Re: [HCP-Users] Troubleshooting error with gradunwarp

2019-06-27 Thread Harms, Michael
Hi, That sounds like this issue, which we haven’t patched quite yet: https://github.com/Washington-University/HCPpipelines/issues/119 Incidentally, you must be running off code in the current master branch, rather than the formally tagged “v4.0.0” release

Re: [HCP-Users] A question about scene file

2019-06-21 Thread Harms, Michael
As part of some other updates to the StructuralQC scenes themselves, I recently created a more sophisticated generation script that should use relative paths within the scene. Please try the just updated master branch of https://github.com/Washington-University/StructuralQC We have tested

Re: [HCP-Users] film_gls error pinv() svd()

2019-06-18 Thread Harms, Michael
-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Moataz Assem Date: Tuesday, June 18, 2019 at 8:00 AM To: "Glasser, Matthew" , "Harms, Michael" , "hcp-users@humanconnectome.org" Subject: RE: [HCP-Users] film_gls error pinv() s

Re: [HCP-Users] film_gls error pinv() svd()

2019-06-17 Thread Harms, Michael
Hmmm. Assuming the problem is reproducible, I think you’ll have to report this, to the FSL list. To provide additional information, it might be helpful to hack the TaskfMRILevel1.sh script to not use the ‘--sa --ms=15 --epith=5’ flags in the call to ‘film_gls’ (or, perhaps easier, just try

Re: [HCP-Users] Training data set for multi-run fix

2019-06-14 Thread Harms, Michael
Hi, I’m not sure if the new training file is ready for public release yet, but just to clarify, to clean short fMRI runs, you really need to use multi-run FIX to get better separation of the signal/noise components. The new training file will help around the margins, but using MR-FIX is

Re: [HCP-Users] RE-POSTING: Duplicate subjects in Connectome in a Box?

2019-06-07 Thread Harms, Michael
Are you sure that there is duplication of actual *data* on the different drives? Just because a subject ID appears on multiple drives doesn’t mean that data under that subject ID is the same on the drives. Cheers, -MH -- Michael Harms, Ph.D.

Re: [HCP-Users] A minor question regarding HCP 7T movie data

2019-06-07 Thread Harms, Michael
Hi, It isn’t surprising that data will be missing in some subjects, due either to problems at the scanner, or problems during processing. Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University

Re: [HCP-Users] Error while running "GenericfMRIVolumeProcessingPipeline.sh"

2019-06-05 Thread Harms, Michael
Try the very latest master, which should resolve this issue. (I was just working on this 30 min ago). Please let us know if it works. -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine

Re: [HCP-Users] Inquiry about data

2019-05-30 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: 温景熙 Date: Thursday, May 30, 2019 at 9:24 PM To: "Glasser, Matthew" , "Harms, Michael

Re: [HCP-Users] Group-averaging of task fMRI data

2019-05-30 Thread Harms, Michael
South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: "Glasser, Matthew" Date: Thursday, May 30, 2019 at 3:52 PM To: Reza Rajimehr , "Harms, Michael" , Nooshin Abbasi Cc: hcp-users Subject: R

Re: [HCP-Users] Group-averaging of task fMRI data

2019-05-30 Thread Harms, Michael
Hi Reza, 1) We’ve already generated Cohen’s d-style effect size maps for all contrasts, using all subjects, as part of the “Group Average Dataset” available at https://db.humanconnectome.org/data/projects/HCP_1200. If you need it computed for a specific subset of subjects, then yes, you can

Re: [HCP-Users] PRISM DWI Parameter Request

2019-05-30 Thread Harms, Michael
Hi, All those details, including an importable VE11C protocol are available at http://protocols.humanconnectome.org/ Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine

Re: [HCP-Users] Downloading movement regressors from HYA release

2019-05-29 Thread Harms, Michael
: Leonardo Tozzi Date: Wednesday, May 29, 2019 at 1:44 PM To: "Harms, Michael" , "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] Downloading movement regressors from HYA release I did and actually some subjects worked, but not these ones: 101006 159441 926862 92735

Re: [HCP-Users] Downloading movement regressors from HYA release

2019-05-29 Thread Harms, Michael
, May 29, 2019 at 11:40 AM To: "Harms, Michael" , "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] Downloading movement regressors from HYA release Dear Michael, I have now downloaded the majority of subjects with: curl -o …/${sub}_${run}_Movement_RelativeRMS.txt

Re: [HCP-Users] A question about the HCP pipeline 4.0.0

2019-05-17 Thread Harms, Michael
Hmmm. What is the specific error message that you are getting? In the 4.0.0 pipelines, the necessary custom scripts that you mentioned are provided with the pipeline distribution, and are contained in the HCPpipelines/FreeSurfer/custom directory. It sounds like you don’t have something

Re: [HCP-Users] volumetric segmentation of subcortical structures

2019-05-16 Thread Harms, Michael
Hi, If you simply want all the FreeSurfer quantification in tabular form, you can select the “Expanded FreeSurfer Data” link under “Quick Downloads”, available here https://db.humanconnectome.org/data/projects/HCP_1200 (You will need a ConnectomeDB account). Cheers, -MH -- Michael Harms,

Re: [HCP-Users] Question on download dMRI.

2019-05-15 Thread Harms, Michael
Hi, If you want to try downloading via https://db.humanconnectome.org and Aspera, simply select the “All Family Subjects” category under “Download Image Data” and then select the “Diffusion” modality on the “Download Packages” page. That will select all 1065 subjects with Diffusion data –

Re: [HCP-Users] Downloading movement regressors from HYA release

2019-05-15 Thread Harms, Michael
Hi, The Movement_RelativeRMS.txt files aren’t part of the specific “${run}_FIX” resource that you tried to reference. If you have access to outputs in our standard file/directory organization (e.g., Amazon S3, Connectome-in-a-Box, or our downloaded “packages”), the Movement_RelativeRMS.txt

Re: [HCP-Users] Quick questions

2019-05-14 Thread Harms, Michael
In the case of the 7T data, the 1/2/3/4 are just used to distinguish the different resting state runs, acquired in different scan sessions. The numbers are not intended to imply that each scan was acquired on a different day. We’d have to look, but I suspect that 1/2 were typically acquired

Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

2019-05-09 Thread Harms, Michael
While I’m not surprised that the ICCs would be lower for an anatomical-based measure for MSMAll than MSMSulc, I am surprised by the magnitude of the change (from 0.9 to 0.65), especially for a parcellated analysis, since only changes in the precise border of the parcellations should be

Re: [HCP-Users] PALM analysis errors with HCP data - data cannot be sorted

2019-04-29 Thread Harms, Michael
Hi, I suggest directing your inquiry to the FSL-Users list. Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.

Re: [HCP-Users] "activation" tables for reporting pscalar results

2019-04-24 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: Joseph Orr Date: Wednesday, April 24, 2019 at 10:51 AM To: "Harms, Michael" Cc:

Re: [HCP-Users] "activation" tables for reporting pscalar results

2019-04-24 Thread Harms, Michael
Why not simply report the parcel name and its values? And consider putting the scene on BALSA, so that others can easily access the data. Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University

Re: [HCP-Users] hp2000 filter not applied to hp2000_clean.nii.gz volume data for some (one?) subjects?

2019-04-23 Thread Harms, Michael
For users that want to follow this, please see: https://github.com/Washington-University/HCPpipelines/issues/108 It has something to do with the fact that we needed to apply manual reclassification of the FIX output in that particular subject/run. Cheers, -MH -- Michael Harms, Ph.D.

Re: [HCP-Users] unequal length of movement regressors

2019-04-22 Thread Harms, Michael
We have seen this occur on rare occasions, and don’t have an explanation for it. Try just running fMRIVolume again. Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine

Re: [HCP-Users] wb_command -metric-tfce

2019-04-20 Thread Harms, Michael
Hi, We suggest you use PALM, since you need to use permutation to determine the distribution of the TFCE metric. Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department

Re: [HCP-Users] DeDriftAndResamplePipeline error

2019-04-20 Thread Harms, Michael
That particular error message can be ignored. We’ll fix the scripts so that it doesn’t occur in the future. Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of

Re: [HCP-Users] Subject list for the HCP Q2 release

2019-04-14 Thread Harms, Michael
FYI: The “prediction of fluid intelligence” aspect of Finn et al (2015) has already been extended to final HCP-YA release via a different research group in this study: https://www.ncbi.nlm.nih.gov/pubmed/30104429 cheers, -MH -- Michael Harms, Ph.D.

Re: [HCP-Users] MSMAllPipeline error

2019-04-13 Thread Harms, Michael
We extended that feature such that it should be an accepted option for all the "ICAFIX"-related scripts, but we haven't had a chance yet to extend it to the context of MSMAll and TaskAnalysis. Hopefully in the near future... -- Michael Harms, Ph.D.

Re: [HCP-Users] file_array objects can not be permuted

2019-04-08 Thread Harms, Michael
Sorry, but I think you are going to have to get support from Anderson and the FSL list for this one. -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134

Re: [HCP-Users] MR ICA+FIX error

2019-04-06 Thread Harms, Michael
doesn't even output anything if it isn't a symlink, while the point is to find the real location whether it is a symlink or not (because it needs other files from that directory). I guess I will make it test whether "$0" is a symlink first. Tim On Mon, Apr 1, 2019 at 9:31 AM Harms, Mic

Re: [HCP-Users] MSM binaries versions

2019-04-04 Thread Harms, Michael
Also, see here https://github.com/ecr05/MSM_HOCR/issues/5 for some info from Emma. -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid

Re: [HCP-Users] ICA+FIX error

2019-04-01 Thread Harms, Michael
Check RS_fMRI_2_hp2000.ica/.fix.log for clues. Also, what’s in the stderr output from the run? -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660

Re: [HCP-Users] Question on fsl 6.0.1

2019-03-29 Thread Harms, Michael
The MR-FIX releases as part of HCPpipelines v4.0.0 should work with FSL 6.0.1. As far as MSMAll and FSL 6.0.1, to my knowledge, we haven't explicitly tested that combination yet. Cheers, -MH -- Michael Harms, Ph.D. --- Associate

Re: [HCP-Users] PostFreesurfer possible bug

2019-03-20 Thread Harms, Michael
8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Shachar Gal Date: Wednesday, March 20, 2019 at 3:32 PM To: "Harms, Michael" Cc: "hcp-users@humanconnectome.org" Subject: Re: [HCP-U

Re: [HCP-Users] PostFreesurfer possible bug

2019-03-20 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: Shachar Gal Date: Wednesday, March 20, 2019 at 3:23 PM To: "Harms, Michael"

Re: [HCP-Users] PostFreesurfer possible bug

2019-03-20 Thread Harms, Michael
Hi, The FreeSurferFolder is located at $StudyFolder/$Subject/T1w/$Subject, which is what PostFreeSurferPipeline.sh is setting up via the following combination of lines: FreeSurferFolder="$Subject" #L101 T1wFolder="$StudyFolder"/"$Subject"/"$T1wFolder" #L137

Re: [HCP-Users] A question about generating quality control scene file for the resting-state data

2019-03-18 Thread Harms, Michael
Running the PostFix script will generate a scene that allows you to review the FIX classification. Don’t recall seeing a surface contour/glitch quite like that before. It definitely merits further investigation. E.g., what do the adjacent slices look like? What does the actual surface look

Re: [HCP-Users] structural preprocessing on Philips data?

2019-03-13 Thread Harms, Michael
Hi, Sounds like a coding error. If you’ve converted your T1w and T2w scans to proper NIFTIs, then you should be able to use those as inputs. Did you review Examples/Scripts/PreFreeSurferPipelineBatch.sh ? If you get it working, let us know how the myelin maps look! Cheers, -MH -- Michael

Re: [HCP-Users] A question about the HCP structural pipeline

2019-03-08 Thread Harms, Michael
/T1w/ contains all the FreeSurfer output. So, /T1w//stats contains the usual FS quantification. -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660

Re: [HCP-Users] rs-fMRI with-in subject comparison

2019-03-04 Thread Harms, Michael
As for a version of the parcellation with network assignments, see here: https://github.com/ColeLab/ColeAnticevicNetPartition cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of

Re: [HCP-Users] extract myelin content of individual subjects in Gordon parcels

2019-03-02 Thread Harms, Michael
As an aside, the S1200 Group Average dataset available at https://db.humanconnectome.org/data/projects/HCP_1200 includes a version of the Gordon parcellation with the parcels reordered according to networks, which is very useful when viewing matrices for network-related structure. Based on

Re: [HCP-Users] generating z-stat file

2019-03-02 Thread Harms, Michael
Hi, You cannot create a z-stat map from a beta map. We suggest that you use PALM to compute group-wise statistics from individual subject beta (cope) maps. Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry

Re: [HCP-Users] ICA FIX output missing

2019-02-26 Thread Harms, Michael
Email: mha...@wustl.edu From: "Glasser, Matthew" Date: Tuesday, February 26, 2019 at 8:19 PM To: NEUROSCIENCE tim , Leonardo Tozzi Cc: "Harms, Michael" , "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] ICA FIX output missing Regarding task analysis,

Re: [HCP-Users] ICA FIX output missing

2019-02-26 Thread Harms, Michael
.edu From: "Glasser, Matthew" Date: Monday, February 25, 2019 at 6:53 PM To: Leonardo Tozzi , "Harms, Michael" , "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] ICA FIX output missing You’ll want to be using wb_command 1.3.2. I am not aware of any modificatio

Re: [HCP-Users] ICA FIX output missing

2019-02-25 Thread Harms, Michael
Hi, The log files for ICA FIX are a bit scattered. In the .ica directory check: .fix_2b_predict.log (from the prediction – i.e,. R code) and .fix.log (from the cleaning stage). And in the .ica/fix directory, check logMatlab.txt (I believe that is from the feature extraction stage). Note that

Re: [HCP-Users] Glasser parcellation with network labels

2019-02-20 Thread Harms, Michael
South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Anita Sinha Date: Wednesday, February 20, 2019 at 9:25 AM To: "Harms, Michael" , "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users]

Re: [HCP-Users] Glasser parcellation with network labels

2019-02-20 Thread Harms, Michael
See this paper: https://www.ncbi.nlm.nih.gov/pubmed/30291974 -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.

Re: [HCP-Users] Some questions about data quality check

2019-02-13 Thread Harms, Michael
Another way to put this is that hippocampus is not cortical (it is part of the medial wall), and thus FreeSurfer does not attempt to generate surfaces that follow the structures in that region. They even have a FAQ on that specific question:

Re: [HCP-Users] Multiple Comparison Correction on Cifti/gifti

2019-02-11 Thread Harms, Michael
Hi, We’d suggest that you use PALM for inference. Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.

Re: [HCP-Users] Imaging Protocols for HCP Version 2019.01.14

2019-02-11 Thread Harms, Michael
Hi, We are working on getting the link functioning. -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel:

Re: [HCP-Users] Sharing HCP-derived brain networks and graph-theoric measures

2019-02-07 Thread Harms, Michael
Supporting “arbitrary” formats requires putting a whole system in place for describing the format, and making it queryable. The good thing is that if the pconn’s are available, users could use those inputs to their own derived graph-theoretic measures. Cheers, -MH -- Michael Harms, Ph.D.

Re: [HCP-Users] Some questions about using HCP structural preprocessing pipeline

2019-02-07 Thread Harms, Michael
Re 1) If you are using a modern version of ‘dcm2niix’, then in the context of the T1 and T2 scans, the values for T1wSampleSpacing and T2wSampleSpacing are available as the “DwellTime” entry in the BIDS-style json sidecar files. Cheers, -MH -- Michael Harms, Ph.D.

Re: [HCP-Users] Transforming Freesurfer .mgz segmented files into HCP_2mm MNI Surface and Volume space

2019-02-01 Thread Harms, Michael
2019 at 4:40 PM To: "Harms, Michael" , "Glasser, Matthew" , "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] Transforming Freesurfer .mgz segmented files into HCP_2mm MNI Surface and Volume space Hi we just used the isotropic T1w scan A. Benjamin Sriva

Re: [HCP-Users] Transforming Freesurfer .mgz segmented files into HCP_2mm MNI Surface and Volume space

2019-01-30 Thread Harms, Michael
Hi, I’m curious, did you run the hippocampal/amygdala segmentation using only a isotropic T1w scan, or did you add in a high in-plane resolution T2w, as is often used for best performance of the hp/amyg segmentation routine? Cheers, -MH -- Michael Harms, Ph.D.

Re: [HCP-Users] Detailed manual rating score of structural images

2019-01-22 Thread Harms, Michael
nifer" Date: Tuesday, January 22, 2019 at 9:48 AM To: Xuhong Liao , hcp-users , "Harms, Michael" Subject: Re: [HCP-Users] Detailed manual rating score of structural images Hi Xuhong, All of the structural data released by HCP is of good or excellent quality (scores of 3-4 on ou

Re: [HCP-Users] Detailed manual rating score of structural images

2019-01-20 Thread Harms, Michael
Hi, https://wiki.humanconnectome.org/pages/viewpage.action?pageId=88901591 -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.

Re: [HCP-Users] CIFTI to Matlab

2019-01-17 Thread Harms, Michael
.Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Anita Sinha Date: Thursday, January 17, 2019 at 4:38 PM To: "Glasser, Matthew" , "Harms, Michael" , "hcp-users@humanconnectome.org" Subject: Re: [HCP

Re: [HCP-Users] CIFTI to Matlab

2019-01-17 Thread Harms, Michael
Hi, It sounds like you don’t have the gifti library properly installed. Within matlab, what happens when you type g = gifti Do you get a gifti structure? Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry

Re: [HCP-Users] dMRI data order for eddy

2019-01-06 Thread Harms, Michael
Hi, Please see comments related to this in Examples/DiffusionPreprocessingBatch.sh. Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660

Re: [HCP-Users] Temporal signal to noise ratio of HCP subjects

2018-12-21 Thread Harms, Michael
Hi, tSNR (and a fairly sophisticated variance partitioning) is available via the “RestingStateStats” pipeline. If you have the full sets of packages from HCP-YA, see the ${subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_stats.txt file, which includes a “tSNR” entry. (Associated

Re: [HCP-Users] Time series data

2018-12-19 Thread Harms, Michael
If you are looking for a network assignment of the parcels in the Glasser parcellation, see: https://github.com/ColeLab/ColeAnticevicNetPartition cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington

Re: [HCP-Users] Noise level estimate from the data

2018-12-17 Thread Harms, Michael
Hi, I don’t think that those values in the .fsf file get used for anything in terms of the HCPpipelines, so in that sense their value is irrelevant. Perhaps Greg will recall if they were set in any meaningful manner way-back when we constructed the design.fsf templates. Cheers, -MH --

Re: [HCP-Users] HCP_FIX

2018-12-14 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: "Glasser, Matthew" Date: Thursday, December 13, 2018 at 2:02 PM To: Shachar Gal Cc: "Harms, Michae

Re: [HCP-Users] fix error, vn maps

2018-12-06 Thread Harms, Michael
ciftisavereset wasn’t compiled in to the existing 1.067 compiled matlab. I just tested a new compiled in which this is fixed. Waiting for Oxford to either update the fix1.067 package, or release a new fix version. Cheers, -MH -- Michael Harms, Ph.D.

Re: [HCP-Users] Number-to-anatomical labels: need help!

2018-12-03 Thread Harms, Michael
Hi, It’s the standard FreeSurfer label table -- $FREESURFER_HOME/FreeSurferColorLUT.txt Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134

Re: [HCP-Users] PALM basic execution error - setup issue?

2018-11-26 Thread Harms, Michael
Hi, The error in palm_miscread.m is telling you that your execution environment isn’t finding ‘wb_command’ in your PATH, so you need to resolve that by setting up your environment appropriately. Cheers, -MH -- Michael Harms, Ph.D. ---

Re: [HCP-Users] HCP_FIX

2018-11-26 Thread Harms, Michael
Hi, The cleaning of the CIFTI data is done automatically in fix_3_clean.m of the FIX distribution, which is called by the fix script itself. The only relevant aspect of hcp_fix to that process is that hcp_fix creates the following symbolic link: if [ -f ../${fmri_orig}_Atlas.dtseries.nii ] ;

Re: [HCP-Users] HCP_FIX

2018-11-22 Thread Harms, Michael
Hi, What is the overall context of this inquiry? Are you getting errors with running the version of hcp_fix in ICAFIX/hcp_fix? If so, simply revert to using the version of hcp_fix supplied with the FIX distribution itself. That doesn’t include some of the enhancements that Matt mentioned

Re: [HCP-Users] Number of cortical vertices in cifti and gifti files

2018-11-16 Thread Harms, Michael
-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Reza Rajimehr Date: Friday, November 16, 2018 at 1:50 PM To: "Harms, Michael" Cc: "Glasser, Matthew" , "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] Number of cortical ver

Re: [HCP-Users] Number of cortical vertices in cifti and gifti files

2018-11-16 Thread Harms, Michael
No, it is more complicated than that. I believe what you need is -cifti-export-dense-mapping Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box

Re: [HCP-Users] List of ALL unrelated subject

2018-11-02 Thread Harms, Michael
Hi, 1) We didn’t repeat the exercise of generating an “unrelated subjects” list following the complete S1200, and rather doubt that we will at this point in time. Sorry. 2) There is no unique “unrelated subjects” list, since you can pick any one participant from each family. We generated

Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh

2018-11-01 Thread Harms, Michael
Hi, Have you configured your R installation correctly, per the FSL FIX Wiki page? https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX/UserGuide cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School

Re: [HCP-Users] Software version for HCP Pipeline (v 3.27.0)

2018-11-01 Thread Harms, Michael
. --- Associate Professor of Psychiatry 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: "Harms, Michael&q

Re: [HCP-Users] Software version for HCP Pipeline (v 3.27.0)

2018-11-01 Thread Harms, Michael
FS: 5.3.0-HCP. We are working toward compatibility with FS 6.x – hopefully in the not too distant future. FSL: latest (5.0.11 currently) Workbench: latest (1.3.2 currently) We know that the following is way out of date, and needs to be updated:

Re: [HCP-Users] Question about dense functional connectome

2018-10-25 Thread Harms, Michael
As an aside, if ‘ft_read_cifti’ is expanding all the data to type double (64 bit), then you are looking at needing > 66 GB to load a 91282x91282 dconn.nii in matlab. I assume that is what is happening based on your experience. If you want to see how far you can get in Matlab, I would at least

Re: [HCP-Users] T1w_acpc_dc_restore_brain.nii.gz

2018-10-09 Thread Harms, Michael
Hi, See http://www.ncbi.nlm.nih.gov/pubmed/23668970 specifically Figure 9. “dc” is the readout distortion correction. “restore” is the bias field correction (for the receive bias field) The gradient distortion correction is not included as part of the filename, so the file could just as well

Re: [HCP-Users] Time-of-day when scans where performed?

2018-10-01 Thread Harms, Michael
Hi, You can find that info in the "3T/7T MRI Session Summary CSVs" available for download via https://db.humanconnectome.org/data/projects/HCP_1200 cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington

Re: [HCP-Users] Intermediate freesurfer files not available through CREST?

2018-09-25 Thread Harms, Michael
st because of data footprint issue on compute clusters). Are those files available via CREST? Thank you! nicola On 09/25/2018 03:17 PM, Harms, Michael wrote: > Hi, > You can obtain the entire FreeSurfer output via the Structural Extended > packages. Perhaps that would be an easier way

Re: [HCP-Users] Intermediate freesurfer files not available through CREST?

2018-09-25 Thread Harms, Michael
Hi, You can obtain the entire FreeSurfer output via the Structural Extended packages. Perhaps that would be an easier way for you to proceed? Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington

Re: [HCP-Users] questions about the motion metrics (Movement_RelativeRMS_mean.txt)

2018-09-18 Thread Harms, Michael
1. The translations are in mm. I don’t recall off the top of head whether the rotations are in degrees or rotations, but I believe that is documented in the release manual. (Or check the HCP Pipeline code). 2. RMS is based on a combination of both the translations and rotations. 3. Yes.

Re: [HCP-Users] Need to truncate dummy scans for 7T data?

2018-09-10 Thread Harms, Michael
Hi, For HCP-YA we did NOT remove any additional frames beyond the couple that Siemens automatically discards. That means that there are indeed some T1-related transient effects in that data. I'd suggest that you simply compute some time-courses averaged over the whole brain (or even better,

Re: [HCP-Users] making a chart/graph out of myelin maps

2018-09-06 Thread Harms, Michael
Hi, You can use -cifti-parcellate with, e.g., the Glasser parcellation. Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid

Re: [HCP-Users] Question regarding intracranial volume

2018-08-30 Thread Harms, Michael
Hi, As the link to the FS page that Jenn provided makes clear, the FS value for “ICV” is solely an estimate derived from the determinant of the talairach transform. You cannot actually measure a true ICV using just a T1w image. Also, be aware that we didn’t QC the accuracy of the talairach

Re: [HCP-Users] QC

2018-08-30 Thread Harms, Michael
Hi, Script to generate scenes for structural QC are available here: https://github.com/Washington-University/StructuralQC The joint lecture/practical on “Data Quality” for the HCP course, available here for the 2017 Course, would be useful for you to review as well:

Re: [HCP-Users] TOPUP Settings

2018-08-30 Thread Harms, Michael
FWIW, the readout distortion effect in the structurals is such a small effect that it is difficult to confirm the appropriate polarities for that correction by trial and error. Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor

Re: [HCP-Users] TOPUP Settings

2018-08-30 Thread Harms, Michael
Hi, Note that UnwarpDir in the PreFreeSurfer script is a very different thing from UnwarpDir in the fMRIVolume script. In the former, it specifies the *readout* direction of the *structurals* -- typically ‘z’ for how we collect T1 and T2 structurals on Siemens scanners (assuming that the

Re: [HCP-Users] help on Simple higher level FEAT analysis

2018-08-20 Thread Harms, Michael
Hi, FSL/FEAT are not currently equipped to handle grayordinate data. We have examples of a “third-level” (across subject) analyses as part of the Practicals in the HCP Course. The content for the 2018 course (in June) will hopefully become available online in the near future. Until then, the

Re: [HCP-Users] DICOM to NIFTI in HCP standard

2018-08-16 Thread Harms, Michael
Hi, Sorry, but not to my knowledge. We use ‘dcm2niix’ currently for DICOM to NIFTI conversion (‘dcm2niix’ generates nice .json files containing a bunch of relevant parameters of the scan). That particular step is pretty straightforward. Then, as part of our “session building” process, we

Re: [HCP-Users] Diffusion Times (Delta and delta) for HCP 1200 release?

2018-08-13 Thread Harms, Michael
Via Essa Yacoub: from Stam's paper - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3720790/ Sampling in q-space includes 3 shells at b=1000, 2000 and 3000 s/mm2 (diffusion times are Δ=43.1 ms and d=10.6 ms, and Gmax=97.4 mT/m after vendor supplied gradient duty cycle optimization). --

Re: [HCP-Users] Finding a significant difference only in one hemisphere

2018-08-08 Thread Harms, Michael
of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Darko Komnenić Date: Wednesday, August 8, 2018 at 2:08 PM To: "Glasser, Matthew" Cc: "Harms, Michael" , "Winkle

Re: [HCP-Users] Finding a significant difference only in one hemisphere

2018-08-07 Thread Harms, Michael
(NIH/NIMH) [E]" Date: Tuesday, August 7, 2018 at 3:02 PM To: Darko Komnenić , "Harms, Michael" Cc: "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] Finding a significant difference only in one hemisphere Hi Darko, The option “-saveglm” in PALM should produce

Re: [HCP-Users] HCPpipelines Task Analysis Level 2 design error

2018-07-27 Thread Harms, Michael
Yes, if you have 4 runs in your level 2, then you probably need to start with fresh templates derived from a 4 run volume analysis. Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of

Re: [HCP-Users] Missing output after running genericfMRISurfaceProcessingPipelineBatch.sh

2018-07-24 Thread Harms, Michael
Are you looking in $SUBJID/MNINonLinear/Results/$fMRIName ? -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.

Re: [HCP-Users] HCP pipeline working directory documentation

2018-07-24 Thread Harms, Michael
Hi, I took a very quick look to see what direction this is heading. One initlal thing I noticed -- the files in $SUBJID/T1w are not in MNI152 space. Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington

Re: [HCP-Users] Generating Field Maps for PreFreeSurferPipelineBatch.sh input

2018-07-22 Thread Harms, Michael
of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Marc Dubin Date: Saturday, July 21, 2018 at 11:13 PM To: "Harms, Michael" Cc: "Glasser, Matthew" , "hcp-users@human

Re: [HCP-Users] Generating Field Maps for PreFreeSurferPipelineBatch.sh input

2018-07-21 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: Marc Dubin Date: Saturday, July 21, 2018 at 10:28 PM To: "Harms, Michael" Cc: "G

Re: [HCP-Users] Generating Field Maps for PreFreeSurferPipelineBatch.sh input

2018-07-19 Thread Harms, Michael
, July 19, 2018 at 9:46 PM To: "Glasser, Matthew" Cc: "Harms, Michael" , "hcp-users@humanconnectome.org" Subject: [HCP-Users] Generating Field Maps for PreFreeSurferPipelineBatch.sh input I used the Matlab DICOM viewer and got BWPPPE as a private f

Re: [HCP-Users] Generating Field Maps for PreFreeSurferPipelineBatch.sh input

2018-07-19 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: on behalf of "Harms, Michael" Date: Thursday, July 19, 2018 at 9:44 PM To: "G

Re: [HCP-Users] Generating Field Maps for PreFreeSurferPipelineBatch.sh input

2018-07-19 Thread Harms, Michael
Dubin Cc: "Harms, Michael" , "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] Generating Field Maps for PreFreeSurferPipelineBatch.sh input I would just pull the numbers directly from the indicated DICOM fields using a DICOM header viewer such as this one: ht

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