Dear All,
I'm trying to load a pretty big diffusion MRI dataset (320x320x260x122). I'm running matlab 2015a 64bit on a linux machine.
I'm using MRIread, which in turn calls load_nifti. I'm getting the following error:
Error using + Out of memory. Type HELP MEMORY for your options.
Error in load_nifti (line 158) hdr.vol = hdr.vol * hdr.scl_slope + hdr.scl_inter;
Error in MRIread (line 158) hdr = load_nifti(fspec,headeronly);
When I load half dataset (320x320x260x61) it works ok. I tried to increase the Maximum array size in Matalb (default 1,000 - now 10,000), but I'm still getting the error. I tried to change machine (which runs matlab 2013a on linux) and it worked fine.
I think this is due to some matlab settings. Can anyone help?
Thanks a lot, Ilaria
------------------------------------------- Ilaria Sani, PhD Postdoctoral Fellow, Freiwald Lab The Rockefeller University 1230 York Ave., New York, NY 10065. Phone: (212) 327 7699 Fax: (212) 327 7698 Email: isani01@rockefeller.eduhttps://rumail.rockefeller.edu/owa/redir.aspx?C=Kqhy3ohui0OLc6NBHS0gx_jC9yHmUtEIuvMTV8kpl1lEP6utIV_5LPRr35l0-k2eSQyLqrMn4XI.&URL=mailto%3assadagopan%40rockefeller.edu
Hi Ilaria
do you have any reason to believe that it isn't just out of memory? If so, there's not much to do other than get more RAM or use a different machine
cheers Bruce
On Thu, 6 Apr 2017, Ilaria Sani wrote:
Dear All,
I’m trying to load a pretty big diffusion MRI dataset (320x320x260x122).
I’m running matlab 2015a 64bit on a linux machine.
I’m using MRIread, which in turn calls load_nifti.
I’m getting the following error:
Error using +
Out of memory. Type HELP MEMORY for your options.
Error in load_nifti (line 158)
hdr.vol = hdr.vol * hdr.scl_slope + hdr.scl_inter;
Error in MRIread (line 158)
hdr = load_nifti(fspec,headeronly);
When I load half dataset (320x320x260x61) it works ok.
I tried to increase the Maximum array size in Matalb (default 1,000 - now 10,000), but I’m still getting the error.
I tried to change machine (which runs matlab 2013a on linux) and it worked fine.
I think this is due to some matlab settings.
Can anyone help?
Thanks a lot,
Ilaria
Ilaria Sani, PhD Postdoctoral Fellow, Freiwald Lab The Rockefeller University 1230 York Ave., New York, NY 10065. Phone: (212) 327 7699 Fax: (212) 327 7698 Email: isani01@rockefeller.edu
Hi Bruce,
Not sure this answer your question...
In matlab workspace, I am able to load data in two halves:
H1=MRIread(half1) H2=MRIread(half2)
And then concatenate the volumes concatenate them var=cat(4,H1,H2).
So, somehow matlab can handle...
However, when those operations are embedded inside a function (like in the case of load_nifti and MRIread) I get the error.
Thanks, Ilaria
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Thursday, April 6, 2017 1:36 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] MRIread (load_nifti)- Out of memory
Hi Ilaria
do you have any reason to believe that it isn't just out of memory? If so, there's not much to do other than get more RAM or use a different machine
cheers Bruce
On Thu, 6 Apr 2017, Ilaria Sani wrote:
Dear All,
I’m trying to load a pretty big diffusion MRI dataset (320x320x260x122).
I’m running matlab 2015a 64bit on a linux machine.
I’m using MRIread, which in turn calls load_nifti.
I’m getting the following error:
Error using +
Out of memory. Type HELP MEMORY for your options.
Error in load_nifti (line 158)
hdr.vol = hdr.vol * hdr.scl_slope + hdr.scl_inter;
Error in MRIread (line 158)
hdr = load_nifti(fspec,headeronly);
When I load half dataset (320x320x260x61) it works ok.
I tried to increase the Maximum array size in Matalb (default 1,000 - now 10,000), but I’m still getting the error.
I tried to change machine (which runs matlab 2013a on linux) and it worked fine.
I think this is due to some matlab settings.
Can anyone help?
Thanks a lot,
Ilaria
Ilaria Sani, PhD Postdoctoral Fellow, Freiwald Lab The Rockefeller University 1230 York Ave., New York, NY 10065. Phone: (212) 327 7699 Fax: (212) 327 7698 Email: isani01@rockefeller.edu
is it a compressed nifti (nii.gz)? If so, try uncompressing it first
On 04/06/2017 02:53 PM, Ilaria Sani wrote:
Hi Bruce,
Not sure this answer your question...
In matlab workspace, I am able to load data in two halves:
H1=MRIread(half1) H2=MRIread(half2)
And then concatenate the volumes concatenate them var=cat(4,H1,H2).
So, somehow matlab can handle...
However, when those operations are embedded inside a function (like in the case of load_nifti and MRIread) I get the error.
Thanks, Ilaria
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Thursday, April 6, 2017 1:36 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] MRIread (load_nifti)- Out of memory
Hi Ilaria
do you have any reason to believe that it isn't just out of memory? If so, there's not much to do other than get more RAM or use a different machine
cheers Bruce
On Thu, 6 Apr 2017, Ilaria Sani wrote:
Dear All,
I’m trying to load a pretty big diffusion MRI dataset (320x320x260x122).
I’m running matlab 2015a 64bit on a linux machine.
I’m using MRIread, which in turn calls load_nifti.
I’m getting the following error:
Error using +
Out of memory. Type HELP MEMORY for your options.
Error in load_nifti (line 158)
hdr.vol = hdr.vol * hdr.scl_slope + hdr.scl_inter;
Error in MRIread (line 158)
hdr = load_nifti(fspec,headeronly);
When I load half dataset (320x320x260x61) it works ok.
I tried to increase the Maximum array size in Matalb (default 1,000 - now 10,000), but I’m still getting the error.
I tried to change machine (which runs matlab 2013a on linux) and it worked fine.
I think this is due to some matlab settings.
Can anyone help?
Thanks a lot,
Ilaria
Ilaria Sani, PhD Postdoctoral Fellow, Freiwald Lab The Rockefeller University 1230 York Ave., New York, NY 10065. Phone: (212) 327 7699 Fax: (212) 327 7698 Email: isani01@rockefeller.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Thanks for the tip. I can load the volume now!
I'm getting different types of errors when I proceed with my analyses though.
Can you help me to understand why it works when data are decompressed and in what way data are different now.
Thanks a lot, Ilaria
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, April 6, 2017 3:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] MRIread (load_nifti)- Out of memory
is it a compressed nifti (nii.gz)? If so, try uncompressing it first
On 04/06/2017 02:53 PM, Ilaria Sani wrote:
Hi Bruce,
Not sure this answer your question...
In matlab workspace, I am able to load data in two halves:
H1=MRIread(half1) H2=MRIread(half2)
And then concatenate the volumes concatenate them var=cat(4,H1,H2).
So, somehow matlab can handle...
However, when those operations are embedded inside a function (like in the case of load_nifti and MRIread) I get the error.
Thanks, Ilaria
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Thursday, April 6, 2017 1:36 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] MRIread (load_nifti)- Out of memory
Hi Ilaria
do you have any reason to believe that it isn't just out of memory? If so, there's not much to do other than get more RAM or use a different machine
cheers Bruce
On Thu, 6 Apr 2017, Ilaria Sani wrote:
Dear All,
I’m trying to load a pretty big diffusion MRI dataset (320x320x260x122).
I’m running matlab 2015a 64bit on a linux machine.
I’m using MRIread, which in turn calls load_nifti.
I’m getting the following error:
Error using +
Out of memory. Type HELP MEMORY for your options.
Error in load_nifti (line 158)
hdr.vol = hdr.vol * hdr.scl_slope + hdr.scl_inter;
Error in MRIread (line 158)
hdr = load_nifti(fspec,headeronly);
When I load half dataset (320x320x260x61) it works ok.
I tried to increase the Maximum array size in Matalb (default 1,000 - now 10,000), but I’m still getting the error.
I tried to change machine (which runs matlab 2013a on linux) and it worked fine.
I think this is due to some matlab settings.
Can anyone help?
Thanks a lot,
Ilaria
Ilaria Sani, PhD Postdoctoral Fellow, Freiwald Lab The Rockefeller University 1230 York Ave., New York, NY 10065. Phone: (212) 327 7699 Fax: (212) 327 7698 Email: isani01@rockefeller.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv ard.edu_mailman_listinfo_freesurfer&d=DwIGCQ&c=JeTkUgVztGMmhKYjxsy2rfo WYibK1YmxXez1G3oNStg&r=d4z88RzwDKeicDL3VVuTqQcuSf1y8Z7V7XewX20Ubmk&m=T wHxSFAJ26NQtkppj0LKxgphSKdwYAmvUro9McGq0Go&s=U95y-XJlyTRcgzsYZ4BI3aWEN BXJrmcsbcj8WCzxjaE&e=
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed... www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
when they are compressed, a shell command is run to decompress it. When a shell command is run from inside matlab, it creates a "fork". This is a new process identical to the original process, meaning that it takes up twice as much memory. When you decompress it, it does not run the shell script or create a fork and so does not take up as much memory.
On 04/06/2017 07:28 PM, Ilaria Sani wrote:
Hi Doug,
Thanks for the tip. I can load the volume now!
I'm getting different types of errors when I proceed with my analyses though.
Can you help me to understand why it works when data are decompressed and in what way data are different now.
Thanks a lot, Ilaria
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, April 6, 2017 3:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] MRIread (load_nifti)- Out of memory
is it a compressed nifti (nii.gz)? If so, try uncompressing it first
On 04/06/2017 02:53 PM, Ilaria Sani wrote:
Hi Bruce,
Not sure this answer your question...
In matlab workspace, I am able to load data in two halves:
H1=MRIread(half1) H2=MRIread(half2)
And then concatenate the volumes concatenate them var=cat(4,H1,H2).
So, somehow matlab can handle...
However, when those operations are embedded inside a function (like in the case of load_nifti and MRIread) I get the error.
Thanks, Ilaria
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Thursday, April 6, 2017 1:36 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] MRIread (load_nifti)- Out of memory
Hi Ilaria
do you have any reason to believe that it isn't just out of memory? If so, there's not much to do other than get more RAM or use a different machine
cheers Bruce
On Thu, 6 Apr 2017, Ilaria Sani wrote:
Dear All,
I’m trying to load a pretty big diffusion MRI dataset (320x320x260x122).
I’m running matlab 2015a 64bit on a linux machine.
I’m using MRIread, which in turn calls load_nifti.
I’m getting the following error:
Error using +
Out of memory. Type HELP MEMORY for your options.
Error in load_nifti (line 158)
hdr.vol = hdr.vol * hdr.scl_slope + hdr.scl_inter;Error in MRIread (line 158)
hdr = load_nifti(fspec,headeronly);
When I load half dataset (320x320x260x61) it works ok.
I tried to increase the Maximum array size in Matalb (default 1,000 - now 10,000), but I’m still getting the error.
I tried to change machine (which runs matlab 2013a on linux) and it worked fine.
I think this is due to some matlab settings.
Can anyone help?
Thanks a lot,
Ilaria
Ilaria Sani, PhD Postdoctoral Fellow, Freiwald Lab The Rockefeller University 1230 York Ave., New York, NY 10065. Phone: (212) 327 7699 Fax: (212) 327 7698 Email: isani01@rockefeller.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv ard.edu_mailman_listinfo_freesurfer&d=DwIGCQ&c=JeTkUgVztGMmhKYjxsy2rfo WYibK1YmxXez1G3oNStg&r=d4z88RzwDKeicDL3VVuTqQcuSf1y8Z7V7XewX20Ubmk&m=T wHxSFAJ26NQtkppj0LKxgphSKdwYAmvUro9McGq0Go&s=U95y-XJlyTRcgzsYZ4BI3aWEN BXJrmcsbcj8WCzxjaE&e=
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed... www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
Ilaria Sani