Error in Tracula-all -prep

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Salah Showiheen

6 Apr 2020 6 Apr '20

11:49 p.m.

External Email - Use Caution

Hi Freesurfer community,

I have an issue that I spent ages trying to figure out and this error has been asked about back in (17/12/2016) and the title is ([Freesurfer] Tracula trac -all preprocessing error.

my error is:

ERROR: fio_pushd: /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/dlabel/mni

There is an issue that the mini folder is empty.

Attached is the log file and the configuration file (tracula_conf.txt)

Regards, Salah

Attachments:

attachment.html (text/html — 3.6 KB)
tracula_conf.txt (text/plain — 6.4 KB)
trac-all.log (application/octet-stream — 139.5 KB)

Show replies by date

Yendiki, Anastasia

8 Apr 8 Apr

10:34 p.m.

Hi Salah - It looks like it didn't find your subject's freesurfer recon when it was doing the pre-processing, so it skipped some steps that you need to go beyond that point. Based on your SUBJECTS_DIR and your subject name, it looked for this file: /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/mri/brain.mgz

Any chance this was missing or unreadable?

a.y ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Salah Showiheen sshowiheen@gmail.com Sent: Monday, April 6, 2020 11:49 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Error in Tracula-all -prep

External Email - Use Caution

Hi Freesurfer community,

I have an issue that I spent ages trying to figure out and this error has been asked about back in (17/12/2016) and the title is ([Freesurfer] Tracula trac -all preprocessing error.

my error is:

ERROR: fio_pushd: /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/dlabel/mni

There is an issue that the mini folder is empty.

Attached is the log file and the configuration file (tracula_conf.txt)

Regards, Salah

Salah Showiheen

10 Apr 10 Apr

12:33 a.m.

External Email - Use Caution

Hi Anastasia,

It is true that this file was missing. When I added it, the processing in trac-all -intra took longer time but comes with an error :

/Applications/freesurfer/tktools/tkregister2.bin: Bad CPU type in executable.

Any hint in fixing this issue or finding if the file (brain,mgz) is unreadable? I was able to open it in freeviewer, though!!

NB: log file is attached.

Regards, Salah

On Thu, Apr 9, 2020 at 12:35 PM Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:

...

Hi Salah - It looks like it didn't find your subject's freesurfer recon when it was doing the pre-processing, so it skipped some steps that you need to go beyond that point. Based on your SUBJECTS_DIR and your subject name, it looked for this file: /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/mri/brain.mgz

Any chance this was missing or unreadable?

a.y

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Salah Showiheen < sshowiheen@gmail.com> *Sent:* Monday, April 6, 2020 11:49 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Error in Tracula-all -prep
    External Email - Use Caution
Hi Freesurfer community,

I have an issue that I spent ages trying to figure out and this error has been asked about back in (17/12/2016) and the title is ([Freesurfer] Tracula trac -all preprocessing error.

my error is:

ERROR: fio_pushd: /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/dlabel/mni

There is an issue that the mini folder is empty.

Attached is the log file and the configuration file (tracula_conf.txt)

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

Yendiki, Anastasia

3:53 p.m.

Hi Salah - You're probably running into this problem: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg64575.html

You can edit the script $FREESURFER_HOME/bin/trac-preproc, search for tkregister2, change it to tkregister2_cmdl, then try again.

a.y ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Salah Showiheen sshowiheen@gmail.com Sent: Friday, April 10, 2020 12:33 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Error in Tracula-all -prep

External Email - Use Caution

Hi Anastasia,

It is true that this file was missing. When I added it, the processing in trac-all -intra took longer time but comes with an error :

/Applications/freesurfer/tktools/tkregister2.bin: Bad CPU type in executable.

Any hint in fixing this issue or finding if the file (brain,mgz) is unreadable? I was able to open it in freeviewer, though!!

NB: log file is attached.

Regards, Salah

On Thu, Apr 9, 2020 at 12:35 PM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Hi Salah - It looks like it didn't find your subject's freesurfer recon when it was doing the pre-processing, so it skipped some steps that you need to go beyond that point. Based on your SUBJECTS_DIR and your subject name, it looked for this file: /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/mri/brain.mgz

Any chance this was missing or unreadable?

a.y ________________________________ 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 Salah Showiheen <sshowiheen@gmail.commailto:sshowiheen@gmail.com> Sent: Monday, April 6, 2020 11:49 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Error in Tracula-all -prep

External Email - Use Caution

Hi Freesurfer community,

I have an issue that I spent ages trying to figure out and this error has been asked about back in (17/12/2016) and the title is ([Freesurfer] Tracula trac -all preprocessing error.

my error is:

ERROR: fio_pushd: /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/dlabel/mni

There is an issue that the mini folder is empty.

Attached is the log file and the configuration file (tracula_conf.txt)

Salah Showiheen

15 Apr 15 Apr

3:42 a.m.

External Email - Use Caution

Thanks Freesurfer developer I have followed what you have suggested and it did work for me.

Thanks once again for your help.

Regards Salah

On Sat, 11 Apr 2020, 5:54 am Yendiki, Anastasia, AYENDIKI@mgh.harvard.edu wrote:

...

Hi Salah - You're probably running into this problem: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg64575.html

You can edit the script $FREESURFER_HOME/bin/trac-preproc, search for tkregister2, change it to tkregister2_cmdl, then try again.

a.y

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Salah Showiheen < sshowiheen@gmail.com> *Sent:* Friday, April 10, 2020 12:33 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Error in Tracula-all -prep
    External Email - Use Caution
Hi Anastasia,

It is true that this file was missing. When I added it, the processing in trac-all -intra took longer time but comes with an error :

/Applications/freesurfer/tktools/tkregister2.bin: Bad CPU type in executable.

Any hint in fixing this issue or finding if the file (brain,mgz) is unreadable? I was able to open it in freeviewer, though!!

NB: log file is attached.

Regards, Salah

On Thu, Apr 9, 2020 at 12:35 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:

Hi Salah - It looks like it didn't find your subject's freesurfer recon when it was doing the pre-processing, so it skipped some steps that you need to go beyond that point. Based on your SUBJECTS_DIR and your subject name, it looked for this file: /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/mri/brain.mgz

Any chance this was missing or unreadable?

a.y

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Salah Showiheen < sshowiheen@gmail.com> *Sent:* Monday, April 6, 2020 11:49 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Error in Tracula-all -prep
    External Email - Use Caution
Hi Freesurfer community,

I have an issue that I spent ages trying to figure out and this error has been asked about back in (17/12/2016) and the title is ([Freesurfer] Tracula trac -all preprocessing error.

my error is:

ERROR: fio_pushd: /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/dlabel/mni

There is an issue that the mini folder is empty.

Attached is the log file and the configuration file (tracula_conf.txt)

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

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

Salah Showiheen

20 Apr 20 Apr

7:08 a.m.

External Email - Use Caution

Hi Freesurfers

I have different type of data set and when I run trac-all I faced exactly the same issue, that I had been saving last time, but this time the file mri/brain.mgz is there!!! However, I think it is unreadable as you said las time that this file is either missing or unreadable. Because it is not missing, I assume it is unreadable.

I have attached recon-all and trac-all files.

Regards, Salah

On Wed, Apr 15, 2020 at 5:42 PM Salah Showiheen sshowiheen@gmail.com wrote:

...

Thanks Freesurfer developer I have followed what you have suggested and it did work for me.

Thanks once again for your help.

Regards Salah

On Sat, 11 Apr 2020, 5:54 am Yendiki, Anastasia, AYENDIKI@mgh.harvard.edu wrote:

...
Hi Salah - You're probably running into this problem: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg64575.html

You can edit the script $FREESURFER_HOME/bin/trac-preproc, search for tkregister2, change it to tkregister2_cmdl, then try again.

a.y

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Salah Showiheen < sshowiheen@gmail.com> *Sent:* Friday, April 10, 2020 12:33 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Error in Tracula-all -prep
    External Email - Use Caution
Hi Anastasia,

It is true that this file was missing. When I added it, the processing in trac-all -intra took longer time but comes with an error :

/Applications/freesurfer/tktools/tkregister2.bin: Bad CPU type in executable.

Any hint in fixing this issue or finding if the file (brain,mgz) is unreadable? I was able to open it in freeviewer, though!!

NB: log file is attached.

Regards, Salah

On Thu, Apr 9, 2020 at 12:35 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:

Hi Salah - It looks like it didn't find your subject's freesurfer recon when it was doing the pre-processing, so it skipped some steps that you need to go beyond that point. Based on your SUBJECTS_DIR and your subject name, it looked for this file: /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/mri/brain.mgz

Any chance this was missing or unreadable?

a.y

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Salah Showiheen < sshowiheen@gmail.com> *Sent:* Monday, April 6, 2020 11:49 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Error in Tracula-all -prep
    External Email - Use Caution
Hi Freesurfer community,

I have an issue that I spent ages trying to figure out and this error has been asked about back in (17/12/2016) and the title is ([Freesurfer] Tracula trac -all preprocessing error.

my error is:

ERROR: fio_pushd: /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/dlabel/mni

There is an issue that the mini folder is empty.

Attached is the log file and the configuration file (tracula_conf.txt)

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

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

Yendiki, Anastasia

3:16 p.m.

When you run the following command, what do you see?

ls -l /Volumes/HD/Post_HARDI/HIRF_Research_84/18/trac_R18/mri ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Salah Showiheen sshowiheen@gmail.com Sent: Monday, April 20, 2020 7:08 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Error in Tracula-all -prep

External Email - Use Caution

Hi Freesurfers

I have attached recon-all and trac-all files.

Regards, Salah

On Wed, Apr 15, 2020 at 5:42 PM Salah Showiheen <sshowiheen@gmail.commailto:sshowiheen@gmail.com> wrote: Thanks Freesurfer developer I have followed what you have suggested and it did work for me.

Thanks once again for your help.

Regards Salah

On Sat, 11 Apr 2020, 5:54 am Yendiki, Anastasia, <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Hi Salah - You're probably running into this problem: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg64575.html

You can edit the script $FREESURFER_HOME/bin/trac-preproc, search for tkregister2, change it to tkregister2_cmdl, then try again.

a.y ________________________________ 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 Salah Showiheen <sshowiheen@gmail.commailto:sshowiheen@gmail.com> Sent: Friday, April 10, 2020 12:33 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Error in Tracula-all -prep

External Email - Use Caution

Hi Anastasia,

It is true that this file was missing. When I added it, the processing in trac-all -intra took longer time but comes with an error :

/Applications/freesurfer/tktools/tkregister2.bin: Bad CPU type in executable.

Any hint in fixing this issue or finding if the file (brain,mgz) is unreadable? I was able to open it in freeviewer, though!!

NB: log file is attached.

Regards, Salah

Any chance this was missing or unreadable?

External Email - Use Caution

Hi Freesurfer community,

I have an issue that I spent ages trying to figure out and this error has been asked about back in (17/12/2016) and the title is ([Freesurfer] Tracula trac -all preprocessing error.

my error is:

ERROR: fio_pushd: /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/dlabel/mni

There is an issue that the mini folder is empty.

Attached is the log file and the configuration file (tracula_conf.txt)

Salah Showiheen

8:56 p.m.

External Email - Use Caution

Hi Anastasia,

Here is what I have within the folder DIR/mri

QUT-gonzo:/ n9800093$ cd Volumes/G_RAID/Backup_Salah/Post_HARDI/HIRF_Research_84/18/Recon_R18/mri/

QUT-gonzo:mri n9800093$ ls -l

total 98496

-rw-rw-r-- 1 n9800093 staff 5616637 17 Apr 16:39 T1.mgz

-rw-rw-r-- 1 n9800093 staff 413271 18 Apr 05:18 aparc+aseg.mgz

-rw-rw-r-- 1 n9800093 staff 411315 18 Apr 05:33 aparc.DKTatlas+aseg.mgz

-rw-rw-r-- 1 n9800093 staff 449897 18 Apr 05:25 aparc.a2009s+aseg.mgz

-rw-rw-r-- 1 n9800093 staff 254587 17 Apr 22:12 aseg.auto.mgz

-rw-rw-r-- 1 n9800093 staff 1544 17 Apr 20:31 aseg.auto_noCCseg.label_intensities.txt

-rw-rw-r-- 1 n9800093 staff 254025 17 Apr 22:10 aseg.auto_noCCseg.mgz

-rw-rw-r-- 1 n9800093 staff 357285 18 Apr 05:33 aseg.mgz

-rw-rw-r-- 1 n9800093 staff 254943 18 Apr 05:11 aseg.presurf.hypos.mgz

-rw-rw-r-- 1 n9800093 staff 254587 17 Apr 22:12 aseg.presurf.mgz

-rw-rw-r-- 1 n9800093 staff 1463192 17 Apr 22:19 brain.finalsurfs.mgz

-rw-rw-r-- 1 n9800093 staff 1496605 17 Apr 22:19 brain.mgz

-rw-rw-r-- 1 n9800093 staff 1495689 17 Apr 16:59 brainmask.auto.mgz

-rw-rw-r-- 1 n9800093 staff 1495689 17 Apr 16:59 brainmask.mgz

-rw-rw-r-- 1 n9800093 staff 557913 17 Apr 17:17 ctrl_pts.mgz

-rw-rw-r-- 1 n9800093 staff 140475 17 Apr 22:25 filled.mgz

-rw-rw-r-- 1 n9800093 staff 114842 18 Apr 05:00 lh.ribbon.mgz

-rw-rw-r-- 1 n9800093 staff 14275 17 Apr 16:36 mri_nu_correct.mni.log

-rw-rw-r-- 1 n9800093 staff 12794 17 Apr 16:32 mri_nu_correct.mni.log.bak

-rw-rw-r-- 1 n9800093 staff 1600004 17 Apr 17:17 norm.mgz

-rw-rw-r-- 1 n9800093 staff 5906417 17 Apr 16:36 nu.mgz

drwxrwxr-x 3 n9800093 staff 102 17 Apr 16:28 orig

-rw-rw-r-- 1 n9800093 staff 5909247 17 Apr 16:29 orig.mgz

-rw-rw-r-- 1 n9800093 staff 5790997 17 Apr 16:32 orig_nu.mgz

-rw-rw-r-- 1 n9800093 staff 13973314 17 Apr 16:29 rawavg.mgz

-rw-rw-r-- 1 n9800093 staff 117517 18 Apr 05:00 rh.ribbon.mgz

-rw-rw-r-- 1 n9800093 staff 220417 18 Apr 05:00 ribbon.mgz

-rw-rw-r-- 1 n9800093 staff 121 17 Apr 22:19 segment.dat

-rw-rw-r-- 1 n9800093 staff 1544 17 Apr 18:03 talairach.label_intensities.txt

-rw-rw-r-- 1 n9800093 staff 214 17 Apr 17:15 talairach.log

-rw-rw-r-- 1 n9800093 staff 214 17 Apr 16:58 talairach_with_skull.log

drwxrwxr-x 13 n9800093 staff 442 17 Apr 22:12 transforms

-rw-rw-r-- 1 n9800093 staff 419883 17 Apr 22:24 wm.asegedit.mgz

-rw-rw-r-- 1 n9800093 staff 421210 17 Apr 22:24 wm.mgz

-rw-rw-r-- 1 n9800093 staff 454934 17 Apr 22:22 wm.seg.mgz

-rw-rw-r-- 1 n9800093 staff 468036 18 Apr 05:43 wmparc.mgz

QUT-gonzo:mri n9800093$

Regards, Salah

On Tue, Apr 21, 2020 at 5:17 AM Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:

...

When you run the following command, what do you see?

ls -l /Volumes/HD/Post_HARDI/HIRF_Research_84/18/trac_R18/mri

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Salah Showiheen < sshowiheen@gmail.com> *Sent:* Monday, April 20, 2020 7:08 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Error in Tracula-all -prep
    External Email - Use Caution
Hi Freesurfers

I have different type of data set and when I run trac-all I faced exactly the same issue, that I had been saving last time, but this time the file mri/brain.mgz is there!!! However, I think it is unreadable as you said las time that this file is either missing or unreadable. Because it is not missing, I assume it is unreadable.

I have attached recon-all and trac-all files.

Regards, Salah

On Wed, Apr 15, 2020 at 5:42 PM Salah Showiheen sshowiheen@gmail.com wrote:

Thanks Freesurfer developer I have followed what you have suggested and it did work for me.

Thanks once again for your help.

Regards Salah

On Sat, 11 Apr 2020, 5:54 am Yendiki, Anastasia, AYENDIKI@mgh.harvard.edu wrote:

Hi Salah - You're probably running into this problem: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg64575.html

You can edit the script $FREESURFER_HOME/bin/trac-preproc, search for tkregister2, change it to tkregister2_cmdl, then try again.

a.y

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Salah Showiheen < sshowiheen@gmail.com> *Sent:* Friday, April 10, 2020 12:33 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Error in Tracula-all -prep
    External Email - Use Caution
Hi Anastasia,

It is true that this file was missing. When I added it, the processing in trac-all -intra took longer time but comes with an error :

/Applications/freesurfer/tktools/tkregister2.bin: Bad CPU type in executable.

Any hint in fixing this issue or finding if the file (brain,mgz) is unreadable? I was able to open it in freeviewer, though!!

NB: log file is attached.

Regards, Salah

On Thu, Apr 9, 2020 at 12:35 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:

Hi Salah - It looks like it didn't find your subject's freesurfer recon when it was doing the pre-processing, so it skipped some steps that you need to go beyond that point. Based on your SUBJECTS_DIR and your subject name, it looked for this file: /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/mri/brain.mgz

Any chance this was missing or unreadable?

a.y

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Salah Showiheen < sshowiheen@gmail.com> *Sent:* Monday, April 6, 2020 11:49 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Error in Tracula-all -prep
    External Email - Use Caution
Hi Freesurfer community,

I have an issue that I spent ages trying to figure out and this error has been asked about back in (17/12/2016) and the title is ([Freesurfer] Tracula trac -all preprocessing error.

my error is:

ERROR: fio_pushd: /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/dlabel/mni

There is an issue that the mini folder is empty.

Attached is the log file and the configuration file (tracula_conf.txt)

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

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

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

Yendiki, Anastasia

10:18 p.m.

These are the contents of a different directory from the one I asked about. TRACULA is looking for your subject's freesurfer recon under /Volumes/HD/Post_HARDI/HIRF_Research_84/18/trac_R18 because your SUBJECTS_DIR is set to /Volumes/HD/Post_HARDI/HIRF_Research_84/18 and your subject name is trac_R18. If you want it to look elsewhere, you have to set your SUBJECTS_DIR accordingly. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Salah Showiheen sshowiheen@gmail.com Sent: Monday, April 20, 2020 8:56 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Error in Tracula-all -prep

External Email - Use Caution

Hi Anastasia,

Here is what I have within the folder DIR/mri

QUT-gonzo:/ n9800093$ cd Volumes/G_RAID/Backup_Salah/Post_HARDI/HIRF_Research_84/18/Recon_R18/mri/

QUT-gonzo:mri n9800093$ ls -l

total 98496

-rw-rw-r-- 1 n9800093 staff 5616637 17 Apr 16:39 T1.mgz

-rw-rw-r-- 1 n9800093 staff 413271 18 Apr 05:18 aparc+aseg.mgz

-rw-rw-r-- 1 n9800093 staff 411315 18 Apr 05:33 aparc.DKTatlas+aseg.mgz

-rw-rw-r-- 1 n9800093 staff 449897 18 Apr 05:25 aparc.a2009s+aseg.mgz

-rw-rw-r-- 1 n9800093 staff 254587 17 Apr 22:12 aseg.auto.mgz

-rw-rw-r-- 1 n9800093 staff 1544 17 Apr 20:31 aseg.auto_noCCseg.label_intensities.txt

-rw-rw-r-- 1 n9800093 staff 254025 17 Apr 22:10 aseg.auto_noCCseg.mgz

-rw-rw-r-- 1 n9800093 staff 357285 18 Apr 05:33 aseg.mgz

-rw-rw-r-- 1 n9800093 staff 254943 18 Apr 05:11 aseg.presurf.hypos.mgz

-rw-rw-r-- 1 n9800093 staff 254587 17 Apr 22:12 aseg.presurf.mgz

-rw-rw-r-- 1 n9800093 staff 1463192 17 Apr 22:19 brain.finalsurfs.mgz

-rw-rw-r-- 1 n9800093 staff 1496605 17 Apr 22:19 brain.mgz

-rw-rw-r-- 1 n9800093 staff 1495689 17 Apr 16:59 brainmask.auto.mgz

-rw-rw-r-- 1 n9800093 staff 1495689 17 Apr 16:59 brainmask.mgz

-rw-rw-r-- 1 n9800093 staff 557913 17 Apr 17:17 ctrl_pts.mgz

-rw-rw-r-- 1 n9800093 staff 140475 17 Apr 22:25 filled.mgz

-rw-rw-r-- 1 n9800093 staff 114842 18 Apr 05:00 lh.ribbon.mgz

-rw-rw-r-- 1 n9800093 staff 14275 17 Apr 16:36 mri_nu_correct.mni.log

-rw-rw-r-- 1 n9800093 staff 12794 17 Apr 16:32 mri_nu_correct.mni.log.bak

-rw-rw-r-- 1 n9800093 staff 1600004 17 Apr 17:17 norm.mgz

-rw-rw-r-- 1 n9800093 staff 5906417 17 Apr 16:36 nu.mgz

drwxrwxr-x 3 n9800093 staff 102 17 Apr 16:28 orig

-rw-rw-r-- 1 n9800093 staff 5909247 17 Apr 16:29 orig.mgz

-rw-rw-r-- 1 n9800093 staff 5790997 17 Apr 16:32 orig_nu.mgz

-rw-rw-r-- 1 n9800093 staff 13973314 17 Apr 16:29 rawavg.mgz

-rw-rw-r-- 1 n9800093 staff 117517 18 Apr 05:00 rh.ribbon.mgz

-rw-rw-r-- 1 n9800093 staff 220417 18 Apr 05:00 ribbon.mgz

-rw-rw-r-- 1 n9800093 staff 121 17 Apr 22:19 segment.dat

-rw-rw-r-- 1 n9800093 staff 1544 17 Apr 18:03 talairach.label_intensities.txt

-rw-rw-r-- 1 n9800093 staff 214 17 Apr 17:15 talairach.log

-rw-rw-r-- 1 n9800093 staff 214 17 Apr 16:58 talairach_with_skull.log

drwxrwxr-x 13 n9800093 staff 442 17 Apr 22:12 transforms

-rw-rw-r-- 1 n9800093 staff 419883 17 Apr 22:24 wm.asegedit.mgz

-rw-rw-r-- 1 n9800093 staff 421210 17 Apr 22:24 wm.mgz

-rw-rw-r-- 1 n9800093 staff 454934 17 Apr 22:22 wm.seg.mgz

-rw-rw-r-- 1 n9800093 staff 468036 18 Apr 05:43 wmparc.mgz

QUT-gonzo:mri n9800093$

Regards, Salah

On Tue, Apr 21, 2020 at 5:17 AM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: When you run the following command, what do you see?

ls -l /Volumes/HD/Post_HARDI/HIRF_Research_84/18/trac_R18/mri ________________________________ 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 Salah Showiheen <sshowiheen@gmail.commailto:sshowiheen@gmail.com> Sent: Monday, April 20, 2020 7:08 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Error in Tracula-all -prep

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Hi Freesurfers

I have attached recon-all and trac-all files.

Regards, Salah

On Wed, Apr 15, 2020 at 5:42 PM Salah Showiheen <sshowiheen@gmail.commailto:sshowiheen@gmail.com> wrote: Thanks Freesurfer developer I have followed what you have suggested and it did work for me.

Thanks once again for your help.

Regards Salah

You can edit the script $FREESURFER_HOME/bin/trac-preproc, search for tkregister2, change it to tkregister2_cmdl, then try again.

a.y ________________________________ 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 Salah Showiheen <sshowiheen@gmail.commailto:sshowiheen@gmail.com> Sent: Friday, April 10, 2020 12:33 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Error in Tracula-all -prep

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Hi Anastasia,

It is true that this file was missing. When I added it, the processing in trac-all -intra took longer time but comes with an error :

/Applications/freesurfer/tktools/tkregister2.bin: Bad CPU type in executable.

Any hint in fixing this issue or finding if the file (brain,mgz) is unreadable? I was able to open it in freeviewer, though!!

NB: log file is attached.

Regards, Salah

Any chance this was missing or unreadable?

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Hi Freesurfer community,

I have an issue that I spent ages trying to figure out and this error has been asked about back in (17/12/2016) and the title is ([Freesurfer] Tracula trac -all preprocessing error.

my error is:

ERROR: fio_pushd: /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/dlabel/mni

There is an issue that the mini folder is empty.

Attached is the log file and the configuration file (tracula_conf.txt)

Regards, Salah _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Salah Showiheen
Yendiki, Anastasia