[HCP-Users] MSMAll Failure Following hcp-fix_multi-run
Hello, I am having issues running MSMAll following hcp-fix_multi-run for a study that I am doing processing for. The particular study that I am processing data for has 6 fMRI scans totalling 2950 timepoints per scanning session. I am certainly aware of the large amount of memory that hcp-fix_multi-run requires as it is fed more timepoints, however, this is completing without issue. I am running HCP version 3.27.0 with MSMAll v2 and FSL 5.0.11. Is there a way to get around this error? If I end up having to break up hcp-fix_multi-run do you have any best practices on how to do this (i.e. 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 mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[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 : #22 :: ERROR: Could not open image /output_dir/sub-9276/ses-52 742/Diffusion/eddy/eddy_unwarped_Neg I'm looking for an intuition as to what could have happened. Best, -Tim ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Separating Parcellated Files
Oh good to know! Thanks Tim! Best, -Tim On Mon, Feb 18, 2019 at 5:39 PM Timothy Coalson wrote: > Parcellated files contain only one value per parcel (per map), so it isn't > a good idea to try to reconstitute them into a spatial map before > analysis. I think the correct thing 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 PALM with >> parcellated surface data. Within the PALM wiki underneath the CIFTI >> examples portion it is suggested to separate cifti files into it's discrete >> pieces, so I tried to separate the parcellated file into the left and right >> hemisphere, however I get a failure. >> >> /home/lnpi14-raid1/timothy-data-lnpi14/DOWNLOADS/workbench/bin_rh_linux64/../exe_rh_linux64/wb_command >> -cifti-separate merged_MyelinMap_MSMSulc.Glasser.pscalar.nii ROW -metric >> CORTEX_LEFT 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 >> >> While running: >> /home/lnpi14-raid1/timothy-data-lnpi14/DOWNLOADS/workbench/bin_rh_linux64/../exe_rh_linux64/wb_command >> -cifti-separate merged_MyelinMap_MSMSulc.Glasser.pscalar.nii COLUMN -metric >> CORTEX_LEFT 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 >> University of Minnesota >> Bioinformatics M.S. Candidate >> Office: 612-624-0783 >> Mobile: 507-259-3434 (texts okay) >> >> ___ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Separating Parcellated Files
Hello, I am attempting to perform an analysis with the tool PALM with parcellated surface data. Within the PALM wiki underneath the CIFTI examples portion it is suggested to separate cifti files into it's discrete pieces, so I tried to separate the parcellated file into the left and right hemisphere, however I get a failure. /home/lnpi14-raid1/timothy-data-lnpi14/DOWNLOADS/workbench/bin_rh_linux64/../exe_rh_linux64/wb_command -cifti-separate merged_MyelinMap_MSMSulc.Glasser.pscalar.nii ROW -metric CORTEX_LEFT 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 While running: /home/lnpi14-raid1/timothy-data-lnpi14/DOWNLOADS/workbench/bin_rh_linux64/../exe_rh_linux64/wb_command -cifti-separate merged_MyelinMap_MSMSulc.Glasser.pscalar.nii COLUMN -metric CORTEX_LEFT 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 University of Minnesota Bioinformatics M.S. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay) ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[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 of Minnesota Bioinformatics M.S. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay) ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[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 how I would do this? Thanks! -Tim ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] FW: FSL FIX no memory with hcp_fix_multi_run
Sort of continuing this conversation, I am occasionally running into another error with hcp_fix_multi_run. I've noticed that within a few concatenation folders I get a error log file, named errorLog.txt with the following message: *Error Time: 09/05/2018 12:42:16* *Error using load* *Unable to read file 'mc/prefiltered_func_data_mcf.par': no such file or directory.* As mentioned I only notice this error on a few participants whereas for others hcp_fix_multi_run completes without issue. Is this an error that is well known? I am inclined to think that this may be a memory issue. -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) On Tue, Aug 21, 2018 at 6:47 PM, Glasser, Matthew wrote: > Sorry that is actually a FSL bug that I have already reported to them. > > You can work around it with (/bin/sh -c '. /usr/local/fsl/etc/fslconf/fsl.sh; > fslmaths filtered_func_data -sub filtered_func_data -add > filtered_func_data_clean filtered_func_data_clean’) > > Matt. > > From: Timothy Hendrickson > Date: Tuesday, August 21, 2018 at 6:36 PM > To: Matt Glasser > > Subject: Re: [HCP-Users] FSL FIX no memory with hcp_fix_multi_run > > Hmm, interesting. The total swap space that is available is approximately > 130GB whereas the total amount of RAM is just as much, that would seem to > me to be plenty enough. > > What other suggestions do you have? > > How important is the FSL call (/bin/sh -c '. > /usr/local/fsl/etc/fslconf/fsl.sh; > fslcpgeom filtered_func_data filtered_func_data_clean') ? Even though the > command does not complete I can still open it with fsleyes and fslinfo > without issue. From my brief research into fslutils fslcpgeom copies header > information. > > Can I perhaps comment out that command so the cleaned dtseries file can be > generated (the following lines of code)? > > -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) > > On Tue, Aug 21, 2018 at 4:36 PM, Glasser, Matthew > wrote: > >> You might need to configure swap space or increase the amount. >> >> Matt. >> >> From: Timothy Hendrickson >> Date: Tuesday, August 21, 2018 at 1:54 PM >> >> To: Timothy Coalson >> Cc: Matt Glasser , "hcp-users@humanconnectome.org" < >> HCP-Users@humanconnectome.org> >> Subject: Re: [HCP-Users] FSL FIX no memory with hcp_fix_multi_run >> >> Okay I have gotten past the previous issue with read_avg, however, I am >> experiencing a new error. >> >> See below: >> >> Error using call_fsl (line 36) >> FSL call (/bin/sh -c '. /usr/local/fsl/etc/fslconf/fsl.sh; fslcpgeom >> filtered_func_data filtered_func_data_clean') failed, Unable to allocate >> memory for copy: Cannot allocate memory >> >> Error in fix_3_clean (line 112) >> >> On Fri, Aug 17, 2018 at 4:53 PM, Timothy Coalson wrote: >> >>> In other words, if you have matlab installed, set the matlab mode to 1 >>> (in settings.sh). If not, you will need the compiled matlab to be up to >>> date with the matlab scripts, and use mode 0. >>> >>> The alternative, figuring out how to build octave to handle larger >>> matrices, sounds like an adventure. >>> >>> Tim >>> >>> >>> On Fri, Aug 17, 2018 at 4:50 PM, Timothy Coalson wrote: >>> >>>> It looks like default builds of octave have an unfortunate limit to the >>>> possible number of elements in any matrix: >>>> >>>> octave:1> test=zeros(6); >>>> error: out of memory or dimension too large for Octave's index type >>>> >>>> The limit appears to be 2 billion elements total (signed 32-bit). >>>> >>>> Tim >>>> >>>> >>>> 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, 2018 at 4:39 PM >>>>> To: Timothy Coalson >>>>> Cc: Matt Glasser , "hcp-users@humanconnectome.org" >>>>> >>>>> Subject: Re: [HCP-Users] FSL FIX no memory with hcp_fix_multi_run >>>>> >>>>> It i
[HCP-Users] Resting State Stats Following hcp_fix_multi_run and MSMAll
Hello, I am working on Resting State Stats following hcp_fix_multi_run and MSMAll. My call to run_RestingStateStats.sh initially failed because it was attempting to point to .fix within the resting state scan directory rather than the hcp_fix_multi_run concatenated directory. Once I changed this it seemed to run, however, I received an error within the .matlab.log *RestingStateStats - Finished fslmaths filtering of motion confounds* *Error using ** *Inner matrix dimensions must agree.* *Error in RestingStateStats (line 232)* *MATLAB:innerdim* This told me that I should change the Movement Regressor path from the resting state scan to the hcp_fix_mult_run concatenation. Here is the full call, I just want to make sure I am providing the correct inputs: */opt/HCP-Pipelines/RestingStateStats/Compiled_RestingStateStats/distrib/run_RestingStateStats.sh /usr/local/R2013a/v81 '/output_dir/sub-7397/ses-51327/MNINonLinear/Results/multiICAFIX/Movement_Regressors_demean' 2000 0.80 '/output_dir/sub-7397/ses-51327/MNINonLinear/Results/multiICAFIX/multiICAFIX_hp2000.ica/filtered_func_data.ica/melodic_mix' '/output_dir/sub-7397/ses-51327/MNINonLinear/Results/multiICAFIX/multiICAFIX_hp2000.ica/.fix' '/opt/workbench/bin_rh_linux64/wb_command' '/output_dir/sub-7397/ses-51327/MNINonLinear/Results/sub-7397_ses-51327_task-rest_run-01_bold/sub-7397_ses-51327_task-rest_run-01_bold_Atlas' '/output_dir/sub-7397/ses-51327/MNINonLinear/Results/sub-7397_ses-51327_task-rest_run-01_bold/sub-7397_ses-51327_task-rest_run-01_bold_Atlas_BiasField.dscalar.nii' '/output_dir/sub-7397/ses-51327/MNINonLinear/Results/sub-7397_ses-51327_task-rest_run-01_bold/RestingStateStats/sub-7397_ses-51327_task-rest_run-01_bold_Atlas' '/360CortSurf_19Vol_parcel.dlabel.nii' 'REVERT' 'stats' 'NONE' 'NONE' >> /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 Institute University of Minnesota Bioinformatics M.S. Candidate Office: 612-624-0783 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] FSL FIX no memory with hcp_fix_multi_run
Okay I have gotten past the previous issue with read_avg, however, I am experiencing a new error. See below: Error using call_fsl (line 36) FSL call (/bin/sh -c '. /usr/local/fsl/etc/fslconf/fsl.sh; fslcpgeom filtered_func_data filtered_func_data_clean') failed, Unable to allocate memory for copy: Cannot allocate memory Error in fix_3_clean (line 112) On Fri, Aug 17, 2018 at 4:53 PM, Timothy Coalson wrote: > In other words, if you have matlab installed, set the matlab mode to 1 (in > settings.sh). If not, you will need the compiled matlab to be up to date > with the matlab scripts, and use mode 0. > > The alternative, figuring out how to build octave to handle larger > matrices, sounds like an adventure. > > Tim > > > On Fri, Aug 17, 2018 at 4:50 PM, Timothy Coalson wrote: > >> It looks like default builds of octave have an unfortunate limit to the >> possible number of elements in any matrix: >> >> octave:1> test=zeros(6); >> error: out of memory or dimension too large for Octave's index type >> >> The limit appears to be 2 billion elements total (signed 32-bit). >> >> Tim >> >> >> 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, 2018 at 4:39 PM >>> To: Timothy Coalson >>> Cc: Matt Glasser , "hcp-users@humanconnectome.org" < >>> HCP-Users@humanconnectome.org> >>> Subject: 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: 507-259-3434 (texts okay) >>> >>> On Fri, Aug 17, 2018 at 4:32 PM, Timothy Coalson wrote: >>> >>>> How much memory does the machine you are running this on have? What is >>>> the number of timepoints and number of voxels of your concatenated input? >>>> Are you trying to run more than one subject at once on the machine? >>>> >>>> I believe the way we are approaching multi-run fix is that we only >>>> concatenate scans that were taken on the same day. >>>> >>>> Tim >>>> >>>> >>>> On Fri, Aug 17, 2018 at 4:24 PM, Timothy Hendrickson >>>> wrote: >>>> >>>>> 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 of Minnesota >>>>> Bioinformatics M.S. Candidate >>>>> Office: 612-624-0783 >>>>> Mobile: 507-259-3434 (texts okay) >>>>> >>>>> On Fri, Aug 17, 2018 at 2:04 PM, Glasser, Matthew >>>>> wrote: >>>>> >>>>>> I have attached an updated version of read_avw_img.m that forces >>>>>> matlab to retain the same precision as the input file rather than >>>>>> converting everything to doubles. >>>>>> >>>>>> Matt. >>>>>> >>>>>> From: on behalf of Timothy >>>>>> Hendrickson >>>>>> Date: Friday, August 17, 2018 at 1:58 PM >>>>>> To: "hcp-users@humanconnectome.org" >>>>>> Subject: [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 secon
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 Bioinformatics M.S. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay) 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, 2018 at 4:39 PM > To: Timothy Coalson > Cc: Matt Glasser , "hcp-users@humanconnectome.org" < > HCP-Users@humanconnectome.org> > Subject: 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: 507-259-3434 (texts okay) > > On Fri, Aug 17, 2018 at 4:32 PM, Timothy Coalson wrote: > >> How much memory does the machine you are running this on have? What is >> the number of timepoints and number of voxels of your concatenated input? >> Are you trying to run more than one subject at once on the machine? >> >> I believe the way we are approaching multi-run fix is that we only >> concatenate scans that were taken on the same day. >> >> Tim >> >> >> On Fri, Aug 17, 2018 at 4:24 PM, Timothy Hendrickson >> wrote: >> >>> 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 of Minnesota >>> Bioinformatics M.S. Candidate >>> Office: 612-624-0783 >>> Mobile: 507-259-3434 (texts okay) >>> >>> On Fri, Aug 17, 2018 at 2:04 PM, Glasser, Matthew >>> wrote: >>> >>>> I have attached an updated version of read_avw_img.m that forces matlab >>>> to retain the same precision as the input file rather than converting >>>> everything to doubles. >>>> >>>> Matt. >>>> >>>> From: on behalf of Timothy >>>> Hendrickson >>>> Date: Friday, August 17, 2018 at 1:58 PM >>>> To: "hcp-users@humanconnectome.org" >>>> Subject: [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 of memory. Type HELP MEMORY for your options.* >>>> >>>> *Error in read_avw_img (line 24)* >>>> >>>> >>>> >>>> *Error in read_avw (line 34)* >>>> >>>> >>>> >>>> *Error in fix_3_clean (line 63)* >>>> >>>> >>>> >>>> *MATLAB:nomem* >>>> >>>> >>>> How much memory does MATLAB require for this, and is there a way to >>>> change this via an argument? >>>> >>>> -Tim >>>> >>>> ___ >>>> HCP-Users mailing list >>>> HCP-Users@humanconnectome.org >>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>> >>>> >>>> -- >>>> >>>> The materials in this message are private and may contain Protected >>>> Healthcare Information or other information of a sensitive nature. If you >>>> are not the intended recipient, be advised that any unauthorized use, >>>> disclosure, copying or the taking of any action in reliance on the contents >>>> of this information is strictly prohibited. If you have received this email >>>> in error, please immediately notify the sender via telephone or return >>>> mail. >>>> >>> >>> ___ >>> HCP-Users mailing list >>> HCP-Users@humanconnectome.org >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> >> >> > > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
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: 507-259-3434 (texts okay) On Fri, Aug 17, 2018 at 4:32 PM, Timothy Coalson wrote: > How much memory does the machine you are running this on have? What is > the number of timepoints and number of voxels of your concatenated input? > Are you trying to run more than one subject at once on the machine? > > I believe the way we are approaching multi-run fix is that we only > concatenate scans that were taken on the same day. > > Tim > > > On Fri, Aug 17, 2018 at 4:24 PM, Timothy Hendrickson > wrote: > >> 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 of Minnesota >> Bioinformatics M.S. Candidate >> Office: 612-624-0783 >> Mobile: 507-259-3434 (texts okay) >> >> On Fri, Aug 17, 2018 at 2:04 PM, Glasser, Matthew >> wrote: >> >>> I have attached an updated version of read_avw_img.m that forces matlab >>> to retain the same precision as the input file rather than converting >>> everything to doubles. >>> >>> Matt. >>> >>> From: on behalf of Timothy >>> Hendrickson >>> Date: Friday, August 17, 2018 at 1:58 PM >>> To: "hcp-users@humanconnectome.org" >>> Subject: [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 of memory. Type HELP MEMORY for your options.* >>> >>> *Error in read_avw_img (line 24)* >>> >>> >>> >>> *Error in read_avw (line 34)* >>> >>> >>> >>> *Error in fix_3_clean (line 63)* >>> >>> >>> >>> *MATLAB:nomem* >>> >>> >>> How much memory does MATLAB require for this, and is there a way to >>> change this via an argument? >>> >>> -Tim >>> >>> ___ >>> HCP-Users mailing list >>> HCP-Users@humanconnectome.org >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> >>> >>> -- >>> >>> The materials in this message are private and may contain Protected >>> Healthcare Information or other information of a sensitive nature. If you >>> are not the intended recipient, be advised that any unauthorized use, >>> disclosure, copying or the taking of any action in reliance on the contents >>> of this information is strictly prohibited. If you have received this email >>> in error, please immediately notify the sender via telephone or return mail. >>> >> >> ___ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
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 of Minnesota Bioinformatics M.S. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay) On Fri, Aug 17, 2018 at 2:04 PM, Glasser, Matthew wrote: > I have attached an updated version of read_avw_img.m that forces matlab to > retain the same precision as the input file rather than converting > everything to doubles. > > Matt. > > From: on behalf of Timothy > Hendrickson > Date: Friday, August 17, 2018 at 1:58 PM > To: "hcp-users@humanconnectome.org" > Subject: [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 of memory. Type HELP MEMORY for your options.* > > *Error in read_avw_img (line 24)* > > > > *Error in read_avw (line 34)* > > > > *Error in fix_3_clean (line 63)* > > > > *MATLAB:nomem* > > > How much memory does MATLAB require for this, and is there a way to change > this via an argument? > > -Tim > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[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 of memory. Type HELP MEMORY for your options.* *Error in read_avw_img (line 24)* *Error in read_avw (line 34)* *Error in fix_3_clean (line 63)* *MATLAB:nomem* How much memory does MATLAB require for this, and is there a way to change this via an argument? -Tim ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] MSMAll
I noticed on the FSL FIX FAQ page the following: Can I use FIX to clean task fMRI data? - Yes, although you will probably need to create a study-specific training dataset Can you speak to how multi run ICA+FIX gets away without needing a study-specific training dataset? -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) On Tue, Jul 24, 2018 at 3:28 PM, Timothy Hendrickson wrote: > 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, Jul 24, 2018 at 3:21 PM, Glasser, Matthew > wrote: > >> The MR+FIX pipeline automatically breaks the runs back up at the end. >> >> Matt. >> >> From: Timothy Hendrickson >> Date: Tuesday, July 24, 2018 at 3:17 PM >> >> To: Matt Glasser >> Cc: "hcp-users@humanconnectome.org" >> Subject: 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 >> Bioinformatics M.S. Candidate >> Office: 612-624-0783 >> Mobile: 507-259-3434 (texts okay) >> >> On Mon, Jul 23, 2018 at 1:31 PM, Glasser, Matthew >> wrote: >> >>> Give it a try, but you may find that you need to split it into two. >>> Make sure you are using the latest released FSL for this. >>> >>> Matt. >>> >>> From: Timothy Hendrickson >>> Date: Monday, July 23, 2018 at 1:26 PM >>> >>> To: Matt Glasser >>> Cc: "hcp-users@humanconnectome.org" >>> Subject: 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 >>> Mobile: 507-259-3434 (texts okay) >>> >>> On Mon, Jul 23, 2018 at 1:12 PM, Glasser, Matthew >>> wrote: >>> >>>> FSL 6.0 hasn’t been released but has some updates to the math library >>>> that makes melodic much faster. Also if you make too large of a merged >>>> file it will crash the old melodic because of some bugs. How many frames >>>> are you wanting to do? >>>> >>>> Peace, >>>> >>>> Matt. >>>> >>>> From: Timothy Hendrickson >>>> Date: Monday, July 23, 2018 at 1:02 PM >>>> To: Matt Glasser >>>> Cc: "hcp-users@humanconnectome.org" >>>> Subject: Re: [HCP-Users] MSMAll >>>> >>>> Thanks Matt. >>>> >>>> With the hcp_fix_multi_run script I notice that in the first few lines >>>> of code there is a line with software requirements which include FIX >= >>>> 1.065 and FSL 6.0 melodic version. I have FIX version = 1.066 and I have >>>> FSL 5.0.9 and melodic version 3.14. Without the FSL 6.0 release 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. Candidate >>>> Office: 612-624-0783 >>>> Mobile: 507-259-3434 (texts okay) >>>> >>>> On Thu, Jul 19, 2018 at 6:26 PM, Glasser, Matthew >>>> wrote: >>>> >>>>> There is a new Multi-run FIX pipeline currently available in the Git >>>>> repository that you can use. I would consider it beta a this time. >>>>> >>>>> Matt. >>>>> >>>>> From: on behalf of Timothy >>>>> Hendrickson >&g
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, Jul 24, 2018 at 3:21 PM, Glasser, Matthew wrote: > The MR+FIX pipeline automatically breaks the runs back up at the end. > > Matt. > > From: Timothy Hendrickson > Date: Tuesday, July 24, 2018 at 3:17 PM > > To: Matt Glasser > Cc: "hcp-users@humanconnectome.org" > Subject: 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 > Bioinformatics M.S. Candidate > Office: 612-624-0783 > Mobile: 507-259-3434 (texts okay) > > On Mon, Jul 23, 2018 at 1:31 PM, Glasser, Matthew > wrote: > >> Give it a try, but you may find that you need to split it into two. Make >> sure you are using the latest released FSL for this. >> >> Matt. >> >> From: Timothy Hendrickson >> Date: Monday, July 23, 2018 at 1:26 PM >> >> To: Matt Glasser >> Cc: "hcp-users@humanconnectome.org" >> Subject: 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 >> Mobile: 507-259-3434 (texts okay) >> >> On Mon, Jul 23, 2018 at 1:12 PM, Glasser, Matthew >> wrote: >> >>> FSL 6.0 hasn’t been released but has some updates to the math library >>> that makes melodic much faster. Also if you make too large of a merged >>> file it will crash the old melodic because of some bugs. How many frames >>> are you wanting to do? >>> >>> Peace, >>> >>> Matt. >>> >>> From: Timothy Hendrickson >>> Date: Monday, July 23, 2018 at 1:02 PM >>> To: Matt Glasser >>> Cc: "hcp-users@humanconnectome.org" >>> Subject: Re: [HCP-Users] MSMAll >>> >>> Thanks Matt. >>> >>> With the hcp_fix_multi_run script I notice that in the first few lines >>> of code there is a line with software requirements which include FIX >= >>> 1.065 and FSL 6.0 melodic version. I have FIX version = 1.066 and I have >>> FSL 5.0.9 and melodic version 3.14. Without the FSL 6.0 release 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. Candidate >>> Office: 612-624-0783 >>> Mobile: 507-259-3434 (texts okay) >>> >>> On Thu, Jul 19, 2018 at 6:26 PM, Glasser, Matthew >>> wrote: >>> >>>> There is a new Multi-run FIX pipeline currently available in the Git >>>> repository that you can use. I would consider it beta a this time. >>>> >>>> Matt. >>>> >>>> From: on behalf of Timothy >>>> Hendrickson >>>> Date: Thursday, July 19, 2018 at 6:24 PM >>>> To: "hcp-users@humanconnectome.org" >>>> Subject: [HCP-Users] MSMAll >>>> >>>> Hello, >>>> >>>> From the HCP course material I noticed that that suggested format to >>>> use MSMAll is to do so immediately after the Minimal Pre-Processing stream >>>> and immediately before subsequent tfMRI and rfMRI processing. As MSMAll >>>> expects the data inputted to be run through ICA-FIX I am curious what 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 >>>> Univers
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 Bioinformatics M.S. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay) On Mon, Jul 23, 2018 at 1:31 PM, Glasser, Matthew wrote: > Give it a try, but you may find that you need to split it into two. Make > sure you are using the latest released FSL for this. > > Matt. > > From: Timothy Hendrickson > Date: Monday, July 23, 2018 at 1:26 PM > > To: Matt Glasser > Cc: "hcp-users@humanconnectome.org" > Subject: 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 > Mobile: 507-259-3434 (texts okay) > > On Mon, Jul 23, 2018 at 1:12 PM, Glasser, Matthew > wrote: > >> FSL 6.0 hasn’t been released but has some updates to the math library >> that makes melodic much faster. Also if you make too large of a merged >> file it will crash the old melodic because of some bugs. How many frames >> are you wanting to do? >> >> Peace, >> >> Matt. >> >> From: Timothy Hendrickson >> Date: Monday, July 23, 2018 at 1:02 PM >> To: Matt Glasser >> Cc: "hcp-users@humanconnectome.org" >> Subject: Re: [HCP-Users] MSMAll >> >> Thanks Matt. >> >> With the hcp_fix_multi_run script I notice that in the first few lines of >> code there is a line with software requirements which include FIX >= 1.065 >> and FSL 6.0 melodic version. I have FIX version = 1.066 and I have FSL >> 5.0.9 and melodic version 3.14. Without the FSL 6.0 release 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. Candidate >> Office: 612-624-0783 >> Mobile: 507-259-3434 (texts okay) >> >> On Thu, Jul 19, 2018 at 6:26 PM, Glasser, Matthew >> wrote: >> >>> There is a new Multi-run FIX pipeline currently available in the Git >>> repository that you can use. I would consider it beta a this time. >>> >>> Matt. >>> >>> From: on behalf of Timothy >>> Hendrickson >>> Date: Thursday, July 19, 2018 at 6:24 PM >>> To: "hcp-users@humanconnectome.org" >>> Subject: [HCP-Users] MSMAll >>> >>> Hello, >>> >>> From the HCP course material I noticed that that suggested format to use >>> MSMAll is to do so immediately after the Minimal Pre-Processing stream and >>> immediately before subsequent tfMRI and rfMRI processing. As MSMAll expects >>> the data inputted to be run through ICA-FIX I am curious what 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 M.S. Candidate >>> Office: 612-624-0783 >>> Mobile: 507-259-3434 (texts okay) >>> >>> ___ >>> HCP-Users mailing list >>> HCP-Users@humanconnectome.org >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> >>> >>> -- >>> >>> The materials in this message are private and may contain Protected >>> Healthcare Information or other information of a sensitive nature. If you >>> are not the intended recipient, be advised that any unauthorized use, >>> disclosure, copying or the taking of any action in reliance on the contents >>> of this information is strictly prohibited. If you have received this email >>> in error, please immediately notify the sender via telephone or return mail. >>> >> >> >> -- >> >> The materials i
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 Mobile: 507-259-3434 (texts okay) On Mon, Jul 23, 2018 at 1:12 PM, Glasser, Matthew wrote: > FSL 6.0 hasn’t been released but has some updates to the math library that > makes melodic much faster. Also if you make too large of a merged file it > will crash the old melodic because of some bugs. How many frames are you > wanting to do? > > Peace, > > Matt. > > From: Timothy Hendrickson > Date: Monday, July 23, 2018 at 1:02 PM > To: Matt Glasser > Cc: "hcp-users@humanconnectome.org" > Subject: Re: [HCP-Users] MSMAll > > Thanks Matt. > > With the hcp_fix_multi_run script I notice that in the first few lines of > code there is a line with software requirements which include FIX >= 1.065 > and FSL 6.0 melodic version. I have FIX version = 1.066 and I have FSL > 5.0.9 and melodic version 3.14. Without the FSL 6.0 release 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. Candidate > Office: 612-624-0783 > Mobile: 507-259-3434 (texts okay) > > On Thu, Jul 19, 2018 at 6:26 PM, Glasser, Matthew > wrote: > >> There is a new Multi-run FIX pipeline currently available in the Git >> repository that you can use. I would consider it beta a this time. >> >> Matt. >> >> From: on behalf of Timothy >> Hendrickson >> Date: Thursday, July 19, 2018 at 6:24 PM >> To: "hcp-users@humanconnectome.org" >> Subject: [HCP-Users] MSMAll >> >> Hello, >> >> From the HCP course material I noticed that that suggested format to use >> MSMAll is to do so immediately after the Minimal Pre-Processing stream and >> immediately before subsequent tfMRI and rfMRI processing. As MSMAll expects >> the data inputted to be run through ICA-FIX I am curious what 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 M.S. Candidate >> Office: 612-624-0783 >> Mobile: 507-259-3434 (texts okay) >> >> ___ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> >> -- >> >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. If you >> are not the intended recipient, be advised that any unauthorized use, >> disclosure, copying or the taking of any action in reliance on the contents >> of this information is strictly prohibited. If you have received this email >> in error, please immediately notify the sender via telephone or return mail. >> > > > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] MSMAll
Thanks Matt. With the hcp_fix_multi_run script I notice that in the first few lines of code there is a line with software requirements which include FIX >= 1.065 and FSL 6.0 melodic version. I have FIX version = 1.066 and I have FSL 5.0.9 and melodic version 3.14. Without the FSL 6.0 release 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. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay) On Thu, Jul 19, 2018 at 6:26 PM, Glasser, Matthew wrote: > There is a new Multi-run FIX pipeline currently available in the Git > repository that you can use. I would consider it beta a this time. > > Matt. > > From: on behalf of Timothy > Hendrickson > Date: Thursday, July 19, 2018 at 6:24 PM > To: "hcp-users@humanconnectome.org" > Subject: [HCP-Users] MSMAll > > Hello, > > From the HCP course material I noticed that that suggested format to use > MSMAll is to do so immediately after the Minimal Pre-Processing stream and > immediately before subsequent tfMRI and rfMRI processing. As MSMAll expects > the data inputted to be run through ICA-FIX I am curious what 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 M.S. Candidate > Office: 612-624-0783 > Mobile: 507-259-3434 (texts okay) > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] MSMAll
Hello, >From the HCP course material I noticed that that suggested format to use MSMAll is to do so immediately after the Minimal Pre-Processing stream and immediately before subsequent tfMRI and rfMRI processing. As MSMAll expects the data inputted to be run through ICA-FIX I am curious what 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 M.S. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay) ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Core Dump ${MSMBINDIR}/msm
Hello,
When I run msm within MSMAll I get a core dump because the* --inmesh file
could not be found:
${NativeFolder}/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii*. I see
that the file is generated within the PostFreeSurfer pipeline if the
MSMSulc registration is specified. I've already run 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
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S. Candidate
Office: 612-624-0783
Mobile: 507-259-3434 (texts okay)
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
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Re: [HCP-Users] Resting State processing
Hi Matthew, The file does not exist. I see now that the PostFreeSurfer pipeline I have locally is different than the latest version found on github (specifically *FreeSurfer2CaretConvertAndRegisterNonlinear.sh). *I see that the line referencing *allparameterssulcDRconf *has been commented out in favor of *MSMSulcStrainFinalconf*, however, this file does not appear to exist either. Which version of MSM HOCR is the most recent that should be used? I am using version 2) On a completely other note why aren't these configuration files already included in the HCP pipelines? It seems very 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: 507-259-3434 (texts okay) On Mon, Jan 8, 2018 at 7:16 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > Does the file exist? That might be the old config file it is looking for > suggesting that you don’t have the latest master. > > Peace, > > Matt. > > From: Timothy Hendrickson <hendr...@umn.edu> > Date: Monday, January 8, 2018 at 9:15 AM > To: "hcp-users@humanconnectome.org" <HCP-Users@humanconnectome.org> > Cc: Matt Glasser <glass...@wustl.edu> > Subject: Re: [HCP-Users] Resting State processing > > Hello all, > > Despite having the most recent version of the hcp pipeline (3.22) and > downloading the MSM configuration binaries, however, I am still receiving > an error when I attempt to run the PreFreeSurfer pipeline with > RegName="MSMSulc". This is the error message I receive: > */opt/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 <(612)%20624-6441> > Mobile: 507-259-3434 <(507)%20259-3434> (texts okay) > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Resting State processing
Hello all, Despite having the most recent version of the hcp pipeline (3.22) and downloading the MSM configuration binaries, however, I am still receiving an error when I attempt to run the PreFreeSurfer pipeline with RegName="MSMSulc". This is the error message I receive: */opt/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 (texts okay) ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[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 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://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Creating Custom dlabel File
HCP users, I would like to create a custom dlabel file with particular ROIs from the Glasser 360 surface atlas. Here is what I have done so far: 1) First I separated individual ROIs into their dscalar files with wb_command -cifti-label-to-roi 2) I can easily visualize all dscalar files within wb_view Now I am stuck trying to take the individual ROI dscalar files and create one dlabel file which merges all ROI dscalar files together. I've tried several different commands including -cifti-create-dense, -cifti-create-dense-from-template, -cifti-create-label without luck. If anyone could 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-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] fMRISurface Pipeline FinalfMRIResolution Variable
HCP users, I did some searching on the list and could not find an answer to my question, I apologize if I missed it. I am attempting to use the HCP preprocessing pipelines to processing resting state data which was acquired with a lower resolution than HCP. I notice that the FinalfMRIResolution 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 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://lists.humanconnectome.org/mailman/listinfo/hcp-users
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, Harms, Michael <mha...@wustl.edu> wrote: > > Which version of FSL are you using? I believe that the > *eddy_unwarped_images.eddy_rotated_bvecs *file will be created by the > version of ‘eddy’ that comes with the newest FSL (5.0.10), but if you are > using FSL 5.0.9, you needed to install the “eddy patch” to get that > functionality. > > cheers, > -MH > > -- > Michael Harms, Ph.D. > --- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 <(314)%20747-6173> > St. Louis, MO 63110 Email: mha...@wustl.edu > > From: <hcp-users-boun...@humanconnectome.org> on behalf of Timothy > Hendrickson <hendr...@umn.edu> > Date: Thursday, July 6, 2017 at 3:24 PM > To: "hcp-users@humanconnectome.org" <HCP-Users@humanconnectome.org> > Subject: [HCP-Users] Diffusion Preprocessing Error/Bug > > Hello, > > I am having trouble running the diffusion preprocessing. Once the > processing gets to eddy_postproc.sh I get the following error: *awk: cmd. > line:1: fatal: cannot open file > `/home/lnpi15-raid3/cgilmore-data-lnpi15/272_CENC/49769/Diffusion/eddy/eddy_unwarped_images.eddy_rotated_bvecs*. > The error is pretty straightforward, but I cannot figure out why the > diffusion preprocessing scripts are not generating the > *eddy_unwarped_images.eddy_rotated_bvecs > *file. I notice that there is a file named > *eddy_unwarped_images.eddy_parameters*. Is this similar to the rotated > bvec file? > > Thanks! > > -Tim > > Timothy Hendrickson > Department of Psychiatry > University of Minnesota > Bioinformatics and Computational Biology M.S. Candidate > Office: 612-624-6441 <(612)%20624-6441> > Mobile: 507-259-3434 <(507)%20259-3434> (texts okay) > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Diffusion Preprocessing Error/Bug
Hello, I am having trouble running the diffusion preprocessing. Once the processing gets to eddy_postproc.sh I get the following error: *awk: cmd. line:1: fatal: cannot open file `/home/lnpi15-raid3/cgilmore-data-lnpi15/272_CENC/49769/Diffusion/eddy/eddy_unwarped_images.eddy_rotated_bvecs*. The error is pretty straightforward, but I cannot figure out why the diffusion preprocessing scripts are not generating the *eddy_unwarped_images.eddy_rotated_bvecs *file. I notice that there is a file named *eddy_unwarped_images.eddy_parameters*. Is this similar to the rotated bvec file? Thanks! -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-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
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 <glass...@wustl.edu> wrote: > They should be identical. > > Peace, > > Matt. > > From: <hcp-users-boun...@humanconnectome.org> on behalf of Timothy > Hendrickson <hendr...@umn.edu> > Date: Wednesday, June 7, 2017 at 9:51 AM > To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: [HCP-Users] Similarity between thickness dscalar files and > freesurfer 5.3 thickness files > > Hello, > > I am curious how similar thickness dscalar files and freesurfer 5.3 > thickness files are. I know that the thickness dscalar files are of course > a by product of the PreFreeSurfer, FreeSurfer, and PostFreeSurfer > pipelines, but what I am unsure about is whether I should expect the > thickness files found within the FreeSurfer directory would be different > than the dscalar files. > > Any help would be much appreciated! > > -Tim > > Timothy Hendrickson > Department of Psychiatry > University of Minnesota > Bioinformatics and Computational Biology M.S. Candidate > Office: 612-624-6441 <(612)%20624-6441> > Mobile: 507-259-3434 <(507)%20259-3434> (texts okay) > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[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) ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
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 for those pipelines. For the structural > pipelines you cannot rerun FreeSurfer after running PostFreeSurfer. > > Matt. > > From: Timothy Hendrickson <hendr...@umn.edu> > Date: Tuesday, February 21, 2017 at 4:26 PM > To: Matt Glasser <glass...@wustl.edu> > Cc: "Harms, Michael" <mha...@wustl.edu>, "hcp-users@humanconnectome.org" < > hcp-users@humanconnectome.org> > > Subject: Re: [HCP-Users] Variation in HCP Minimal Preprocessing Pipeline > Differences Across Releases > > Darn. Alright I will reprocess the fMRI and DTI data. It sounds like the > structural pipeline has not been changed so I would not have to reprocess > that right? > > I am curious are the pipelines associated with the fMRI and DTI data smart > enough to overwrite data files or do I have to totally delete files and > start over? > > -Tim > > Timothy Hendrickson > Department of Psychiatry > University of Minnesota > Office: 612-624-6441 <(612)%20624-6441> > Mobile: 507-259-3434 <(507)%20259-3434> (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 important changes for >> fMRIVolume (change in the way bias field correction is done) and >> potentially also some changes in the diffusion pipeline. While it would >> probably work fine, I would recommend rerunning if it isn’t too painful. >> >> Peace, >> >> Matt. >> >> From: <hcp-users-boun...@humanconnectome.org> on behalf of Timothy >> Hendrickson <hendr...@umn.edu> >> Date: Tuesday, February 21, 2017 at 11:07 AM >> To: "Harms, Michael" <mha...@wustl.edu> >> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >> Subject: Re: [HCP-Users] Variation in HCP Minimal Preprocessing Pipeline >> Differences Across Releases >> >> I can see that several changes/additions have been made to 3.21, but I >> asked whether there is a difference in *just* the minimal preprocessing >> pipelines (i.e. PreFreeSurfer, FreeSurfer, PostFreeSurfer, fMRIVolume, >> fMRISurface, and Diffusion) between 3.4.0 and 3.21. >> >> I can ask this a different way, do MSMAll, DeDriftAndResample, PostFix, >> RestingStateStats, ICAFIX, and TaskfMRIAnalysis scripts rely specifically >> on data preprocessed from a particular version? My impression was that >> perhaps MSMAll, DeDriftAndResample, PostFix, RestingStateStats, ICAFIX, and >> TaskfMRIAnalysis act on top of minimally preprocessed data. Is this wrong? >> >> -Tim >> >> Timothy Hendrickson >> Department of Psychiatry >> University of Minnesota >> Office: 612-624-6441 <(612)%20624-6441> >> Mobile: 507-259-3434 <(507)%20259-3434> (texts okay) >> >> On Tue, Feb 21, 2017 at 10:59 AM, Harms, Michael <mha...@wustl.edu> >> wrote: >> >>> >>> There have been a lot of changes/additions from 3.4.0 to 3.21. If you >>> are starting a new study, it would be preferable for you to start with the >>> latest version. >>> >>> cheers, >>> -MH >>> >>> -- >>> Michael Harms, Ph.D. >>> --- >>> Conte Center for the Neuroscience of Mental Disorders >>> Washington University School of Medicine >>> Department of Psychiatry, Box 8134 >>> 660 South Euclid Ave.Tel: 314-747-6173 <(314)%20747-6173> >>> St. Louis, MO 63110Email: mha...@wustl.edu >>> >>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Timothy >>> Hendrickson <hendr...@umn.edu> >>> Date: Tuesday, February 21, 2017 at 9:38 AM >>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >>> Subject: [HCP-Users] Variation in HCP Minimal Preprocessing Pipeline >>> Differences Across Releases >>> >>> Hello, >>> >>> I have been using version 3.4.0 of the HCP Minimal Preprocessing >>> Pipeline to process my HCP compatible data. >>> I've used 3.4.0 to run the structural (PreFreeSurfer, FreeSurfer, >>> PostFreeSurfer), fMRI (fMRIVolume, and fMRISurface), and diffusion >>> sub-pipelines. I have now downloaded
Re: [HCP-Users] Variation in HCP Minimal Preprocessing Pipeline Differences Across Releases
Darn. Alright I will reprocess the fMRI and DTI data. It sounds like the structural pipeline has not been changed so I would not have to reprocess that right? I am curious are the pipelines associated with the fMRI and DTI data smart enough to overwrite data files or do I have to totally delete 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 important changes for fMRIVolume > (change in the way bias field correction is done) and potentially also some > changes in the diffusion pipeline. While it would probably work fine, I > would recommend rerunning if it isn’t too painful. > > Peace, > > Matt. > > From: <hcp-users-boun...@humanconnectome.org> on behalf of Timothy > Hendrickson <hendr...@umn.edu> > Date: Tuesday, February 21, 2017 at 11:07 AM > To: "Harms, Michael" <mha...@wustl.edu> > Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] Variation in HCP Minimal Preprocessing Pipeline > Differences Across Releases > > I can see that several changes/additions have been made to 3.21, but I > asked whether there is a difference in *just* the minimal preprocessing > pipelines (i.e. PreFreeSurfer, FreeSurfer, PostFreeSurfer, fMRIVolume, > fMRISurface, and Diffusion) between 3.4.0 and 3.21. > > I can ask this a different way, do MSMAll, DeDriftAndResample, PostFix, > RestingStateStats, ICAFIX, and TaskfMRIAnalysis scripts rely specifically > on data preprocessed from a particular version? My impression was that > perhaps MSMAll, DeDriftAndResample, PostFix, RestingStateStats, ICAFIX, and > TaskfMRIAnalysis act on top of minimally preprocessed data. Is this wrong? > > -Tim > > Timothy Hendrickson > Department of Psychiatry > University of Minnesota > Office: 612-624-6441 <(612)%20624-6441> > Mobile: 507-259-3434 <(507)%20259-3434> (texts okay) > > On Tue, Feb 21, 2017 at 10:59 AM, Harms, Michael <mha...@wustl.edu> wrote: > >> >> There have been a lot of changes/additions from 3.4.0 to 3.21. If you >> are starting a new study, it would be preferable for you to start with the >> latest version. >> >> cheers, >> -MH >> >> -- >> Michael Harms, Ph.D. >> --- >> Conte Center for the Neuroscience of Mental Disorders >> Washington University School of Medicine >> Department of Psychiatry, Box 8134 >> 660 South Euclid Ave.Tel: 314-747-6173 <(314)%20747-6173> >> St. Louis, MO 63110Email: mha...@wustl.edu >> >> From: <hcp-users-boun...@humanconnectome.org> on behalf of Timothy >> Hendrickson <hendr...@umn.edu> >> Date: Tuesday, February 21, 2017 at 9:38 AM >> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >> Subject: [HCP-Users] Variation in HCP Minimal Preprocessing Pipeline >> Differences Across Releases >> >> Hello, >> >> I have been using version 3.4.0 of the HCP Minimal Preprocessing Pipeline >> to process my HCP compatible data. >> I've used 3.4.0 to run the structural (PreFreeSurfer, FreeSurfer, >> PostFreeSurfer), fMRI (fMRIVolume, and fMRISurface), and diffusion >> sub-pipelines. I have now downloaded version 3.21 and notice several >> additional sub-pipelines such as MSMAll, DeDriftAndResample, PostFix, >> RestingStateStats, ICAFIX, and TaskfMRIAnalysis to name a few. I am curious >> whether I can use minimally preprocessed data from 3.4.0 and shoehorn it >> into the additional sub-pipelines just mentioned. >> >> I am 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 <(612)%20624-6441> >> Mobile: 507-259-3434 <(507)%20259-3434> (texts okay) >> >> ___ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> >> -- >> >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. If you >> are not the intended recipient, be advised that any unauthorized use, >> disclosure, copy
Re: [HCP-Users] Variation in HCP Minimal Preprocessing Pipeline Differences Across Releases
I can see that several changes/additions have been made to 3.21, but I asked whether there is a difference in *just* the minimal preprocessing pipelines (i.e. PreFreeSurfer, FreeSurfer, PostFreeSurfer, fMRIVolume, fMRISurface, and Diffusion) between 3.4.0 and 3.21. I can ask this a different way, do MSMAll, DeDriftAndResample, PostFix, RestingStateStats, ICAFIX, and TaskfMRIAnalysis scripts rely specifically on data preprocessed from a particular version? My impression was that perhaps MSMAll, DeDriftAndResample, PostFix, RestingStateStats, ICAFIX, and TaskfMRIAnalysis act on top 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/additions from 3.4.0 to 3.21. If you are > starting a new study, it would be preferable for you to start with the > latest version. > > cheers, > -MH > > -- > Michael Harms, Ph.D. > --- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 <(314)%20747-6173> > St. Louis, MO 63110 Email: mha...@wustl.edu > > From: <hcp-users-boun...@humanconnectome.org> on behalf of Timothy > Hendrickson <hendr...@umn.edu> > Date: Tuesday, February 21, 2017 at 9:38 AM > To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: [HCP-Users] Variation in HCP Minimal Preprocessing Pipeline > Differences Across Releases > > Hello, > > I have been using version 3.4.0 of the HCP Minimal Preprocessing Pipeline > to process my HCP compatible data. > I've used 3.4.0 to run the structural (PreFreeSurfer, FreeSurfer, > PostFreeSurfer), fMRI (fMRIVolume, and fMRISurface), and diffusion > sub-pipelines. I have now downloaded version 3.21 and notice several > additional sub-pipelines such as MSMAll, DeDriftAndResample, PostFix, > RestingStateStats, ICAFIX, and TaskfMRIAnalysis to name a few. I am curious > whether I can use minimally preprocessed data from 3.4.0 and shoehorn it > into the additional sub-pipelines just mentioned. > > I am 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 <(612)%20624-6441> > Mobile: 507-259-3434 <(507)%20259-3434> (texts okay) > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Variation in HCP Minimal Preprocessing Pipeline Differences Across Releases
Hello, I have been using version 3.4.0 of the HCP Minimal Preprocessing Pipeline to process my HCP compatible data. I've used 3.4.0 to run the structural (PreFreeSurfer, FreeSurfer, PostFreeSurfer), fMRI (fMRIVolume, and fMRISurface), and diffusion sub-pipelines. I have now downloaded version 3.21 and notice several additional sub-pipelines such as MSMAll, DeDriftAndResample, PostFix, RestingStateStats, ICAFIX, and TaskfMRIAnalysis to name a few. I am curious whether I can use minimally preprocessed data from 3.4.0 and shoehorn it into the additional sub-pipelines just mentioned. I am 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 mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/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) ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
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)
On Tue, Dec 6, 2016 at 8:21 AM, Timothy Hendrickson <hendr...@umn.edu>
wrote:
> Yes thank you!
>
> On Dec 6, 2016 8:13 AM, "Dierker, Donna" <do...@wustl.edu> wrote:
>
>> TimH - you mean this one?
>>
>> On Jul 7, 2016, at 10:26 AM, Dierker, Donna <do...@wustl.edu> wrote:
>>
>> You need to adjust your overlay settings; see attached capture. 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 how to observe significance levels with a
>> threshold of p<0.05.
>>
>> Respectfully,
>>
>> -Tim
>>
>> You need to adjust your overlay settings; see attached capture. Make
>> sure
>> Threshold Type is set to On.
>>
>>
>> From:
>> hcp-users-boun...@humanconnectome.org
>>
>> <
>> hcp-users-boun...@humanconnectome.org
>> > on behalf of Dev vasu
>> <
>> vasudevamurthy.devulapa...@gmail.com
>> >
>> Sent: Thursday, July 7, 2016 10:03:28 AM
>> To: Dierker, Donna
>> Cc: <
>> hcp-users@humanconnectome.org
>> >
>> Subject: Re: [HCP-Users] thresholding the data to p-value
>>
>> Dear madam,
>>
>> I don't want to write to an ROI volume, i just want to observe activation
>> levels with a threshold of p<0.05.
>>
>>
>> Thanks
>> Vasudev
>>
>> On 7 July 2016 at 16:31, Dierker, Donna
>> <
>> do...@wustl.edu<mailto:do...@wustl.edu
>> >> wrote:
>>
>> Hi Vasudev,
>>
>>
>> I'm pretty sure wb_view can display voxels within a range of values
>> (inside
>> upper and lower limit), but I think you mean threshold and write a ROI
>> volume.
>> For that, try:
>>
>>
>> wb_command -metric-math "(x<${Pthresh})" ${PthreshFile} -var x
>> ${PstatFile}
>>
>>
>> Donna
>>
>>
>> From:
>>
>> hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun.
>> ..@humanconnectome.org
>> >
>>
>> <
>> hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun.
>> ..@humanconnectome.org
>> >>
>> on behalf of Dev vasu
>> <
>> vasudevamurthy.devulapa...@gmail.com<mailto:vasudevamurthy.
>> devulapa...@gmail.com
>> >>
>> Sent: Wednesday, July 6, 2016 12:04:50 PM
>> To: Harms, Michael;
>> <
>> hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org
>> >>
>> Subject: [HCP-Users] thresholding the data to p-value
>>
>>
>>
>> Dear sir,
>>
>> I would like to threshold my results to a p-value of p<0.05 and i
>> couldn't do
>> it from workbench GUI, I can only threshold the data to 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
>>
>>
>>
>> --
>>
>> The materials in this message are private and may contain Protected
>> Healthcare Information or other information of a sensitive nature. If you
>> are not the intended recipient, be advised that any unauthorized use,
>> disclosure, copying or the taking of any action in reliance on the contents
>> of this information is strictly prohibited. If you have received this email
>> in error, please immediately notify the sender via telephone or return mail.
>>
>
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] thresholding the data to p-value
Yes thank you!
On Dec 6, 2016 8:13 AM, "Dierker, Donna" <do...@wustl.edu> wrote:
> TimH - you mean this one?
>
> On Jul 7, 2016, at 10:26 AM, Dierker, Donna <do...@wustl.edu> wrote:
>
> You need to adjust your overlay settings; see attached capture. 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 how to observe significance levels with a threshold
> of p<0.05.
>
> Respectfully,
>
> -Tim
>
> You need to adjust your overlay settings; see attached capture. Make sure
> Threshold Type is set to On.
>
>
> From:
> hcp-users-boun...@humanconnectome.org
>
> <
> hcp-users-boun...@humanconnectome.org
> > on behalf of Dev vasu
> <
> vasudevamurthy.devulapa...@gmail.com
> >
> Sent: Thursday, July 7, 2016 10:03:28 AM
> To: Dierker, Donna
> Cc: <
> hcp-users@humanconnectome.org
> >
> Subject: Re: [HCP-Users] thresholding the data to p-value
>
> Dear madam,
>
> I don't want to write to an ROI volume, i just want to observe activation
> levels with a threshold of p<0.05.
>
>
> Thanks
> Vasudev
>
> On 7 July 2016 at 16:31, Dierker, Donna
> <
> do...@wustl.edu<mailto:do...@wustl.edu
> >> wrote:
>
> Hi Vasudev,
>
>
> I'm pretty sure wb_view can display voxels within a range of values
> (inside
> upper and lower limit), but I think you mean threshold and write a ROI
> volume.
> For that, try:
>
>
> wb_command -metric-math "(x<${Pthresh})" ${PthreshFile} -var x
> ${PstatFile}
>
>
> Donna
>
>
> From:
>
> hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@
> humanconnectome.org
> >
>
> <
> hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@
> humanconnectome.org
> >>
> on behalf of Dev vasu
> <
> vasudevamurthy.devulapa...@gmail.com<mailto:vasudevamurth
> y.devulapa...@gmail.com
> >>
> Sent: Wednesday, July 6, 2016 12:04:50 PM
> To: Harms, Michael;
> <
> hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org
> >>
> Subject: [HCP-Users] thresholding the data to p-value
>
>
>
> Dear sir,
>
> I would like to threshold my results to a p-value of p<0.05 and i couldn't
> do
> it from workbench GUI, I can only threshold the data to 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
>
>
>
> --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] thresholding the data to p-value
Hi Donna,
Could you please re-attach the screen capture that you took for
Vasudev? I cannot find it...
I also am looking into how to observe significance levels with a
threshold of p<0.05.
Respectfully,
-Tim
You need to adjust your overlay settings; see attached capture. Make sure
Threshold Type is set to On.
From: hcp-users-boun...@humanconnectome.org
<hcp-users-boun...@humanconnectome.org> on behalf of Dev vasu
<vasudevamurthy.devulapa...@gmail.com>
Sent: Thursday, July 7, 2016 10:03:28 AM
To: Dierker, Donna
Cc: <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] thresholding the data to p-value
Dear madam,
I don't want to write to an ROI volume, i just want to observe activation
levels with a threshold of p<0.05.
Thanks
Vasudev
On 7 July 2016 at 16:31, Dierker, Donna
<do...@wustl.edu<mailto:do...@wustl.edu <do...@wustl.edu>>> wrote:
Hi Vasudev,
I'm pretty sure wb_view can display voxels within a range of values (inside
upper and lower limit), but I think you mean threshold and write a ROI volume.
For that, try:
wb_command -metric-math "(x<${Pthresh})" ${PthreshFile} -var x ${PstatFile}
Donna
From:
hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org
<hcp-users-boun...@humanconnectome.org>>
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org
<hcp-users-boun...@humanconnectome.org>>>
on behalf of Dev vasu
<vasudevamurthy.devulapa...@gmail.com<mailto:vasudevamurthy.devulapa...@gmail.com
<vasudevamurthy.devulapa...@gmail.com>>>
Sent: Wednesday, July 6, 2016 12:04:50 PM
To: Harms, Michael;
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org
<hcp-users@humanconnectome.org>>>
Subject: [HCP-Users] thresholding the data to p-value
Dear sir,
I would like to threshold my results to a p-value of p<0.05 and i couldn't do
it from workbench GUI, I can only threshold the data to 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)
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Re: [HCP-Users] Myelin Map Summary Statistics
Thanks Matt. Hmm I am still confused. So here is my command to extract myelin for the entire cortex: wb_command -cifti-stats 43387.MyelinMap.32k_fs_LR.dscalar.nii -reduce MEAN. Since -cifti-stats requires the -reduce flag the data I receive is only one number. What I am hoping to accomplish is to extract the average surface myelin for the left and right hemisphere and all surface ROIs. For example with freesurfer I can rather easily generate a stats file which informs me a measurement (of my choosing) at each particular location. For example see attached: lh.allSite.aparc.thickness.csv. I 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> wrote: > You should be able to do that with the commands Tim mentioned with the > -roi sub option. > > Peace, > > Matt. > > From: <hcp-users-boun...@humanconnectome.org> on behalf of Timothy > Hendrickson <hendr...@umn.edu> > Date: Wednesday, November 2, 2016 at 11:42 AM > To: Timothy Coalson <tsc...@mst.edu> > Cc: "hcp-users@humanconnectome.org" <HCP-Users@humanconnectome.org> > Subject: Re: [HCP-Users] Myelin Map Summary Statistics > > Hmm, I have a follow up question. I can extract average myelin for the > entire cortex rather easily however I am having more trouble extracting > hemispheric and ROI information. > Suggestions? > > Timothy Hendrickson > Department of Psychiatry > University of Minnesota > Mobile: 507-259-3434 (texts okay) > > On Mon, Oct 31, 2016 at 3:45 PM, Timothy Coalson <tsc...@mst.edu> wrote: > >> Take a look at http://www.humanconnectome.org/software/workbench-command >> .php?function=-cifti-weighted-stats and/or http://www.humanconnect >> ome.org/software/workbench-command.php?function=-cifti-stats . >> >> Tim >> >> >> On Mon, Oct 31, 2016 at 3:32 PM, Timothy Hendrickson <hendr...@umn.edu> >> wrote: >> >>> HCP experts, >>> >>> Is there a way to extract myelin values from individual dscalar CIFTI >>> files? >>> What I am looking for is an average myelin value at the hemispheric and >>> ROI level. >>> >>> -Tim >>> >>> Timothy Hendrickson >>> Department of Psychiatry >>> University of Minnesota >>> Mobile: 507-259-3434 (texts okay) >>> >>> ___ >>> HCP-Users mailing list >>> HCP-Users@humanconnectome.org >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> >> >> > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users Subject Number,lh_bankssts_thickness,lh_caudalanteriorcingulate_thickness,lh_caudalmiddlefrontal_thickness,lh_cuneus_thickness,lh_entorhinal_thickness,lh_fusiform_thickness,lh_inferiorparietal_thickness,lh_inferiortemporal_thickness,lh_isthmuscingulate_thickness,lh_lateraloccipital_thickness,lh_lateralorbitofrontal_thickness,lh_lingual_thickness,lh_medialorbitofrontal_thickness,lh_middletemporal_thickness,lh_parahippocampal_thickness,lh_paracentral_thickness,lh_parsopercularis_thickness,lh_parsorbitalis_thickness,lh_parstriangularis_thickness,lh_pericalcarine_thickness,lh_postcentral_thickness,lh_posteriorcingulate_thickness,lh_precentral_thickness,lh_precuneus_thickness,lh_rostralanteriorcingulate_thickness,lh_rostralmiddlefrontal_thickness,lh_superiorfrontal_thickness,lh_superiorparietal_thickness,lh_superiortemporal_thickness,lh_supramarginal_thickness,lh_frontalpole_thickness,lh_temporalpole_thickness,lh_transversetemporal_thickness,lh_insula_thickness,lh_MeanThickness_thickness CCA239,2.84
