Your environmental variables need to be set in the environment you use.
I don’t think the environment gets carried through when you use “sudo”.
That’s why your status messages show things like:
Working in SUBJECTS_DIR: /analise//
$SUBJECTS_DIR didn’t get interpreted.
You can double check by trying: sudo printenv
which will give you a list of your environmental variables.
You probably can get it to work with something like:
sudo ( source Script_With_EnvironmentalVariableSettings; long_mris_slopes
--qdec $SUBJECTS_DIR/qdec … )
or even
sudo ( export FREESURFER_HOME=/ABC/DEF ; export
SUBJECTS_DIR=${FREESURFER_HOME/subjects ; long_mris_slopes --qdec
$SUBJECTS_DIR/qdec … )
Regards,
Don
[Signature0001]
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
From: [email protected]
[mailto:[email protected]] On Behalf Of carolina.mr
Sent: Tuesday, February 24, 2015 5:37 AM
To: [email protected]
Subject: [Freesurfer] Longitudinal post processing
Hello,
I am trying to make the Two Stage Longitudinal processing and when I give the
command to prepare the data with QCACHE.
I've already set up the environment for FREESURFER_HOME, but it keeps appearing
the error message:
ERROR: FREESURFER_HOME not defined in environment
ERROR 1 : mri_label2label mapping the label failed?
Following, there is a copy of my command and the error messages that appeared.
sudo long_mris_slopes --qdec $SUBJECTS_DIR/qdec/longRRMSP01.qdec.table.dat
--meas thickness --hemi lh \ --do-avg --do-rate --do-pc1 --do-spc --do-stack
--do-label \ --time years --qcache $SUBJECTS_DIR/fsaverage/ --sd $SUBJECTS_DIR/
Password:
Parsing the qdec table: /analise//qdec/longRRMSP01.qdec.table.dat
Working in SUBJECTS_DIR: /analise//
Working on hemi: lh
Subject-Template: P01_TP
INFO: 2 TPs in P01_TP , mean age: 2.25
===============================================================================
SUBJECT P01_TP Intersecting Within-Subject Cortex Label
cp /analise//P01_RM1.long.P01_TP/label/lh.cortex.label
/analise//P01_TP/label/lh.long.cortex.label
mris_label_calc intersect /analise//P01_RM2.long.P01_TP/label/lh.cortex.label
/analise//P01_TP/label/lh.long.cortex.label
/analise//P01_TP/label/lh.long.cortex.label
===============================================================================
SUBJECT P01_TP mapping label to QCache
mri_label2label --srclabel /analise//P01_TP/label/lh.long.cortex.label
--srcsubject P01_TP --trglabel
/analise//P01_TP/label/lh.long.cortex./analise//fsaverage/.label --trgsubject
/analise//fsaverage/ --regmethod surface --hemi lh
srclabel = /analise//P01_TP/label/lh.long.cortex.label
srcsubject = P01_TP
trgsubject = /analise//fsaverage/
trglabel = /analise//P01_TP/label/lh.long.cortex./analise//fsaverage/.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
ERROR: FREESURFER_HOME not defined in environment
ERROR 1 : mri_label2label mapping the label failed?
Thank you, Carolina
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