validation error

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Mahmoud

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Apr 18, 2018, 4:49:39 PM4/18/18
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Hi everyone,

I created this Nifti folder and its content on desktop of my PC.


I am using this BIDS validator (http://incf.github.io/bids-validator/) to validate my file conversion and it gives me an error file (attached) but I don't understand what is going wrong here.

I appreciate if someone could give me a hint.

Thank you!
Mahmoud
sub-00008_03_errors.txt

Chris Gorgolewski

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Apr 18, 2018, 5:28:52 PM4/18/18
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Hi,

A few things:

1. Labels cannot include underscores "_". So `sub-0000803` instead of `sub-0000803` (it seems that you got an explicit error about this)
2. It's `T1w` not `T1W`. similar with T2w
3. Suffixes need to be at the end of the filename so `sub-0000803_ses-2_acq-MPRAGE_run-1_T1w.nii.gz`

I hope this helps. You can check out more examples of BIDS datasets on http://OpenNeuro.org

Best,
Chris

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Mahmoud

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Apr 18, 2018, 9:35:01 PM4/18/18
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Dear Chris,

Thanks for your advice.
Our subject ID has to have two parts because of they have meanings. Is there any way to keep them separate?

Thank you,
Mahmoud

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Chris Gorgolewski

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Apr 18, 2018, 9:44:15 PM4/18/18
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You could use a letter to separate them.

Best,
Chris


Best,
Chris

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eric...@gmail.com

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Apr 19, 2018, 10:05:43 AM4/19/18
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Would a period (aka. dot) be an acceptable delimiter in BIDS?

Chris Gorgolewski

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Apr 19, 2018, 10:31:56 AM4/19/18
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Not currently. It's restricted to letters and numbers.

Best,
Chris

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Mahmoud

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Apr 25, 2018, 2:53:15 PM4/25/18
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Hi everyone,

What is wrong with this file naming: sub-00008T03_ses-1_task-rest_acq-TR720_run-1AP_bold.nii.gz
I'm getting an error from bids validator that "Files with such naming scheme are not part of BIDS specification"

I am trying to include PA and AP in file names, not sure where to put it. I tried _acq-TR720AP_ but did not work either.

Thanks,
Mahmoud

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Tal Yarkoni

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Apr 25, 2018, 3:02:49 PM4/25/18
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I don't know if this is the only problem, but runs can only have numerical values. So at minimum, the "run-1AP" part of your filename should be "run-1".

You could potentially put AP in either "session" or "subject", as those are allowed to be strings.


On Wed, Apr 25, 2018 at 1:52 PM, Mahmoud <zeyd...@gmail.com> wrote:
Hi everyone,

What is wrong with this file naming: sub-00008T03_ses-1_task-rest_acq-TR720_run-1AP_bold.nii.gz
I'm getting an error from bids validator that "Files with such naming scheme are not part of BIDS specification"

I am trying to include PA and AP in file names, not sure where to put it. I tried _acq-TR720AP_ but did not work either.

Thanks,
Mahmoud

Chris Gorgolewski

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Apr 25, 2018, 3:32:12 PM4/25/18
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The general pattern is:
sub-<participant_label>[_ses-<session_label>]_task-<task_label>[_acq-<label>][_rec-<label>][_run-<index>][_echo-<index>]_bold.nii[.gz]

So
sub-00008T03/ses-1/sub-00008T03_ses-1_task-rest_acq-TR720AP_run-1_bold.nii.gz

should work.

Best,
Chris


On Wed, Apr 25, 2018 at 12:02 PM Tal Yarkoni <tyar...@gmail.com> wrote:

I don't know if this is the only problem, but runs can only have numerical values. So at minimum, the "run-1AP" part of your filename should be "run-1".

You could potentially put AP in either "session" or "subject", as those are allowed to be strings.

On Wed, Apr 25, 2018 at 1:52 PM, Mahmoud <zeyd...@gmail.com> wrote:
Hi everyone,

What is wrong with this file naming: sub-00008T03_ses-1_task-rest_acq-TR720_run-1AP_bold.nii.gz
I'm getting an error from bids validator that "Files with such naming scheme are not part of BIDS specification"

I am trying to include PA and AP in file names, not sure where to put it. I tried _acq-TR720AP_ but did not work either.

Thanks,
Mahmoud

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Mahmoud

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Apr 25, 2018, 5:31:58 PM4/25/18
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Hi Chris,

Could you please take a look at the attached file? My file name is exactly like yours but I still receive errors.


Thank you,
Mahmoud

On Wed, Apr 25, 2018 at 3:31 PM, Chris Gorgolewski <krzysztof....@gmail.com> wrote:
The general pattern is:
sub-<participant_label>[_ses-<session_label>]_task-<task_label>[_acq-<label>][_rec-<label>][_run-<index>][_echo-<index>]_bold.nii[.gz]

So
sub-00008T03/ses-1/sub-00008T03_ses-1_task-rest_acq-TR720AP_run-1_bold.nii.gz

should work.

Best,
Chris

On Wed, Apr 25, 2018 at 12:02 PM Tal Yarkoni <tyar...@gmail.com> wrote:

I don't know if this is the only problem, but runs can only have numerical values. So at minimum, the "run-1AP" part of your filename should be "run-1".

You could potentially put AP in either "session" or "subject", as those are allowed to be strings.

On Wed, Apr 25, 2018 at 1:52 PM, Mahmoud <zeyd...@gmail.com> wrote:
Hi everyone,

What is wrong with this file naming: sub-00008T03_ses-1_task-rest_acq-TR720_run-1AP_bold.nii.gz
I'm getting an error from bids validator that "Files with such naming scheme are not part of BIDS specification"

I am trying to include PA and AP in file names, not sure where to put it. I tried _acq-TR720AP_ but did not work either.

Thanks,
Mahmoud
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sourcedata_errors.txt

Chris Gorgolewski

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Apr 25, 2018, 5:40:56 PM4/25/18
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Hi,

Thanks for sharing the log.

All the errors I see there concern missing or malformed metadata in the JSON files - not actual file names. It seems you got the filenames right and now you need to fix the metadata.

Best,
Chris


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Mahmoud

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Apr 25, 2018, 5:53:27 PM4/25/18
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Hi Chris,

Thanks for your response. But I'm seeing errors other than JSON. Please see below:

Error 1;
You have to define 'RepetitionTime' for this file.

sub-00008T03_ses-1_task-rest_acq-TR720AP_run-1_bold.nii.gz
128563.655 KB | application/gzip
Location:

sourcedata/sub-00008T03/ses-1/func/sub-00008T03_ses-1_task-rest_acq-TR720AP_run-1_bold.nii.gz
Reason:

You have to define 'RepetitionTime' for this file. It can be included one of the following locations: /bold.json, /task-rest_bold.json, /task-rest_acq-TR720AP_bold.json, /sub-00008T03/sub-00008T03_bold.json, /sub-00008T03/sub-00008T03_task-rest_bold.json, /sub-00008T03/sub-00008T03_task-rest_acq-TR720AP_bold.json, /sub-00008T03/ses-1/sub-00008T03_ses-1_bold.json, /sub-00008T03/ses-1/sub-00008T03_ses-1_task-rest_bold.json, /sub-00008T03/ses-1/sub-00008T03_ses-1_task-rest_acq-TR720AP_bold.json, /sub-00008T03/ses-1/func/sub-00008T03_ses-1_task-rest_acq-TR720AP_run-1_bold.json

Error: 2
You have to define 'TaskName' for this file.

sub-00008T03_ses-1_task-rest_acq-TR720AP_run-1_bold.nii.gz
128563.655 KB | application/gzip
Location:

sourcedata/sub-00008T03/ses-1/func/sub-00008T03_ses-1_task-rest_acq-TR720AP_run-1_bold.nii.gz
Reason:

You have to define 'TaskName' for this file. It can be included one of the following locations: /bold.json, /task-rest_bold.json, /task-rest_acq-TR720AP_bold.json, /sub-00008T03/sub-00008T03_bold.json, /sub-00008T03/sub-00008T03_task-rest_bold.json, /sub-00008T03/sub-00008T03_task-rest_acq-TR720AP_bold.json, /sub-00008T03/ses-1/sub-00008T03_ses-1_bold.json, /sub-00008T03/ses-1/sub-00008T03_ses-1_task-rest_bold.json, /sub-00008T03/ses-1/sub-00008T03_ses-1_task-rest_acq-TR720AP_bold.json, /sub-00008T03/ses-1/func/sub-00008T03_ses-1_task-rest_acq-TR720AP_run-1_bold.json

Thanks,
Mahmoud

On Wed, Apr 25, 2018 at 5:40 PM, Chris Gorgolewski <krzysztof....@gmail.com> wrote:
Hi,

Thanks for sharing the log.

All the errors I see there concern missing or malformed metadata in the JSON files - not actual file names. It seems you got the filenames right and now you need to fix the metadata.

Best,
Chris

On Wed, Apr 25, 2018 at 2:31 PM Mahmoud <zeyd...@gmail.com> wrote:
Hi Chris,

Could you please take a look at the attached file? My file name is exactly like yours but I still receive errors.


Thank you,
Mahmoud
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Chris Gorgolewski

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Apr 25, 2018, 6:01:38 PM4/25/18
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Hi Mahmoud,

These errors are related to missing metadata in JSON files. Have a look at the detailed explanation of the error:

You have to define 'RepetitionTime' for this file. It can be included one of the following locations: /bold.json, /task-rest_bold.json, /task-rest_acq-TR720AP_bold.json, /sub-00008T03/sub-00008T03_bold.json, /sub-00008T03/sub-00008T03_task-rest_bold.json, /sub-00008T03/sub-00008T03_task-rest_acq-TR720AP_bold.json, /sub-00008T03/ses-1/sub-00008T03_ses-1_bold.json, /sub-00008T03/ses-1/sub-00008T03_ses-1_task-rest_bold.json, /sub-00008T03/ses-1/sub-00008T03_ses-1_task-rest_acq-TR720AP_bold.json, /sub-00008T03/ses-1/func/sub-00008T03_ses-1_task-rest_acq-TR720AP_run-1_bold.json

Maybe checking out some example datasets will help to make things bit more clear: https://github.com/INCF/BIDS-examples

Best,
Chris


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Mahmoud

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Apr 25, 2018, 6:48:52 PM4/25/18
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Thanks, Chirs.

That solved the problem.

Best,
Mahmoud

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Mahmoud

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Apr 30, 2018, 6:04:34 PM4/30/18
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Hi Chris,

I have a b0 dwi that is acquired in the opposite direction to our main dwi (67 volumes) for purpose of distortion correction.
This b0 has just one volume and dcm2niix does not create bval or bvec files for it. So, I create these files in my script by writing a "0" for bval and a column of three zeros "0\n0\n\0" for bvec.

sub-00106T03_ses-3_acq-b0_run-1_dwi.bval
sub-00106T03_ses-3_acq-b0_run-1_dwi.bvec

However, the bids validator outputs this error:
Location:

sourcedata/sub-00106T03/ses-3/dwi/sub-00106T03_ses-3_acq-b0_run-1_dwi.nii.gz
Reason:

The number of volumes in this scan does not match the number of volumes in the corresponding .bvec and .bval files.

Could you please advise?

Thanks,
Mahmoud


On Wed, Apr 25, 2018 at 6:48 PM, Mahmoud <zeyd...@gmail.com> wrote:
Thanks, Chirs.

That solved the problem.

Best,
Mahmoud

Chris Gorgolewski

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Apr 30, 2018, 6:20:38 PM4/30/18
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Hi,

Since this single volume image was acquired to perform distortion correction it should go into fmap folder. More specifically

sub-00106T03/ses-3/fmap/sub-00106T03_ses-3_dir-LR_epi.nii.gz
sub-00106T03/ses-3/fmap/sub-00106T03_ses-3_dir-LR_epi.json
(replace LR with an appropriate intuitive label of your choosing describing the phase encoding direction)

Where the JSON file should include IntendedFor and PhaseEncodingDirection fields. See section 8.3.5.4 of http://bids.neuroimaging.io/bids_spec1.1.0.pdf  for more details

Best,
Chris


On Mon, Apr 30, 2018 at 3:04 PM Mahmoud <zeyd...@gmail.com> wrote:
Hi Chris,

I have a b0 dwi that is acquired in the opposite direction to our main dwi (67 volumes) for purpose of distortion correction.
This b0 has just one volume and dcm2niix does not create bval or bvec files for it. So, I create these files in my script by writing a "0" for bval and a column of three zeros "0\n0\n\0" for bvec.

sub-00106T03_ses-3_acq-b0_run-1_dwi.bval
sub-00106T03_ses-3_acq-b0_run-1_dwi.bvec

However, the bids validator outputs this error:
Location:

sourcedata/sub-00106T03/ses-3/dwi/sub-00106T03_ses-3_acq-b0_run-1_dwi.nii.gz
Reason:

The number of volumes in this scan does not match the number of volumes in the corresponding .bvec and .bval files.

Could you please advise?

Thanks,
Mahmoud

On Wed, Apr 25, 2018 at 6:48 PM, Mahmoud <zeyd...@gmail.com> wrote:
Thanks, Chirs.

That solved the problem.

Best,
Mahmoud

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Mahmoud

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Apr 30, 2018, 6:39:56 PM4/30/18
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Hi Chris,

Thanks for your response. But, this is not really a field map image. Should I still put it the fmap directory?
And in some other older instances, we've acquired this b0 volume in this way: (6 averages of b0s plus one dwi) I guess this was because of some limitations in an older version of Simens MRI software. In this case dcm2niix provides me with bvec and bval files.
How should I treat these volumes?

Thanks,
Mahmoud

On Mon, Apr 30, 2018 at 6:20 PM, Chris Gorgolewski <krzysztof....@gmail.com> wrote:
Hi,

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Chris Gorgolewski

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Apr 30, 2018, 6:52:48 PM4/30/18
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On Mon, Apr 30, 2018 at 3:39 PM Mahmoud <zeyd...@gmail.com> wrote:
Hi Chris,

Thanks for your response. But, this is not really a field map image. Should I still put it the fmap directory?
Yup - this is what I would recommend (due to the intention of the acqusition to perform distortion correction and the fact, that b0 alone does not actually measure diffusion).

And in some other older instances, we've acquired this b0 volume in this way: (6 averages of b0s plus one dwi) I guess this was because of some limitations in an older version of Simens MRI software. In this case dcm2niix provides me with bvec and bval files.
How should I treat these volumes?
This is a bit of an edge case. I would still put it into fmap, but skip the single diffusion weighted volume.
 

Thanks,
Mahmoud

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