Fails conversion with tonii_all

[mschneider1711]

Describe the bug
A clear and concise description of what the bug is.
When I want to convert multiple datasets with tonii_all at the same time I get a bug that the input folder is not valid.

When I comment out the section where it checks if the parent folder is a pv_dataset it works and all my files are converted into nifti.
My folder structur is:

Expected behavior
In my case the BidsData folder should not be recognized as a pv_dataset and therefore the script should not stop at this point.

Desktop (please complete the following information):

• Windows 11
• Version v.0.3.10

@Aswendt-Lab
@arefks
@maswendt

[gdevenyi]

Please share the complete command you are using.

[mschneider1711]

That's the command I'm using:

[gdevenyi]

And what are the contents of one of the subfolders of BidsData?

[mschneider1711]

It is the raw dataset.

[gdevenyi]

Ok, the error is as expected. The tonii_all command is intended to be run on a single dataset, whereas you are running it on multiple datasets.

The error could be better in terms of what it says, since it wrongly indicates you're running on a single scan.

I think the solution here is an optional flag to tonii_all --recursive which will recurse down directories.

[mschneider1711]

Unfortunately I get the same error when using it on a single dataset:

[dvm-shlee]

@mschneider1711, apologies for the delayed response. Have you managed to resolve the issue? If not, could you please share the contents of the /Data folder located under /BidsData?

It seems there might be a misunderstanding causing the brkraw tonii_all command to treat BidsData as a single raw data set, whereas your initial method should have worked as expected. I am actively working on addressing issues within the BrkRaw package and expect to have enhancements ready by mid-May. If you're still encountering problems, I can assist you in testing with the new module, which should present fewer issues than the current version. Please consider that the complete code will be ready by May 15th.

[MrImaging]

I experienced this issue as well and could resolve it/work around it by zipping the raw data sets/folders, which then allowed me to apply tonii_all to multiple subjects and sessions simultaneuosly

[neginnes]

Hi,
I face the same issue as described here. This is while when using brkraw v0.2.14 I am able to use tonii_all to convert full study (it generates a new data folder and categorizes the converted outputs in Anat, DWI and Func folders). However v0.2.14 doesn't provide bval and bvec files for DWI and therefor I switched to v0.3.11. Unfortunately, zipping the entire study or the scans within it also didn't help me with using this version of brkraw to successfully convert the whole study. Has anyone found a solution to this problem?
Is there any way to get the same output at brkraw v0.2.14 from the latest version?

Below, I am sharing the raw folder structure and my error.

.
├── 1
│   ├── acqp
│   ├── AdjRefgProfiles.dat
│   ├── AdjStatePerScan
│   ├── configscan
│   ├── fid
│   ├── method
│   ├── pdata
│   │   └── 1
│   │       ├── 2dseq
│   │       ├── id
│   │       ├── methreco
│   │       ├── procs
│   │       ├── reco
│   │       └── visu_pars
│   ├── pulseprogram
│   ├── specpar
│   ├── spnam0
│   ├── spnam40
│   ├── uxnmr.info
│   ├── uxnmr.par
│   └── visu_pars
├── 10
│   ├── acqp
│   ├── AdjStatePerScan
│   ├── configscan
│   ├── fid
│   ├── method
│   ├── pdata
│   │   └── 1
│   │       ├── 2dseq
│   │       ├── id
│   │       ├── procs
│   │       ├── reco
│   │       └── visu_pars
│   ├── pulseprogram
│   ├── specpar
│   ├── spnam0
│   ├── uxnmr.info
│   ├── uxnmr.par
│   └── visu_pars
├── 11
│   ├── acqp
│   ├── AdjStatePerScan
│   ├── configscan
│   ├── fid
│   ├── method
│   ├── pdata
│   │   └── 1
│   │       ├── 2dseq
│   │       ├── id
│   │       ├── procs
│   │       ├── reco
│   │       └── visu_pars
│   ├── pulseprogram
│   ├── specpar
│   ├── spnam0
│   ├── uxnmr.info
│   ├── uxnmr.par
│   └── visu_pars
├── 12
│   ├── acqp
│   ├── AdjStatePerScan
│   ├── configscan
│   ├── fid
│   ├── method
│   ├── pdata
│   │   ├── 1
│   │   │   ├── 2dseq
│   │   │   ├── id
│   │   │   ├── methreco
│   │   │   ├── procs
│   │   │   ├── reco
│   │   │   ├── roi
│   │   │   └── visu_pars
│   │   └── 2
│   │       ├── 2dseq
│   │       ├── d3proc
│   │       ├── id
│   │       ├── isa
│   │       ├── roi
│   │       └── visu_pars
│   ├── pulseprogram
│   ├── specpar
│   ├── spnam40
│   ├── uxnmr.info
│   ├── uxnmr.par
│   └── visu_pars
├── 13
│   ├── acqp
│   ├── AdjRefgProfiles.dat
│   ├── AdjStatePerScan
│   ├── configscan
│   ├── fid
│   ├── method
│   ├── pdata
│   │   └── 1
│   │       ├── 2dseq
│   │       ├── id
│   │       ├── methreco
│   │       ├── procs
│   │       ├── reco
│   │       └── visu_pars
│   ├── pulseprogram
│   ├── specpar
│   ├── spnam0
│   ├── spnam40
│   ├── uxnmr.info
│   ├── uxnmr.par
│   └── visu_pars
├── 14
│   ├── acqp
│   ├── AdjRefgProfiles.dat
│   ├── AdjStatePerScan
│   ├── configscan
│   ├── fid
│   ├── method
│   ├── pdata
│   │   └── 1
│   │       ├── 2dseq
│   │       ├── id
│   │       ├── methreco
│   │       ├── procs
│   │       ├── reco
│   │       └── visu_pars
│   ├── pulseprogram
│   ├── specpar
│   ├── spnam0
│   ├── spnam40
│   ├── uxnmr.info
│   ├── uxnmr.par
│   └── visu_pars
├── 15
│   ├── acqp
│   ├── AdjStatePerScan
│   ├── configscan
│   ├── fid
│   ├── method
│   ├── pdata
│   │   └── 1
│   │       ├── 2dseq
│   │       ├── id
│   │       ├── methreco
│   │       ├── procs
│   │       ├── reco
│   │       └── visu_pars
│   ├── pulseprogram
│   ├── specpar
│   ├── spnam0
│   ├── uxnmr.info
│   ├── uxnmr.par
│   └── visu_pars
├── 2
│   ├── acqp
│   ├── AdjStatePerScan
│   ├── configscan
│   ├── method
│   ├── pdata
│   │   └── 1
│   │       ├── id
│   │       ├── methreco
│   │       └── reco
│   ├── pulseprogram
│   ├── specpar
│   ├── spnam0
│   ├── uxnmr.info
│   └── uxnmr.par
├── 3
│   ├── acqp
│   ├── AdjStatePerScan
│   ├── configscan
│   ├── fid
│   ├── method
│   ├── pdata
│   │   └── 1
│   │       ├── 2dseq
│   │       ├── id
│   │       ├── procs
│   │       ├── reco
│   │       └── visu_pars
│   ├── pulseprogram
│   ├── specpar
│   ├── spnam1
│   ├── uxnmr.info
│   ├── uxnmr.par
│   └── visu_pars
├── 4
│   ├── acqp
│   ├── AdjStatePerScan
│   ├── configscan
│   ├── fid
│   ├── method
│   ├── pdata
│   │   └── 1
│   │       ├── 2dseq
│   │       ├── id
│   │       ├── procs
│   │       ├── reco
│   │       └── visu_pars
│   ├── pulseprogram
│   ├── specpar
│   ├── uxnmr.info
│   ├── uxnmr.par
│   └── visu_pars
├── 5
│   ├── acqp
│   ├── AdjStatePerScan
│   ├── configscan
│   ├── fid
│   ├── method
│   ├── pdata
│   │   └── 1
│   │       ├── 2dseq
│   │       ├── id
│   │       ├── procs
│   │       ├── reco
│   │       └── visu_pars
│   ├── pulseprogram
│   ├── specpar
│   ├── uxnmr.info
│   ├── uxnmr.par
│   └── visu_pars
├── 6
│   ├── acqp
│   ├── AdjStatePerScan
│   ├── configscan
│   ├── fid
│   ├── method
│   ├── pdata
│   │   └── 1
│   │       ├── 2dseq
│   │       ├── id
│   │       ├── procs
│   │       ├── reco
│   │       └── visu_pars
│   ├── pulseprogram
│   ├── specpar
│   ├── uxnmr.info
│   ├── uxnmr.par
│   └── visu_pars
├── 7
│   ├── acqp
│   ├── AdjStatePerScan
│   ├── configscan
│   ├── fid
│   ├── method
│   ├── pdata
│   │   └── 1
│   │       ├── 2dseq
│   │       ├── id
│   │       ├── procs
│   │       ├── reco
│   │       └── visu_pars
│   ├── pulseprogram
│   ├── specpar
│   ├── spnam40
│   ├── uxnmr.info
│   ├── uxnmr.par
│   └── visu_pars
├── 8
│   ├── acqp
│   ├── AdjStatePerScan
│   ├── configscan
│   ├── fid
│   ├── method
│   ├── pdata
│   │   └── 1
│   │       ├── 2dseq
│   │       ├── id
│   │       ├── procs
│   │       ├── reco
│   │       └── visu_pars
│   ├── pulseprogram
│   ├── specpar
│   ├── spnam1
│   ├── spnam40
│   ├── uxnmr.info
│   ├── uxnmr.par
│   └── visu_pars
├── 9
│   ├── acqp
│   ├── AdjStatePerScan
│   ├── configscan
│   ├── fid
│   ├── method
│   ├── pdata
│   │   └── 1
│   │       ├── 2dseq
│   │       ├── id
│   │       ├── procs
│   │       ├── reco
│   │       └── visu_pars
│   ├── pulseprogram
│   ├── specpar
│   ├── spnam0
│   ├── uxnmr.info
│   ├── uxnmr.par
│   └── visu_pars
├── AdjResult
│   ├── 2.16.756.5.5.100.279771525.10448.1725383903.18
│   │   └── result.jcamp
│   ├── 2.16.756.5.5.100.279771525.14755.1725384542.18
│   │   └── result.jcamp
│   ├── 2.16.756.5.5.100.279771525.18160.1725384808.18
│   │   └── result.jcamp
│   ├── 2.16.756.5.5.100.279771525.21172.1725385167.18
│   │   └── result.jcamp
│   ├── 2.16.756.5.5.100.279771525.21497.1725382381.11
│   │   └── result.jcamp
│   ├── 2.16.756.5.5.100.279771525.21497.1725382381.12
│   │   └── result.jcamp
│   ├── 2.16.756.5.5.100.279771525.21497.1725382381.13
│   │   └── result.jcamp
│   ├── 2.16.756.5.5.100.279771525.21497.1725382381.14
│   │   └── result.jcamp
│   ├── 2.16.756.5.5.100.279771525.22653.1725385466.19
│   │   └── result.jcamp
│   ├── 2.16.756.5.5.100.279771525.24293.1725385764.20
│   │   └── result.jcamp
│   ├── 2.16.756.5.5.100.279771525.25000.1725382610.15
│   │   └── result.jcamp
│   ├── 2.16.756.5.5.100.279771525.25000.1725382610.16
│   │   └── result.jcamp
│   ├── 2.16.756.5.5.100.279771525.25000.1725382610.17
│   │   └── result.jcamp
│   ├── 2.16.756.5.5.100.279771525.25000.1725382610.18
│   │   └── result.jcamp
│   ├── 2.16.756.5.5.100.279771525.26645.1725386224.21
│   │   └── result.jcamp
│   ├── 2.16.756.5.5.100.279771525.28505.1725382870.19
│   │   └── result.jcamp
│   ├── 2.16.756.5.5.100.279771525.7087.1725383497.22
│   │   └── result.jcamp
│   ├── 2.16.756.5.5.100.279771525.8357.1725381337.10
│   │   └── result.jcamp
│   ├── 2.16.756.5.5.100.279771525.8357.1725381337.7
│   │   └── result.jcamp
│   ├── 2.16.756.5.5.100.279771525.8357.1725381337.8
│   │   └── result.jcamp
│   ├── 2.16.756.5.5.100.279771525.8357.1725381337.9
│   │   └── result.jcamp
│   ├── 2.16.756.5.5.100.279771525.8508.1725383642.18
│   │   └── result.jcamp
│   └── 2.16.756.5.5.100.279771525.9476.1725383773.18
│       └── result.jcamp
├── AdjStatePerStudy
├── ResultState
├── ScanProgram.scanProgram
└── subject

brkraw tonii_all Raw/
[Error] Invalid input path: Raw/
         The input path indicates raw data itself. 
        You must input the parents folder instead of path of the raw data
        If you want to convert single session raw data, use (tonii) instead.
NoneType: None
Traceback (most recent call last):
  File "/home/negin/envs/my3env/bin/brkraw", line 11, in <module>
    load_entry_point('brkraw==0.3.10', 'console_scripts', 'brkraw')()
  File "/home/negin/envs/my3env/lib/python3.8/site-packages/brkraw/scripts/brkraw.py", line 219, in main
    raise InvalidApproach(invalid_error_message)
brkraw.lib.errors.InvalidApproach: [Error] Invalid input path: Raw/

I also tried using 'info' but that also failed:

brkraw info Raw/
Traceback (most recent call last):
  File "/home/negin/envs/my3env/bin/brkraw", line 11, in <module>
    load_entry_point('brkraw==0.3.10', 'console_scripts', 'brkraw')()
  File "/home/negin/envs/my3env/lib/python3.8/site-packages/brkraw/scripts/brkraw.py", line 111, in main
    study.info()
  File "/home/negin/envs/my3env/lib/python3.8/site-packages/brkraw/lib/loader.py", line 721, in info
    dim, cls = self._get_dim_info(visu_pars)
  File "/home/negin/envs/my3env/lib/python3.8/site-packages/brkraw/lib/loader.py", line 867, in _get_dim_info
    if not all(map(lambda x: x == 'spatial', dim_desc)):
TypeError: 'NoneType' object is not iterable

@dvm-shlee