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.edu> wrote:

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.edu> wrote:

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.edu> wrote:

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

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 

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.edu> wrote:

Hi Mona - Here's how you add something to your Unix path:

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.

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.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.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:

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.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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