Endless thanks. I'll try and update you. Andrea
----Messaggio originale---- Da: fischl@nmr.mgh.harvard.edu Data: 9-apr-2014 17.16 A: "Andrea Tateo"andrea.tateo@virgilio.it Cc: "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu Ogg: Re: R: Re: R: Re: [Freesurfer] Problem of size
on the recon-all command line On Wed, 9 Apr 2014, Andrea Tateo wrote:
I use « recon-all -debug -s 001 -autorecon-all »
and after
« mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o 001_rawavg.mgz --regheader aseg.mgz »
Where can I specify "-cw256" ?
----Messaggio originale---- Da: fischl@nmr.mgh.harvard.edu Data: 9-apr-2014 16.56 A: "Andrea Tateo"andrea.tateo@virgilio.it Cc: "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu Ogg: Re: R: Re: [Freesurfer] Problem of size
Hi Andrea
will it fit in 256? You can try specifying -cw256
cheers Bruce
On Wed, 9 Apr 2014, Andrea Tateo wrote:
Hi Bruce,
thanks for the quick response.
I report the full error message:
WARNING==================++++++++++++++++++++++++==========================
=======
====== The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 312 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). ==================================================++++++++++++++++++++++++=
==============
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ readingfrom/lustre/home/tateo/Simulazione_FREESURF_GRID_2/Segmentazione/SUB_1006_3
/001
/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -0) j_ras = (0, 0, -1) k_ras = (-0, 1, -0) Original Data has (1, 1, 1) mm size and (256, 256, 312) voxels. Data is conformed to 1 mm size and 312 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writingto/lustre/home/tateo/Simulazione_FREESURF_GRID_2/Segmentazione/SUB_1006_3/0
01
/mri/orig.mgz...
ERROR! FOV=312.000 > 256 Include the flag -cw256 with recon-all!
Thank you very much
Andrea
----Messaggio originale---- Da: fischl@nmr.mgh.harvard.edu Data: 9-apr-2014 14.45 A: "Andrea Tateo"andrea.tateo@virgilio.it, "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Problem of size
Hi Andrea
what size are your voxels? Do you really need an FOV that big? If not, you could extract the central 256mm using mri_extract. And I believe this is just a warning - does recon-all complete?
cheers Bruce
On Wed, 9 Apr 2014, Andrea Tateo wrote:
Hi FreeSurfer expert,
I have a problem with command "recon-all".
In recon-all.log I can read:
«The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot
fit
in 256^3 mm^3 volume.
The resulting volume will have 312 slices.
If you find problems, please let us know
(freesurfer@nmr.mgh.harvard.edu).»
I hope are there anyone to help me.
Thank for your help.
Andrea
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