314-747-6173
St. Louis, MO 63110
Email: mha...@wustl.edu
From: Harms, Michael mha...@wustl.edu
Date: Thursday, September 4, 2014 9:23 AM
To: Satrajit Ghosh sa...@mit.edu, Harms, Michael mha...@wustl.edu
Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org
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
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. So,
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
Hi,
See this page for details. You'll need to complete a C2P agreement.
https://www.cmrr.umn.edu/multiband/
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of
Yes, the first volume should be *one* of the b=0 images (check the bvals file). Note that b=0 volumes are interspersed throughout the acquisition.
For the preprocessed data, all the available dMRI data is concatenated into that single data.nii.gz file (and the bvec, bvals to match). The
To: Harms, Michael mha...@wustl.edu
Subject: Re: [HCP-Users] ROI extraction of rest fmri data
Sorry if my questions sound naive. I am a beginner in fmri(esp rfmri )field.
Since I'm working on Q1 data, I do not remember any CIFTI/grayordinate versions of the data (There were 3 kinds of rfmri data
63110
Email: mha...@wustl.edu
From: Mahsa Alizade shalchy ma.shal...@yahoo.com
Reply-To: Mahsa Alizade shalchy ma.shal...@yahoo.com
Date: Tuesday, October 14, 2014 5:15 PM
To: Harms, Michael mha...@wustl.edu, Hcp-users hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] ROI extraction
of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.
Tel: 314-747-6173
St. Louis, MO 63110
Email: mha...@wustl.edu
From: Book, Gregory gregory.b...@hhchealth.org
Date: Thursday, October 16, 2014 10:11 AM
To: Harms, Michael mha...@wustl.edu, hcp-users@humanconnectome.org hcp-users
Yes, you can use that output in subsequent stats processing.
Regarding the motion, you need to compare against the uncorrected time series at the same time points. Was there very large motion at those time points? Large motion that occurs in the middle of a volume acquisition is
On Oct 24, 2014, at 2:46 PM, Harms, Michael wrote:
Hi Gaurav,
As the pipelines currently stand, they haven't yet been extended to
incorporate manual FS edits. It shouldn't be overly difficult for
someone familiar with FS editing and the various stages in FS to modify
the pipelines
-Original Message-
From: Harms, Michael [mailto:mha...@wustl.edu]
Sent: Tuesday, October 28, 2014 1:28 PM
To: Book, Gregory; Harms, Michael; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] GenericfMRIVolumeProcessingPipelineBatch motion
correction
So, what did the result from 'mcflirt
the middle timepoint
instead of either the sbref or the mean of the first 10 images?
-G
-Original Message-
From: Harms, Michael [mailto:mha...@wustl.edu]
Sent: Wednesday, October 29, 2014 10:45 AM
To: Book, Gregory; Harms, Michael; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users
FWIW, while you should use DICOM field (0019, 1018) as Matt said, I believe that the correct formula to come close to that would be:
DwellTime = 1 / (PixelBandwidthInReadOutDirection * nReadOut * 2)
where
PixelBandwidthInReadOutDirection = DICOM (0018,0095)
nReadOut = MatrixSize in the
Hi,
The file has zstat in its name, so it is the z-statistic from the Level 3 group model across 440 related subjects (R440). You could compute a p-value from a standard normal distribution, but those p-values will not be fully accurate, because as we
note in the data release manual, the
From: Long longspac...@gmail.com
Date: Wednesday, November 26, 2014 10:55 AM
To: Harms, Michael mha...@wustl.edu
Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] How to threshold the task data?
Dear Michael,
Thank you for your reply! I loaded right
: 314-747-6173
St. Louis, MO 63110
Email: mha...@wustl.edu
From: Long longspac...@gmail.com
Date: Wednesday, November 26, 2014 3:12 PM
To: Harms, Michael mha...@wustl.edu
Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] How to threshold the task data
Hi,
I haven't used the 'ciftisavereset' function, but a dscalar.nii should have grayordinates as the first dimension, so try saving the transpose of your data (i.e., an [nGrayOrdinates x 1] vector).
cheers,
-MH
--
Michael Harms, Ph.D.
The value of PhaseEncodingDirectionPositive in the shadow field (0029,1020) reflects the combination of both Phase enc. dir. on the Routine tab (e.g., AP vs. PA) AND the setting of Invert RO/PE Polarity on the Sequence/Special tab.
As long as you have one of each polarity, you can use the
PM
To: Matt Glasser glass...@wusm.wustl.edu, Harms, Michael mha...@wustl.edu, hcp-users@humanconnectome.org
hcp-users@humanconnectome.org
Subject: 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
of Psychiatry, Box 8134
660 South Euclid Ave.
Tel: 314-747-6173
St. Louis, MO 63110
Email: mha...@wustl.edu
From: Book, Gregory gregory.b...@hhchealth.org
Date: Monday, December 15, 2014 4:17 PM
To: Harms, Michael mha...@wustl.edu, Matt Glasser glass...@wusm.wustl.edu, hcp-users
...@wustl.edu
From: Book, Gregory gregory.b...@hhchealth.org
Date: Wednesday, December 17, 2014 8:34 AM
To: Harms, Michael mha...@wustl.edu, Matt Glasser glass...@wusm.wustl.edu, hcp-users@humanconnectome.org
hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] spin echo phase encoding direction
Hi Ariel,
Thanks for you interest in novel analyses of HCP dMRI data. Unfortunately, individual channel coil images are not available and we don't have an easy mechanism to generate them from the raw k-space data at this point in time.
Best,
-MH
--
Michael Harms, Ph.D.
For Lifespan, there should be pair of SpinEchoFieldMap scans that you use for correction of the T1w/T2w scans instead. You'll need to change the launch script appropriately to use the different approach.
cheers,
-MH
--
Michael Harms, Ph.D.
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.
Tel: 314-747-6173
St. Louis, MO 63110
Email: mha...@wustl.edu
From: 최용호 chldydgh0...@gmail.com
Date: Thursday, January 15, 2015 9:14 AM
To: Harms, Michael mha...@wustl.edu
Subject: Re
Hi,
You're going to need to provide more specifics, such as exactly what commands you used.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
of Psychiatry, Box 8134
660 South Euclid Ave.
Tel: 314-747-6173
St. Louis, MO 63110
Email: mha...@wustl.edu
From: yamur osmanova yamur.osmanova1...@gmail.com
Date: Wednesday, January 21, 2015 2:13 PM
To: Harms, Michael mha...@wustl.edu
Cc: hcp-users@humanconnectome.org hcp-users
Hi,
Is this HCP data, or data collected on a different Siemens scanner?
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Not only that, but just because a given physiological trace exists, doesn't necessarily mean that it is a *good* trace. There is going to be considerable variability in the quality of the physiological measurements, which presents a challenge in using
them in a large scale study. I'm sure
We are working on developing a script that will use randomise and permutation testing to accomplish that, but don't have anything to share at this time.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center
If you are willing to use 'matlab', another option is to load the dlabel.nii into matlab, and then using the FIND command you can easily get a list of all the indices corresponding to a given (numeric) label ID.
cheers,
-MH
--
Michael Harms, Ph.D.
Hi,
You'll want to refer to the relevant functions in the FSLnets package.
I did something very similar to what you are trying to do recently. Here is the code that you want to use if you are trying to replicate the distributed netmats (pconn's) from the distributed time-series:
...@umn.edu
Date: Monday, March 30, 2015 6:54 PM
To: Harms, Michael mha...@wustl.edu
Cc: Stephen Smith st...@fmrib.ox.ac.uk, hcp-users@humanconnectome.org hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] netmats in HCP
Dear Dr. Harms,
Thank you very much for your codes. They are very
Organization: University of Minnesota
Date: Tuesday, March 31, 2015 12:09 PM
To: Jennifer Elam el...@pcg.wustl.edu, Harms, Michael mha...@wustl.edu, hcp-users@humanconnectome.org
hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Discrepancy of number of subjects with complete dMRI datasets
Not sure if this will help your purposes, but the HCP500-PTN(ParcellationTimeseriesNetmats)distribution includes the following:
melodic_IC_sum.nii.gz: ICA spatial maps projected from the surface into the volume, for reporting purposes. MNI152 space.
I don't think we have any group ICA
Correct on the mapping to the group ICA components.
The order in the concatenated time series file is:
REST1_LR
REST1_RL
REST2_LR
REST2_RL
Note that, in case it matters to you, the LR scan does NOT necessarily precede the RL scan temporally within each scan session.
HI Arjuna,
We don't have much experience here with using SPM. If SPM has a mode for specifying acquisition time (rather than order), then yes, I would think that you should just be able to use the times specified in that file.
Also, since you found the timing file, I assume you've seen
/ ( 2 * ( sqrt ( 2 * l ( 2 ) ) ) ) | bc -l`
So even more precise.;-)
On Apr 13, 2015, at 8:59 AM, Harms, Michael mha...@wustl.edu wrote:
Hi,
Just wanted to mention, for purposes of documenting in this thread, that technically the conversion from FWHM to sigma is:
sigma = FWHM/2.355
http
Hi,
Just wanted to mention, for purposes of documenting in this thread, that technically the conversion from FWHM to sigma is:
sigma = FWHM/2.355
http://en.wikipedia.org/wiki/Full_width_at_half_maximum
I believe the FEAT just uses 2 rather than 2.355 in the denominator for the calculation
It is the conversion factor from Hz to radians/sec: 2*pi = 6.283
You want to leave that as is.
cheers,
MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Take a look also at the recent posts. There are unfortunately some unresolved issues about myelin maps acquired on the GE platform not looking the same as they do when derived from Siemens data.
cheers,
-MH
--
Michael Harms, Ph.D.
for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.
Tel: 314-747-6173
St. Louis, MO 63110
Email: mha...@wustl.edu
From: Michael Dwyer mgdw...@bnac.net
Date: Sunday, June 21, 2015 11:17 AM
To: Harms, Michael mha
Alternatively, if you don't want to go through that process, and are content with using ~ 100 subjects, you can conveniently get a list of 100 unrelated subjects via the 100 Unrelated Subjects grouping that we already have populated in ConnectomeDB.
cheers,
-MH
--
Michael Harms, Ph.D.
The cifti-matlab tools, as currently constituted, load the medial wall,
whereas the python implementation does not. That is why the two yield a
differing number of grayordinates.
The cifti-matlab tools are a bit of a work in progress. If you simply
want to load the grayordinates, excluding the
Yes, _ts2 are dual regression; _ts3 are the eigentimeseries. See the section Description of released files in the pdf with the PTN distribution.
Steve can comment on the matching issue, but I wonder if the 0's that get added to the pseudo-NIFTI file to fill out the matrix dimensions
Yes, that should be fine. You'll probably want to use the GDC -- gradient distortion corrected -- version of the structurals that we supplied in the packages as your input structurals (and then turn off gradient distortion correction in the script).
Also, you can choose between using the T1
oops, meant to type, "Sorry, that's not available b/c it is never generated".
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry,
Hi Craig,
In our usage, the "scout" is indeed the SBRef for a given fMRI scan (although the pipelines are set up such that you can use other "scouts").
What we call "SpinEchoFieldMap_{RL,LR}" during scan collection are not field maps per se, but rather the actual reversed-PE, SE EPIs
Typically, we care more about the "relative" (frame-to-frame) motion. If you wanted to exclude based on the mean across the whole run you could use the number in the "Movement_RelativeRMS_mean.txt" file. If you wanted to implement a censoring/scrubbing
of individual frames you could use
Hi Vishal,
There is a version of the hard parcellation from Gordon et al. (Cerebral Cortex, 2014) available as a CIFTI 'dlabel.nii' file, if you are interested in that.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for
; that these two subjects (ID: 528446 and 209733) were removed.
>
> Best,
> Niklas
>
> On 28/10/15 16:43, Harms, Michael wrote:
>>
>> Hi,
>> If you download the "Structural Extended Preprocessed" package for each
>>subject you want,
This might be something that it would be worthwhile for us to process once and then make available to everyone, possibly via a simple spreadsheet initially, but hopefully incorporated into the database as a variable at some later point. Along those lines,
is there an existing script
Hi Mark,
The locked sequences that we are using for HCP, and on which those protocol print-outs are based, are based on a fairly old (at this point) version of the CMRR sequences, for which Fatsat = none actually means that a gradient reversal based method of
fat suppression is used rather
Sorry, but no -- not currently. The T2w is a fundamental component of HCP acquisitions and pipelines, so stuff related to it is embedded into the pipelines.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the
t; Also, the FreeSurfer-generated aparc and aparc.a2009s non-overlapping
> parcellations for each subject are available on the 32k_fs_LR mesh and
> 164k mesh in the Structural preprocessed package for each subject. These
> are available as GIFTI label files per hemisphere and as CIFTI dlabe
Hi,
No such option in ft_read_cifti currently.
I've added Robert in case he wants to comment.
You should be able to remove the NaN and get a standard ordering. If you want to check, you can use the 'ciftiopen.m' alternative for loading CIFTI and compare that you get the same ordering.
MO 63110
Email: mha...@wustl.edu
From: , Michael <michael.stev...@hhchealth.org>
Date: Monday, August 31, 2015 3:16 PM
To: "Harms, Michael" <mha...@wustl.edu>, Stephen Smith <st...@fmrib.ox.ac.uk>
Cc: "hcp-users@humanconnectome.org" <hcp-users@humancon
Yes, that is correct. (The SBRef for the BOLD scans are gradient-echo images).
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry,
t the Desikan–Killiany atlas is adaptive to each subject. And the metric used for parcel alignment will show some differences to the metric used to align the HCP vertices, hence a variable parcel:vertex
mapping will occur, right?
Thanks for the clarification,
M@
On 16/9/15 16:10 , "Harms,
..@york.ac.uk>
Date: Thursday, November 26, 2015 6:00 AM
To: "Harms, Michael" <mha...@wustl.edu>
Subject: Re: [HCP-Users] MRI parameters
Hi Michael,
Apologies, I probably did not make myself very clear.
I set up my scan protocol, assuming that the parameters I used would
Hi,
You should be able to obtain the files via REST calls into the database.
See previous post in the list archives for an example of how to do so.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental
, MO 63110
Email: mha...@wustl.edu
From: Joelle Zimmermann <joelle.t.zimmerm...@gmail.com>
Date: Wednesday, December 9, 2015 3:08 PM
To: "Harms, Michael" <mha...@wustl.edu>
Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
Subject
Determining the recon version ("r177" vs "r227") of old Q1-Q3 released data is different for dMRI vs. fMRI.
For fMRI, we have not ever changed the image reconstruction algorithm for a
given subject's data across data releases. So the "fMRI_3T_ReconVrs" variable that is currently
63110
Email: mha...@wustl.edu
From: Joelle Zimmermann <joelle.t.zimmerm...@gmail.com>
Date: Thursday, December 17, 2015 9:10 AM
To: "Harms, Michael" <mha...@wustl.edu>
Cc: Greg Burgess <gcburg...@gmail.com>, "hcp-users@humanconnectome.org" <hcp-use
Hi,
See inline below.
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.
Tel: 314-747-6173
St.
arson-Prior, PhD
University of Arkansas for Medical Sciences
Department of Psychiatry
4301 W. Markham #554
Little Rock AR 72205
email: ljlarsonpr...@uams.edu
ph: 501-526-8100
mobile: 314-303-3498
On 12/14/15, 1:33 PM, "hcp-users-boun...@humanconnectome.org on behalf of
Harms, Mic
Does the MEG specific processing not already contain what you need?
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South
Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.
Tel: 314-747-6173
St. Louis, MO 63110
Email: mha...@wustl.edu
From: Gregory Butron <gregorybut...@gmail.com>
Date: Monday, December 14, 2015 2:03 PM
To: "Harms, Michael&q
Hi,
The only purely anatomical parcellation that is available currently are those provided by FreeSurfer, which you seem to be familiar with.
If you are interested in a functional parcellation, there is the Gordon et al. parcellation derived from non-HCP rfMRI data. A parcellation that
Hi Peka,
I'm not quite sure what you have, but an axial FLAIR scan with CLEAR applied seems like it would be a structural scan, not a field map.
Even if you have a dual-echo gradient echo field map acquisition, I'm afraid that the pipelines haven't been extended yet to incorporate whatever
To Steve's point and the issue of memory: A critical distinction is whether you are intending to work with dense connectomes or parcellated connectomes. In the context of parcellated connectomes, both Steve and myself have found a small advantage in
reproducibility if you compute a
I don't know if this is it, but off the top of my head, how exactly did you set up your SUBJECTS_DIR? I assume that you are trying to aggregate stats into a table across a number of subjects after having downloaded the "Structural Extended" packages?
The location of the FS data in the HCP
As a brief follow-up to this: As you see from Steve's pasted code, the order of the time series in the PTN is based solely on the file name in ConnectomeDB. Importantly, nothing in the REST{1,2}_{LR,RL} naming tells you whether the LR run came first,
or vice-versa. All you know for sure
University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.
Tel: 314-747-6173
St. Louis, MO 63110
Email: mha...@wustl.edu
From: Stephen Smith <st...@fmrib.ox.ac.uk>
Date: Wednesday, November 25, 2015 11:34 AM
To: "Harms, Michael" <mha...@wus
All subject currently hosted in the WU-Minn HCP project on ConnectomDB were processed in a consistent manner using the "500 subject release" pipelines. The release field refers to when they were originally released, and probably isn't of much use to you.
(Where it is relevant, is that if
el: 314-747-6173
St. Louis, MO 63110
Email: mha...@wustl.edu
From: "Mark A. Pinsk" <mpi...@gmail.com>
Date: Monday, November 30, 2015 1:32 PM
To: "Harms, Michael" <mha...@wustl.edu>
Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome
The particular choice of TR/TE may vary between studies, but for a given study they are typically fixed for all the participants.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
What are your settings on all the parameters on the Sequence:Special tab?
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box
St. Louis, MO 63110
Email: mha...@wustl.edu
From: Gregory Butron <gregorybut...@gmail.com>
Date: Tuesday, January 12, 2016 at 1:15 PM
To: jan-mathijs schoffelen <jm.schoffe...@gmail.com>
Cc: "Harms, Michael" <mha...@wustl.edu>, "hcp-users@humanconnectome.or
Every subject that goes through the structural pipeline will have a T1w_acpc_dc_restore.nii.gz file. Could you give some specific subject IDs for which that isn’t the case, so that our IT folks can look into what be going on with Amazon S3?
cheers,
-MH
--
Michael Harms, Ph.D.
Hi,
We have not QC’ed the physiological traces. If you start working with that data, we would appreciate it if you could give us feedback on your experience.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte
Hi,
We just recently discovered that the OFP03 parcellation was missing from the distributed dlabel file.
See this in the HCP-User list archives for a fixed version:
http://www.mail-archive.com/hcp-users%40humanconnectome.org/msg02609.html
cheers,
-MH
--
Tuesday, June 14, 2016 at 10:36 AM
To: "Harms, Michael" <mha...@wustl.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
Subject: RE: [HCP-Users] Area 25 grayordinates
Thanks Michael,
That was actually me who asked that original
It looks like that fMRI at least are an oblique acquisition? Is the T1 oblique as well?
I’ve never been able to get oblique acquisitions to behave nicely in wb_view 1.1.0, but haven’t had opportunity to test it yet under 1.2.0. Hopefully one of the wb_view developers can give
Date: Tuesday, May 31, 2016 at 10:12 AM
To: "Harms, Michael" <mha...@wustl.edu>, "Dierker, Donna" <do...@wustl.edu>, "hcp-users@humanconnectome.org"
<hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] [SPAM] ERROR: mpr2mni305 failed in FreesurferP
Hi,
If I may, why VBM? VBM is prone to a number of interpretational issues, as opposed to say cortical thickness, which is already available for you as part of the HCP processing.
cheers,
-MH
--
Michael Harms, Ph.D.
hcp-users-boun...@humanconnectome.org> on behalf of Dev vasu <vasudevamurthy.devulapa...@gmail.com>
Date: Tuesday, June 21, 2016 at 2:02 PM
To: "Harms, Michael" <mha...@wustl.edu>
Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
Subject:
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St. Louis, MO 63110
Email: mha...@wustl.edu
From: Dev vasu <vasudevamurthy.devulapa...@gmail.com>
Date: Tuesday, June 21, 2016 at 2:36 PM
To: "Harms, Michael" <mha...@wustl.edu>
Cc: "hcp-users@humanconnectome.org" <hcp-users@huma
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Email: mha...@wustl.edu
From: <hcp-users-boun...@humanconnectome.org> on behalf of Dev vasu <vasudevamurthy.devulapa...@gmail.com>
Date: Thursday, June 23, 2016 at 10:02 AM
To: "Har
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