[HCP-Users] MSMAll Failure Following hcp-fix_multi-run

. should it be a mix of tfMRI and rsfMRI, etc)? Best, -Tim Timothy Hendrickson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University of Minnesota Bioinformatics M.S. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay

[HCP-Users] Diffusion Preprocessing Failure

Hello, I am attempting to run the diffusion preprocessing with HCP version 3.27.0 with the GPU enabled eddy, however I receive an error that "eddy_unwarped_Neg" could not be opened, see below: START: eddy_postproc JAC resampling has been used. Eddy Output is now combined. Image Exception :

Re: [HCP-Users] Separating Parcellated Files

ing to do is to put them through PALM in a > way that doesn't use spatial information (no tfce, no smoothing, etc). > > Tim > > > On Mon, Feb 18, 2019, 4:27 PM Timothy Hendrickson > wrote: > >> Hello, >> >> I am attempting to perform an analysis with the tool PAL

[HCP-Users] Separating Parcellated Files

merged_MyelinMap_MSMSulc.Glasser.L.func.gii -metric CORTEX_RIGHT merged_MyelinMap_MSMSulc.Glasser.R.func.gii ERROR: specified direction does not contain brain models Any suggestions? Thank you! -Tim Timothy Hendrickson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute

[HCP-Users] Extract Individual Maps from CIFTI File

Hello, I have a dlabel CIFTI file with multiple maps within it. If I would like to use the dlabel file from just one of the maps how do I extract just that map? Thanks! -Tim Timothy Hendrickson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University

[HCP-Users] dlabel file with FSL HistThal Atlas

Hello, I am attempting to use the HistThal Atlas: https://github.com/CobraLab/atlases/tree/master/colin27-subcortical as the subcortical portion of a cifti file with the intention of creating a way to incorporate it into a dlabel file. Is there some sort of how-to that you can point me to as to

Re: [HCP-Users] FW: FSL FIX no memory with hcp_fix_multi_run

Timothy Hendrickson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University of Minnesota Bioinformatics M.S. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay) On Tue, Aug 21, 2018 at 6:47 PM, Glasser, Matthew wrote: > Sorry that is actually a

[HCP-Users] Resting State Stats Following hcp_fix_multi_run and MSMAll

' >> /output_dir/sub-7397/ses-51327/MNINonLinear/Results/sub-7397_ses-51327_task-rest_run-01_bold/RestingStateStats/ses-51327_sub-7397_ses-51327_task-rest_run-01_bold.matlab.log 2>&1* -Tim Timothy Hendrickson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institu

Re: [HCP-Users] FSL FIX no memory with hcp_fix_multi_run

im >> >> >> On Fri, Aug 17, 2018 at 4:42 PM, Glasser, Matthew >> wrote: >> >>> Is everything 64bit? Do you have swap space? >>> >>> Matt. >>> >>> From: Timothy Hendrickson >>> Date: Friday, August 17, 20

Re: [HCP-Users] FSL FIX no memory with hcp_fix_multi_run

Everything is 64bit. I was testing on my local workstation. I'll shift it over to a more powerful system (128gb memory) if you think it is purely a memory issue. Timothy Hendrickson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University of Minnesota

Re: [HCP-Users] FSL FIX no memory with hcp_fix_multi_run

It is one participant, with 2950 timepoints and 2mm isotropic voxels. The machine has 32gb of memory. -Tim Timothy Hendrickson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University of Minnesota Bioinformatics M.S. Candidate Office: 612-624-0783 Mobile: 507

Re: [HCP-Users] FSL FIX no memory with hcp_fix_multi_run

Hmm, now I am getting a different error... Elapsed time is 1.67516 seconds. Elapsed time is 2.38414 seconds. error: out of memory or dimension too large for Octave's index type Timothy Hendrickson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University

[HCP-Users] FSL FIX no memory with hcp_fix_multi_run

Hello, I am attempting to run FIX cleanup on a rather large dataset (several fMRI scans concatenated together via hcp_fix_multi_run) and am running into the following error: * In fix_3_clean at 45 * *Elapsed time is 1.153074 seconds.* *Elapsed time is 1.077840 seconds.* *Error using fread* *Out

Re: [HCP-Users] MSMAll

Hendrickson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University of Minnesota Bioinformatics M.S. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay) On Tue, Jul 24, 2018 at 3:28 PM, Timothy Hendrickson wrote: > Sorry for the dumb question

Re: [HCP-Users] MSMAll

Sorry for the dumb question, I should have read the code further. Thanks! Timothy Hendrickson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University of Minnesota Bioinformatics M.S. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay) On Tue

Re: [HCP-Users] MSMAll

So once I finish with the multiICAFIX pipeline I wold have to manually separate the concatenated cleaned nifti file and then run MSMAll on those scans. Is that right? Timothy Hendrickson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University of Minnesota

Re: [HCP-Users] MSMAll

I handle processing for several studies, an upward bound for the studies I handle would be approximately 3000 frames. Timothy Hendrickson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University of Minnesota Bioinformatics M.S. Candidate Office: 612-624-0783

Re: [HCP-Users] MSMAll

ase handy to me I am not sure what melodic version would be considered equivalent "FSL 6.0". Could you shed some light on this for me? -Tim Timothy Hendrickson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University of Minnesota Bioinformatics M.S. Can

[HCP-Users] MSMAll

t I should be doing with tfMRI data (i.e. what mods do I have to make to hcp_fix, etc). If you could provide me a code snippet/s that would be great! -Tim Timothy Hendrickson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University of Minnesota Bioinformatics

[HCP-Users] Core Dump ${MSMBINDIR}/msm

minimal preprocessing on this study with FS as registration name. While I will ultimately switch all of my processing to MSMSulc I would like to keep the preprocessing I have done with FS there. What file should I use then for inmesh? -Tim Timothy Hendrickson Neuroimaging Analyst/Staff Scientist

Re: [HCP-Users] Resting State processing

burdensome to require each user to mimic the exact version of the MSM binaries that *FreeSurfer2CaretConvertAndRegisterNonlinear.sh *expects. -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Bioinformatics and Computational Biology M.S. Candidate Office: 612-624-6441 Mobile: 507

Re: [HCP-Users] Resting State processing

/local/hcp-pipelines-3.22.0/Pipelines-3.22.0/MSMBinaries/allparameterssulcDRconf: Couldn't open the file!* -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Bioinformatics and Computational Biology M.S. Candidate Office: 612-624-6441 Mobile: 507-259-3434 (

[HCP-Users] HCP Longitudinal Pipeline

HCP experts, I did some research on the HCP users list and if I missed this question I apologize. I am curious what the timeline for a HCP longitudinal processing pipeline public release? Is there possibly a beta version that I may gain access to in order to use? -Tim Timothy Hendrickson

[HCP-Users] Creating Custom dlabel File

assist it would be much appreciated. -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Bioinformatics and Computational Biology M.S. Candidate Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) ___ HCP-Users mailing list HCP

[HCP-Users] fMRISurface Pipeline FinalfMRIResolution Variable

variable expects one number as input. I have two questions about this. 1. Is this in reference to one particular resolution direction (X,Y,Z), if so which one? 2. If the pipeline expects an isotropic acquisition, how does one enter in an anistropic acquisition? Thanks! Timothy Hendrickson

Re: [HCP-Users] Diffusion Preprocessing Error/Bug

I've been using FSL 5.0.7. It sounds like I need to download 5.0.10. Thanks Michael Timothy Hendrickson Department of Psychiatry University of Minnesota Bioinformatics and Computational Biology M.S. Candidate Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) On Thu, Jul 6, 2017 at 3:30 PM

[HCP-Users] Diffusion Preprocessing Error/Bug

Timothy Hendrickson Department of Psychiatry University of Minnesota Bioinformatics and Computational Biology M.S. Candidate Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) ___ HCP-Users mailing list HCP-Users@humanconnectome.org http

Re: [HCP-Users] Similarity between thickness dscalar files and freesurfer 5.3 thickness files

Okay, I thought as much. Thanks for clarifying Matt! Timothy Hendrickson Department of Psychiatry University of Minnesota Bioinformatics and Computational Biology M.S. Candidate Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) On Wed, Jun 7, 2017 at 10:37 AM, Glasser, Matthew <gl

[HCP-Users] hcp_fix bug

I am getting very similar errors to Nallin. Has this been resolved? Timothy Hendrickson Department of Psychiatry University of Minnesota Bioinformatics and Computational Biology M.S. Candidate Office: 612-624-6441 Mobile: 507-259-3434 (texts okay

Re: [HCP-Users] Variation in HCP Minimal Preprocessing Pipeline Differences Across Releases

Okay good to know. Thank you Matt. -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) On Tue, Feb 21, 2017 at 4:28 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > I think it is okay to over write

Re: [HCP-Users] Variation in HCP Minimal Preprocessing Pipeline Differences Across Releases

files and start over? -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) On Tue, Feb 21, 2017 at 3:34 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > I had a look over this and there are some importan

Re: [HCP-Users] Variation in HCP Minimal Preprocessing Pipeline Differences Across Releases

of minimally preprocessed data. Is this wrong? -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) On Tue, Feb 21, 2017 at 10:59 AM, Harms, Michael <mha...@wustl.edu> wrote: > > There have been a lot of changes/ad

[HCP-Users] Variation in HCP Minimal Preprocessing Pipeline Differences Across Releases

hoping I can get away with not reprocessing all of my data through the minimal preprocessing! Thank you! -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) ___ HCP-Users

[HCP-Users] 2016 Course Material Download

Hello, I am curious when I can expect the 2016 Course Material tutorial data to be available for download? Respectfully, -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay

Re: [HCP-Users] thresholding the data to p-value

Can you please clarify what the fields "Show Data Inside Thresholds" and "Show Data Outside Thresholds" represent? I'm confused by the wording... -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay)

Re: [HCP-Users] thresholding the data to p-value

e. Make sure > Threshold Type is set to On. > > > > > On Dec 5, 2016, at 11:16 AM, Timothy Hendrickson <hendr...@umn.edu> wrote: > > Hi Donna, > > Could you please re-attach the screen capture that you took for Vasudev? I > cannot find it... > I also am looking into ho

Re: [HCP-Users] thresholding the data to p-value

o percentage changes. Please kindly let me know how i can possibly threshold the results to real p-stats. Thanks Vasudev Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Myelin Map Summary Statistics

apologize for the continued questions. I am fairly new to HCP data and am still learning the in and outs :) -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) On Wed, Nov 2, 2016 at 1:20 PM, Glasser, Matthew <glass...@wustl.edu>