recon-all crash errors (fMRIPrep)

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Rubina Chandnani

13 Sep 2021 13 Sep '21

11:58 a.m.

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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

Attachments:

attachment.html (text/html — 3.4 KB)
crash-20210913-154933-root-recon_report-2a675116-390a-4e11-8875-0057ef5ffe7e.txt (text/plain — 2.2 KB)
crash-20210913-155007-root-mri_coreg-6c2151a1-2ace-4e5b-85a3-195d48489f06.txt (text/plain — 4.2 KB)
crash-20210913-155039-root-mri_coreg-99b294b4-4343-4182-9ee0-76d927b39bea.txt (text/plain — 4.2 KB)
crash-20210913-155113-root-mri_coreg-b6908d99-a9a0-4332-aaa1-afdfc8745bf8.txt (text/plain — 4.2 KB)

Show replies by date

Rosalia Dacosta Aguayo

13 Sep 13 Sep

12:06 p.m.

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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:

...

    External Email - Use Caution
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1OD1LaDDNuRcHWG7eUXpMYktVjLebxvJU4LrqWiw6B4CWCT...

Rubina Chandnani

12:12 p.m.

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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)

External Email - Use Caution

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.ukmailto:rubinachandnani@hotmail.co.uk> wrote:

External Email - Use Caution

Hi there,

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,

Rosalia Dacosta Aguayo

12:16 p.m.

External Email - Use Caution

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:

...

    External Email - Use Caution
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)
    External Email - Use Caution
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:
    External Email - Use Caution
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1lhK2R5Q3Kkl5BmEqLpxH_LnMzAZIOUm9GN0h4fF_euEU9a... https://secure-web.cisco.com/1OD1LaDDNuRcHWG7eUXpMYktVjLebxvJU4LrqWiw6B4CWCTju7gFYdND--NcWELBCV-xpF7FJ-i14NPAbIpf1i0aoo71BDif4c_BTviEHfhJu6bEzVjzwDLiBkltb21PGV-mQ6NW8wei--YsZWjsP9w5EufNj35bviEK_t52Jbu3-85aalWVgDasgtDGQtNQFnhipGZO854swSWlOnTqTxv6ZOEBDwTQ0pY2ce4cO0qdTWhcWA6HkXlKVOGaqQuSk7MfJuJ4x0bOB9KvEXxmp1Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1lhK2R5Q3Kkl5BmEqLpxH_LnMzAZIOUm9GN0h4fF_euEU9a...

Rubina Chandnani

12:26 p.m.

External Email - Use Caution

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)

External Email - Use Caution

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.ukmailto:rubinachandnani@hotmail.co.uk> wrote:

External Email - Use Caution

Hi Rosie,

I used MRIcroGL to convert DICOMs to Niftis.

Kind regards,

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

External Email - Use Caution

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.ukmailto:rubinachandnani@hotmail.co.uk> wrote:

External Email - Use Caution

Hi there,

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,

Rosalia Dacosta Aguayo

12:32 p.m.

External Email - Use Caution

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:

...

    External Email - Use Caution
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)
    External Email - Use Caution
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:
    External Email - Use Caution
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)
    External Email - Use Caution
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:
    External Email - Use Caution
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1WKvOazW0HmDrBzSzroMjtpuFeneFGv-T0IcXiLgyqbDzQG... https://secure-web.cisco.com/1OD1LaDDNuRcHWG7eUXpMYktVjLebxvJU4LrqWiw6B4CWCTju7gFYdND--NcWELBCV-xpF7FJ-i14NPAbIpf1i0aoo71BDif4c_BTviEHfhJu6bEzVjzwDLiBkltb21PGV-mQ6NW8wei--YsZWjsP9w5EufNj35bviEK_t52Jbu3-85aalWVgDasgtDGQtNQFnhipGZO854swSWlOnTqTxv6ZOEBDwTQ0pY2ce4cO0qdTWhcWA6HkXlKVOGaqQuSk7MfJuJ4x0bOB9KvEXxmp1Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1WKvOazW0HmDrBzSzroMjtpuFeneFGv-T0IcXiLgyqbDzQG... https://secure-web.cisco.com/1lhK2R5Q3Kkl5BmEqLpxH_LnMzAZIOUm9GN0h4fF_euEU9ah_3vTJjAm1ozq_Nh1GHffMbn155j-AbqLPvZrFd-fz8JtJjuYO3U1jWOcjRhKulton-2wlbxmBq2tgpHAk2rSHMJGOB_EqW3GK6vbvGjIhacXtdGLNf_-KNb1Geo26KoxVQ-x9ZPx_YiKbbVl_bYQlNhfLUFqFKBp4qBOmjrH3PvrH6cjUHGguCMCWu1xN-4dVaVR_yIYHDHrZWru-COGsNBmmawaZwMAzRBAE7g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1WKvOazW0HmDrBzSzroMjtpuFeneFGv-T0IcXiLgyqbDzQG...

Rubina Chandnani

12:37 p.m.

External Email - Use Caution

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)

External Email - Use Caution

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.ukmailto:rubinachandnani@hotmail.co.uk> wrote:

External Email - Use Caution

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

External Email - Use Caution

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.ukmailto:rubinachandnani@hotmail.co.uk> wrote:

External Email - Use Caution

Hi Rosie,

I used MRIcroGL to convert DICOMs to Niftis.

Kind regards,

External Email - Use Caution

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.ukmailto:rubinachandnani@hotmail.co.uk> wrote:

External Email - Use Caution

Hi there,

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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/123KGsTJpVqPFnVXmtBVPH17IxdsuVMMnBIBXn0p7uMw5on...https://secure-web.cisco.com/1OD1LaDDNuRcHWG7eUXpMYktVjLebxvJU4LrqWiw6B4CWCTju7gFYdND--NcWELBCV-xpF7FJ-i14NPAbIpf1i0aoo71BDif4c_BTviEHfhJu6bEzVjzwDLiBkltb21PGV-mQ6NW8wei--YsZWjsP9w5EufNj35bviEK_t52Jbu3-85aalWVgDasgtDGQtNQFnhipGZO854swSWlOnTqTxv6ZOEBDwTQ0pY2ce4cO0qdTWhcWA6HkXlKVOGaqQuSk7MfJuJ4x0bOB9KvEXxmp1Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/123KGsTJpVqPFnVXmtBVPH17IxdsuVMMnBIBXn0p7uMw5on...https://secure-web.cisco.com/1lhK2R5Q3Kkl5BmEqLpxH_LnMzAZIOUm9GN0h4fF_euEU9ah_3vTJjAm1ozq_Nh1GHffMbn155j-AbqLPvZrFd-fz8JtJjuYO3U1jWOcjRhKulton-2wlbxmBq2tgpHAk2rSHMJGOB_EqW3GK6vbvGjIhacXtdGLNf_-KNb1Geo26KoxVQ-x9ZPx_YiKbbVl_bYQlNhfLUFqFKBp4qBOmjrH3PvrH6cjUHGguCMCWu1xN-4dVaVR_yIYHDHrZWru-COGsNBmmawaZwMAzRBAE7g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/123KGsTJpVqPFnVXmtBVPH17IxdsuVMMnBIBXn0p7uMw5on...https://secure-web.cisco.com/1WKvOazW0HmDrBzSzroMjtpuFeneFGv-T0IcXiLgyqbDzQGyi42mBjG9y5Td72fB6dnNZeFLDcXsmZ2P-lh9R_WEHCt3PgScyMCSx6MHmYkSxu8-YXTRY_9hA_fkZiJi7scKEfAzTQAMUW_kAusgsD23G_aPYKefWKYMcS12i5Gh9TeLHTdu_rYDgz_LHhncgametrnYHGSX0UnBYw_kVvoDlGP6OHEDogIY5ndwoQNlYxy7R3tl0ZML2C3_FV88n3op_1kptw1l6VoUtPGomtg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

Rubina Chandnani

1:19 p.m.

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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:

[cid:d2936560-dddf-4635-a174-955bebf30be9]

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)

External Email - Use Caution

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)

External Email - Use Caution

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.ukmailto:rubinachandnani@hotmail.co.uk> wrote:

External Email - Use Caution

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

External Email - Use Caution

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.ukmailto:rubinachandnani@hotmail.co.uk> wrote:

External Email - Use Caution

Hi Rosie,

I used MRIcroGL to convert DICOMs to Niftis.

Kind regards,

External Email - Use Caution

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.ukmailto:rubinachandnani@hotmail.co.uk> wrote:

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Hi there,

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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1gS_EKUgmzBKXmxjs92IEUmb246_aRM2aNDbQTNV-3GINhM...https://secure-web.cisco.com/1OD1LaDDNuRcHWG7eUXpMYktVjLebxvJU4LrqWiw6B4CWCTju7gFYdND--NcWELBCV-xpF7FJ-i14NPAbIpf1i0aoo71BDif4c_BTviEHfhJu6bEzVjzwDLiBkltb21PGV-mQ6NW8wei--YsZWjsP9w5EufNj35bviEK_t52Jbu3-85aalWVgDasgtDGQtNQFnhipGZO854swSWlOnTqTxv6ZOEBDwTQ0pY2ce4cO0qdTWhcWA6HkXlKVOGaqQuSk7MfJuJ4x0bOB9KvEXxmp1Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1gS_EKUgmzBKXmxjs92IEUmb246_aRM2aNDbQTNV-3GINhM...https://secure-web.cisco.com/1lhK2R5Q3Kkl5BmEqLpxH_LnMzAZIOUm9GN0h4fF_euEU9ah_3vTJjAm1ozq_Nh1GHffMbn155j-AbqLPvZrFd-fz8JtJjuYO3U1jWOcjRhKulton-2wlbxmBq2tgpHAk2rSHMJGOB_EqW3GK6vbvGjIhacXtdGLNf_-KNb1Geo26KoxVQ-x9ZPx_YiKbbVl_bYQlNhfLUFqFKBp4qBOmjrH3PvrH6cjUHGguCMCWu1xN-4dVaVR_yIYHDHrZWru-COGsNBmmawaZwMAzRBAE7g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1gS_EKUgmzBKXmxjs92IEUmb246_aRM2aNDbQTNV-3GINhM...https://secure-web.cisco.com/1WKvOazW0HmDrBzSzroMjtpuFeneFGv-T0IcXiLgyqbDzQGyi42mBjG9y5Td72fB6dnNZeFLDcXsmZ2P-lh9R_WEHCt3PgScyMCSx6MHmYkSxu8-YXTRY_9hA_fkZiJi7scKEfAzTQAMUW_kAusgsD23G_aPYKefWKYMcS12i5Gh9TeLHTdu_rYDgz_LHhncgametrnYHGSX0UnBYw_kVvoDlGP6OHEDogIY5ndwoQNlYxy7R3tl0ZML2C3_FV88n3op_1kptw1l6VoUtPGomtg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

Douglas N. Greve

15 Sep 15 Sep

3:56 p.m.

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)

External Email - Use Caution

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)

External Email - Use Caution

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 mailto:rubinachandnani@hotmail.co.uk> wrote:

        External Email - Use Caution

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

        External Email - Use Caution

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
<mailto:rubinachandnani@hotmail.co.uk>> wrote:

            External Email - Use Caution

    Hi Rosie,

    I used MRIcroGL to convert DICOMs to Niftis.

    Kind regards,

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

            External Email - Use Caution

    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
    <mailto:rubinachandnani@hotmail.co.uk>> wrote:

                External Email - Use Caution

        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
        _______________________________________________
        Freesurfer mailing list
        Freesurfer@nmr.mgh.harvard.edu
        <mailto:Freesurfer@nmr.mgh.harvard.edu>
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Rubina Chandnani

4:04 p.m.

External Email - Use Caution

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:

External Email - Use Caution

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:

[cid:part1.B5332F80.F43BE9DF@mgh.harvard.edu]

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

External Email - Use Caution

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

External Email - Use Caution

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.ukmailto:rubinachandnani@hotmail.co.uk> wrote:

External Email - Use Caution

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

External Email - Use Caution

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.ukmailto:rubinachandnani@hotmail.co.uk> wrote:

External Email - Use Caution

Hi Rosie,

I used MRIcroGL to convert DICOMs to Niftis.

Kind regards,

External Email - Use Caution

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.ukmailto:rubinachandnani@hotmail.co.uk> wrote:

External Email - Use Caution

Hi there,

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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1tN5ZJ3Qt0onz60QpHhwPP3EI1vdce16AWX1V6rNPnYCP77...https://secure-web.cisco.com/1OD1LaDDNuRcHWG7eUXpMYktVjLebxvJU4LrqWiw6B4CWCTju7gFYdND--NcWELBCV-xpF7FJ-i14NPAbIpf1i0aoo71BDif4c_BTviEHfhJu6bEzVjzwDLiBkltb21PGV-mQ6NW8wei--YsZWjsP9w5EufNj35bviEK_t52Jbu3-85aalWVgDasgtDGQtNQFnhipGZO854swSWlOnTqTxv6ZOEBDwTQ0pY2ce4cO0qdTWhcWA6HkXlKVOGaqQuSk7MfJuJ4x0bOB9KvEXxmp1Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1tN5ZJ3Qt0onz60QpHhwPP3EI1vdce16AWX1V6rNPnYCP77...https://secure-web.cisco.com/1lhK2R5Q3Kkl5BmEqLpxH_LnMzAZIOUm9GN0h4fF_euEU9ah_3vTJjAm1ozq_Nh1GHffMbn155j-AbqLPvZrFd-fz8JtJjuYO3U1jWOcjRhKulton-2wlbxmBq2tgpHAk2rSHMJGOB_EqW3GK6vbvGjIhacXtdGLNf_-KNb1Geo26KoxVQ-x9ZPx_YiKbbVl_bYQlNhfLUFqFKBp4qBOmjrH3PvrH6cjUHGguCMCWu1xN-4dVaVR_yIYHDHrZWru-COGsNBmmawaZwMAzRBAE7g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1tN5ZJ3Qt0onz60QpHhwPP3EI1vdce16AWX1V6rNPnYCP77...https://secure-web.cisco.com/1WKvOazW0HmDrBzSzroMjtpuFeneFGv-T0IcXiLgyqbDzQGyi42mBjG9y5Td72fB6dnNZeFLDcXsmZ2P-lh9R_WEHCt3PgScyMCSx6MHmYkSxu8-YXTRY_9hA_fkZiJi7scKEfAzTQAMUW_kAusgsD23G_aPYKefWKYMcS12i5Gh9TeLHTdu_rYDgz_LHhncgametrnYHGSX0UnBYw_kVvoDlGP6OHEDogIY5ndwoQNlYxy7R3tl0ZML2C3_FV88n3op_1kptw1l6VoUtPGomtg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

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Douglas N. Greve
Rosalia Dacosta Aguayo
Rubina Chandnani