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It seems to me like it's Freesurfer errors. When I run fMRIPrep with fs-no-reconall in the code on Ubuntu 20.04, it runs smoothly (i.e., no errors).

I already turned to the fMRIPrep list and they can't seem to narrow down the source of these errors, which is why I turned to Freesurfer mailing list.
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@MGH.HARVARD.EDU>
Sent: Wednesday, September 15, 2021 9:56 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all crash errors (fMRIPrep)
 
Are these fMRIPrep errors or freesurfer errors? If fMRIprep, then you should questions to the fMRIprep list

On 9/13/2021 1:19 PM, Rubina Chandnani wrote:

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Hi again,

I don't know if this is useful (or not) but I took a screenshot of one of the functional BOLD image files (that is producing errors) and this is shown below:



Is there something I need to change for the transformation not to give an error?

Thank you and best regards,

Rubina

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Rubina Chandnani <rubinachandnani@hotmail.co.uk>
Sent: Monday, September 13, 2021 6:37 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all crash errors (fMRIPrep)
 

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That's correct. It worked perfectly fine for the first 17 participants. 

I don't know if there's some interaction between my operating system (Windows) and the gzip file failing.

I hope someone can point out how I can overcome this error?

Many thanks for your prompt reply, Rosie.

Best regards,

Rubina
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Rosalia Dacosta Aguayo <rdacostaa@gmail.com>
Sent: Monday, September 13, 2021 6:32 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all crash errors (fMRIPrep)
 

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I do not know for sure. Somebody on the list will hopefully answer your question.

I understand you used the same procedure that you used for the first 17 subjects. I would visually inspect the dicoms to see if there is any trouble with them.

Kind regards,
Rosie




On Mon, Sep 13, 2021 at 6:26 PM Rubina Chandnani <rubinachandnani@hotmail.co.uk> wrote:

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This data was collected by someone else but they used Siemens.

If there is something wrong with the transformation, what can I do in this case?

Thank you and best regards,

Rubina
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Rosalia Dacosta Aguayo <rdacostaa@gmail.com>
Sent: Monday, September 13, 2021 6:16 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all crash errors (fMRIPrep)
 

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It's weird as it seems something is not working properly with the transformation.

Which scanner did you use? Siemens, LG, Philips, Canon?

Kind regards,
Rosie




On Mon, Sep 13, 2021 at 6:12 PM Rubina Chandnani <rubinachandnani@hotmail.co.uk> wrote:

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Hi Rosie,

I used MRIcroGL to convert DICOMs to Niftis.

Kind regards,

Rubina
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Rosalia Dacosta Aguayo <rdacostaa@gmail.com>
Sent: Monday, September 13, 2021 6:06 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all crash errors (fMRIPrep)
 

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Hi Rubina,

How did you gzip your data? Which software did you use?

Kind regards,
Rosie




On Mon, Sep 13, 2021 at 5:59 PM Rubina Chandnani <rubinachandnani@hotmail.co.uk> wrote:

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Hi there,

I'm getting in touch because I'm consistently running into a repeated recon-all error. I've tried so many suggestions (from Neurostars) and I was wondering if you can maybe suggest an alternative to running the Freesurfer license.

I used this code on Ubuntu 20.04 on Windows (it worked smoothly for 17 participants and failed on the remaining participants I need to run pre-processing):

fmriprep-docker /mnt/c/Users/rubin/BIDS /mnt/c/Users/rubin/derivatives participant --participant-label sub-M1121053 --fs-license-file /mnt/c/Users/rubin/fs-license/license.txt --low-mem

More specifically, I get these errors (please see 4 attachments). I also tried gzipping the files (with .gz at the end of the files) but even that failed.

Are there any suggestions that you can offer that would help resolve these errors?

I look forward to hearing from you.

If there is anything you need from my end, please do get in touch with me.

Thank you and best regards,

Rubina Chandnani
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