Sebastian,

Hi, can you post the data to our upload site for us to recreate the problem? The upload site where upload data is visible only by us is:

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

That's the easiest way to track down the segfault.

Nick

On Fri, 2009-04-24 at 14:21 -0700, Sebastian Moeller wrote:

Dear fellow surfers,

in the process of hoisting my monkey scripts for processing of anatomical data from stable3 (3.0.5, boy some programms really expect completely different arguments now, :)) to the cutting edge 4.3.0 I am encountering some problems. On an intel mac (leopard 10.5.6) mri_normalize leads to segmentation faults, while the centos4_x86_64 version of 4.3.0 mri_normalize, happily performs the normalization using the same commandline. Here is bugr's output:

---

FREESURFER_HOME: /opt/freesurfer/

Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v4.3.0

Kernel info: Darwin 9.6.2 i386

---

Please include the following additional information in your report:

1. subject name

n/a, non human primate data; selfmade scripts, mri_info of nu.mgz: hms-beagle:myscripts_anat moeller$ mri_info ../mri/nu.mgz Volume information for ../mri/nu.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: 1450.00 msec, TE: 3.05 msec, TI: 800.00 msec, flip angle: 10.00 degrees nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 13.3323 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 2.5991 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 40.7345

talairach xfm :
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
               -1.0000   0.0000   0.0000   141.3323
     		        0.0000   0.0000   1.0000  -125.4009
                0.0000  -1.0000   0.0000   168.7345
                0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant -1

ras to voxel transform:
               -1.0000   0.0000   0.0000   141.3323
               -0.0000  -0.0000  -1.0000   168.7345
               -0.0000   1.0000  -0.0000   125.4009
                0.0000   0.0000   0.0000     1.0000
So to my knowledge nu.mgz looks okay, it displays okay in tkmedit

2. the entire command-line executed

mri_normalize -n 1 -no1d -gentle ../mri/nu.mgz ../mri/T1.mgz

adding -nosnr or removing -gentle does not solve the problem, it always segfaults with the following output

3. the error message generated

performing 3d normalization 1 times disabling 1d normalization... performing kinder gentler normalization... reading from ../mri/nu.mgz... normalizing image... computing initial normalization using SNR... Segmentation fault

4. optionally include the subject's /script/recon-all.log

See also: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Any idea, what I can do?