Error in loading wmparc2diff.mgz

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Patlak PET/MRI

Ramesh Babu

31 Jan 2025 31 Jan '25

7:50 a.m.

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Dear Expert,

I am finding an error in loading wmparc2diff.mgz in freeview. The error report from the terminal is; $ freeview -v lowb.nii.gz $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz:colormap=lut -f $SUBJECTS_DIR/$subj/surf/lh.white:edgecolor=green $SUBJECTS_DIR/$subj/surf/rh.white:edgecolor=green -viewport coronal error: mghRead(/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz, -1): could not open file MRIread failed: Unable to read from /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

Please see the attached file and give your suggestions.

Regards Ramesh

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Ramesh Babu

31 Jan 31 Jan

8:04 a.m.

External Email - Use Caution

Sorry, I forgot to attach the files with the earlier message.

Dear Expert,

I am finding an error in loading wmparc2diff.mgz in freeview. The error report from the terminal is;

$ freeview -v lowb.nii.gz $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz:colormap=lut -f $SUBJECTS_DIR/$subj/surf/lh.white:edgecolor=green $SUBJECTS_DIR/$subj/surf/rh.white:edgecolor=green -viewport coronal error: mghRead(/mnt/data_analysis/freesurfer_data/diffusion_ recons/sub01/mri/wmparc2diff.mgz, -1): could not open file MRIread failed: Unable to read from /mnt/data_analysis/freesurfer_ data/diffusion_recons/sub01/mri/wmparc2diff.mgz

In the attached Error-1 file it shows error after entering the command in the terminal. Error-2 file - trying to load the file manually. You cannot see the wmparc2diff.mgz file though it is created and located in the folder.

Please see the attached files and give your suggestions.

Regards Ramesh

On Fri, Jan 31, 2025 at 6:20 PM Ramesh Babu mgrameshbabu2013@gmail.com wrote:

...

Dear Expert,

I am finding an error in loading wmparc2diff.mgz in freeview. The error report from the terminal is; $ freeview -v lowb.nii.gz $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz:colormap=lut -f $SUBJECTS_DIR/$subj/surf/lh.white:edgecolor=green $SUBJECTS_DIR/$subj/surf/rh.white:edgecolor=green -viewport coronal error: mghRead(/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz, -1): could not open file MRIread failed: Unable to read from /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

Please see the attached file and give your suggestions.

Regards Ramesh

Huang, Yujing

8:10 a.m.

Can you check if the volume exists? ls -l /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

I only see wmparc.mgz in your listed directory.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Ramesh Babu Sent: Friday, January 31, 2025 8:05 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Error in loading wmparc2diff.mgz

External Email - Use Caution Sorry, I forgot to attach the files with the earlier message.

Dear Expert,

I am finding an error in loading wmparc2diff.mgz in freeview. The error report from the terminal is;

$ freeview -v lowb.nii.gz $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz:colormap=lut -f $SUBJECTS_DIR/$subj/surf/lh.white:edgecolor=green $SUBJECTS_DIR/$subj/surf/rh.white:edgecolor=green -viewport coronal error: mghRead(/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz, -1): could not open file MRIread failed: Unable to read from /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

Please see the attached files and give your suggestions.

Regards Ramesh

On Fri, Jan 31, 2025 at 6:20 PM Ramesh Babu <mgrameshbabu2013@gmail.commailto:mgrameshbabu2013@gmail.com> wrote: Dear Expert,

Please see the attached file and give your suggestions.

Regards Ramesh

Ramesh Babu

8:18 a.m.

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Dear Yujing,

Thank you for your prompt reply. Yes, it exists.

$ ls -l /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diﬀ.mgz

-rwxrwxrwx 1 root root 65906 Jan 31 18:00 /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diﬀ.mgz

But while loading manually it is not detected. Also, I used the "all types" option, but same issue.

Thanks Ramesh

On Fri, Jan 31, 2025 at 6:41 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

...

Can you check if the volume exists?

ls -l /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

I only see wmparc.mgz in your listed directory.

Yujing

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Ramesh Babu *Sent:* Friday, January 31, 2025 8:05 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Error in loading wmparc2diff.mgz
   External Email - Use Caution        *
Sorry, I forgot to attach the files with the earlier message.

Dear Expert,

I am finding an error in loading wmparc2diff.mgz in freeview. The error report from the terminal is;

$ freeview -v lowb.nii.gz $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz:colormap=lut -f $SUBJECTS_DIR/$subj/surf/lh.white:edgecolor=green $SUBJECTS_DIR/$subj/surf/rh.white:edgecolor=green -viewport coronal error: mghRead(/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz, -1): could not open file MRIread failed: Unable to read from /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

In the attached Error-1 file it shows error after entering the command in the terminal.

Error-2 file - trying to load the file manually. You cannot see the wmparc2diff.mgz file though it is created and located in the folder.

Please see the attached files and give your suggestions.

Regards

Ramesh

On Fri, Jan 31, 2025 at 6:20 PM Ramesh Babu mgrameshbabu2013@gmail.com wrote:

Dear Expert,

I am finding an error in loading wmparc2diff.mgz in freeview. The error report from the terminal is;

$ freeview -v lowb.nii.gz $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz:colormap=lut -f $SUBJECTS_DIR/$subj/surf/lh.white:edgecolor=green $SUBJECTS_DIR/$subj/surf/rh.white:edgecolor=green -viewport coronal error: mghRead(/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz, -1): could not open file MRIread failed: Unable to read from /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

Please see the attached file and give your suggestions.

Regards

Ramesh

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1nJs0ku4hfI3bgUTpG3lchmSHRheODGVWj3X0BijKpWtnHQ... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1IjBx51WZFzV_9W6gQF6k68Pbwhuf1Xo6C9wN4JZhonF40R... < https://secure-web.cisco.com/1IjBx51WZFzV_9W6gQF6k68Pbwhuf1Xo6C9wN4JZhonF40R... .

Huang, Yujing

8:24 a.m.

Can you try these two commands? 1. freeview /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz 2. mri_info /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Ramesh Babu Sent: Friday, January 31, 2025 8:19 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Error in loading wmparc2diff.mgz

External Email - Use Caution Dear Yujing,

Thank you for your prompt reply. Yes, it exists.

$ ls -l /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diﬀ.mgz -rwxrwxrwx 1 root root 65906 Jan 31 18:00 /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diﬀ.mgz

But while loading manually it is not detected. Also, I used the "all types" option, but same issue.

Thanks Ramesh

On Fri, Jan 31, 2025 at 6:41 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Can you check if the volume exists? ls -l /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

I only see wmparc.mgz in your listed directory.

Yujing

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 Ramesh Babu Sent: Friday, January 31, 2025 8:05 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Error in loading wmparc2diff.mgz

External Email - Use Caution Sorry, I forgot to attach the files with the earlier message.

Dear Expert,

I am finding an error in loading wmparc2diff.mgz in freeview. The error report from the terminal is;

$ freeview -v lowb.nii.gz $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz:colormap=lut -f $SUBJECTS_DIR/$subj/surf/lh.white:edgecolor=green $SUBJECTS_DIR/$subj/surf/rh.white:edgecolor=green -viewport coronal error: mghRead(/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz, -1): could not open file MRIread failed: Unable to read from /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

Please see the attached files and give your suggestions.

Regards Ramesh

On Fri, Jan 31, 2025 at 6:20 PM Ramesh Babu <mgrameshbabu2013@gmail.commailto:mgrameshbabu2013@gmail.com> wrote: Dear Expert,

Please see the attached file and give your suggestions.

Regards Ramesh _______________________________________________ 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/freesurfer https://secure-web.cisco.com/1nJs0ku4hfI3bgUTpG3lchmSHRheODGVWj3X0BijKpWtnHQ9epN43J_vDLzxgMAcgl7bm_lnQdyw690eER7tGFhcYtORahRj0JjIKxODg3RoKkgeyoAJgCbpSZVsbna4P1gRod5bndciuMUg2deoZP5rUGtE__NZEn0WIoWB-RMPgsz6Bd2-QDLrobMWG7-qFrrLR1jAC5LutNvY95oJrORtDzSwJ4Pm8n2gulRlsx7whaT3z7-jtEmWJNEHSpXk3eX49gOZ8gpaAie2T9v0onZoNHegi3MSZM3eJws9lj-Y2QqXRgbZXAVkcyJdHR0SSvg8gHBUd7SGMExw7mt3WhQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline https://secure-web.cisco.com/1IjBx51WZFzV_9W6gQF6k68Pbwhuf1Xo6C9wN4JZhonF40RkDjkIZdm1VwzmRsvb4ROp0AZcPhM-y4G0wIj371btjfQowkTksuBGqDS8RpQ0J07hqGAhrSdHKoF0lIdl8iLmRvDHrZKjltFvH1Sd6qe-GLtrLHEJaqchYRKXWStLLlh5wRMAWM-q9DWyscvfoKc_jApvea5K95XAsIVw9OyUgARB5bb0ndgoP7rAehXrlTcGO9z_q6GLfa7xqUL__H9_HMRdIPAKOmZtumdAxuOxThPRFHtjaQrapgsr7wB-SkmsXXT-D2p9cHIji093dMJVqIdOMVCoSz6RhWWuUEA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline https://secure-web.cisco.com/1IjBx51WZFzV_9W6gQF6k68Pbwhuf1Xo6C9wN4JZhonF40RkDjkIZdm1VwzmRsvb4ROp0AZcPhM-y4G0wIj371btjfQowkTksuBGqDS8RpQ0J07hqGAhrSdHKoF0lIdl8iLmRvDHrZKjltFvH1Sd6qe-GLtrLHEJaqchYRKXWStLLlh5wRMAWM-q9DWyscvfoKc_jApvea5K95XAsIVw9OyUgARB5bb0ndgoP7rAehXrlTcGO9z_q6GLfa7xqUL__H9_HMRdIPAKOmZtumdAxuOxThPRFHtjaQrapgsr7wB-SkmsXXT-D2p9cHIji093dMJVqIdOMVCoSz6RhWWuUEA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .

Ramesh Babu

10:31 a.m.

External Email - Use Caution

Dear Yujing,

For the command, freeview /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

MRIread failed: Unable to read from /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

$ mri_info /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz error: mghRead(/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz, -1): could not open file

Thank you Ramesh

On Fri, Jan 31, 2025 at 6:54 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

...

Can you try these two commands?

freeview

/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

mri_info

/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Ramesh Babu *Sent:* Friday, January 31, 2025 8:19 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Error in loading wmparc2diff.mgz
   External Email - Use Caution        *
Dear Yujing,

Thank you for your prompt reply. Yes, it exists.

$ ls -l /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diﬀ.mgz

-rwxrwxrwx 1 root root 65906 Jan 31 18:00 /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diﬀ .mgz

But while loading manually it is not detected. Also, I used the "all types" option, but same issue.

Thanks

Ramesh

On Fri, Jan 31, 2025 at 6:41 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

Can you check if the volume exists?

ls -l /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

I only see wmparc.mgz in your listed directory.

Yujing

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Ramesh Babu *Sent:* Friday, January 31, 2025 8:05 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Error in loading wmparc2diff.mgz
   External Email - Use Caution        *
Sorry, I forgot to attach the files with the earlier message.

Dear Expert,

I am finding an error in loading wmparc2diff.mgz in freeview. The error report from the terminal is;

$ freeview -v lowb.nii.gz $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz:colormap=lut -f $SUBJECTS_DIR/$subj/surf/lh.white:edgecolor=green $SUBJECTS_DIR/$subj/surf/rh.white:edgecolor=green -viewport coronal error: mghRead(/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz, -1): could not open file MRIread failed: Unable to read from /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

In the attached Error-1 file it shows error after entering the command in the terminal.

Error-2 file - trying to load the file manually. You cannot see the wmparc2diff.mgz file though it is created and located in the folder.

Please see the attached files and give your suggestions.

Regards

Ramesh

On Fri, Jan 31, 2025 at 6:20 PM Ramesh Babu mgrameshbabu2013@gmail.com wrote:

Dear Expert,

I am finding an error in loading wmparc2diff.mgz in freeview. The error report from the terminal is;

$ freeview -v lowb.nii.gz $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz:colormap=lut -f $SUBJECTS_DIR/$subj/surf/lh.white:edgecolor=green $SUBJECTS_DIR/$subj/surf/rh.white:edgecolor=green -viewport coronal error: mghRead(/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz, -1): could not open file MRIread failed: Unable to read from /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

Please see the attached file and give your suggestions.

Regards

Ramesh

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/17Ew-YRAyE28k0stLB_GZfCnrSZeKM945PbXAZ_3R26_DVc... https://secure-web.cisco.com/1nJs0ku4hfI3bgUTpG3lchmSHRheODGVWj3X0BijKpWtnHQ9epN43J_vDLzxgMAcgl7bm_lnQdyw690eER7tGFhcYtORahRj0JjIKxODg3RoKkgeyoAJgCbpSZVsbna4P1gRod5bndciuMUg2deoZP5rUGtE__NZEn0WIoWB-RMPgsz6Bd2-QDLrobMWG7-qFrrLR1jAC5LutNvY95oJrORtDzSwJ4Pm8n2gulRlsx7whaT3z7-jtEmWJNEHSpXk3eX49gOZ8gpaAie2T9v0onZoNHegi3MSZM3eJws9lj-Y2QqXRgbZXAVkcyJdHR0SSvg8gHBUd7SGMExw7mt3WhQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1i9F9cDRo5Gysn3-YC_k-YM1Qqk-zzI0229v_UYmLEIPdPp... https://secure-web.cisco.com/1IjBx51WZFzV_9W6gQF6k68Pbwhuf1Xo6C9wN4JZhonF40RkDjkIZdm1VwzmRsvb4ROp0AZcPhM-y4G0wIj371btjfQowkTksuBGqDS8RpQ0J07hqGAhrSdHKoF0lIdl8iLmRvDHrZKjltFvH1Sd6qe-GLtrLHEJaqchYRKXWStLLlh5wRMAWM-q9DWyscvfoKc_jApvea5K95XAsIVw9OyUgARB5bb0ndgoP7rAehXrlTcGO9z_q6GLfa7xqUL__H9_HMRdIPAKOmZtumdAxuOxThPRFHtjaQrapgsr7wB-SkmsXXT-D2p9cHIji093dMJVqIdOMVCoSz6RhWWuUEA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1i9F9cDRo5Gysn3-YC_k-YM1Qqk-zzI0229v_UYmLEIPdPp... https://secure-web.cisco.com/1IjBx51WZFzV_9W6gQF6k68Pbwhuf1Xo6C9wN4JZhonF40RkDjkIZdm1VwzmRsvb4ROp0AZcPhM-y4G0wIj371btjfQowkTksuBGqDS8RpQ0J07hqGAhrSdHKoF0lIdl8iLmRvDHrZKjltFvH1Sd6qe-GLtrLHEJaqchYRKXWStLLlh5wRMAWM-q9DWyscvfoKc_jApvea5K95XAsIVw9OyUgARB5bb0ndgoP7rAehXrlTcGO9z_q6GLfa7xqUL__H9_HMRdIPAKOmZtumdAxuOxThPRFHtjaQrapgsr7wB-SkmsXXT-D2p9cHIji093dMJVqIdOMVCoSz6RhWWuUEA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/17Ew-YRAyE28k0stLB_GZfCnrSZeKM945PbXAZ_3R26_DVc... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1i9F9cDRo5Gysn3-YC_k-YM1Qqk-zzI0229v_UYmLEIPdPp... < https://secure-web.cisco.com/1i9F9cDRo5Gysn3-YC_k-YM1Qqk-zzI0229v_UYmLEIPdPp... .

Ramesh Babu

2 Feb 2 Feb

11:34 a.m.

External Email - Use Caution

Dear Experts,

May I know why wmparc2diff is unreadable? Please suggest.

Thank you Ramesh

On Fri, Jan 31, 2025, 9:01 PM Ramesh Babu mgrameshbabu2013@gmail.com wrote:

...

Dear Yujing,

For the command, freeview /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

MRIread failed: Unable to read from /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

$ mri_info /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz error: mghRead(/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz, -1): could not open file

Thank you Ramesh

On Fri, Jan 31, 2025 at 6:54 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

...
Can you try these two commands?

freeview

/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

mri_info

/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Ramesh Babu *Sent:* Friday, January 31, 2025 8:19 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Error in loading wmparc2diff.mgz
   External Email - Use Caution        *
Dear Yujing,

Thank you for your prompt reply. Yes, it exists.

$ ls -l /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diﬀ.mgz

-rwxrwxrwx 1 root root 65906 Jan 31 18:00 /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diﬀ .mgz

But while loading manually it is not detected. Also, I used the "all types" option, but same issue.

Thanks

Ramesh

On Fri, Jan 31, 2025 at 6:41 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

Can you check if the volume exists?

ls -l /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

I only see wmparc.mgz in your listed directory.

Yujing

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Ramesh Babu *Sent:* Friday, January 31, 2025 8:05 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Error in loading wmparc2diff.mgz
   External Email - Use Caution        *
Sorry, I forgot to attach the files with the earlier message.

Dear Expert,

I am finding an error in loading wmparc2diff.mgz in freeview. The error report from the terminal is;

$ freeview -v lowb.nii.gz $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz:colormap=lut -f $SUBJECTS_DIR/$subj/surf/lh.white:edgecolor=green $SUBJECTS_DIR/$subj/surf/rh.white:edgecolor=green -viewport coronal error: mghRead(/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz, -1): could not open file MRIread failed: Unable to read from /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

In the attached Error-1 file it shows error after entering the command in the terminal.

Error-2 file - trying to load the file manually. You cannot see the wmparc2diff.mgz file though it is created and located in the folder.

Please see the attached files and give your suggestions.

Regards

Ramesh

On Fri, Jan 31, 2025 at 6:20 PM Ramesh Babu mgrameshbabu2013@gmail.com wrote:

Dear Expert,

I am finding an error in loading wmparc2diff.mgz in freeview. The error report from the terminal is;

$ freeview -v lowb.nii.gz $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz:colormap=lut -f $SUBJECTS_DIR/$subj/surf/lh.white:edgecolor=green $SUBJECTS_DIR/$subj/surf/rh.white:edgecolor=green -viewport coronal error: mghRead(/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz, -1): could not open file MRIread failed: Unable to read from /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

Please see the attached file and give your suggestions.

Regards

Ramesh

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/1WwQJM2x8cynpquVqqhJebMIVs0ZsFXqqlDQNVfOwqazuOS... https://secure-web.cisco.com/1nJs0ku4hfI3bgUTpG3lchmSHRheODGVWj3X0BijKpWtnHQ9epN43J_vDLzxgMAcgl7bm_lnQdyw690eER7tGFhcYtORahRj0JjIKxODg3RoKkgeyoAJgCbpSZVsbna4P1gRod5bndciuMUg2deoZP5rUGtE__NZEn0WIoWB-RMPgsz6Bd2-QDLrobMWG7-qFrrLR1jAC5LutNvY95oJrORtDzSwJ4Pm8n2gulRlsx7whaT3z7-jtEmWJNEHSpXk3eX49gOZ8gpaAie2T9v0onZoNHegi3MSZM3eJws9lj-Y2QqXRgbZXAVkcyJdHR0SSvg8gHBUd7SGMExw7mt3WhQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/12fl5bduiyAPgvMzzZFQQHl3o0iYt0q2N5z7Dd9kqY4BfBs... https://secure-web.cisco.com/1IjBx51WZFzV_9W6gQF6k68Pbwhuf1Xo6C9wN4JZhonF40RkDjkIZdm1VwzmRsvb4ROp0AZcPhM-y4G0wIj371btjfQowkTksuBGqDS8RpQ0J07hqGAhrSdHKoF0lIdl8iLmRvDHrZKjltFvH1Sd6qe-GLtrLHEJaqchYRKXWStLLlh5wRMAWM-q9DWyscvfoKc_jApvea5K95XAsIVw9OyUgARB5bb0ndgoP7rAehXrlTcGO9z_q6GLfa7xqUL__H9_HMRdIPAKOmZtumdAxuOxThPRFHtjaQrapgsr7wB-SkmsXXT-D2p9cHIji093dMJVqIdOMVCoSz6RhWWuUEA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/12fl5bduiyAPgvMzzZFQQHl3o0iYt0q2N5z7Dd9kqY4BfBs... https://secure-web.cisco.com/1IjBx51WZFzV_9W6gQF6k68Pbwhuf1Xo6C9wN4JZhonF40RkDjkIZdm1VwzmRsvb4ROp0AZcPhM-y4G0wIj371btjfQowkTksuBGqDS8RpQ0J07hqGAhrSdHKoF0lIdl8iLmRvDHrZKjltFvH1Sd6qe-GLtrLHEJaqchYRKXWStLLlh5wRMAWM-q9DWyscvfoKc_jApvea5K95XAsIVw9OyUgARB5bb0ndgoP7rAehXrlTcGO9z_q6GLfa7xqUL__H9_HMRdIPAKOmZtumdAxuOxThPRFHtjaQrapgsr7wB-SkmsXXT-D2p9cHIji093dMJVqIdOMVCoSz6RhWWuUEA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1WwQJM2x8cynpquVqqhJebMIVs0ZsFXqqlDQNVfOwqazuOS... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/12fl5bduiyAPgvMzzZFQQHl3o0iYt0q2N5z7Dd9kqY4BfBs... < https://secure-web.cisco.com/12fl5bduiyAPgvMzzZFQQHl3o0iYt0q2N5z7Dd9kqY4BfBs... .

Douglas N. Greve

3 Feb 3 Feb

9:19 a.m.

Does that file exist?

On 2/2/2025 11:34 AM, Ramesh Babu wrote:

...

External Email - Use Caution

Dear Experts,

May I know why wmparc2diff is unreadable? Please suggest.

Thank you Ramesh

On Fri, Jan 31, 2025, 9:01 PM Ramesh Babu mgrameshbabu2013@gmail.com wrote:

Dear Yujing,

For the command,
freeview
/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

MRIread failed: Unable to read from
/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

$ mri_info
/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz
error:
mghRead(/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz,
-1): could not open file

Thank you
Ramesh




On Fri, Jan 31, 2025 at 6:54 PM Huang, Yujing
<YHUANG43@mgh.harvard.edu> wrote:

    Can you try these two commands?

    1. freeview
    /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

    2. mri_info
    /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

    *From:*freesurfer-bounces@nmr.mgh.harvard.edu
    <freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Ramesh
    Babu
    *Sent:* Friday, January 31, 2025 8:19 AM
    *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
    *Subject:* Re: [Freesurfer] Error in loading wmparc2diff.mgz

    *        External Email - Use Caution *

    Dear Yujing,

    Thank you for your prompt reply. Yes, it exists.

    $ ls -l
    /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diﬀ.mgz

    -rwxrwxrwx 1 root root 65906 Jan 31 18:00
    /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diﬀ.mgz

    But while loading manually it is not detected. Also, I used
    the "all types" option, but same issue.

    Thanks

    Ramesh

    On Fri, Jan 31, 2025 at 6:41 PM Huang, Yujing
    <YHUANG43@mgh.harvard.edu> wrote:

        Can you check if the volume exists?

        ls -l
        /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

        I only see wmparc.mgz in your listed directory.

        Yujing

        *From:*freesurfer-bounces@nmr.mgh.harvard.edu
        <freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of
        *Ramesh Babu
        *Sent:* Friday, January 31, 2025 8:05 AM
        *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
        *Subject:* Re: [Freesurfer] Error in loading wmparc2diff.mgz

        *        External Email - Use Caution *

        Sorry, I forgot to attach the files with the earlier message.

        Dear Expert,

        I am finding an error in loading wmparc2diff.mgz in
        freeview. The error report from the terminal is;

        $ freeview -v lowb.nii.gz
        $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz:colormap=lut -f
        $SUBJECTS_DIR/$subj/surf/lh.white:edgecolor=green
        $SUBJECTS_DIR/$subj/surf/rh.white:edgecolor=green
        -viewport coronal
        error:
        mghRead(/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz,
        -1): could not open file
        MRIread failed: Unable to read from
        /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

        In the attached Error-1 file it shows error after entering
        the command in the terminal.

        Error-2 file - trying to load the file manually. You
        cannot see the wmparc2diff.mgz file though it is created
        and located in the folder.

        Please see the attached files and give your suggestions.

        Regards

        Ramesh

        On Fri, Jan 31, 2025 at 6:20 PM Ramesh Babu
        <mgrameshbabu2013@gmail.com> wrote:

            Dear Expert,

            I am finding an error in loading wmparc2diff.mgz in
            freeview. The error report from the terminal is;

            $ freeview -v lowb.nii.gz
            $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz:colormap=lut
            -f $SUBJECTS_DIR/$subj/surf/lh.white:edgecolor=green
            $SUBJECTS_DIR/$subj/surf/rh.white:edgecolor=green
            -viewport coronal
            error:
            mghRead(/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz,
            -1): could not open file
            MRIread failed: Unable to read from
            /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

            Please see the attached file and give your suggestions.

            Regards

            Ramesh

        _______________________________________________
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        The information in this e-mail is intended only for the
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    The information in this e-mail is intended only for the person
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    .

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

Ramesh Babu

4 Feb 4 Feb

6:20 a.m.

External Email - Use Caution

Dear Experts,

I found the issue. Few scripts I copy pasted from the website which caused font change. After typing in the terminal it works better now.

Thank You Ramesh

On Mon, Feb 3, 2025 at 7:50 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:

...

Does that file exist?

On 2/2/2025 11:34 AM, Ramesh Babu wrote:
    External Email - Use Caution
Dear Experts,

May I know why wmparc2diff is unreadable? Please suggest.

Thank you Ramesh

On Fri, Jan 31, 2025, 9:01 PM Ramesh Babu mgrameshbabu2013@gmail.com wrote:

...
Dear Yujing,

For the command, freeview /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

MRIread failed: Unable to read from /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

$ mri_info /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz error: mghRead(/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz, -1): could not open file

Thank you Ramesh

On Fri, Jan 31, 2025 at 6:54 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

...
Can you try these two commands?

freeview

/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

mri_info

/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Ramesh Babu *Sent:* Friday, January 31, 2025 8:19 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Error in loading wmparc2diff.mgz
   External Email - Use Caution        *
Dear Yujing,

Thank you for your prompt reply. Yes, it exists.

$ ls -l /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diﬀ.mgz

-rwxrwxrwx 1 root root 65906 Jan 31 18:00 /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diﬀ .mgz

But while loading manually it is not detected. Also, I used the "all types" option, but same issue.

Thanks

Ramesh

On Fri, Jan 31, 2025 at 6:41 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

Can you check if the volume exists?

ls -l /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

I only see wmparc.mgz in your listed directory.

Yujing

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Ramesh Babu *Sent:* Friday, January 31, 2025 8:05 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Error in loading wmparc2diff.mgz
   External Email - Use Caution        *
Sorry, I forgot to attach the files with the earlier message.

Dear Expert,

I am finding an error in loading wmparc2diff.mgz in freeview. The error report from the terminal is;

$ freeview -v lowb.nii.gz $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz:colormap=lut -f $SUBJECTS_DIR/$subj/surf/lh.white:edgecolor=green $SUBJECTS_DIR/$subj/surf/rh.white:edgecolor=green -viewport coronal error: mghRead(/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz, -1): could not open file MRIread failed: Unable to read from /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

In the attached Error-1 file it shows error after entering the command in the terminal.

Error-2 file - trying to load the file manually. You cannot see the wmparc2diff.mgz file though it is created and located in the folder.

Please see the attached files and give your suggestions.

Regards

Ramesh

On Fri, Jan 31, 2025 at 6:20 PM Ramesh Babu mgrameshbabu2013@gmail.com wrote:

Dear Expert,

I am finding an error in loading wmparc2diff.mgz in freeview. The error report from the terminal is;

$ freeview -v lowb.nii.gz $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz:colormap=lut -f $SUBJECTS_DIR/$subj/surf/lh.white:edgecolor=green $SUBJECTS_DIR/$subj/surf/rh.white:edgecolor=green -viewport coronal error: mghRead(/mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz, -1): could not open file MRIread failed: Unable to read from /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz

Please see the attached file and give your suggestions.

Regards

Ramesh

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Douglas N. Greve
Huang, Yujing
Ramesh Babu