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brainlife / app-tractographyQualityCheck

Compute many statistics from your input tractogram and any (optionally input) associated classification structure. These statistics can be used to facilitate quality assurance on your tractography and segmentation, or as part of subject/group level quantative analysis for a research project. See the output section of README.MD for more details.
MIT License
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Brace indexing is not supported for variables of this type. #5

Open soichih opened 4 years ago

soichih commented 4 years ago

I ran this App for John Thompson's data, and I ran into this error message.

Brace indexing is not supported for variables of this type.

Error in bsc_makeFGsFromClassification (line 57)

Error in wma_quantAllWMNorm (line 40)

Error in bsc_feAndSegQualityCheck (line 59)

Error in main (line 46)

MATLAB:cellRefFromNonCell

real    7m28.904s
user    46m23.600s
sys 19m28.525s

image

Here is the full stdout log.

Creating container runtime...
Exploding layer: sha256:5667fdb72017d1fb364744ca1abf7b6f3bbe9c98c3786f294a461c2866db69ab.tar.gz
Exploding layer: sha256:d83811f270d56d34a208f721f3dbf1b9242d1900ad8981fc7071339681998a31.tar.gz
Exploding layer: sha256:ee671aafb583e2321880e275c94d49a49185006730e871435cd851f42d2a775d.tar.gz
Exploding layer: sha256:7fc152dfb3a6b5c9a436b49ff6cd72ed7eb5f1fd349128b50ee04c3c5c2355fb.tar.gz
Exploding layer: sha256:38a9a12bd26ba74f33f9f44da5fb2922ae758ee7252ade74ca140236581a952a.tar.gz
Exploding layer: sha256:0bbf4cf7d7db6f9f7bae7de86415bde09229b640b4835831d8b0bba809800c51.tar.gz
Exploding layer: sha256:40fec727362bf0b0accb4d296f1fba69fe9b757039ecf78710bb1b9d2ba0bb8b.tar.gz
Exploding layer: sha256:dc836274419492605d4361fc611002abc547a9cb43eb73dca6ccc81ddfeb277a.tar.gz
Exploding layer: sha256:990274eae3adc1b2add71b2d952a4814999f93f6c2144589a0a6b4cd2958c896.tar.gz
Exploding layer: sha256:a783742cea938a8858ced4c2885f6bb35f8b00e867979443691d15eedede3051.tar.gz
Exploding layer: sha256:a246aede5303a36a2d9e31a2fa4bf1aed07845df360ef3fe4f54ac94db4b6094.tar.gz
Exploding layer: sha256:1e49489b055e7f80ca59bd27346dbeab3fad7da75da71807c0362601410d2438.tar.gz
Exploding layer: sha256:79c3875b675d44a5150010d52fe69c8e6adbd350287881cb17392045977192e3.tar.gz
Exploding layer: sha256:8921f39da08b13431bd18412f1b6dd5f480fee272edca58f36e01eae00d22084.tar.gz
Warning: Class 'sptensor' is an unknown object class or does not have a valid 'loadobj' method.  Element(s) of this class in array 'fe' have been converted to structures.
> In main (line 21)

 fe structure loaded
 fe structure loaded
 fg structure loaded.  
 fg structure is in acpc coordpace 

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> In wma_quantTract (line 169)
  In wma_quantWBFG (line 50)
  In wma_quantAllWMNorm (line 28)
  In bsc_feAndSegQualityCheck (line 59)
  In main (line 46)

 0 NaN values detected in fe.life.fit.weights
 fg structure loaded.  
 fg structure is in acpc coordpace 

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 100 percent completeWarning: \n Endpoint and midpoint stats not run due to overly large tract
> In wma_quantTract (line 169)
  In wma_quantWBFG (line 90)
  In wma_quantAllWMNorm (line 28)
  In bsc_feAndSegQualityCheck (line 59)
  In main (line 46)

 fe structure loaded
 fg structure loaded.  
 fg structure is in acpc coordpace 

 creating tract 1 with 94 streamlines
 creating tract 2 with 36 streamlines
 creating tract 3 with 44 streamlines
 creating tract 4 with 38 streamlines
 creating tract 5 with 1 streamlines
 creating tract 6 with 23 streamlines
 creating tract 7 with 200 streamlines
 creating tract 8 with 300 streamlines
 creating tract 9 with 51 streamlines
 creating tract 10 with 41 streamlines
 creating tract 11 with 15 streamlines
 creating tract 12 with 239 streamlines
 creating tract 13 with 75 streamlines
 creating tract 14 with 332 streamlines
 creating tract 15 with 342 streamlines
 creating tract 16 with 100 streamlines
 creating tract 17 with 154 streamlines
 creating tract 18 with 276 streamlines
 creating tract 19 with 539 streamlines
 creating tract 20 with 355 streamlines
 creating tract 21 with 781 streamlines
 creating tract 22 with 177 streamlines
 creating tract 23 with 3295 streamlines
 creating tract 24 with 1406 streamlines
 creating tract 25 with 4703 streamlines
 creating tract 26 with 4006 streamlines
 creating tract 27 with 80 streamlines
 creating tract 28 with 21 streamlines
 creating tract 29 with 10 streamlines
 creating tract 30 with 31 streamlines
 creating tract 31 with 44 streamlines
 creating tract 32 with 10 streamlines
 creating tract 33 with 29 streamlines
 creating tract 34 with 205 streamlines
 creating tract 35 with 4 streamlines
 creating tract 36 with 68 streamlines
 creating tract 37 with 37 streamlines
 creating tract 38 with 55 streamlines
 creating tract 39 with 70 streamlines
 creating tract 40 with 41 streamlines
 creating tract 41 with 200 streamlines
 creating tract 42 with 7 streamlines
 creating tract 43 with 22 streamlines
 creating tract 44 with 27 streamlines
 creating tract 45 with 100 streamlines
 creating tract 46 with 564 streamlines
 creating tract 47 with 1431 streamlines
 creating tract 48 with 14 streamlines
 creating tract 49 with 5 streamlines
 creating tract 50 with 5 streamlines
 creating tract 51 with 5 streamlines
 creating tract 52 with 7 streamlines
 creating tract 53 with 14 streamlines
 creating tract 54 with 145 streamlines
 creating tract 55 with 2358 streamlines
 creating tract 56 with 721 streamlines
 245680 positively weighted fibers found in fe structure
 23953 pre-life streamlines classified 

 8791 post-life streamlines classified 

 fg structure loaded.  
 fg structure is in acpc coordpace
DanNBullock commented 4 years ago

https://github.com/DanNBullock/wma_tools/blob/cda6115a1765357f4eadaa8ecddf1702494bc49c/bsc_makeFGsFromClassification.m#L57

Index field is a vector of doubles, updating function to reflect this.

DanNBullock commented 4 years ago

fixed here: https://github.com/DanNBullock/wma_tools/commit/ae863769e7e732c3bcf730f30ac13a59be402b8d#diff-868949b0a70657b7ea767d3966047654

Would recomend replacing instances of this fgs from classification function with V4 (https://github.com/DanNBullock/wma_tools/blob/master/bsc_makeFGsFromClassification_v4.m)

DanNBullock commented 4 years ago

Recommend recompile with fix.

soichih commented 4 years ago

I've git pull wma_tool and recompiled main.m for master branch. I will test it and cut a new version if it works.

I am not sure what you mean by this

Would recomend replacing instances of this fgs from classification function with V4 ( https://github.com/DanNBullock/wma_tools/blob/master/bsc_makeFGsFromClassification_v4.m )

Here is the main.m that I am using for this App

https://github.com/brainlife/app-tractographyQualityCheck/blob/master/main.m

Are you suggesting to make any changes to main.m?

Soichi

On Sun, Feb 16, 2020 at 5:43 PM Daniel Bullock notifications@github.com wrote:

Recommend recompile with fix.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/brainlife/app-tractographyQualityCheck/issues/5?email_source=notifications&email_token=AAHBR6CUDEAKQ5NKN6JBAJTRDG6QFA5CNFSM4KWHJAY2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEL4UYIA#issuecomment-586763296, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAHBR6AGTNHW2N5XZCVX3M3RDG6QFANCNFSM4KWHJAYQ .

DanNBullock commented 4 years ago

I can go through my code later and replace instances of the v1 with v4, but it doesn't strike me as particularly urgent.

I dont see any instances of makeFGsFromClassification in the main.m so there would be no changes to make there. makeFGsFromClassification appears to be called deeper in other functions.

soichih commented 4 years ago

OK. Thanks for patching it quickly. I will let you know how the test job goes.

On Sun, Feb 16, 2020 at 6:01 PM Daniel Bullock notifications@github.com wrote:

I can go through my code later and replace instances of the v1 with v4, but it doesn't strike me as particularly urgent.

I dont see any instances of makeFGsFromClassification in the main.m so there would be no changes to make there. makeFGsFromClassification appears to be called deeper in other functions.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/brainlife/app-tractographyQualityCheck/issues/5?email_source=notifications&email_token=AAHBR6ENRACHB4B4VTBHTO3RDHATJA5CNFSM4KWHJAY2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEL4VFWY#issuecomment-586765019, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAHBR6HRWBPXFNTTV6W24GTRDHATJANCNFSM4KWHJAYQ .

soichih commented 4 years ago

The test job progressed a bit more than previous, but it failed again with the similar error message.

WARNING: Warning reading tar header: Ignoring malformed pax extended attribute
Brace indexing is not supported for variables of this type.

Error in wma_quantAllWMNorm (line 63)

Error in bsc_feAndSegQualityCheck (line 59)

Error in main (line 46)

MATLAB:cellRefFromNonCell

real    11m30.205s
user    48m52.766s
sys 21m44.390s
...
 creating tract 14 with 585 streamlines
 creating tract 15 with 158 streamlines
 creating tract 16 with 115 streamlines
 creating tract 17 with 242 streamlines
 creating tract 18 with 495 streamlines
 creating tract 19 with 269 streamlines
 creating tract 20 with 877 streamlines
 creating tract 21 with 132 streamlines
 creating tract 22 with 4281 streamlines
 creating tract 23 with 1981 streamlines
 creating tract 24 with 4913 streamlines
 creating tract 25 with 3971 streamlines
 creating tract 26 with 93 streamlines
 creating tract 27 with 21 streamlines
 creating tract 28 with 12 streamlines
 creating tract 29 with 57 streamlines
 creating tract 30 with 143 streamlines
 creating tract 31 with 13 streamlines
 creating tract 32 with 18 streamlines
 creating tract 33 with 158 streamlines
 creating tract 34 with 11 streamlines
 creating tract 35 with 101 streamlines
 creating tract 36 with 76 streamlines
 creating tract 37 with 75 streamlines
 creating tract 38 with 42 streamlines
 creating tract 39 with 65 streamlines
 creating tract 40 with 96 streamlines
 creating tract 41 with 4 streamlines
 creating tract 42 with 58 streamlines
 creating tract 43 with 30 streamlines
 creating tract 44 with 86 streamlines
 creating tract 45 with 645 streamlines
 creating tract 46 with 1236 streamlines
 creating tract 47 with 44 streamlines
 creating tract 48 with 14 streamlines
 creating tract 49 with 16 streamlines
 creating tract 50 with 2 streamlines
 creating tract 51 with 13 streamlines
 creating tract 52 with 5 streamlines
 creating tract 53 with 144 streamlines
 creating tract 54 with 2599 streamlines
 creating tract 55 with 1097 streamlines
 233047 positively weighted fibers found in fe structure
 26971 pre-life streamlines classified 

 8865 post-life streamlines classified 

 fg structure loaded.  
 fg structure is in acpc coordpace 

 50 percent complete
 100 percent complete
 forcepsMajor