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trac-all -prep error

Nasiriavanaki, Zahra,M.D.

5 Dec 2021 5 Dec '21

12:21 p.m.

Hello,

I’ve been running the trac-all -prep step and I faced this error:

ConvertTransformFile 3 /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt --hm --ras ConvertTransformFile: Command not found. Linux bee.nmr.mgh.harvard.eduhttp://bee.nmr.mgh.harvard.edu 3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec 3 14:29:56 EST 2021

Could you please let me know what the problem is? I’m running it in dev environment.

Thanks, Mona

Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry | MGH/HMS Department of Radiology | MGH/HMS 149 13th Street, 149-2615 Boston, MA, USA, 02129

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Yendiki, Anastasia

6 Dec 6 Dec

10:44 a.m.

Hi Mona - You need to add the location of the ANTs executables to your path.

Best, Anastasia.

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Nasiriavanaki, Zahra,M.D. ZNASIRIAVANAKI@mgh.harvard.edu Sent: Sunday, December 5, 2021 12:21 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Tracula error

Hello,

I’ve been running the trac-all -prep step and I faced this error:

trac-preproc exited with ERRORS at Fri Dec 3 14:29:56 EST 2021

Could you please let me know what the problem is? I’m running it in dev environment.

Thanks, Mona

Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry | MGH/HMS Department of Radiology | MGH/HMS 149 13th Street, 149-2615 Boston, MA, USA, 02129

Nasiriavanaki, Zahra,M.D.

7 Dec 7 Dec

1:30 p.m.

Hi Anastasia,

I did add the ANTs to my path, but am still getting that same error.

I adde the path : setenv ANTSPATH /usr/pubsw/packages/ANTS/2.3.4/bin to the .csh file which has all the TRACULA configuration info, and also to the bash script that I’m running the trac-all from: export ANTSPATH=/usr/pubsw/packages/ANTS/2.3.4/bin

Is there anything else I should do?

Thanks, Mona

On Dec 6, 2021, at 10:44 AM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Hi Mona - You need to add the location of the ANTs executables to your path.

Best, Anastasia.

________________________________ 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 Nasiriavanaki, Zahra,M.D. <ZNASIRIAVANAKI@mgh.harvard.edumailto:ZNASIRIAVANAKI@mgh.harvard.edu> Sent: Sunday, December 5, 2021 12:21 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Tracula error

Hello,

I’ve been running the trac-all -prep step and I faced this error:

ConvertTransformFile 3 /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt --hm --ras ConvertTransformFile: Command not found. Linux bee.nmr.mgh.harvard.eduhttp://bee.nmr.mgh.harvard.edu/ 3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec 3 14:29:56 EST 2021

Could you please let me know what the problem is? I’m running it in dev environment.

Thanks, Mona

Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry | MGH/HMS Department of Radiology | MGH/HMS 149 13th Street, 149-2615 Boston, MA, USA, 02129

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

Yendiki, Anastasia

8 Dec 8 Dec

6:37 p.m.

Hi Mona - Here's how you add something to your Unix path: https://unix.stackexchange.com/questions/3809/how-can-i-make-a-program-execu...

In your case you'd replace /path/to/file with $ANTSPATH.

Anastasia.

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Nasiriavanaki, Zahra,M.D. ZNASIRIAVANAKI@mgh.harvard.edu Sent: Tuesday, December 7, 2021 1:30 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula error

Hi Anastasia,

I did add the ANTs to my path, but am still getting that same error.

Is there anything else I should do?

Thanks, Mona

On Dec 6, 2021, at 10:44 AM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Hi Mona - You need to add the location of the ANTs executables to your path.

Best, Anastasia.

Hello,

I’ve been running the trac-all -prep step and I faced this error:

ConvertTransformFile 3 /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt --hm --ras ConvertTransformFile: Command not found. Linux bee.nmr.mgh.harvard.eduhttp://bee.nmr.mgh.harvard.edu/ 3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec 3 14:29:56 EST 2021

Could you please let me know what the problem is? I’m running it in dev environment.

Thanks, Mona

Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry | MGH/HMS Department of Radiology | MGH/HMS 149 13th Street, 149-2615 Boston, MA, USA, 02129

Nasiriavanaki, Zahra,M.D.

14 Dec 14 Dec

11:40 a.m.

Hello,

I was running the "trac-all -bedp” section, when I got the below error. I appreciate it much if you please let me know what the issue is.

Thanks, Mona

----- Bedpostx Monitor ----- An error ocurred. Please check file /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri.bedpostX/logs/bedpostx_pre.e9769 Killed

bedpostx_pre.e9769: /usr/pubsw/packages/fsl/6.0.4/bin/bedpostx_preproc.sh: line 77: 9819 Illegal instruction (core dumped) ${FSLDIR}/bin/fslslice ${subjdir}/data /usr/pubsw/packages/fsl/6.0.4/bin/bedpostx_preproc.sh: line 78: 9837 Illegal instruction (core dumped) ${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask

On Dec 8, 2021, at 6:37 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Hi Mona - Here's how you add something to your Unix path: https://unix.stackexchange.com/questions/3809/how-can-i-make-a-program-execu...

In your case you'd replace /path/to/file with $ANTSPATH.

Anastasia.

________________________________ 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 Nasiriavanaki, Zahra,M.D. <ZNASIRIAVANAKI@mgh.harvard.edumailto:ZNASIRIAVANAKI@mgh.harvard.edu> Sent: Tuesday, December 7, 2021 1:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Tracula error

Hi Anastasia,

I did add the ANTs to my path, but am still getting that same error.

Is there anything else I should do?

Thanks, Mona

On Dec 6, 2021, at 10:44 AM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Hi Mona - You need to add the location of the ANTs executables to your path.

Best, Anastasia.

Hello,

I’ve been running the trac-all -prep step and I faced this error:

ConvertTransformFile 3 /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt --hm --ras ConvertTransformFile: Command not found. Linux bee.nmr.mgh.harvard.eduhttp://bee.nmr.mgh.harvard.edu/ 3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec 3 14:29:56 EST 2021

Could you please let me know what the problem is? I’m running it in dev environment.

Thanks, Mona

Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry | MGH/HMS Department of Radiology | MGH/HMS 149 13th Street, 149-2615 Boston, MA, USA, 02129

Yendiki, Anastasia

12:03 p.m.

Hard to tell from the two lines. Did any files get created in bedpostX output directory? ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Nasiriavanaki, Zahra,M.D. ZNASIRIAVANAKI@mgh.harvard.edu Sent: Tuesday, December 14, 2021 11:40 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula error

Hello,

I was running the "trac-all -bedp” section, when I got the below error. I appreciate it much if you please let me know what the issue is.

Thanks, Mona

----- Bedpostx Monitor ----- An error ocurred. Please check file /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri.bedpostX/logs/bedpostx_pre.e9769 Killed

On Dec 8, 2021, at 6:37 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Hi Mona - Here's how you add something to your Unix path: https://unix.stackexchange.com/questions/3809/how-can-i-make-a-program-execu...

In your case you'd replace /path/to/file with $ANTSPATH.

Anastasia.

________________________________ 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 Nasiriavanaki, Zahra,M.D. <ZNASIRIAVANAKI@mgh.harvard.edumailto:ZNASIRIAVANAKI@mgh.harvard.edu> Sent: Tuesday, December 7, 2021 1:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Tracula error

Hi Anastasia,

I did add the ANTs to my path, but am still getting that same error.

Is there anything else I should do?

Thanks, Mona

On Dec 6, 2021, at 10:44 AM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Hi Mona - You need to add the location of the ANTs executables to your path.

Best, Anastasia.

Hello,

I’ve been running the trac-all -prep step and I faced this error:

ConvertTransformFile 3 /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt --hm --ras ConvertTransformFile: Command not found. Linux bee.nmr.mgh.harvard.eduhttp://bee.nmr.mgh.harvard.edu/ 3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec 3 14:29:56 EST 2021

Could you please let me know what the problem is? I’m running it in dev environment.

Thanks, Mona

Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry | MGH/HMS Department of Radiology | MGH/HMS 149 13th Street, 149-2615 Boston, MA, USA, 02129

Nasiriavanaki, Zahra,M.D.

12:18 p.m.

Yes.

dmri.bedpostX has these files in it:

diff_slices empty xfms empty bvals bvecs monitor nodiff_brain_mask.nii.gz logs: monitor empty bedpostx_pre.e9769 bedpostx_pre.e47281 bedpostx_pre.o9769 bedpostx_pre.o47281

Hard to tell from the two lines. Did any files get created in bedpostX output directory? ________________________________ 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 Nasiriavanaki, Zahra,M.D. <ZNASIRIAVANAKI@mgh.harvard.edumailto:ZNASIRIAVANAKI@mgh.harvard.edu> Sent: Tuesday, December 14, 2021 11:40 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Tracula error

Hello,

I was running the "trac-all -bedp” section, when I got the below error. I appreciate it much if you please let me know what the issue is.

Thanks, Mona

----- Bedpostx Monitor ----- An error ocurred. Please check file /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri.bedpostX/logs/bedpostx_pre.e9769 Killed

On Dec 8, 2021, at 6:37 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Hi Mona - Here's how you add something to your Unix path: https://unix.stackexchange.com/questions/3809/how-can-i-make-a-program-execu...

In your case you'd replace /path/to/file with $ANTSPATH.

Anastasia.

________________________________ 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 Nasiriavanaki, Zahra,M.D. <ZNASIRIAVANAKI@mgh.harvard.edumailto:ZNASIRIAVANAKI@mgh.harvard.edu> Sent: Tuesday, December 7, 2021 1:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Tracula error

Hi Anastasia,

I did add the ANTs to my path, but am still getting that same error.

Is there anything else I should do?

Thanks, Mona

On Dec 6, 2021, at 10:44 AM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Hi Mona - You need to add the location of the ANTs executables to your path.

Best, Anastasia.

Hello,

I’ve been running the trac-all -prep step and I faced this error:

ConvertTransformFile 3 /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt --hm --ras ConvertTransformFile: Command not found. Linux bee.nmr.mgh.harvard.eduhttp://bee.nmr.mgh.harvard.edu/ 3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec 3 14:29:56 EST 2021

Could you please let me know what the problem is? I’m running it in dev environment.

Thanks, Mona

Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry | MGH/HMS Department of Radiology | MGH/HMS 149 13th Street, 149-2615 Boston, MA, USA, 02129

Yendiki, Anastasia

12:40 p.m.

Any chance you're low on disk space? ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Nasiriavanaki, Zahra,M.D. ZNASIRIAVANAKI@mgh.harvard.edu Sent: Tuesday, December 14, 2021 12:18 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula error

Yes.

dmri.bedpostX has these files in it:

diff_slices empty xfms empty bvals bvecs monitor nodiff_brain_mask.nii.gz logs: monitor empty bedpostx_pre.e9769 bedpostx_pre.e47281 bedpostx_pre.o9769 bedpostx_pre.o47281

Hello,

I was running the "trac-all -bedp” section, when I got the below error. I appreciate it much if you please let me know what the issue is.

Thanks, Mona

----- Bedpostx Monitor ----- An error ocurred. Please check file /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri.bedpostX/logs/bedpostx_pre.e9769 Killed

On Dec 8, 2021, at 6:37 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Hi Mona - Here's how you add something to your Unix path: https://unix.stackexchange.com/questions/3809/how-can-i-make-a-program-execu...

In your case you'd replace /path/to/file with $ANTSPATH.

Anastasia.

________________________________ 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 Nasiriavanaki, Zahra,M.D. <ZNASIRIAVANAKI@mgh.harvard.edumailto:ZNASIRIAVANAKI@mgh.harvard.edu> Sent: Tuesday, December 7, 2021 1:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Tracula error

Hi Anastasia,

I did add the ANTs to my path, but am still getting that same error.

Is there anything else I should do?

Thanks, Mona

On Dec 6, 2021, at 10:44 AM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Hi Mona - You need to add the location of the ANTs executables to your path.

Best, Anastasia.

Hello,

I’ve been running the trac-all -prep step and I faced this error:

ConvertTransformFile 3 /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt --hm --ras ConvertTransformFile: Command not found. Linux bee.nmr.mgh.harvard.eduhttp://bee.nmr.mgh.harvard.edu/ 3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec 3 14:29:56 EST 2021

Could you please let me know what the problem is? I’m running it in dev environment.

Thanks, Mona

Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry | MGH/HMS Department of Radiology | MGH/HMS 149 13th Street, 149-2615 Boston, MA, USA, 02129

Nasiriavanaki, Zahra,M.D.

12:41 p.m.

How much space would I need to run this?

Thanks, Mona

On Dec 14, 2021, at 12:40 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Any chance you're low on disk space? ________________________________ 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 Nasiriavanaki, Zahra,M.D. <ZNASIRIAVANAKI@mgh.harvard.edumailto:ZNASIRIAVANAKI@mgh.harvard.edu> Sent: Tuesday, December 14, 2021 12:18 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Tracula error

Yes.

dmri.bedpostX has these files in it:

diff_slices empty xfms empty bvals bvecs monitor nodiff_brain_mask.nii.gz logs: monitor empty bedpostx_pre.e9769 bedpostx_pre.e47281 bedpostx_pre.o9769 bedpostx_pre.o47281

Hello,

I was running the "trac-all -bedp” section, when I got the below error. I appreciate it much if you please let me know what the issue is.

Thanks, Mona

----- Bedpostx Monitor ----- An error ocurred. Please check file /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri.bedpostX/logs/bedpostx_pre.e9769 Killed

On Dec 8, 2021, at 6:37 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Hi Mona - Here's how you add something to your Unix path: https://unix.stackexchange.com/questions/3809/how-can-i-make-a-program-execu...

In your case you'd replace /path/to/file with $ANTSPATH.

Anastasia.

________________________________ 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 Nasiriavanaki, Zahra,M.D. <ZNASIRIAVANAKI@mgh.harvard.edumailto:ZNASIRIAVANAKI@mgh.harvard.edu> Sent: Tuesday, December 7, 2021 1:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Tracula error

Hi Anastasia,

I did add the ANTs to my path, but am still getting that same error.

Is there anything else I should do?

Thanks, Mona

On Dec 6, 2021, at 10:44 AM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Hi Mona - You need to add the location of the ANTs executables to your path.

Best, Anastasia.

Hello,

I’ve been running the trac-all -prep step and I faced this error:

ConvertTransformFile 3 /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt --hm --ras ConvertTransformFile: Command not found. Linux bee.nmr.mgh.harvard.eduhttp://bee.nmr.mgh.harvard.edu/ 3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec 3 14:29:56 EST 2021

Could you please let me know what the problem is? I’m running it in dev environment.

Thanks, Mona

Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry | MGH/HMS Department of Radiology | MGH/HMS 149 13th Street, 149-2615 Boston, MA, USA, 02129

Yendiki, Anastasia

12:50 p.m.

Is there a dmri/data.nii.gz? Can you run mri_info on it please? ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Nasiriavanaki, Zahra,M.D. ZNASIRIAVANAKI@mgh.harvard.edu Sent: Tuesday, December 14, 2021 12:41 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula error

How much space would I need to run this?

Thanks, Mona

On Dec 14, 2021, at 12:40 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Yes.

dmri.bedpostX has these files in it:

diff_slices empty xfms empty bvals bvecs monitor nodiff_brain_mask.nii.gz logs: monitor empty bedpostx_pre.e9769 bedpostx_pre.e47281 bedpostx_pre.o9769 bedpostx_pre.o47281

Hello,

I was running the "trac-all -bedp” section, when I got the below error. I appreciate it much if you please let me know what the issue is.

Thanks, Mona

----- Bedpostx Monitor ----- An error ocurred. Please check file /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri.bedpostX/logs/bedpostx_pre.e9769 Killed

On Dec 8, 2021, at 6:37 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Hi Mona - Here's how you add something to your Unix path: https://unix.stackexchange.com/questions/3809/how-can-i-make-a-program-execu...

In your case you'd replace /path/to/file with $ANTSPATH.

Anastasia.

________________________________ 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 Nasiriavanaki, Zahra,M.D. <ZNASIRIAVANAKI@mgh.harvard.edumailto:ZNASIRIAVANAKI@mgh.harvard.edu> Sent: Tuesday, December 7, 2021 1:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Tracula error

Hi Anastasia,

I did add the ANTs to my path, but am still getting that same error.

Is there anything else I should do?

Thanks, Mona

On Dec 6, 2021, at 10:44 AM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Hi Mona - You need to add the location of the ANTs executables to your path.

Best, Anastasia.

Hello,

I’ve been running the trac-all -prep step and I faced this error:

ConvertTransformFile 3 /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt --hm --ras ConvertTransformFile: Command not found. Linux bee.nmr.mgh.harvard.eduhttp://bee.nmr.mgh.harvard.edu/ 3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec 3 14:29:56 EST 2021

Could you please let me know what the problem is? I’m running it in dev environment.

Thanks, Mona

Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry | MGH/HMS Department of Radiology | MGH/HMS 149 13th Street, 149-2615 Boston, MA, USA, 02129

Nasiriavanaki, Zahra,M.D.

12:59 p.m.

Yes, here it is:

Volume information for data.nii.gz type: nii dimensions: 120 x 120 x 69 x 132 voxel sizes: 2.000000, 2.000000, 2.000000 type: SHORT (4) fov: 240.000 dof: 0 xstart: -120.0, xend: 120.0 ystart: -120.0, yend: 120.0 zstart: -69.0, zend: 69.0 TR: 3000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 132 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = -0.0000, c_r = -1.7665 : x_a = -0.0000, y_a = 1.0000, z_a = -0.0000, c_a = -0.6018 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -5.1718 Orientation : LAS Primary Slice Direction: axial

voxel to ras transform: -2.0000 0.0000 -0.0000 118.2335 -0.0000 2.0000 -0.0000 -120.6018 0.0000 0.0000 2.0000 -74.1718 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -8

ras to voxel transform: -0.5000 -0.0000 -0.0000 59.1168 -0.0000 0.5000 -0.0000 60.3009 -0.0000 -0.0000 0.5000 37.0859 -0.0000 -0.0000 -0.0000 1.0000

On Dec 14, 2021, at 12:50 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Is there a dmri/data.nii.gz? Can you run mri_info on it please? ________________________________ 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 Nasiriavanaki, Zahra,M.D. <ZNASIRIAVANAKI@mgh.harvard.edumailto:ZNASIRIAVANAKI@mgh.harvard.edu> Sent: Tuesday, December 14, 2021 12:41 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Tracula error

How much space would I need to run this?

Thanks, Mona

On Dec 14, 2021, at 12:40 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Yes.

dmri.bedpostX has these files in it:

diff_slices empty xfms empty bvals bvecs monitor nodiff_brain_mask.nii.gz logs: monitor empty bedpostx_pre.e9769 bedpostx_pre.e47281 bedpostx_pre.o9769 bedpostx_pre.o47281

Hello,

I was running the "trac-all -bedp” section, when I got the below error. I appreciate it much if you please let me know what the issue is.

Thanks, Mona

----- Bedpostx Monitor ----- An error ocurred. Please check file /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri.bedpostX/logs/bedpostx_pre.e9769 Killed

On Dec 8, 2021, at 6:37 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Hi Mona - Here's how you add something to your Unix path: https://unix.stackexchange.com/questions/3809/how-can-i-make-a-program-execu...

In your case you'd replace /path/to/file with $ANTSPATH.

Anastasia.

________________________________ 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 Nasiriavanaki, Zahra,M.D. <ZNASIRIAVANAKI@mgh.harvard.edumailto:ZNASIRIAVANAKI@mgh.harvard.edu> Sent: Tuesday, December 7, 2021 1:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Tracula error

Hi Anastasia,

I did add the ANTs to my path, but am still getting that same error.

Is there anything else I should do?

Thanks, Mona

On Dec 6, 2021, at 10:44 AM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Hi Mona - You need to add the location of the ANTs executables to your path.

Best, Anastasia.

Hello,

I’ve been running the trac-all -prep step and I faced this error:

ConvertTransformFile 3 /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt --hm --ras ConvertTransformFile: Command not found. Linux bee.nmr.mgh.harvard.eduhttp://bee.nmr.mgh.harvard.edu/ 3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec 3 14:29:56 EST 2021

Could you please let me know what the problem is? I’m running it in dev environment.

Thanks, Mona

Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry | MGH/HMS Department of Radiology | MGH/HMS 149 13th Street, 149-2615 Boston, MA, USA, 02129

Nasiriavanaki, Zahra,M.D.

15 Dec 15 Dec

11:15 p.m.

Hello,

I wanted to follow up on this question. I appreciate it much if you could suggest me any solutions. I checked my space and I have 3.5 T free space, so It’s definitely not a space problem.

Thanks, Mona

On Dec 14, 2021, at 12:59 PM, Nasiriavanaki, Zahra,M.D. <ZNASIRIAVANAKI@mgh.harvard.edumailto:ZNASIRIAVANAKI@mgh.harvard.edu> wrote:

Yes, here it is:

voxel to ras transform: -2.0000 0.0000 -0.0000 118.2335 -0.0000 2.0000 -0.0000 -120.6018 0.0000 0.0000 2.0000 -74.1718 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -8

ras to voxel transform: -0.5000 -0.0000 -0.0000 59.1168 -0.0000 0.5000 -0.0000 60.3009 -0.0000 -0.0000 0.5000 37.0859 -0.0000 -0.0000 -0.0000 1.0000

On Dec 14, 2021, at 12:50 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

How much space would I need to run this?

Thanks, Mona

On Dec 14, 2021, at 12:40 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Yes.

dmri.bedpostX has these files in it:

diff_slices empty xfms empty bvals bvecs monitor nodiff_brain_mask.nii.gz logs: monitor empty bedpostx_pre.e9769 bedpostx_pre.e47281 bedpostx_pre.o9769 bedpostx_pre.o47281

Hello,

I was running the "trac-all -bedp” section, when I got the below error. I appreciate it much if you please let me know what the issue is.

Thanks, Mona

----- Bedpostx Monitor ----- An error ocurred. Please check file /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri.bedpostX/logs/bedpostx_pre.e9769 Killed

On Dec 8, 2021, at 6:37 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Hi Mona - Here's how you add something to your Unix path: https://unix.stackexchange.com/questions/3809/how-can-i-make-a-program-execu...

In your case you'd replace /path/to/file with $ANTSPATH.

Anastasia.

________________________________ 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 Nasiriavanaki, Zahra,M.D. <ZNASIRIAVANAKI@mgh.harvard.edumailto:ZNASIRIAVANAKI@mgh.harvard.edu> Sent: Tuesday, December 7, 2021 1:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Tracula error

Hi Anastasia,

I did add the ANTs to my path, but am still getting that same error.

Is there anything else I should do?

Thanks, Mona

On Dec 6, 2021, at 10:44 AM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Hi Mona - You need to add the location of the ANTs executables to your path.

Best, Anastasia.

Hello,

I’ve been running the trac-all -prep step and I faced this error:

ConvertTransformFile 3 /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt --hm --ras ConvertTransformFile: Command not found. Linux bee.nmr.mgh.harvard.eduhttp://bee.nmr.mgh.harvard.edu/ 3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec 3 14:29:56 EST 2021

Could you please let me know what the problem is? I’m running it in dev environment.

Thanks, Mona

Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry | MGH/HMS Department of Radiology | MGH/HMS 149 13th Street, 149-2615 Boston, MA, USA, 02129

Yendiki, Anastasia

23 Dec 23 Dec

2:26 p.m.

Hi Mona - It's hard to tell from the 2 lines of output that you sent. Do you see any other output?

Anastasia. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Nasiriavanaki, Zahra,M.D. ZNASIRIAVANAKI@mgh.harvard.edu Sent: Wednesday, December 15, 2021 11:15 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula error

Hello,

I wanted to follow up on this question. I appreciate it much if you could suggest me any solutions. I checked my space and I have 3.5 T free space, so It’s definitely not a space problem.

Thanks, Mona

On Dec 14, 2021, at 12:59 PM, Nasiriavanaki, Zahra,M.D. <ZNASIRIAVANAKI@mgh.harvard.edumailto:ZNASIRIAVANAKI@mgh.harvard.edu> wrote:

Yes, here it is:

voxel to ras transform: -2.0000 0.0000 -0.0000 118.2335 -0.0000 2.0000 -0.0000 -120.6018 0.0000 0.0000 2.0000 -74.1718 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -8

ras to voxel transform: -0.5000 -0.0000 -0.0000 59.1168 -0.0000 0.5000 -0.0000 60.3009 -0.0000 -0.0000 0.5000 37.0859 -0.0000 -0.0000 -0.0000 1.0000

On Dec 14, 2021, at 12:50 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

How much space would I need to run this?

Thanks, Mona

On Dec 14, 2021, at 12:40 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Yes.

dmri.bedpostX has these files in it:

diff_slices empty xfms empty bvals bvecs monitor nodiff_brain_mask.nii.gz logs: monitor empty bedpostx_pre.e9769 bedpostx_pre.e47281 bedpostx_pre.o9769 bedpostx_pre.o47281

Hello,

I was running the "trac-all -bedp” section, when I got the below error. I appreciate it much if you please let me know what the issue is.

Thanks, Mona

----- Bedpostx Monitor ----- An error ocurred. Please check file /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri.bedpostX/logs/bedpostx_pre.e9769 Killed

On Dec 8, 2021, at 6:37 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Hi Mona - Here's how you add something to your Unix path: https://unix.stackexchange.com/questions/3809/how-can-i-make-a-program-execu...

In your case you'd replace /path/to/file with $ANTSPATH.

Anastasia.

________________________________ 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 Nasiriavanaki, Zahra,M.D. <ZNASIRIAVANAKI@mgh.harvard.edumailto:ZNASIRIAVANAKI@mgh.harvard.edu> Sent: Tuesday, December 7, 2021 1:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Tracula error

Hi Anastasia,

I did add the ANTs to my path, but am still getting that same error.

Is there anything else I should do?

Thanks, Mona

On Dec 6, 2021, at 10:44 AM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Hi Mona - You need to add the location of the ANTs executables to your path.

Best, Anastasia.

Hello,

I’ve been running the trac-all -prep step and I faced this error:

ConvertTransformFile 3 /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt --hm --ras ConvertTransformFile: Command not found. Linux bee.nmr.mgh.harvard.eduhttp://bee.nmr.mgh.harvard.edu/ 3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec 3 14:29:56 EST 2021

Could you please let me know what the problem is? I’m running it in dev environment.

Thanks, Mona

Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry | MGH/HMS Department of Radiology | MGH/HMS 149 13th Street, 149-2615 Boston, MA, USA, 02129

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Nasiriavanaki, Zahra,M.D.
Yendiki, Anastasia