open-discussion > dramms does not correctly read input files
Jul 15, 2019  08:07 PM | Seonjoo Lee
dramms does not correctly read input files
When I used an old version, it worked fine. But lately I downlosded new versions in ios, dramms does not seem to recognize inputs correctly.

I tried pretty much all available versions, and they all have same issues. Is the code written errorously for mac (it does not make sense for me...) or is there any configuration that I missed here?

Here's an example snapshot. The error occured that somehow dramms code errorneously included '/' in front of the input file name.




seonjoosMacBook:127_S_0844-S22283-T1 seonjoolee$ /opt/sbia/dramms-1.4.3/bin/dramms -v -S 127_S_0844-S22283-T1_brain001.img -T MNI152_T1_1mm_brain001.hdr -O img_sub_2_mni.nii -D def_sub_2_mni.nii
dyld: Library not loaded: /usr/local/opt/readline/lib/libreadline.7.dylib
Referenced from: /usr/local/bin/awk
Reason: image not found
usage: dirname path
usage: dirname path
Automatically mapping regularization weights and label factor to roughly the range [0,1]
Regularization = .35555555555555555554
Label factor = 0.50

Number of Gabor scales = 3
-------------------------------------------------------------------------------------------
DRAMMS: Deformable image Registration via Attribute Matching and Mutual-Saliency weighting
-------------------------------------------------------------------------------------------
----------------------------------------
Registering from
127_S_0844-S22283-T1_brain001.img (in directory )
to
MNI152_T1_1mm_brain001.hdr (in directory ),
Registered image will be
img_sub_2_mni.nii (in directory /Users/seonjoolee/Dropbox/127_S_0844-S22283-T1)
and deformation will be
def_sub_2_mni.nii (in directory /Users/seonjoolee/Dropbox/127_S_0844-S22283-T1).
Both registered image and deformation field will be in the same space as MNI152_T1_1mm_brain001.hdr.
----------------------------------------
Gabor attributes will be computed at 3 scales and in 4 orientations
During discrete optimization, number of samples: 5
Manipulation method of control points: 1
Regularization weight: 0.2
Input mask: NULL
Temporary working directory: /var/folders/57/31_68nmx40z1h0nkbp6l05bh0000gn/T/dramms-RtNDnS
Temporary attribute directory: /var/folders/57/31_68nmx40z1h0nkbp6l05bh0000gn/T/dramms-RtNDnS/features
Intermediate results directory: /var/folders/57/31_68nmx40z1h0nkbp6l05bh0000gn/T/dramms-RtNDnS/intermediate
Changed to directory /var/folders/57/31_68nmx40z1h0nkbp6l05bh0000gn/T/dramms-RtNDnS/intermediate
Step 1: Convert images to byte datatype...
Failed to read image from file /127_S_0844-S22283-T1_brain001.img!
Command /opt/sbia/dramms-1.4.3/lib/ConvertImage -s -e --reset-scaling -t uchar -m 0 -M 255 /127_S_0844-S22283-T1_brain001.img A_byte.nii.gz failed
seonjoosMacBook:127_S_0844-S22283-T1 seonjoolee$ /opt/sbia/dramms-1.4.3/bin/dramms -v -S 127_S_0844-S22283-T1_brain001.hdr -T MNI152_T1_1mm_brain001.hdr -O img_sub_2_mni.nii -D def_sub_2_mni.nii
dyld: Library not loaded: /usr/local/opt/readline/lib/libreadline.7.dylib
Referenced from: /usr/local/bin/awk
Reason: image not found
usage: dirname path
usage: dirname path
Automatically mapping regularization weights and label factor to roughly the range [0,1]
Regularization = .35555555555555555554
Label factor = 0.50
Number of Gabor scales = 3
-------------------------------------------------------------------------------------------
DRAMMS: Deformable image Registration via Attribute Matching and Mutual-Saliency weighting
-------------------------------------------------------------------------------------------
----------------------------------------
Registering from
127_S_0844-S22283-T1_brain001.hdr (in directory )
to
MNI152_T1_1mm_brain001.hdr (in directory ),
Registered image will be
img_sub_2_mni.nii (in directory /Users/seonjoolee/Dropbox/127_S_0844-S22283-T1)
and deformation will be
def_sub_2_mni.nii (in directory /Users/seonjoolee/Dropbox/127_S_0844-S22283-T1).
Both registered image and deformation field will be in the same space as MNI152_T1_1mm_brain001.hdr.
----------------------------------------
Gabor attributes will be computed at 3 scales and in 4 orientations
During discrete optimization, number of samples: 5
Manipulation method of control points: 1
Regularization weight: 0.2
Input mask: NULL
Temporary working directory: /var/folders/57/31_68nmx40z1h0nkbp6l05bh0000gn/T/dramms-ynxIZ8
Temporary attribute directory: /var/folders/57/31_68nmx40z1h0nkbp6l05bh0000gn/T/dramms-ynxIZ8/features
Intermediate results directory: /var/folders/57/31_68nmx40z1h0nkbp6l05bh0000gn/T/dramms-ynxIZ8/intermediate
Changed to directory /var/folders/57/31_68nmx40z1h0nkbp6l05bh0000gn/T/dramms-ynxIZ8/intermediate
Step 1: Convert images to byte datatype...
Failed to read image from file /127_S_0844-S22283-T1_brain001.hdr!