crashes if studyinfo is N/A

[yarikoptic]

the promise is that tool could be used on any 4D nifti but the code seems to rely on having some 'studyinfo':

$> ls -l phantom_3_1.nii.gz                             
-rw-r--r-- 1 yoh yoh 21181951 Nov  7 14:40 phantom_3_1.nii.gz

$> stabilitycalc /tmp phantom_3_1.nii.gz 0              
reading input file...
[4, 64, 64, 40, 121, 1, 1, 1]
cat: /tmp/studyinfo: No such file or directory
cat: /tmp/studyinfo: No such file or directory
cat: /tmp/studyinfo: No such file or directory
cat: /tmp/studyinfo: No such file or directory
Traceback (most recent call last):
  File "/usr/bin/stabilitycalc", line 423, in <module>
    theyear=studydate[0:4]
TypeError: 'NoneType' object has no attribute '__getitem__'

[bbfrederick]

Ah, yes. I will fix that. Sorry!

Sent from my iPhone - expect random autocorrection errors.

On Nov 7, 2013, at 6:57 PM, Yaroslav Halchenko notifications@github.com wrote:

the promise is that tool could be used on any 4D nifti but the code seems to rely on having some 'studyinfo':

$> ls -l phantom_3_1.nii.gz
-rw-r--r-- 1 yoh yoh 21181951 Nov 7 14:40 phantom_3_1.nii.gz

$> stabilitycalc /tmp phantom_3_1.nii.gz 0
reading input file...
[4, 64, 64, 40, 121, 1, 1, 1]
cat: /tmp/studyinfo: No such file or directory
cat: /tmp/studyinfo: No such file or directory
cat: /tmp/studyinfo: No such file or directory
cat: /tmp/studyinfo: No such file or directory
Traceback (most recent call last):
File "/usr/bin/stabilitycalc", line 423, in
theyear=studydate[0:4]
TypeError: 'NoneType' object has no attribute 'getitem'
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[bbfrederick]

Actually, there is a workaround for the time being - call stabilitycalc with 7 arguments (just add 4 arguments after what you put in - they will be ignored, but that will flip an internal switch to ignore studyinfo).

i.e.:
stabilitycalc /tmp phantom_3_1.nii.gz 0 0 0 0 0

Try that and tell me if it works.

Blaise

On Nov 7, 2013, at 6:57 PM, Yaroslav Halchenko notifications@github.com wrote:

the promise is that tool could be used on any 4D nifti but the code seems to rely on having some 'studyinfo':

$> ls -l phantom_3_1.nii.gz
-rw-r--r-- 1 yoh yoh 21181951 Nov 7 14:40 phantom_3_1.nii.gz

$> stabilitycalc /tmp phantom_3_1.nii.gz 0
reading input file...
[4, 64, 64, 40, 121, 1, 1, 1]
cat: /tmp/studyinfo: No such file or directory
cat: /tmp/studyinfo: No such file or directory
cat: /tmp/studyinfo: No such file or directory
cat: /tmp/studyinfo: No such file or directory
Traceback (most recent call last):
File "/usr/bin/stabilitycalc", line 423, in
theyear=studydate[0:4]
TypeError: 'NoneType' object has no attribute 'getitem'
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[yarikoptic]

nope

$> stabilitycalc /tmp phantom_3_1.nii.gz 0 0 0 0  
processing as individual coil element file
reading input file...
[4, 64, 64, 40, 121, 1, 1, 1]
cat: /tmp/studyinfo: No such file or directory
cat: /tmp/studyinfo: No such file or directory
cat: /tmp/studyinfo: No such file or directory
cat: /tmp/studyinfo: No such file or directory
Traceback (most recent call last):
  File "/usr/bin/stabilitycalc", line 423, in <module>
    theyear=studydate[0:4]
TypeError: 'NoneType' object has no attribute '__getitem__'

[bbfrederick]

Add one more zero and try again - I think I told you one too few…

On Nov 8, 2013, at 10:45 AM, Yaroslav Halchenko notifications@github.com wrote:

nope

$> stabilitycalc /tmp phantom_3_1.nii.gz 0 0 0 0
processing as individual coil element file
reading input file...
[4, 64, 64, 40, 121, 1, 1, 1]
cat: /tmp/studyinfo: No such file or directory
cat: /tmp/studyinfo: No such file or directory
cat: /tmp/studyinfo: No such file or directory
cat: /tmp/studyinfo: No such file or directory
Traceback (most recent call last):
File "/usr/bin/stabilitycalc", line 423, in
theyear=studydate[0:4]
TypeError: 'NoneType' object has no attribute 'getitem'

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[bbfrederick]

Yes, looking at what you sent, you used one too few zeros.

On Nov 8, 2013, at 10:45 AM, Yaroslav Halchenko notifications@github.com wrote:

nope

$> stabilitycalc /tmp phantom_3_1.nii.gz 0 0 0 0
processing as individual coil element file
reading input file...
[4, 64, 64, 40, 121, 1, 1, 1]
cat: /tmp/studyinfo: No such file or directory
cat: /tmp/studyinfo: No such file or directory
cat: /tmp/studyinfo: No such file or directory
cat: /tmp/studyinfo: No such file or directory
Traceback (most recent call last):
File "/usr/bin/stabilitycalc", line 423, in
theyear=studydate[0:4]
TypeError: 'NoneType' object has no attribute 'getitem'

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[yarikoptic]

nah -- tried with many zeros

$> stabilitycalc $PWD 20131125_092404fMRI_SG0SENSEs003a001.nii.gz 0 0 0 0
processing as individual coil element file
reading input file...
[4, 80, 80, 30, 157, 1, 1, 1]
cat: /tmp/philips-qa/studyinfo: No such file or directory
cat: /tmp/philips-qa/studyinfo: No such file or directory
cat: /tmp/philips-qa/studyinfo: No such file or directory
cat: /tmp/philips-qa/studyinfo: No such file or directory
Traceback (most recent call last):
  File "/usr/bin/stabilitycalc", line 423, in <module>
    theyear=studydate[0:4]
TypeError: 'NoneType' object has no attribute '__getitem__'
2 17604 ->1.....................................:Fri 20 Dec 2013 04:36:56 PM EST:.
novo:/tmp/philips-qa
$> stabilitycalc $PWD 20131125_092404fMRI_SG0SENSEs003a001.nii.gz 0 0 0 0 0
usage: stabilitycalc directoryname inputfile numskip [xcenter ycenter zcenter]

required arguments:
    directoryname   - the directory where the 4D NIFTI file is located
    inputfile   - the name of the 4D NIFTI file
    numskip     - the number of tr periods to skip at the beginning of the file

optional arguments:
    xcenter ycenter zcenter - use this location as the center of mass of the phantom
2 17605.....................................:Fri 20 Dec 2013 04:36:58 PM EST:.
novo:/tmp/philips-qa
$> stabilitycalc $PWD 20131125_092404fMRI_SG0SENSEs003a001.nii.gz 0 0 0 0 0 0
usage: stabilitycalc directoryname inputfile numskip [xcenter ycenter zcenter]

required arguments:
    directoryname   - the directory where the 4D NIFTI file is located
    inputfile   - the name of the 4D NIFTI file
    numskip     - the number of tr periods to skip at the beginning of the file

optional arguments:
    xcenter ycenter zcenter - use this location as the center of mass of the phantom