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

2018-08-17 Thread Timothy Coalson 
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
> 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.
>

 ___
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 HCP-Users@humanconnectome.org
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>>>
>>>
>>
>> --
>>
>> 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

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

2018-08-17 Thread Timothy Coalson 
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

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 HCP-Users@humanconnectome.org
 http://lists.humanconnectome.org/mailman/listinfo/hcp-users


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

2018-08-17 Thread Timothy Hendrickson 
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.
>

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

2018-08-17 Thread Glasser, Matthew 
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>>
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>>
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


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intended recipient, be advised that any unauthorized use, disclosure, copying 
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strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.


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intended recipient, be advised that any unauthorized use, disclosure, copying 
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Re: [HCP-Users] FSL FIX no memory with hcp_fix_multi_run

2018-08-17 Thread Timothy Hendrickson 
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
>>
>
>

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

2018-08-17 Thread Timothy Coalson 
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
>

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

2018-08-17 Thread Timothy Hendrickson 
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
>
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Re: [HCP-Users] FSL FIX no memory with hcp_fix_multi_run

2018-08-17 Thread Glasser, Matthew 
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>>
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


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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 
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read_avw_img.m
Description: read_avw_img.m

[HCP-Users] FSL FIX no memory with hcp_fix_multi_run

2018-08-17 Thread Timothy Hendrickson 
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

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