epitome failed for IMOB during registrations
colinhawco opened this issue · 9 comments
My epitome failed.
/projects/colin/epitome/IMOB-COLIN/
Here is where in the log I think it failed:
FSL: Linear registration pathway calculator
Calculates EPI <--> T1 <--> MNI152 (included in AFNI distribution)
- Using data quality: high,
- Cost function: corratio,
- Degrees of freedom preset 6,
- Generates EPI template registered to T1 & vice-versa (sessionwise),
Image Exception : #22 :: ERROR: Could not open image /projects/colin/epitome/IMOB-COLIN/H160_CAMH/T1/SESS01/anat_T1_brain
It assumes the anat is called anat_T!_brain I guess.
the contents of that folder are:
anat_aparc2009_fs.nii.gz anat_aparc_fs.nii.gz anat_T1_fs.nii.gz
I am not sure if freesurfer was supposed to spit out anat_T!_brain?
from your proclist, what does the output of epi-fsexport say? anat_T1_fs.nii.gz should be converted to anat_t1_brain using AFNI (is AFNI available?)
You mean this file? It has an error in it but I am unclear.
-bash: module: line 1: syntax error: unexpected end of file
-bash: error importing function definition for module' /bin/bash: module: line 1: syntax error: unexpected end of file /bin/bash: error importing function definition formodule'
But it looks to me like freesurfer failed? The freesurfer outputs went
to /projects/colin/freesurfer. I can't see obvious issues (there are files
in there), but I am not at all familiar with freesurfer.
On 6 August 2015 at 16:39, Joseph Viviano notifications@github.com wrote:
from your proclist, what does the output of epi-fsexport say?
anat_T1_fs.nii.gz should be converted to anat_t1_brain using AFNI (is AFNI
available?)—
Reply to this email directly or view it on GitHub
#23 (comment)
.
Hi Colin, freesurfer worked. The conversion of the freesurfer oriented t1 to Afni oriented t1 failed. Is Afni installed properly? Where are you running this?
We were running on Anne's old machine which is tesla I believe. AFNi will
run on it but as you may recall we made a setup file for epitome which
called the relevant modules. But I can't remember where that setup file
was!
On 6 August 2015 at 17:36, Joseph Viviano notifications@github.com wrote:
Hi Colin, freesurfer worked. The conversion of the freesurfer oriented t1
to Afni oriented t1 failed. Is Afni installed properly? Where are you
running this?—
Reply to this email directly or view it on GitHub
#23 (comment)
.
how are you tryibng to run epitome? I just ran the epi-fsexport line from your proclist with no issues.
exact command:
epi-fsexport /projects/colin/epitome IMOB-COLIN
from:
/projects/colin/epitome/IMOB-COLIN/proclist_150724_161704_150724-colinexample.sh
Update?
I will take another look tomorrow.
On Aug 9, 2015 2:40 PM, "Joseph Viviano" notifications@github.com wrote:
Update?
—
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#23 (comment)
.
I'm closing this as it seems like things are working out on your end?