Hi Alan - On the tutorial page you need to follow the directions under "If
you are not at an organized course", and $TUTORIAL_DATA is whatever
directory you have downloaded the tutorial data in.
Please address questions to the list and not to me personally, as other
people may have the same issue and this way the answers get archived.
Thanks,
a.y
On Mon, 5 Aug 2013, Alan Francis wrote:
Hi Anastasia:
Sorry about being a pest. One more question. I am running the Tutorial data
to get a better understanding of Tracula. When I type $TUTORIAL_DATA, it
keeps saying Undefined variable. Could you please help me.
Thanks,
Alan
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D
ATA/diffusion_recons] : setenv FREESURFER_HOME
/usr/local/freesurfer/stable5_3_0/
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D
ATA/diffusion_recons] : source $FREESURFER_HOME/Set
SetUpFreeSurfer.csh* SetUpFreeSurfer.sh*
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D
ATA/diffusion_recons] : source $FREESURFER_HOME/SetUpFreeSurfer.csh
-------- freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer/stable5_3_0/
FSFAST_HOME /usr/local/freesurfer/stable5_3_0//fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /usr/local/freesurfer/stable5_3_0//subjects
MNI_DIR /usr/local/freesurfer/stable5_3_0//mni
FSL_DIR /usr/pubsw/packages/fsl/current
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D
ATA/diffusion_recons] : setenv SUBJECTS_DIR $TUTORIAL_DATA/d
$TUTORIAL_DATA/ not found
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D
ATA/diffusion_recons] : setenv SUBJECTS_DIR /autofs/space/d
dali_001/ dali_002/ dali_003/
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D
ATA/diffusion_recons] : setenv
SUBJECTS_DIR/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_DA
TA/diffusion_recons/
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D
ATA/diffusion_recons] : gedit
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial &
TUTORIAL_DATA: Undefined variable.
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D
ATA/diffusion_recons] : gedit
/TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial &
[1] 32742
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D
ATA/diffusion_recons] : trac-all -prep -c
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial
TUTORIAL_DATA: Undefined variable.
On Fri, Aug 2, 2013 at 7:16 PM, Alan Francis <alandarkene...@gmail.com>
wrote:
thanks again.
On Fri, Aug 2, 2013 at 3:51 PM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
It can have any name you want. You just have to type the
right name next to the "-c ..."
On Fri, 2 Aug 2013, Alan Francis wrote:
Sorry. I have another question. Should I name
the config file dmrirc.txt or
is there any other name?
thank you so much,
Alan
On Fri, Aug 2, 2013 at 2:45 PM, Alan Francis
<alandarkene...@gmail.com>
wrote:
Thanks Anastasia.
On Fri, Aug 2, 2013 at 2:26 PM, Anastasia
Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
Hi Alan - All the "set ..." commands for
tracula need to
be in a configuration file. You then
pass that
configuration file as an argument to the
"-c" option of
trac-all. See tutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Hope this helps,
a.y
On Fri, 2 Aug 2013, Alan Francis wrote:
Hi Anastasia and others:
I have been trying to run Trac all on
five brains.
It keeps giving me the
error message:
ERROR: run list is longer than subject
list
My run list is equal to the subject
list: Here is
the environment:
Thanks for your help,
Alan
Martinos Center for Biomedical Imaging
__________________________________________________________________
--------
freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
--------
Setting up environment for
FreeSurfer/FS-FAST (and
FSL)
FREESURFER_HOME
/usr/local/freesurfer/stable5_3_0/
FSFAST_HOME
/usr/local/freesurfer/stable5_3_0//fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR
/usr/local/freesurfer/stable5_3_0//subjects
MNI_DIR
/usr/local/freesurfer/stable5_3_0//mni
FSL_DIR
/usr/pubsw/packages/fsl/current
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] : setenv SUBJECTS_DIR
/autofs/space/d
dali_001/ dali_002/ dali_003/
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons]
:setenvSUBJECTS_DIR/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.
3_Data
/diffusion_r
econs/
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] : set dtroot = /autofs/space/d
dali_001/ dali_002/ dali_003/
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] :
setdtroot=/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diff
usion_
r
econs/
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] : set subjlist = (101/ 102/ 103/
104/ 105/)
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] : set dcmroot = /autofs/space/d
dali_001/ dali_002/ dali_003/
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] :
setdcmroot=/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/dif
fusion_
r
econs/
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] :
setdcmlist=(101/Diffusion_Recons/20080424_182054563000-000012-000001DTIValeras
012a001
.
nii \
?102/Diffusion_Recons/20080911_101015358000-000010-000001DIFFUSIONHighResva
l
erabi1002s010a001.nii \
?103/Diffusion_Recons/20080911_140753578000-000010-000001DIFFUSIONHighResva
l
eraBI1003s010a001.nii \
?104/Diffusion_Recons/20080915_160812745000-000010-000001DIFFUSIONHighResVa
l
eraBI104s010a001.nii \
?105/Diffusion_Recons/20080917_190940899000-000016-000001DIFFUSIONHighResVa
l
eraBI105s016a001.nii \
? )
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] : set runlist = (101/ 102/ 103/ 104/
bem/ mri/ stats/
touch/
Diffusion_Recons/ scripts/ surf/
trash/
label/ src/ tmp/
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] : set runlist = (101/ 102/ 103/ 104/
105/)
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] : set bvecfile =
/autofs/space/dbvecs.txt
dali_001/ dali_002/ dali_003/
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] :
setbvecfile=/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/di
ffusion_
r
econs/bvecs.txt
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] :
setbvalfile=/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/di
ffusion_
r
econs/bvals.txt
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] : set doeddy = 1
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] : set dorotbvecs = 1
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] : set usemaskanat = 1
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] : set thrbet = 0.3
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] : set doregflt = 0
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] : set doregbbr = 1
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] : set doregmni = 1
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] : set doregcvs = 0
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] : set mnitemp =
$FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] : set cvstemp = cvs_avg35
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] : set cvstempdir =
$FREESURFER_HOME/subjects
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] : set pathlist = ( lh.cst_AS rh.cst_AS
\
? lh.ilf_AS rh.ilf_AS \
? lh.unc_AS rh.unc_AS \
? fmajor_PP fminor_PP \
? lh.atr_PP rh.atr_PP \
? lh.cab_PP rh.cab_PP \
? lh.ccg_PP rh.ccg_PP \
? lh.slfp_PP rh.slfp_PP \
? lh.slft_PP rh.slft_PP )
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] : set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5
4 4 5 5 5
5)
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] : trac-all -prep -c /autofs/space/d
dali_001/ dali_002/ dali_003/
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_
Data/diffusion_
recons] :
trac-all-prep-c/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diff
usion
_r
econs/
ERROR: run list is longer than subject list
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