Re: [HCP-Users] FSL FIX no memory with hcp_fix_multi_run
Do you have a movement regressor file for all runs of all subjects? That is what it is suggesting and probably is not related to memory. Matt. From: Timothy Hendrickson mailto:hendr...@umn.edu>> Date: Thursday, September 6, 2018 at 4:55 AM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: Timothy Coalson mailto:tsc...@mst.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:HCP-Users@humanconnectome.org>> Subject: Re: FW: [HCP-Users] 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 mailto:glass...@wustl.edu>> 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 mailto:hendr...@umn.edu>> Date: Tuesday, August 21, 2018 at 6:36 PM To: Matt Glasser mailto:glass...@wustl.edu>> 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 mailto:glass...@wustl.edu>> wrote: You might need to configure swap space or increase the amount. Matt. From: Timothy Hendrickson mailto:hendr...@umn.edu>> Date: Tuesday, August 21, 2018 at 1:54 PM To: Timothy Coalson mailto:tsc...@mst.edu>> Cc: Matt Glasser mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto: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 mailto:tsc...@mst.edu>> 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 mailto:tsc...@mst.edu>> 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 mailto:glass...@wustl.edu>> wrote: Is everything 64bit? Do you have swap space? Matt. From: Timothy Hendrickson mailto:hendr...@umn.edu>> Date: Friday, August 17, 2018 at 4:39 PM To: Timothy Coalson mailto:tsc...@mst.edu>> Cc: Matt Glasser mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:HCP-Users@humanconnectome.org>> Subject: R
Re: [HCP-Users] FSL FIX no memory with hcp_fix_multi_run
You might need to configure swap space or increase the amount. Matt. From: Timothy Hendrickson mailto:hendr...@umn.edu>> Date: Tuesday, August 21, 2018 at 1:54 PM To: Timothy Coalson mailto:tsc...@mst.edu>> Cc: Matt Glasser mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto: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 mailto:tsc...@mst.edu>> 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 mailto:tsc...@mst.edu>> 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 mailto:glass...@wustl.edu>> wrote: Is everything 64bit? Do you have swap space? Matt. From: Timothy Hendrickson mailto:hendr...@umn.edu>> Date: Friday, August 17, 2018 at 4:39 PM To: Timothy Coalson mailto:tsc...@mst.edu>> Cc: Matt Glasser mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto: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 mailto:tsc...@mst.edu>> 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 mailto:hendr...@umn.edu>> 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 mailto:glass...@wustl.edu>> 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: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Hendrickson mailto:hendr...@umn.edu>> Date: Friday, August 17, 2018 at 1:58 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto: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<mailto: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,
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
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 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 &g
Re: [HCP-Users] FSL FIX no memory with hcp_fix_multi_run
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 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
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
Is everything 64bit? Do you have swap space? Matt. From: Timothy Hendrickson mailto:hendr...@umn.edu>> Date: Friday, August 17, 2018 at 4:39 PM To: Timothy Coalson mailto:tsc...@mst.edu>> Cc: Matt Glasser mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto: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 mailto:tsc...@mst.edu>> 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 mailto:hendr...@umn.edu>> 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 mailto:glass...@wustl.edu>> 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: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Hendrickson mailto:hendr...@umn.edu>> Date: Friday, August 17, 2018 at 1:58 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto: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<mailto: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<mailto: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
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
Re: [HCP-Users] FSL FIX no memory with hcp_fix_multi_run
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: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Hendrickson mailto:hendr...@umn.edu>> Date: Friday, August 17, 2018 at 1:58 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto: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<mailto: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 read_avw_img.m Description: read_avw_img.m
[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
