Hi,
We are on a Intel Mac and are facing a memory problem with mri_glmfit. We want to apply it to a 4D volume consisting of 72 3D volumes of 256 * 256 * 256 voxels each, with 1 byte per voxel. During processing we get the error message that it could not allocate 262144 bytes for the 9313th slice. We noticed the info "changing y type to float" that was issued. We are wondering if there is a workaround for this.
Ed
Hi Ed,
how much RAM do you have in your machine? Bruce
On Wed, 11 May 2011, Ed Gronenschild wrote:
Hi,
We are on a Intel Mac and are facing a memory problem with mri_glmfit. We want to apply it to a 4D volume consisting of 72 3D volumes of 256 * 256 * 256 voxels each, with 1 byte per voxel. During processing we get the error message that it could not allocate 262144 bytes for the 9313th slice. We noticed the info "changing y type to float" that was issued. We are wondering if there is a workaround for this.
Ed
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
16 GB
On 11 May 2011, at 15:24, Bruce Fischl wrote:
Hi Ed,
how much RAM do you have in your machine? Bruce
On Wed, 11 May 2011, Ed Gronenschild wrote:
Hi,
We are on a Intel Mac and are facing a memory problem with mri_glmfit. We want to apply it to a 4D volume consisting of 72 3D volumes of 256 * 256 * 256 voxels each, with 1 byte per voxel. During processing we get the error message that it could not allocate 262144 bytes for the 9313th slice. We noticed the info "changing y type to float" that was issued. We are wondering if there is a workaround for this.
Ed
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do you have other stuff running?
On Wed, 11 May 2011, Ed Gronenschild wrote:
16 GB
On 11 May 2011, at 15:24, Bruce Fischl wrote:
Hi Ed,
how much RAM do you have in your machine? Bruce
On Wed, 11 May 2011, Ed Gronenschild wrote:
Hi,
We are on a Intel Mac and are facing a memory problem with mri_glmfit. We want to apply it to a 4D volume consisting of 72 3D volumes of 256 * 256 * 256 voxels each, with 1 byte per voxel. During processing we get the error message that it could not allocate 262144 bytes for the 9313th slice. We noticed the info "changing y type to float" that was issued. We are wondering if there is a workaround for this.
Ed
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 http://www.partners.org/complianceline . 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.
I did. However, without any other concurrent process running I get exactly the same problem. I guess that this is due to the 2GB limit which can be allocated on a 32 bits machine.
On 11 May 2011, at 15:40, Bruce Fischl wrote:
do you have other stuff running?
On Wed, 11 May 2011, Ed Gronenschild wrote:
16 GB
On 11 May 2011, at 15:24, Bruce Fischl wrote:
Hi Ed,
how much RAM do you have in your machine? Bruce
On Wed, 11 May 2011, Ed Gronenschild wrote:
Hi,
We are on a Intel Mac and are facing a memory problem with mri_glmfit. We want to apply it to a 4D volume consisting of 72 3D volumes of 256 * 256 * 256 voxels each, with 1 byte per voxel. During processing we get the error message that it could not allocate 262144 bytes for the 9313th slice. We noticed the info "changing y type to float" that was issued. We are wondering if there is a workaround for this.
Ed
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 http://www.partners.org/complianceline . 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.
oh, yes, that's definitely not enough:
4*256*256*256*72/(1024*1024) ans = 4608
On Wed, 11 May 2011, Ed Gronenschild wrote:
I did. However, without any other concurrent process running I get exactly the same problem. I guess that this is due to the 2GB limit which can be allocated on a 32 bits machine.
On 11 May 2011, at 15:40, Bruce Fischl wrote:
do you have other stuff running?
On Wed, 11 May 2011, Ed Gronenschild wrote:
16 GB
On 11 May 2011, at 15:24, Bruce Fischl wrote:
Hi Ed,
how much RAM do you have in your machine? Bruce
On Wed, 11 May 2011, Ed Gronenschild wrote:
Hi,
We are on a Intel Mac and are facing a memory problem with mri_glmfit. We want to apply it to a 4D volume consisting of 72 3D volumes of 256 * 256 * 256 voxels each, with 1 byte per voxel. During processing we get the error message that it could not allocate 262144 bytes for the 9313th slice. We noticed the info "changing y type to float" that was issued. We are wondering if there is a workaround for this.
Ed
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 http://www.partners.org/complianceline . 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.
OK, so there's no workaround from your side?
There are many empty voxels in the volumes, so as a workaround I'm going to crop the volumes and hope that they will fit in the 2GB.
On 11 May 2011, at 15:51, Bruce Fischl wrote:
oh, yes, that's definitely not enough:
4*256*256*256*72/(1024*1024) ans = 4608
On Wed, 11 May 2011, Ed Gronenschild wrote:
I did. However, without any other concurrent process running I get exactly the same problem. I guess that this is due to the 2GB limit which can be allocated on a 32 bits machine.
On 11 May 2011, at 15:40, Bruce Fischl wrote:
do you have other stuff running?
On Wed, 11 May 2011, Ed Gronenschild wrote:
16 GB
On 11 May 2011, at 15:24, Bruce Fischl wrote:
Hi Ed,
how much RAM do you have in your machine? Bruce
On Wed, 11 May 2011, Ed Gronenschild wrote:
Hi,
We are on a Intel Mac and are facing a memory problem with mri_glmfit. We want to apply it to a 4D volume consisting of 72 3D volumes of 256 * 256 * 256 voxels each, with 1 byte per voxel. During processing we get the error message that it could not allocate 262144 bytes for the 9313th slice. We noticed the info "changing y type to float" that was issued. We are wondering if there is a workaround for this.
Ed
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 http://www.partners.org/complianceline . 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.
no easy one that springs to mind, sorry. Doug: any ideas?
Bruce
On Wed, 11 May 2011, Ed Gronenschild wrote:
OK, so there's no workaround from your side?
There are many empty voxels in the volumes, so as a workaround I'm going to crop the volumes and hope that they will fit in the 2GB.
On 11 May 2011, at 15:51, Bruce Fischl wrote:
oh, yes, that's definitely not enough:
4*256*256*256*72/(1024*1024) ans = 4608
On Wed, 11 May 2011, Ed Gronenschild wrote:
I did. However, without any other concurrent process running I get exactly the same problem. I guess that this is due to the 2GB limit which can be allocated on a 32 bits machine.
On 11 May 2011, at 15:40, Bruce Fischl wrote:
do you have other stuff running?
On Wed, 11 May 2011, Ed Gronenschild wrote:
16 GB
On 11 May 2011, at 15:24, Bruce Fischl wrote:
Hi Ed,
how much RAM do you have in your machine? Bruce
On Wed, 11 May 2011, Ed Gronenschild wrote:
> Hi, > > We are on a Intel Mac and are facing a memory problem with mri_glmfit. > We want to apply it to a 4D volume consisting of 72 3D volumes > of 256 * 256 * 256 voxels each, with 1 byte per voxel. During > processing we get the error message that it could not allocate > 262144 bytes for the 9313th slice. > We noticed the info "changing y type to float" that was issued. > We are wondering if there is a workaround for this. > > Ed > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >
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 http://www.partners.org/complianceline . 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.
It has to be float because that's what it uses internally. Can you break the volume up into slices? If so, then you can analyze each separately then combine the results back together (can't do correction for multiple comparisons though).
doug
On 5/11/11 10:19 AM, Bruce Fischl wrote:
no easy one that springs to mind, sorry. Doug: any ideas?
Bruce
On Wed, 11 May 2011, Ed Gronenschild wrote:
OK, so there's no workaround from your side?
There are many empty voxels in the volumes, so as a workaround I'm going to crop the volumes and hope that they will fit in the 2GB.
On 11 May 2011, at 15:51, Bruce Fischl wrote:
oh, yes, that's definitely not enough:
4*256*256*256*72/(1024*1024) ans = 4608 On Wed, 11 May 2011, Ed Gronenschild wrote:
I did. However, without any other concurrent process running I get exactly the same problem. I guess that this is due to the 2GB limit which can be allocated on a 32 bits machine.
On 11 May 2011, at 15:40, Bruce Fischl wrote:
do you have other stuff running?
On Wed, 11 May 2011, Ed Gronenschild wrote:
16 GB
On 11 May 2011, at 15:24, Bruce Fischl wrote:
> Hi Ed, > > how much RAM do you have in your machine? > Bruce > > > On Wed, 11 May 2011, Ed > Gronenschild wrote: > >> Hi, >> >> We are on a Intel Mac and are facing a memory problem with mri_glmfit. >> We want to apply it to a 4D volume consisting of 72 3D volumes >> of 256 * 256 * 256 voxels each, with 1 byte per voxel. During >> processing we get the error message that it could not allocate >> 262144 bytes for the 9313th slice. >> We noticed the info "changing y type to float" that was issued. >> We are wondering if there is a workaround for this. >> >> Ed >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > 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 > http://www.partners.org/complianceline . 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. >
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Ed Gronenschild