What is inside your mri folder? And make sure you are not running out of disk space as that would cause the 0 length files Cheers Bruce

On Apr 17, 2022, at 9:04 PM, HYE JUNG YOUN hyejung7890@amc.seoul.kr wrote:



External Email - Use Caution Hi,

Just re-sending this message in case it didn’t go through to the developers, I am still searching for a solution to this problem.

I also found out that the originally converted mri.mgz , brainmask.mgz files are probably re-written – its file size changed to 0kB after I ran the code I sent in my previous email. Where do you think I went wrong?

Thanks for your help. H

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of HYE JUNG YOUN Sent: Wednesday, April 13, 2022 9:39 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Failed to load MRI error

External Email - Use Caution Dear freesurfer devleopers,

I am experiencing an error while loading freeview using the following code: [image001.png]

This always worked for me but now when I try to load and view it, a message “failed to load MRI” pops up on freeview after loading T1.mgz.

From the terminal it says:

error: mghRead(/Applications/freesurfer/7.2.0/subjects/211025/1079_4/mri/wm.mgz, -1): read error

MRIread failed: Unable to read from /Applications/freesurfer/7.2.0/subjects/211025/1079_4/mri/wm.mgz

Also, when I check the mri containing file, eg: 1079_4 folder, after loading freeview, the folder contains automatically generated –v and –f file.

[image002.png] I have seen a few similar errors on google and mail archive but they did not solve my issue. I would very much appreciate any solution to this.

Thank you in advance.

Best, HJ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Can you send us the recon-all.log file from the scripts dir?

On Apr 17, 2022, at 9:35 PM, HYE JUNG YOUN hyejung7890@amc.seoul.kr wrote:



External Email - Use Caution Hi Bruce,

Here’s what it looks like : [image003.png] [image004.png]

I got enough disk space.

Thanks!

H

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Fischl, Bruce Sent: Monday, April 18, 2022 10:08 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Failed to load MRI error

What is inside your mri folder? And make sure you are not running out of disk space as that would cause the 0 length files Cheers Bruce

On Apr 17, 2022, at 9:04 PM, HYE JUNG YOUN <hyejung7890@amc.seoul.krmailto:hyejung7890@amc.seoul.kr> wrote:

External Email - Use Caution Hi,

Just re-sending this message in case it didn’t go through to the developers, I am still searching for a solution to this problem.

I also found out that the originally converted mri.mgz , brainmask.mgz files are probably re-written – its file size changed to 0kB after I ran the code I sent in my previous email. Where do you think I went wrong?

Thanks for your help. H

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 HYE JUNG YOUN Sent: Wednesday, April 13, 2022 9:39 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Failed to load MRI error

External Email - Use Caution Dear freesurfer devleopers,

I am experiencing an error while loading freeview using the following code: [image005.png]

This always worked for me but now when I try to load and view it, a message “failed to load MRI” pops up on freeview after loading T1.mgz.

From the terminal it says:

error: mghRead(/Applications/freesurfer/7.2.0/subjects/211025/1079_4/mri/wm.mgz, -1): read error

MRIread failed: Unable to read from /Applications/freesurfer/7.2.0/subjects/211025/1079_4/mri/wm.mgz

Also, when I check the mri containing file, eg: 1079_4 folder, after loading freeview, the folder contains automatically generated –v and –f file.

[image006.png] I have seen a few similar errors on google and mail archive but they did not solve my issue. I would very much appreciate any solution to this.

Thank you in advance.

Best, HJ _______________________________________________ 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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1ZmwWGKHrQWCPm8fK7XhdeZpGYWQjUpWeL2xrbVxFDPlEUyJki9Cpto93jjT6E3kBudpId-QDN_rwRbK3NwjQtJRYT9do3euQz1x5mydfJnzQ14JelzFbwIKuNazG5bnDJfxifHap_UM6aVulQjk5qy5kPKFOPEviPlflnrRvZqp6W3lCLWS1hKAm-me1Jm3Qr8c1XrPk1kxGExd0vXmvXLN7-xojQip7J9mMPxPz198Vv19CKsoaiEtNbzwRpOIRC8ohNIqxHxmUgEOB6kdsI_3jPAHKs9TcN1dZHXyZkZYwdUE7fFrrFZqj0-CTruQTsAWzBYGgF4PWVStEWuU9uA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Is this for a subject that you can’t load the wm.mgz for? It doesn’t show any errors. Is the wm.mgz zero length? I don’t see how those things can both be true unless you overwrote it at some point. If you haven’t manually edited this subject maybe you should just rerun it?

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of HYE JUNG YOUN Sent: Monday, April 18, 2022 2:44 AM To: 'Freesurfer support list' freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Failed to load MRI error

External Email - Use Caution Hi Bruce, Please find the attached log file.

Thanks.

H

It might be that the wm.mgz file is corrupted. What happens if you run mri_info wm.mgz

On 4/18/2022 8:02 PM, HYE JUNG YOUN wrote:

External Email - Use Caution

Hi Bruce,

Do you mean that I should re-do the recon-all process?

I tried to re run freeview but it did not work. And Yes I  think the files have been overwritten at some point which I am trying to figure out to avoid making the same mistake in the future.

However, the question is I have done the exact same process I always did to view mri files on freeview. I have set and used the same subject directory, used the same code, and etc.

Here’s the code I used:

Which gives me this:

Then, when I check mri folder, notice the selected files have been overwritten (I think) and are shown as 0 byte in size.

Can you see where I went wrong to overwrite those files?

Thank you for your help.

Best, H

*From:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Fischl, Bruce *Sent:* Monday, April 18, 2022 10:35 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Failed to load MRI error

Is this for a subject that you can’t load the wm.mgz for? It doesn’t show any errors. Is the wm.mgz zero length? I don’t see how those things can both be true unless you overwrote it at some point. If you haven’t manually edited this subject maybe you should just rerun it?

*From:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *HYE JUNG YOUN *Sent:* Monday, April 18, 2022 2:44 AM *To:* 'Freesurfer support list' freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Failed to load MRI error

*        External Email - Use Caution *

Hi Bruce,

Please find the attached log file.

Thanks.

H

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

I don't know where you went wrong. You can try to regenerate just that file with cd $SUBJECTS_DIR/subject/mri mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz delete the old wm.mgz first

On 4/21/2022 9:48 PM, HYE JUNG YOUN wrote:

External Email - Use Caution

Hi,

Then I get :

Error: mghRead(/Applications/Freesurfer/7.2.0/subjects/211025/1270_1301/mri/wm.mgz, -1): read error

Should I go through recon all process for all files I have ?

Can you perhaps tell me where I have possibly gone wrong?

I simply just used the code I always used for freeview then this happened. I’d like to avoid making same mistakes I might have made.

Thanks for your help!

*From:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Douglas N. Greve *Sent:* Friday, April 22, 2022 2:59 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Failed to load MRI error

It might be that the wm.mgz file is corrupted. What happens if you run mri_info wm.mgz

On 4/18/2022 8:02 PM, HYE JUNG YOUN wrote:

*        External Email - Use Caution *

Hi Bruce,

Do you mean that I should re-do the recon-all process?

I tried to re run freeview but it did not work. And Yes I  think
the files have been overwritten at some point which I am trying to
figure out to avoid making the same mistake in the future.

However, the question is I have done the exact same process I
always did to view mri files on freeview. I have set and used the
same subject directory, used the same code, and etc.

Here’s the code I used:

Which gives me this:

Then, when I check mri folder, notice the selected files have been
overwritten (I think) and are shown as 0 byte in size.

Can you see where I went wrong to overwrite those files?

Thank you for your help.

Best,
H

*From:*freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu>
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of
*Fischl, Bruce
*Sent:* Monday, April 18, 2022 10:35 PM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] Failed to load MRI error

Is this for a subject that you can’t load the wm.mgz for? It
doesn’t show any errors. Is the wm.mgz zero length? I don’t see
how those things can both be true unless you overwrote it at some
point. If you haven’t manually edited this subject maybe you
should just rerun it?

*From:*freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *HYE JUNG YOUN
*Sent:* Monday, April 18, 2022 2:44 AM
*To:* 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] Failed to load MRI error

*        External Email - Use Caution *

Hi Bruce,

Please find the attached log file.

Thanks.

H



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