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
<ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> wrote:
Is there a dmri/data.nii.gz? Can you run mri_info on it please?
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Nasiriavanaki, Zahra,M.D.
<znasiriavan...@mgh.harvard.edu<mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 14, 2021 12:41 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto: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
<ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> wrote:
Any chance you're low on disk space?
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Nasiriavanaki, Zahra,M.D.
<znasiriavan...@mgh.harvard.edu<mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 14, 2021 12:18 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto: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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Nasiriavanaki, Zahra,M.D.
<znasiriavan...@mgh.harvard.edu<mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 14, 2021 11:40 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto: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
<ayend...@mgh.harvard.edu<mailto:ayend...@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-executable-from-everywhere
In your case you'd replace /path/to/file with $ANTSPATH.
Anastasia.
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Nasiriavanaki, Zahra,M.D.
<znasiriavan...@mgh.harvard.edu<mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 7, 2021 1:30 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto: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
<ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Mona - You need to add the location of the ANTs executables to your path.
Best,
Anastasia.
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Nasiriavanaki, Zahra,M.D.
<znasiriavan...@mgh.harvard.edu<mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Sunday, December 5, 2021 12:21 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu<mailto: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<http://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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