About No BOLD images found

[Edenkut]

Hi, I am a beginner using the prfmodel.
I have completed the preprocessing of fMRI and am now trying the pRF model.
I plan to try prfanalyze-vista and set the path according to the BIDS structure based on the results of garikoitz/prfsynth.
However, I encountered a situation where "No BOLD images found!" appears, and I cannot solve it.

[garikoitz]

Can you please send the output error messages, the whole output? maybe we will be able to understand what went wrong. nevertheless we are updating the Docker based container as we speak, we will update the information and the readme soon

…

On Thu, Mar 23, 2023 at 11:53 AM Eden KUT ***@***.***> wrote: Hi, I am a beginner using the prfmodel. I have completed the preprocessing of fMRI and am now trying the pRF model. I plan to try prfanalyze-vista and set the path according to the BIDS structure based on the results of garikoitz/prfsynth. However, I encountered a situation where "No BOLD images found!" appears, and I cannot solve it. — Reply to this email directly, view it on GitHub <#83>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABCZAV7H5O2CLUSX737VKR3W5QTT3ANCNFSM6AAAAAAWFAYA7U> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Edenkut]

Thank you for your reply.

**Here is command info**

docker run --rm -it \ -v $basedir:/flywheel/v0/input \ -v $basedir:/flywheel/v0/output \ -v $basedir/prfanalyze-vista-config_sub-126_sess-nyu3t01.json:/flywheel/v0/input/config.json:ro \ garikoitz/prfanalyze-vista

Error:

no BIDS directory found!

I had two mgz files and a stimulus file. The command I used seems to be for the fmri_bold file.
Could you give me some guidance on how to use prfanalyze-vista within the mgz file and stimulus file?
Thank you in advance for your reply.

[garikoitz]

Hi, the basedir should be the study dir: The base docker is doing this looking for the BIDS: output_dir = '/flywheel/v0/output' input_dir = '/flywheel/v0/input' bids_dir = os.path.join(input_dir, 'BIDS’) if not os.path.isdir(bids_dir): die('no BIDS directory found!') Instead of "latest", you should install "2.2.1_3.1.1" version of the container, can you docker pull prfanalyze-vista:2.2.1_3.1.1 and test please? thanks! Gari

…

On Wed, Apr 12, 2023 at 4:24 AM Eden KUT ***@***.***> wrote: Thank you for your reply. There is my BID folder which I follow the guidance and built similar one. BIDS ├── README ├── dataset_description.json ├── derivatives │ ├── prfanalyze-vista │ │ └── sub-wlsubj126 │ │ └── ses-nyu3t01 │ │ └── sub-wlsubj126_ses-nyu3t01_task-prf_acq-normal_options.json │ └── prfanalyze-vista_temp000 │ └── sub-wlsubj126 │ └── ses-nyu3t01 │ └── sub-wlsubj126_ses-nyu3t01_task-prf_acq-normal_options.json ├── stimuli │ └── sub-wlsubj126_ses-nyu3t01_task-prf_apertures.nii.gz └── sub-wlsubj126 └── ses-nyu3t01 └── func ├── sub-wlsubj126_ses-nyu3t01_task-prf_acq-normal_run-01_bold.json ├── sub-wlsubj126_ses-nyu3t01_task-prf_acq-normal_run-01_bold.nii.gz ├── sub-wlsubj126_ses-nyu3t01_task-prf_events.json └── sub-wlsubj126_ses-nyu3t01_task-prf_events.tsv **Here is command info** docker run --rm -it \ -v $basedir:/flywheel/v0/input \ -v $basedir:/flywheel/v0/output \ -v $basedir/prfanalyze-vista-config_sub-126_sess-nyu3t01.json:/flywheel/v0/input/config.json:ro \ garikoitz/prfanalyze-vista Error: no BIDS directory found! — Reply to this email directly, view it on GitHub <#83 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABCZAV56X6A4H5FYURVHZ6DXAYG4PANCNFSM6AAAAAAWFAYA7U> . You are receiving this because you commented.Message ID: ***@***.***>

[Edenkut]

Thanks, I installed prfanalyze-vista:2.2.1_3.1.1 .

No BOLD images found!
It still happened.

Acually, I had two mgz files and a stimulus file. The command I used is for the fmri_bold file, which had been preprocessed.

The real directory tree is like the following info:
├── BIDS
│   ├── README
│   ├── dataset_description.json
│   └── sub-wlsubj126
│   └── ses-nyu3t01
│   └── func
│   ├── average_L_hemi.mgz
│   └── average_R_hemi.mgz
├── prfanalyze-vista-config_sub-001_sess-20200320.json
└── stimuli
└── sub-wlsubj126_ses-nyu3t01_task-prf_apertures.nii.gz

No events file?
I got the suggestion that "If you are using our data from OpenNeuro (https://openneuro.org/datasets/ds003787/versions/1.0.1), all you should need to reproduce the pRFs are the .mgz files in _derivatives/fmriprep/sub-wlsubj126/ses-nyu3t01/func_. Once you average these .mgz files together, then you have your data as input for the pRF model. The file you want to include as the stimulus to prfanalyze-vista is the .nii.gz file in _derivatives/stimulus_apertures/sub-wlsubj126/ses-nyu3t01/_. Both the .mgz data and the .nii.gz file are 192s long and then you shouldn't get that error. "

Could you guide me on using prfanalyze-vista within the mgz and stimulus file?

Thank you in advance for getting back to me.

[Edenkut]

Sorry for the unclear directory tree.
Here is the correct info:├── BIDS
│ ├── README
│ ├── dataset_description.json
│ └── sub-wlsubj126
│ └── ses-nyu3t01
│ └── func
│ ├── average_L_hemi.mgz
│ └── average_R_hemi.mgz
├── prfanalyze-vista-config_sub-001_sess-20200320.json
└── stimuli
└── sub-wlsubj126_ses-nyu3t01_task-prf_apertures.nii.gz

[garikoitz]

this is weird, we will have a look and get back to you, thanks! Gari

…

On Fri, Apr 14, 2023 at 5:01 AM Eden KUT ***@***.***> wrote: Sorry for the unclear directory tree. Here is the correct info:├── BIDS │ ├── README │ ├── dataset_description.json │ └── sub-wlsubj126 │ └── ses-nyu3t01 │ └── func │ ├── average_L_hemi.mgz │ └── average_R_hemi.mgz ├── prfanalyze-vista-config_sub-001_sess-20200320.json └── stimuli └── sub-wlsubj126_ses-nyu3t01_task-prf_apertures.nii.gz — Reply to this email directly, view it on GitHub <#83 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABCZAV7ZHGO2ONJDKZPGVQLXBC4YXANCNFSM6AAAAAAWFAYA7U> . You are receiving this because you commented.Message ID: ***@***.***>