Re: [HCP-Users] dMRI gradient table

2013-06-27 Thread Harms, Michael
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

Re: [HCP-Users] dMRI gradient table

2013-06-27 Thread Harms, Michael
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

Re: [HCP-Users] HCP-dMRI gradient table on a TRIO - any experience?

2013-07-08 Thread Harms, Michael
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

Re: [HCP-Users] Only 40 preprocessed diffusion data in Q2 and Q1 reproc?

2013-09-08 Thread Harms, Michael
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

Re: [HCP-Users] Behavioral Data

2014-01-06 Thread Harms, Michael
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

Re: [HCP-Users] details about a sequence parameter for DWI

2014-03-01 Thread Harms, Michael
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 --

Re: [HCP-Users] details about a sequence parameter for DWI

2014-03-10 Thread Harms, Michael
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

Re: [HCP-Users] a problem in opening multi-volume .nii file

2014-03-19 Thread Harms, 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 challenging

Re: [HCP-Users] Easier navigation in volume 3 pane view?

2014-04-24 Thread Harms, Michael
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

Re: [HCP-Users] A Question about tfMRI_X_RL_Atlas.dtseries.nii preprocessing steps

2014-05-02 Thread Harms, Michael
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

Re: [HCP-Users] Creating Group Average Resting State fMRI

2014-05-20 Thread Harms, Michael
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

Re: [HCP-Users] prisma and off line reconstruction

2014-09-03 Thread Harms, Michael
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

Re: [HCP-Users] freesurfer directory structure for 32k average

2014-09-04 Thread Harms, Michael
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

Re: [HCP-Users] Subject directories missing from connectome in a box

2014-09-11 Thread Harms, Michael
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

Re: [HCP-Users] Subject directories missing from connectome in a box

2014-09-11 Thread Harms, Michael
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,

Re: [HCP-Users] The diffusion data of subject 173132 are corrupted.

2014-09-21 Thread Harms, Michael
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

Re: [HCP-Users] how to download the multi-band pulse sequence?

2014-10-01 Thread Harms, Michael
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

Re: [HCP-Users] Finding the B0 Image

2014-10-13 Thread Harms, Michael
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

Re: [HCP-Users] ROI extraction of rest fmri data

2014-10-14 Thread Harms, Michael
Hi Mahsa, I think you are going to have to be more specific for anyone to be able to help you. What is your goal? And what tools are you using and how are you trying to apply the masking. For example, if you are trying to work with the resting state volume data in Matlab/SPM, you may find

Re: [HCP-Users] ROI extraction of rest fmri data

2014-10-14 Thread Harms, Michael
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

Re: [HCP-Users] ROI extraction of rest fmri data

2014-10-14 Thread Harms, Michael
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

Re: [HCP-Users] ROI extraction of rest fmri data

2014-10-15 Thread Harms, Michael
shalchy ma.shal...@yahoo.com Date: Wednesday, October 15, 2014 5:12 AM To: Harms, Michael mha...@wustl.edu Subject: Re: [HCP-Users] ROI extraction of rest fmri data Dear MH How could I convert it to standard images? (i.e I could not use afni, because afni does not recognize the data) Many

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

2014-10-16 Thread Harms, Michael
Hi Greg, Are you trying to re-process the HCP unprocessed data through the HCP pipelines? If so, the grad coefficients from a stock Skyra scanner will not be the correct ones for the HCP Connectom scanner (which has a completely different, customized gradient set, from a stock Skyra). In

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

2014-10-16 Thread Harms, Michael
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

Re: [HCP-Users] GenericfMRIVolumeProcessingPipelineBatch motion correction

2014-10-24 Thread Harms, Michael
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

Re: [HCP-Users] freesurfer errors

2014-10-24 Thread Harms, Michael
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

Re: [HCP-Users] GenericfMRIVolumeProcessingPipelineBatch motion correction

2014-10-28 Thread Harms, Michael
are from volumes 450-600. The voxel size of the raw image is 3x3x3 and the final resolution set in the GenericfMRIVolumeProcessingPipeline script is 3x3x3. I can try running it again without the sbref image and see what happens. -G -Original Message- From: Harms, Michael [mailto:mha

Re: [HCP-Users] GenericfMRIVolumeProcessingPipelineBatch motion correction

2014-10-29 Thread Harms, Michael
-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

Re: [HCP-Users] GenericfMRIVolumeProcessingPipelineBatch motion correction

2014-10-31 Thread Harms, Michael
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

Re: [HCP-Users] PreFreeSurferPipeline

2014-11-25 Thread Harms, Michael
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

Re: [HCP-Users] How to threshold the task data?

2014-11-26 Thread Harms, Michael
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

Re: [HCP-Users] How to threshold the task data?

2014-11-26 Thread Harms, Michael
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

Re: [HCP-Users] How to threshold the task data?

2014-11-26 Thread Harms, Michael
: 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

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

2014-12-10 Thread Harms, Michael
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.

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

2014-12-15 Thread Harms, Michael
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

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

2014-12-15 Thread Harms, Michael
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

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

2014-12-15 Thread Harms, Michael
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

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

2014-12-18 Thread Harms, Michael
...@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

Re: [HCP-Users] Separate coils for DWI data

2015-01-23 Thread Harms, Michael
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.

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

2015-02-03 Thread Harms, Michael
Hi, I'm not sure what those numbers for your T1w scan refer to. For fMRI data, you will need either a traditional gradient echo field map, or a phase-encoding reversed pair of scans for distortion correction. Glasser et al. 2013 is the published reference for the HCP pipelines. cheers,

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

2015-02-06 Thread Harms, Michael
Hi, Which version of the pipeline scripts are you working off? I would suggest that you try referencing the latest pre-release version available at https://github.com/Washington-University/Pipelines/releases/ which appears to contain a good number of embedded comments in its

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

2015-02-06 Thread Harms, Michael
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.

Re: [HCP-Users] Gradient nonlinearity correction (gradient coefficient file)

2015-01-15 Thread Harms, Michael
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

Re: [HCP-Users] failed to find header file for 'rfMRI_REST1_LR'

2015-01-21 Thread Harms, Michael
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

Re: [HCP-Users] failed to find header file for 'rfMRI_REST1_LR'

2015-01-21 Thread Harms, Michael
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

Re: [HCP-Users] Gradient nonlinearity correction (gradient coefficient file)

2015-01-15 Thread Harms, Michael
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

Re: [HCP-Users] Incorporating physiological monitoring data

2015-02-16 Thread Harms, Michael
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

Re: [HCP-Users] cluster extent thresholding on surface

2015-01-11 Thread Harms, Michael
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

Re: [HCP-Users] List of grayordinates belonging to each ROI-cifti parcellate

2015-01-06 Thread Harms, Michael
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.

Re: [HCP-Users] netmats in HCP

2015-03-30 Thread Harms, Michael
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:

Re: [HCP-Users] netmats in HCP

2015-03-31 Thread Harms, Michael
...@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

Re: [HCP-Users] Discrepancy of number of subjects with complete dMRI datasets for download and those listed in the CSV file

2015-03-31 Thread Harms, Michael
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

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

2015-03-02 Thread Harms, Michael
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

Re: [HCP-Users] Dense Connectome Time Courses

2015-03-04 Thread Harms, Michael
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.

Re: [HCP-Users] Slice Timing Correction

2015-05-07 Thread Harms, Michael
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

Re: [HCP-Users] rsfc preprocessing

2015-04-13 Thread Harms, Michael
/ ( 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

Re: [HCP-Users] rsfc preprocessing

2015-04-13 Thread Harms, Michael
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

Re: [HCP-Users] TopupPreprocessingAll.sh

2015-06-04 Thread Harms, Michael
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

Re: [HCP-Users] Freesurfer pipeline and subject's native surfaces

2015-06-04 Thread Harms, Michael
Hi, Are you comparing the FS output in '$subject/T1w/$subject/surf/{lh,rh}.white' to '$subject/T1w/Native/$subject.{L,R}.white.native.surf.gii? Because those should indeed have the same number of vertices and faces for a given hemisphere. Rather than using 'mris_convert', what happens if

Re: [HCP-Users] Myelin mapping with FLAIR

2015-06-19 Thread Harms, Michael
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.

Re: [HCP-Users] Myelin mapping with FLAIR

2015-06-21 Thread Harms, Michael
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

Re: [HCP-Users] Selecting a subsample of unrelated persons from node-timeseries data

2015-06-24 Thread Harms, Michael
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.

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

2015-06-02 Thread Harms, Michael
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

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

2015-07-31 Thread Harms, Michael
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

Re: [HCP-Users] Structural processing of HCP lifespan data

2015-07-23 Thread Harms, Michael
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

Re: [HCP-Users] Total brain size correction

2015-07-14 Thread Harms, Michael
Hi, Couple things: 1) Values for each structure are NOT already adjusted for total brain size. 2) I would use a regression (covariate) approach for controlling for brain size (not taking the ratio for each individual structure). 3) I would NOT use FS_InterCranial_Vol, as it is an estimate

Re: [HCP-Users] native fMRI

2015-10-22 Thread Harms, Michael
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,

Re: [HCP-Users] Clarifying the use of "scout" in the preprocessing scripts

2015-11-11 Thread Harms, Michael
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

Re: [HCP-Users] help for head motion parameters threshold

2015-11-11 Thread Harms, Michael
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

Re: [HCP-Users] Hcp Data with non-overlapping parcellations

2015-11-04 Thread Harms, Michael
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

Re: [HCP-Users] Running TRACULA on the HCP data

2015-11-03 Thread Harms, Michael
; 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,

Re: [HCP-Users] eddy_parameters file

2015-10-16 Thread Harms, Michael
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

Re: [HCP-Users] fat suppression and diffusion scans

2015-07-09 Thread Harms, Michael
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

Re: [HCP-Users] Easy way to have PreFreeSurferBatch.sh not process the T2w?

2015-07-09 Thread Harms, Michael
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

Re: [HCP-Users] Hcp Data with non-overlapping parcellations

2015-11-18 Thread Harms, Michael
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

Re: [HCP-Users] ft_read_cifti too many grayordinates

2015-08-31 Thread Harms, Michael
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.

Re: [HCP-Users] TOPUP options with HCP scripts - Phase Encoding and Voxel Size incompatibilty with EPI

2015-09-01 Thread Harms, Michael
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

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

2015-10-05 Thread Harms, Michael
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,

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

2015-09-18 Thread Harms, Michael
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,

Re: [HCP-Users] MRI parameters

2015-11-27 Thread Harms, Michael
..@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

Re: [HCP-Users] Transformation matrices of HCP 500 Subject Release

2015-12-02 Thread Harms, Michael
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

Re: [HCP-Users] FIX-denoised

2015-12-09 Thread Harms, Michael
, 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

Re: [HCP-Users] Verifying HCP data versions

2015-12-15 Thread Harms, Michael
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

Re: [HCP-Users] ROI parcellation

2015-12-15 Thread Harms, Michael
ou could point me to where the volumetric functional BOLD data in T1 space is (I cannot locate it in the FIX extended package - this only seems to have func already normalized to MNI), I could directly apply the aparc+aseg parcellation (that's in T1 space) to this. Thanks, Joelle On Tue, Dec 1

Re: [HCP-Users] Diffusion processing

2015-12-14 Thread Harms, Michael
The dir{95,96,97} labels in the "raw" (unprocessed) NIFTI files represent the total number of frames acquired in that acquisition, including the b=0. cheers, -MH --  Michael Harms, Ph.D. --- Conte Center for the Neuroscience of

Re: [HCP-Users] ROI parcellation

2015-12-17 Thread Harms, Michael
 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

Re: [HCP-Users] FIX-denoised

2015-12-09 Thread Harms, Michael
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.

Re: [HCP-Users] File 001.mgz

2015-12-14 Thread Harms, Michael
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

Re: [HCP-Users] File 001.mgz

2015-12-14 Thread Harms, Michael
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

Re: [HCP-Users] File 001.mgz

2015-12-14 Thread Harms, Michael
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

Re: [HCP-Users] ROI parcellation

2015-12-15 Thread Harms, Michael
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

Re: [HCP-Users] Field Map

2016-01-06 Thread Harms, Michael
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

Re: [HCP-Users] Phase Encoding left-to-right and right-to-left

2015-11-25 Thread Harms, Michael
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

Re: [HCP-Users] Qdec questions

2015-11-25 Thread Harms, Michael
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

Re: [HCP-Users] phase encoding and group ICA

2015-11-25 Thread Harms, Michael
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

Re: [HCP-Users] Phase Encoding left-to-right and right-to-left

2015-11-25 Thread Harms, Michael
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

Re: [HCP-Users] Demographic and behavioral subject data

2015-11-30 Thread Harms, Michael
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

Re: [HCP-Users] aliasing in diffusion images

2015-11-30 Thread Harms, Michael
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

Re: [HCP-Users] MRI parameters

2015-11-18 Thread Harms, Michael
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

Re: [HCP-Users] aliasing in diffusion images

2015-11-23 Thread Harms, Michael
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

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