Re: [Freesurfer] cannot allocate memory

Hi Doug,

Thanks. I was wondering if you think this would do the job: 1) use fmcpr.nii.gz 2) split it to 3d volumes 3) do mri_vol2vol for all the volumes separely 4) concatenate the resampled volumes together to get a 4d volume. If you don't think this is a good approach, I appreciate it if you could walk me through the steps.

Thanks in advance for your help Best regards, Ehsan

On Tue, Mar 22, 2016 at 3:53 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

The problem is not the command, it is the size of the data it generates. You can try reducing the size of the anatomical to a bounding box around the brain. This is a bit tricky as you also have to compute a new registration. I can help step you through the process if you want to go in that direction.

On 03/22/2016 11:50 AM, Ehsan Tadayon wrote:

...

Hi Doug,

Thanks for your response. What I'm trying to do is to get each voxel's times course in structural space and I was under the impression that mri_vol2vol --mov func.nii would be the right way to go. Would you please let me know what the best way would be to do this?

best, Ehsan,.

On Wed, Mar 16, 2016 at 11:27 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

that's going to create a pretty big volume as it will map your
functional time course to a 256^3 float volume. If you have 100
time points, then that will be about 7G.

On 3/16/16 3:27 PM, Ehsan Tadayon wrote:

...

Hi Bruce,

Thanks for your response. I'm using :

freesurfer version:
freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 on OS X Yosemite
10.10.5 with 16 GB 1333 MHz DDR3 memory. The command that I'm using:

mri_vol2vol --mov func.nii.gz --fstarg --reg register.dat --o
func.anat.nii.gz

Thanks in advance for your help.

best regards,
Ehsan.




On Tue, Mar 15, 2016 at 11:49 PM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>
wrote:

    Hi Ehsan

    We need the full command line and screen output and also what
    your hardware and software environments are to help you.
    Certainly sounds like you ran out of memory though

    Cheers
    Bruce

    > On Mar 15, 2016, at 11:41 PM, Ehsan Tadayon
    <ehsan.tadayon84@gmail.com
    <mailto:ehsan.tadayon84@gmail.com>> wrote:
    >
    > Ehsan

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The information in this e-mail is intended only for the person to
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