Yes, the problem is rawavg.mgz. When was it created? How many runs do you have in this data set? You can also try using your input volume subject/mri/orig/001.mgz (or what ever it is called). If you only have one run, then rawavg.mgz should just be a copy of 001.mgz

doug

On 11/12/2012 11:54 AM, Gabriel Gonzalez Escamilla wrote:

Here yu are:

mri_info brain.mgz Volume information for brain.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 11.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = 0.0000, c_r = 2.1879 : x_a = -0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 11.6591 : x_s = -0.0000, y_s = -1.0000, z_s = -0.0000, c_s = -17.2780 talairach xfm : Orientation : LIA Primary Slice Direction: coronal

voxel to ras transform: -1.0000 -0.0000 0.0000 130.1879 -0.0000 0.0000 1.0000 -116.3409 -0.0000 -1.0000 -0.0000 110.7220 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -1

ras to voxel transform: -1.0000 0.0000 0.0000 130.1879 0.0000 -0.0000 -1.0000 110.7220 -0.0000 1.0000 -0.0000 116.3409 0.0000 0.0000 0.0000 1.0000

mri_info rawavg.mgz MRIalloc: could not allocate -512234304 frame

Cannot allocate memory

As I see, the problem comes from the rawavg.mgz, if I do convert the dicoms into mgz, would this solve the problem, right? or there's anything else I can do?

Regards, Gabriel

El 12/11/12, *Douglas N Greve * greve@nmr.mgh.harvard.edu escribió:

...

Can you send the result of mri_info brain.mgz mri_info rawavg.mgz doug

On 11/12/2012 10:27 AM, Gabriel Gonzalez Escamilla wrote:

...

Dear FS experts,

I'm trying to convert one skull-stripped image from the FS segmentation to a nifti in native space, but I'm having some troubles with it.

I'm doing everything with the a to d steps a) cd /root/trabajo/freesurfer/subjects/s00x/mri/ b) mri_vol2vol --interp nearest --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz --regheader c) mri_mask -T 2 rawavg.mgz brain2raw.mgz brainraw.mgz d) mri_convert -odt float brainraw.mgz brain.nii

but in step b always get the following error:

mri_vol2vol --interp nearest --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz --regheader movvol brain.mgz targvol rawavg.mgz outvol brain2raw.mgz invert 0 tal 0 talres 2 regheader 1 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1352942991 MRIalloc: could not allocate -512234304 frame

Cannot allocate memory

Any ideas how to solve this? Should I to re-run any recon?

Many thanks in advanced, Gabriel

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

---

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.