# Using mne-bids to convert CTF data to bids format

**URL:** <https://mne.discourse.group/t/using-mne-bids-to-convert-ctf-data-to-bids-format/5336>\
**Category:** Support & Discussions\
**Tags:** mne-bids, mne-bids-pipeline\
**Created:** [July 27, 2022, 11:46am UTC](https://mne.discourse.group/t/using-mne-bids-to-convert-ctf-data-to-bids-format/5336 "2022-07-27T11:46:47Z")\
**Posts on this page:** 20\
**Page:** 1

<div class="post-metadata">

**Author:** ![tghafari](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/tghafari/32/1779_2.png) [@tghafari](https://mne.discourse.group/u/tghafari)\
**Post date:** [July 27, 2022, 11:46am UTC](https://mne.discourse.group/t/using-mne-bids-to-convert-ctf-data-to-bids-format/5336/1 "2022-07-27T11:46:47Z")

</div>

Hi all,

I am trying to convert a set of MEG data collected by CTF scanner (extension: .ds) to BIDS format, using mne-bids. it raises the error below on all the files I try.

[WinError 183] Cannot create a file when that file already exists: ‘Z\MEG\_data\MNE-pilot-data-bids\sub-02\ses-01\meg\sub-02\_ses-01\_task-SpAtt\_run-01\_meg.ds\MarkerFile.mrk.bak’ → ‘Z\MEG\_data\MNE-pilot-data-bids\sub-02\ses-01\meg\sub-02\_ses-01\_task-SpAtt\_run-01\_meg.ds\sub-02\_ses-01\_task-SpAtt\_run-01\_meg.bak’

All the files in the ‘MNE-pilot-data-bids’ are created by write\_raw\_bids from mne\_bids yet it still raises an error about the file that has been created by itself.

This error does not happen with .fif files (Elekta/Megin scanner files).

- MNE version: 1.0.3

- operating system: Windows 10

- code snippet:

```python
write_raw_bids(raw, bids_path, events_data=events_data, 
               event_id=events_id, overwrite=True)

```

I appreciate any help,  
Thanks,  
Tara

---

<div class="post-metadata">

**Author:** ![sappelhoff](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/sappelhoff/32/3276_2.png) [@sappelhoff](https://mne.discourse.group/u/sappelhoff)\
**Post date:** [July 27, 2022, 12:35pm UTC](https://mne.discourse.group/t/using-mne-bids-to-convert-ctf-data-to-bids-format/5336/2 "2022-07-27T12:35:32Z")

</div>

Hi Tara, thanks for the report.

- is this the full traceback or is there more information in the error message?
- Have you tried this on another operating system (Linux, Mac?)
- Can you make a part of the data available and prepare a minimal working example (MWE) so that we can potentially reproduce the bug?

---

<div class="post-metadata">

**Author:** ![tghafari](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/tghafari/32/1779_2.png) [@tghafari](https://mne.discourse.group/u/tghafari)\
**Post date:** [July 28, 2022, 12:02pm UTC](https://mne.discourse.group/t/using-mne-bids-to-convert-ctf-data-to-bids-format/5336/3 "2022-07-28T12:02:33Z")

</div>

Hi Stefan,

Thanks for your timely reply.

- Below please find the full traceback of the error message:

```python
Traceback (most recent call last):

  File "C:\Users\ghafarit\AppData\Local\Temp\ipykernel_11684\1508003131.py", line 1, in <module>
    write_raw_bids(raw, bids_path, events_data=events_data,

  File "<decorator-gen-585>", line 12, in write_raw_bids

  File "C:\Users\ghafarit\Anaconda3\envs\mne\lib\site-packages\mne_bids\write.py", line 1755, in write_raw_bids
    copyfile_ctf(raw_fname, bids_path)

  File "C:\Users\ghafarit\Anaconda3\envs\mne\lib\site-packages\mne_bids\copyfiles.py", line 164, in copyfile_ctf
    os.rename(op.join(dest, fname),

FileExistsError: [WinError 183] Cannot create a file when that file already exists: 'Z:\\MEG_data\\MNE-pilot-data-bids\\sub-02\\ses-01\\meg\\sub-02_ses-01_task-SpAtt_run-01_meg.ds\\MarkerFile.mrk.bak' -> 'Z:\\MEG_data\\MNE-pilot-data-bids\\sub-02\\ses-01\\meg\\sub-02_ses-01_task-SpAtt_run-01_meg.ds\\sub-02_ses-01_task-SpAtt_run-01_meg.bak'

```

- I’m afraid I don’t have access to any other operating system at the moment.

- below please find an MWE:  
[mTBI-predict/00\_MWE\_for\_mne\_bids.py at main · tghafari/mTBI-predict · GitHub](https://github.com/tghafari/mTBI-predict/blob/main/Equipment%20testing/00_MWE_for_mne_bids.py)

- Could you please help me and say how would you suggest I share a small (400Mb) MEG dataset with you? I am happy to share it but don’t have a preference where to.

Thanks,  
Tara

---

<div class="post-metadata">

**Author:** ![richard](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/richard/32/15_2.png) [@richard](https://mne.discourse.group/u/richard)\
**Post date:** [July 28, 2022, 12:39pm UTC](https://mne.discourse.group/t/using-mne-bids-to-convert-ctf-data-to-bids-format/5336/4 "2022-07-28T12:39:41Z")

</div>

Hello @tghafari, just a minor note: I edited your post to make the traceback more readable: I simply selected it with my mouse and clicked on the “Preformatted text” in the toolbar. This ensures that blocks of code and tracebacks appear with syntax highlighting.

Best wishes,  
Richard

---

<div class="post-metadata">

**Author:** ![tghafari](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/tghafari/32/1779_2.png) [@tghafari](https://mne.discourse.group/u/tghafari)\
**Post date:** [July 28, 2022, 12:40pm UTC](https://mne.discourse.group/t/using-mne-bids-to-convert-ctf-data-to-bids-format/5336/5 "2022-07-28T12:40:42Z")

</div>

Hi Richard,

Sorry I realized I forgot to do that only after I noticed the correction you made.

Thank you,  
Tara

---

<div class="post-metadata">

**Author:** ![richard](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/richard/32/15_2.png) [@richard](https://mne.discourse.group/u/richard)\
**Post date:** [July 28, 2022, 12:40pm UTC](https://mne.discourse.group/t/using-mne-bids-to-convert-ctf-data-to-bids-format/5336/6 "2022-07-28T12:40:51Z")

</div>

> [@tghafari](#):
>
> I am happy to share it but don’t have a preference where to.

Google Drive will do, or perhaps iCloud if you have an iCloud account; or OneDrive, since you’re on Windows. Anything.

Best wishes,  
Richard

---

<div class="post-metadata">

**Author:** ![tghafari](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/tghafari/32/1779_2.png) [@tghafari](https://mne.discourse.group/u/tghafari)\
**Post date:** [July 28, 2022, 12:49pm UTC](https://mne.discourse.group/t/using-mne-bids-to-convert-ctf-data-to-bids-format/5336/7 "2022-07-28T12:49:42Z")

</div>

Thanks,

- [this is the MEG data](https://drive.google.com/drive/folders/1Eo2k7oNe_-B7Ja-ZuwCxbhB51LUANNZR?usp=sharing)

- [and this is the events file](https://drive.google.com/file/d/1txu5FQAVH4JHgzMN0glJ7PXn4pJOUlSP/view?usp=sharing)

Bests,  
Tara

---

<div class="post-metadata">

**Author:** ![sappelhoff](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/sappelhoff/32/3276_2.png) [@sappelhoff](https://mne.discourse.group/u/sappelhoff)\
**Post date:** [July 28, 2022, 4:39pm UTC](https://mne.discourse.group/t/using-mne-bids-to-convert-ctf-data-to-bids-format/5336/8 "2022-07-28T16:39:55Z")

</div>

Thanks for sharing the data and a MWE! Unfortunately I cannot reproduce this issue on Ubuntu 18.04 with mne-bids development version

```python

ds directory : /home/stefanappelhoff/Downloads/bla/phantom_mTBIPredict_20220714_spatttrigcheck.ds
    res4 data read.
    hc data read.
    Separate EEG position data file read.
    Quaternion matching (desired vs. transformed):
     -16.72 87.41 0.00 mm <-> -16.72 87.41 -0.00 mm (orig : -73.60 56.20 -232.49 mm) diff = 0.000 mm
      16.72 -87.41 0.00 mm <-> 16.72 -87.41 -0.00 mm (orig : 73.16 -44.49 -231.10 mm) diff = 0.000 mm
     102.70 0.00 0.00 mm <-> 102.70 0.00 0.00 mm (orig : 71.68 76.79 -213.22 mm) diff = 0.000 mm
    Coordinate transformations established.
    Polhemus data for 3 HPI coils added
    Device coordinate locations for 3 HPI coils added
    64 extra points added to Polhemus data.
    Measurement info composed.
Finding samples for /home/stefanappelhoff/Downloads/bla/phantom_mTBIPredict_20220714_spatttrigcheck.ds/phantom_mTBIPredict_20220714_spatttrigcheck.meg4: 
    System clock channel is available, checking which samples are valid.
    1 x 180000 = 180000 samples from 526 chs
Current compensation grade : 0
ds directory : /home/stefanappelhoff/Downloads/bla/phantom_mTBIPredict_20220714_spatttrigcheck.ds
    res4 data read.
    hc data read.
    Separate EEG position data file read.
    Quaternion matching (desired vs. transformed):
     -16.72 87.41 0.00 mm <-> -16.72 87.41 -0.00 mm (orig : -73.60 56.20 -232.49 mm) diff = 0.000 mm
      16.72 -87.41 0.00 mm <-> 16.72 -87.41 -0.00 mm (orig : 73.16 -44.49 -231.10 mm) diff = 0.000 mm
     102.70 0.00 0.00 mm <-> 102.70 0.00 0.00 mm (orig : 71.68 76.79 -213.22 mm) diff = 0.000 mm
    Coordinate transformations established.
    Polhemus data for 3 HPI coils added
    Device coordinate locations for 3 HPI coils added
    64 extra points added to Polhemus data.
    Measurement info composed.
Finding samples for /home/stefanappelhoff/Downloads/bla/phantom_mTBIPredict_20220714_spatttrigcheck.ds/phantom_mTBIPredict_20220714_spatttrigcheck.meg4: 
    System clock channel is available, checking which samples are valid.
    1 x 180000 = 180000 samples from 526 chs
Current compensation grade : 0
Writing '/home/stefanappelhoff/Downloads/out/participants.tsv'...
Writing '/home/stefanappelhoff/Downloads/out/participants.json'...
Writing '/home/stefanappelhoff/Downloads/out/sub-02/ses-01/meg/sub-02_ses-01_coordsystem.json'...
Writing '/home/stefanappelhoff/Downloads/out/sub-02/ses-01/meg/sub-02_ses-01_coordsystem.json'...
Used Annotations descriptions: ['block end', 'block number 1', 'catch trial', 'cue offset', 'cue onset left', 'cue onset right', 'dot onset left', 'dot onset right', 'response button press', 'stim onset']
Writing '/home/stefanappelhoff/Downloads/out/sub-02/ses-01/meg/sub-02_ses-01_task-SpAtt_run-01_events.tsv'...
Writing '/home/stefanappelhoff/Downloads/out/dataset_description.json'...
/home/stefanappelhoff/Desktop/bids/mne-bids/mne_bids/read.py:130: RuntimeWarning: This filename (/home/stefanappelhoff/Downloads/bla/phantom_mTBIPredict_20220714_spatttrigcheck-eve.ds) does not conform to MNE naming conventions. All events files should end with .eve, -eve.fif, -eve.fif.gz, -eve.lst, -eve.txt, _eve.fif, _eve.fif.gz, _eve.lst, _eve.txt or -annot.fif
  events = read_events(events_data).astype(int)
    Coordinate transformations established.
Writing '/home/stefanappelhoff/Downloads/out/sub-02/ses-01/meg/sub-02_ses-01_task-SpAtt_run-01_meg.json'...
Writing '/home/stefanappelhoff/Downloads/out/sub-02/ses-01/meg/sub-02_ses-01_task-SpAtt_run-01_channels.tsv'...
Reading 0 ... 179999 = 0.000 ... 299.998 secs...
Copying data files to sub-02_ses-01_task-SpAtt_run-01_meg.ds
Writing '/home/stefanappelhoff/Downloads/out/sub-02/ses-01/sub-02_ses-01_scans.tsv'...
Wrote /home/stefanappelhoff/Downloads/out/sub-02/ses-01/sub-02_ses-01_scans.tsv entry with meg/sub-02_ses-01_task-SpAtt_run-01_meg.ds.
BIDSPath(
root: /home/stefanappelhoff/Downloads/out
datatype: meg
basename: sub-02_ses-01_task-SpAtt_run-01_meg.ds)

```

Here is my `mne sys_info` output:

```python
Platform: Linux-5.4.0-122-generic-x86_64-with-glibc2.27
Python: 3.10.4 (main, Mar 31 2022, 08:41:55) [GCC 7.5.0]
Executable: /home/stefanappelhoff/miniconda3/envs/mne_bids/bin/python
CPU: x86_64: 8 cores
Memory: 31.2 GB

mne: 1.1.dev0
numpy: 1.22.4 {}
scipy: 1.8.1
matplotlib: 3.5.2 {backend=QtAgg}

sklearn: Not found
numba: Not found
nibabel: 3.2.2
nilearn: Not found
dipy: Not found
cupy: Not found
pandas: 1.4.2
pyvista: Not found
pyvistaqt: Not found
ipyvtklink: Not found
vtk: Not found
qtpy: 2.0.1 {PyQt5=5.9.7}
ipympl: Not found
pyqtgraph: Not found
pooch: v1.6.0

mne_bids: 0.11.dev0
mne_nirs: Not found
mne_features: Not found
mne_qt_browser: Not found
mne_connectivity: 0.4dev0
mne_icalabel: Not found

```

---

<div class="post-metadata">

**Author:** ![tghafari](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/tghafari/32/1779_2.png) [@tghafari](https://mne.discourse.group/u/tghafari)\
**Post date:** [July 28, 2022, 4:48pm UTC](https://mne.discourse.group/t/using-mne-bids-to-convert-ctf-data-to-bids-format/5336/9 "2022-07-28T16:48:47Z")

</div>

Thank Stefan,

Could you please share the final output for folder structure and file names created by write\_raw\_bids?  
And just to confirm did you run my script or did you have to change parts of it in order for it to run without error?

Bests,  
Tara

---

<div class="post-metadata">

**Author:** ![sappelhoff](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/sappelhoff/32/3276_2.png) [@sappelhoff](https://mne.discourse.group/u/sappelhoff)\
**Post date:** [July 28, 2022, 5:10pm UTC](https://mne.discourse.group/t/using-mne-bids-to-convert-ctf-data-to-bids-format/5336/10 "2022-07-28T17:10:41Z")

</div>

Sure, see below:

I ran your script and only adjusted the data path, see: `/home/stefanappelhoff/Downloads/bla/phantom_mTBIPredict_20220714_spatttrigcheck.ds` (the events file you uploaded separately is also in the `bla` folder). Everything ran without error.

```python
.
├── dataset_description.json
├── participants.json
├── participants.tsv
├── README
└── sub-02
    └── ses-01
        ├── meg
        │ ├── sub-02_ses-01_coordsystem.json
        │ ├── sub-02_ses-01_task-SpAtt_run-01_channels.tsv
        │ ├── sub-02_ses-01_task-SpAtt_run-01_events.tsv
        │ ├── sub-02_ses-01_task-SpAtt_run-01_meg.ds
        │ │ ├── BadChannels
        │ │ ├── bad.segments
        │ │ ├── ClassFile.cls
        │ │ ├── DigTrigChannelInfo.txt
        │ │ ├── hz.ds
        │ │ │ ├── BadChannels
        │ │ │ ├── hz.acq
        │ │ │ ├── hz.hc
        │ │ │ ├── hz.hist
        │ │ │ ├── hz.infods
        │ │ │ ├── hz.meg4
        │ │ │ ├── hz.newds
        │ │ │ └── hz.res4
        │ │ ├── MarkerFile.mrk
        │ │ ├── sub-02_ses-01_task-SpAtt_run-01_meg.acq
        │ │ ├── sub-02_ses-01_task-SpAtt_run-01_meg.bak
        │ │ ├── sub-02_ses-01_task-SpAtt_run-01_meg.eeg
        │ │ ├── sub-02_ses-01_task-SpAtt_run-01_meg.hc
        │ │ ├── sub-02_ses-01_task-SpAtt_run-01_meg.hist
        │ │ ├── sub-02_ses-01_task-SpAtt_run-01_meg.infods
        │ │ ├── sub-02_ses-01_task-SpAtt_run-01_meg.meg4
        │ │ ├── sub-02_ses-01_task-SpAtt_run-01_meg.newds
        │ │ └── sub-02_ses-01_task-SpAtt_run-01_meg.res4
        │ └── sub-02_ses-01_task-SpAtt_run-01_meg.json
        └── sub-02_ses-01_scans.tsv

5 directories, 31 files

```

---

<div class="post-metadata">

**Author:** ![richard](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/richard/32/15_2.png) [@richard](https://mne.discourse.group/u/richard)\
**Post date:** [July 28, 2022, 5:14pm UTC](https://mne.discourse.group/t/using-mne-bids-to-convert-ctf-data-to-bids-format/5336/11 "2022-07-28T17:14:41Z")

</div>

@tghafari Which version of MNE-BIDS are you using?

@sappelhoff apparently used the development version, which may have fixes that are not included in previous releases 🤔

---

<div class="post-metadata">

**Author:** ![tghafari](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/tghafari/32/1779_2.png) [@tghafari](https://mne.discourse.group/u/tghafari)\
**Post date:** [July 28, 2022, 5:53pm UTC](https://mne.discourse.group/t/using-mne-bids-to-convert-ctf-data-to-bids-format/5336/12 "2022-07-28T17:53:09Z")

</div>

@sappelhoff thanks, all seems great on your side.

@richard I am using mne 1.0.3.

Can I even upgrade to the development version? or what do you recommend I do?

Thanks

---

<div class="post-metadata">

**Author:** ![richard](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/richard/32/15_2.png) [@richard](https://mne.discourse.group/u/richard)\
**Post date:** [July 28, 2022, 6:40pm UTC](https://mne.discourse.group/t/using-mne-bids-to-convert-ctf-data-to-bids-format/5336/13 "2022-07-28T18:40:51Z")

</div>

Hello,

> [@tghafari](#):
>
> @richard I am using mne 1.0.3.

I was asking about MNE-BIDS 🙂

Could you please share the output of the following Python commands:

```python
import mne
mne.sys_info()

```

Thanks!

---

<div class="post-metadata">

**Author:** ![tghafari](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/tghafari/32/1779_2.png) [@tghafari](https://mne.discourse.group/u/tghafari)\
**Post date:** [July 29, 2022, 10:11am UTC](https://mne.discourse.group/t/using-mne-bids-to-convert-ctf-data-to-bids-format/5336/14 "2022-07-29T10:11:11Z")

</div>

Hi @richard,

Sorry I misread your message.

below please see my sys\_info:

```python
Platform: Windows-10-10.0.19042-SP0
Python: 3.9.12 | packaged by conda-forge | (main, Mar 24 2022, 23:17:03) [MSC v.1929 64 bit (AMD64)]
Executable: C:\Users\ghafarit\Anaconda3\envs\mne\python.exe
CPU: Intel64 Family 6 Model 140 Stepping 1, GenuineIntel: 8 cores
Memory: 31.7 GB

mne: 1.0.3
numpy: 1.21.6 {blas=NO_ATLAS_INFO, lapack=lapack}
scipy: 1.8.0
matplotlib: 3.5.2 {backend=module://matplotlib_inline.backend_inline}

sklearn: 1.1.0
numba: 0.55.1
nibabel: 3.2.2
nilearn: 0.9.1
dipy: 1.5.0
cupy: Not found
pandas: 1.4.2
pyvista: 0.34.0 {OpenGL 4.5.0 - Build 30.0.101.1404 via Intel(R) Iris(R) Xe Graphics}
pyvistaqt: 0.9.0
ipyvtklink: 0.2.2
vtk: 9.1.0
PyQt5: 5.12.3
ipympl: Not found
pooch: v1.6.0

mne_bids: 0.10
mne_nirs: Not found
mne_features: Not found
mne_qt_browser: 0.3.1
mne_connectivity: Not found

```

thanks,  
Tara

---

<div class="post-metadata">

**Author:** ![sappelhoff](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/sappelhoff/32/3276_2.png) [@sappelhoff](https://mne.discourse.group/u/sappelhoff)\
**Post date:** [July 29, 2022, 11:14am UTC](https://mne.discourse.group/t/using-mne-bids-to-convert-ctf-data-to-bids-format/5336/15 "2022-07-29T11:14:16Z")

</div>

@tghafari please see if running `python -m pip install --upgrade https://api.github.com/repos/mne-tools/mne-bids/zipball/main` solves your issue (this is installing the mne-bids development version. To revert it, run `pip uninstall mne_bids`, followed by another `pip install mne_bids` … this will get you back to the “stable” version)

---

<div class="post-metadata">

**Author:** ![tghafari](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/tghafari/32/1779_2.png) [@tghafari](https://mne.discourse.group/u/tghafari)\
**Post date:** [August 2, 2022, 9:47am UTC](https://mne.discourse.group/t/using-mne-bids-to-convert-ctf-data-to-bids-format/5336/16 "2022-08-02T09:47:12Z")

</div>

Thanks Stefan,  
This also didn’t help, the same error was raised:

```python
File "C:\Users\ghafarit\AppData\Local\Temp\ipykernel_18068\3279010892.py", line 1, in <module>
    write_raw_bids(raw, bids_path, events_data=events_data,

  File "<decorator-gen-585>", line 12, in write_raw_bids

  File "C:\Users\ghafarit\Anaconda3\envs\mne\lib\site-packages\mne_bids\write.py", line 1755, in write_raw_bids
    copyfile_ctf(raw_fname, bids_path)

  File "C:\Users\ghafarit\Anaconda3\envs\mne\lib\site-packages\mne_bids\copyfiles.py", line 164, in copyfile_ctf
    os.rename(op.join(dest, fname),

FileExistsError: [WinError 183] Cannot create a file when that file already exists: 'Z:\\MEG_data\\MNE-pilot-data-bids\\sub-02\\ses-01\\meg\\sub-02_ses-01_task-SpAtt_run-01_meg.ds\\MarkerFile.mrk.bak' -> 'Z:\\MEG_data\\MNE-pilot-data-bids\\sub-02\\ses-01\\meg\\sub-02_ses-01_task-SpAtt_run-01_meg.ds\\sub-02_ses-01_task-SpAtt_run-01_meg.bak'

```

Do you have any suggestions? Could this be solely resulted by my OS?

Thanks,  
Tara

---

<div class="post-metadata">

**Author:** ![sappelhoff](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/sappelhoff/32/3276_2.png) [@sappelhoff](https://mne.discourse.group/u/sappelhoff)\
**Post date:** [August 2, 2022, 10:11am UTC](https://mne.discourse.group/t/using-mne-bids-to-convert-ctf-data-to-bids-format/5336/17 "2022-08-02T10:11:20Z")

</div>

This function is triggering the error: [https://github.com/mne-tools/mne-bids/blob/ace2a7d55ba943bb3cc0437ded1ac850c71ae278/mne\_bids/copyfiles.py#L137-L166](https://github.com/mne-tools/mne-bids/blob/ace2a7d55ba943bb3cc0437ded1ac850c71ae278/mne_bids/copyfiles.py#L137-L166)

specifically, the `os.rename` part of it.

Now let’s look at `os.rename`: [os — Miscellaneous operating system interfaces — Python 3.12.0 documentation](https://docs.python.org/3/library/os.html#os.rename)

it says:

> On Windows, if _dst_ exists a [`FileExistsError`](https://docs.python.org/3/library/exceptions.html#FileExistsError) is always raised.

Interestingly it doesn’t say so for unix systems (linux, macos) – so this might be why I cannot reproduce your problem.

I think the solution might be that if `write_raw_bids` is called with `overwrite=True` (so the files already exist), then we should first completely remove the existing files before writing them again … because apparently the overwriting via `os.rename` doesn’t work on Windows.

Or we could look into using `os.replace` instead, see: If you want cross-platform overwriting of the destination, use [`replace()`](https://docs.python.org/3/library/os.html#os.replace). (also from the os.rename docs)

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<div class="post-metadata">

**Author:** ![sappelhoff](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/sappelhoff/32/3276_2.png) [@sappelhoff](https://mne.discourse.group/u/sappelhoff)\
**Post date:** [August 2, 2022, 10:24am UTC](https://mne.discourse.group/t/using-mne-bids-to-convert-ctf-data-to-bids-format/5336/18 "2022-08-02T10:24:09Z")

</div>

@tghafari could you please try to install my fix and try it out? See also: [fix: replace instead of rename for win support by sappelhoff · Pull Request #1035 · mne-tools/mne-bids · GitHub](https://github.com/mne-tools/mne-bids/pull/1035)

```bash
pip uninstall mne_bids
pip install git+ssh://git@github.com/sappelhoff/mne-bids.git@fix/ctf/rename

```

if you want to go back to your previous version, just do:

```bash
pip uninstall mne_bids
pip install mne_bids

```

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<div class="post-metadata">

**Author:** ![tghafari](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/tghafari/32/1779_2.png) [@tghafari](https://mne.discourse.group/u/tghafari)\
**Post date:** [August 3, 2022, 10:28am UTC](https://mne.discourse.group/t/using-mne-bids-to-convert-ctf-data-to-bids-format/5336/19 "2022-08-03T10:28:42Z")

</div>

Hi @sappelhoff ,

Thanks for your reply.  
I’m afraid I don’t have access right to try the fix you suggested. below is the error:

```python
(base) C:\Users\ghafarit>pip install git+ssh://git@github.com/sappelhoff/mne-bids.git@fix/ctf/rename
Collecting git+ssh:// **** @github.com/sappelhoff/mne-bids.git@fix/ctf/rename
  Cloning ssh:// **** @github.com/sappelhoff/mne-bids.git (to revision fix/ctf/rename) to c:\users\ghafarit\appdata\local\temp\pip-req-build-fjnpdfx4
  Running command git clone -q 'ssh:// **** @github.com/sappelhoff/mne-bids.git' 'C:\Users\ghafarit\AppData\Local\Temp\pip-req-build-fjnpdfx4'
  Host key verification failed.
  fatal: Could not read from remote repository.

  Please make sure you have the correct access rights
  and the repository exists.
WARNING: Discarding git+ssh:// ****@github.com/sappelhoff/mne-bids.git@fix/ctf/rename. Command errored out with exit status 128: git clone -q 'ssh://**** @github.com/sappelhoff/mne-bids.git' 'C:\Users\ghafarit\AppData\Local\Temp\pip-req-build-fjnpdfx4' Check the logs for full command output.
ERROR: Command errored out with exit status 128: git clone -q 'ssh:// **** @github.com/sappelhoff/mne-bids.git' 'C:\Users\ghafarit\AppData\Local\Temp\pip-req-build-fjnpdfx4' Check the logs for full command output.

```

Is there something I should have done before I can have access?

Thanks,  
Tara

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<div class="post-metadata">

**Author:** ![sappelhoff](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/sappelhoff/32/3276_2.png) [@sappelhoff](https://mne.discourse.group/u/sappelhoff)\
**Post date:** [August 3, 2022, 11:29am UTC](https://mne.discourse.group/t/using-mne-bids-to-convert-ctf-data-to-bids-format/5336/21 "2022-08-03T11:29:18Z")

</div>

The fix has already been merged – you can install it via `python -m pip install --upgrade https://api.github.com/repos/mne-tools/mne-bids/zipball/main` now 🙂

[Next page](https://mne.discourse.group/t/using-mne-bids-to-convert-ctf-data-to-bids-format/5336.md?page=2)