Error: Negative or NULL limit value

[JanD]

Dear BrainVISA Experts,

When I ran the Morphologist 2012 pipeline, I got the following (error) messages:

------------

Skip unselected node: Check SPAM models installation
Skip unselected node: AC/PC Or Normalization

!! VIP Error: Negative or NULL limit value!
!! VIP Error: Execution aborted in function '(distmap)VipComputeFrontPropagationConnectivityDistanceMap'
[this is printed 4 times]

Computing left hemisphere grey-white classification...
Computing right hemisphere grey-white classification...
Detecting left spherical cortex interface...

in Grey White Surface 2012 1 System command exited with non null value : 42
in Morphologist 2012 1 System command exited with non null value : 42

------------

I'm using BrainVISA 4.2.1 on a Mid-2010 MacBook Pro running OS X Lion (10.7) with 8 GB of RAM.

Here are some details on the T1 image as given by fslhd:
sizeof_hdr 348
data_type INT16
dim0 3
dim1 256
dim2 336
dim3 384
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 4
nbyper 2
bitpix 16
pixdim0 0.0000000000
pixdim1 0.6999130249
pixdim2 0.7031250000
pixdim3 0.7031250000
pixdim4 0.0000000000
pixdim5 0.0000000000
pixdim6 0.0000000000
pixdim7 0.0000000000
vox_offset 352
cal_max 0.0000
cal_min 0.0000
scl_slope 1.000000
scl_inter 0.000000
phase_dim 0
freq_dim 0
slice_dim 0
slice_name Unknown
slice_code 0
slice_start 0
slice_end 0
slice_duration 0.000000
time_offset 0.000000
intent Unknown
intent_code 0
intent_name
intent_p1 0.000000
intent_p2 0.000000
intent_p3 0.000000
qform_name Scanner Anat
qform_code 1
qto_xyz:1 -0.698119 0.050292 -0.001256 82.847603
qto_xyz:2 0.050062 0.701324 0.000072 -93.874680
qto_xyz:3 -0.001252 0.000018 0.703124 -166.730972
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name Scanner Anat
sform_code 1
sto_xyz:1 -0.698119 0.050292 -0.001212 82.847603
sto_xyz:2 0.050062 0.701324 0.000070 -93.874680
sto_xyz:3 -0.001208 0.000017 0.703124 -166.730972
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Right-to-Left
sform_yorient Posterior-to-Anterior
sform_zorient Inferior-to-Superior
file_type NIFTI-1+
file_code 1
descrip FSL4.1

This is the first time that I'm using BrainVISA, so I'm not really sure what causes the error message. I saw this posting: http://brainvisa.info/forum/viewtopic.php?f=2&t=1626, but have the impression that the parameters mentioned in the reply are okay in my image (also see attached image).

Any help would be greatly appreciated!

Best,
Jan

[riviere]

Hi Jan,

Have you checked if the values in the image can be negative ? Morphologist expects positive values only, so this might be the cause of the problem (but I'm not sure it is, here).
The importation process takes care of rescaling values in some cases, but maybe not all.
If there are negatives values, then you may need to rescale manually. You can do it using the AimsFileConvert command with appropriate options ("-r --omin 0 --omax 4095" is generally OK and are the values used by the import process when it performs rescaling).

Denis

[JanD]

Hi Denis,

Thank you very much for your quick reply. I checked the values in the image histogram, but there were no negative values. However, to be on the safe side, I re-converted the Dicom images using dcm2nii (I had used MRIconvert before), scaled the values using AimsFileConvert, re-calculated 'Prepare Subject for Anatomical Pipeline', and then re-ran Morphologist 2012. Same error message as before. I also tried Morphologist 2011, with the same result. Do you perhaps have any other ideas on what the problem might be?

Thanks again,
Jan

[riviere]

Hi Jan,

I have tested your data. I get the same message "Negative or NULL limit value", but for me it does not stop the processing. The pipeline continues to the end. The quality of the segmentation is not very good (the GM segmentation grows in the dura, and the white matter also goes in the grey, especially in the central regions) but it produces segmentations and sulci. It may require a bit of tuning to get better segmentations (but I have not spent time on it). I don't know exactly why this strange message is issued, I will investigate.

Denis