Hi Priti,
Thanks so much for your prompt reply!
I have specified all our specs like you suggested below. However, I'm a bit
confused as I thought this shouldn't be necessary as we feed TRACULA with
original GE DICOM files. Doesn't TRACULA read this info from the DICOM
headers?
Also, it looks like TRACULA assumes that there is only one folder (sequence)
per subject. However, as we repeat ours we have 2 per subject meaning I'd
like to point to 2 different folders with the 1st image of each defining the
sequence like
set dcmlist = 014/MRI/AxDTI1/IM-0013-0001.dcm &
set dcmlist = 014/MRI/AxDTI2/IM-0014-0001.dcm
Additionally, I got some errors running trac-preproc with just one series (I
include my dmrirc at the end of this message). Any clue where I screw up
here?
Thanks so much!
Ansgar
New invocation of trac-preproc
ajfurst
VALinux1
Linux VALinux1 2.6.35.14-95.fc14.x86_64 #1 SMP Tue Aug 16 21:01:58 UTC 2011
x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 64 kbytes
maxproc 1024
total used free shared buffers cached
Mem: 8062732 3565084 4497648 0 197864 2413064
-/+ buffers/cache: 954156 7108576
Swap: 10158076 2288 10155788
#-------------------------------------
/usr/local/freesurfer/bin/trac-preproc
#-------------------------------------
#@# Image corrections Tue Sep 20 17:10:45 PDT 2011
mri_convert /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1/IM-0013-0001.dcm
/home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.nii.gz
mri_convert /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1/IM-0013-0001.dcm
/home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1/IM-0013-0001.dcm...
Starting DICOMRead2()
dcmfile = /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1/IM-0013-0001.dcm
dcmdir = /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1
Ref Series No = 13
Found 2032 files, checking for dicoms
Found 2030 dicom files in series.
First Sorting
Computing Slice Direction
Vs: 0.051 -0.354 2.4743
Vs: 0.0203999 -0.141599 0.989714
Second Sorting
Counting frames
nframes = 35
nslices = 58
ndcmfiles = 2030
PE Dir = COL (dicom read)
TransferSyntaxUID: --1.2.840.10008.1.2--
jpegUID: --1.2.840.10008.1.2.4--
Loading pixel data
TR=6600.00, TE=84.20, TI=0.00, flip angle=90.00
i_ras = (-0.999791, -0.00289925, -0.0202339)
j_ras = (0, -0.989897, 0.141789)
k_ras = (-0.0203999, 0.141599, 0.989714)
writing to /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.nii.gz...
mri_probedicom --i /home/ajfurst/Data/WRIISC/014/MRI/AxDTI1/IM-0013-0001.dcm
> /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dcminfo.dat
cp /home/ajfurst/Data/WRIISC/scripts/30+5gradtable.txt
/home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.mghdti.bvecs
cp /home/ajfurst/Data/WRIISC/scripts/bvalfile_1sess.txt
/home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.mghdti.bvals
flip4fsl /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.nii.gz
/home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 2.19727
fslswapdim /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.nii.gz x -y z
/home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.nii.gz
INFO: left-right orientation was flipped by fslswapdim
fslorient -forceradiological
/home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.nii.gz
INFO: found
/home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.mghdti.bvals, converting
to FSL format
INFO: found
/home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig.mghdti.bvecs, converting
to FSL format
mv -f /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.mghdti.bvecs
/home/ajfurst/Data/WRIISC/TRACULA/014/dmri/bvecs
mv -f /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.mghdti.bvals
/home/ajfurst/Data/WRIISC/TRACULA/014/dmri/bvals
eddy_correct /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_orig_flip.nii.gz
/home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi.nii.gz 0
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0000
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0001
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0002
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0003
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0004
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0005
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0006
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0007
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0008
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0009
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0010
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0011
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0012
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0013
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0014
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0015
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0016
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0017
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0018
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0019
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0020
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0021
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0022
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0023
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0024
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0025
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0026
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0027
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0028
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0029
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0030
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0031
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0032
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0033
processing /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi_tmp0034
mv -f /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/bvecs
/home/ajfurst/Data/WRIISC/TRACULA/014/dmri/bvecs.norot
xfmrot /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi.ecclog
/home/ajfurst/Data/WRIISC/TRACULA/014/dmri/bvecs.norot
/home/ajfurst/Data/WRIISC/TRACULA/014/dmri/bvecs
fslroi /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi.nii.gz
/home/ajfurst/Data/WRIISC/TRACULA/014/dmri/lowb.nii.gz 0 5
fslmaths /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/lowb.nii.gz -Tmean
/home/ajfurst/Data/WRIISC/TRACULA/014/dmri/lowb.nii.gz
bet /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/lowb.nii.gz
/home/ajfurst/Data/WRIISC/TRACULA/014/dmri/lowb_brain.nii.gz -m -f 0.3
mv -f /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/lowb_brain_mask.nii.gz
/home/ajfurst/Data/WRIISC/TRACULA/014/dlabel/diff
#-------------------------------------
#@# Inter-subject registration Tue Sep 20 17:42:31 PDT 2011
flirt -in /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/lowb_brain.nii.gz -ref
/usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out
/home/ajfurst/Data/WRIISC/TRACULA/014/dmri/lowb_brain_mni.nii.gz -omat
/home/ajfurst/Data/WRIISC/TRACULA/014/dmri/xfms/diff2mni.mat -cost
mutualinfo
convert_xfm -omat
/home/ajfurst/Data/WRIISC/TRACULA/014/dmri/xfms/mni2diff.mat -inverse
/home/ajfurst/Data/WRIISC/TRACULA/014/dmri/xfms/diff2mni.mat
#-------------------------------------
#@# Masks Tue Sep 20 17:44:14 PDT 2011
#-------------------------------------
#@# Tensor fit Tue Sep 20 17:44:14 PDT 2011
dtifit -k /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dwi.nii.gz -m
/home/ajfurst/Data/WRIISC/TRACULA/014/dlabel/diff/lowb_brain_mask.nii.gz -r
/home/ajfurst/Data/WRIISC/TRACULA/014/dmri/bvecs -b
/home/ajfurst/Data/WRIISC/TRACULA/014/dmri/bvals -o
/home/ajfurst/Data/WRIISC/TRACULA/014/dmri/dtifit
0 256 0 256 0 58
0 slices processed
1 slices processed
2 slices processed
3 slices processed
4 slices processed
5 slices processed
6 slices processed
7 slices processed
8 slices processed
9 slices processed
10 slices processed
11 slices processed
12 slices processed
13 slices processed
14 slices processed
15 slices processed
16 slices processed
17 slices processed
18 slices processed
19 slices processed
20 slices processed
21 slices processed
22 slices processed
23 slices processed
24 slices processed
25 slices processed
26 slices processed
27 slices processed
28 slices processed
29 slices processed
30 slices processed
31 slices processed
32 slices processed
33 slices processed
34 slices processed
35 slices processed
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46 slices processed
47 slices processed
48 slices processed
49 slices processed
50 slices processed
51 slices processed
52 slices processed
53 slices processed
54 slices processed
55 slices processed
56 slices processed
57 slices processed
#-------------------------------------
#@# Priors Tue Sep 20 17:44:44 PDT 2011
/usr/local/freesurfer/bin/dmri_train --outdir
/home/ajfurst/Data/WRIISC/TRACULA/014/dlabel/mni --out
lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt
rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt
fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt
rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt
lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt
rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt
--slist /tmp/subj33.014.9330.txt --trk dlabel/mni/lh.cst_AS.flt.trk
dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk
dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk
dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk
dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk
dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk
dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk
dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk
dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk
dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask
dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0
--rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz
dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz
dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz
dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz
dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz
dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz
dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz
dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz
dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz
dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz
dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz
dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz
dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz
dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz
dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz
dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz
dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz
dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz
dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask
/home/ajfurst/Data/WRIISC/TRACULA/014/dlabel/mni/lowb_brain_mask.flt.nii.gz
--fa /home/ajfurst/Data/WRIISC/TRACULA/014/dmri/mni/dtifit_FA.flt.nii.gz
--ncpts 5 --debug
ERROR: fio_pushd: /home/ajfurst/Data/WRIISC/TRACULA/014/dlabel/mni
ERROR: must specify brain mask volume for output subject
Linux VALinux1 2.6.35.14-95.fc14.x86_64 #1 SMP Tue Aug 16 21:01:58 UTC 2011
x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Tue Sep 20 17:44:44 PDT 2011
==============================================================================================
# Run command file generated automatically by trac-all
#
setenv FREESURFER_HOME /usr/local/freesurfer
setenv SUBJECTS_DIR /home/ajfurst/Data/WRIISC
set dtroot = (/home/ajfurst/Data/WRIISC/TRACULA)
set subj = (014)
#
# Processing steps to be performed
#
set docorr = (1)
set dointra = (1)
set dointer = (1)
set domasks = (1)
set dotensor = (1)
set dopriors = (1)
#
# Options for image corrections and tensor fit
#
set dcmroot = (/home/ajfurst/Data/WRIISC)
set dcmfile = (014/MRI/AxDTI1/IM-0013-0001.dcm)
set bvecfile = (/home/ajfurst/Data/WRIISC/scripts/30+5gradtable.txt)
set bvalfile = (/home/ajfurst/Data/WRIISC/scripts/bvalfile_1sess.txt)
set nb0 = (5)
set dob0 = (0)
set b0mfile = ()
set b0pfile = ()
set echospacing = ()
set doeddy = (1)
set dorotbvecs = (1)
set thrbet = (0.3)
#
# Options for registrations
#
set doregflt = (1)
set doregbbr = (1)
set doregmni = (1)
set doregcvs = (0)
set mnitemp = (/usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz)
set cvstempdir = (/usr/local/freesurfer/subjects)
set cvstemp = (cvs_avg35)
#
# Options for path reconstructions
#
set usemaskanat = (1)
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)
set ncptlist = (5)
set trainsubjlist = (/usr/local/freesurfer/trctrain/trc001
/usr/local/freesurfer/trctrain/trc002 /usr/local/freesurfer/trctrain/trc003
/usr/local/freesurfer/trctrain/trc004 /usr/local/freesurfer/trctrain/trc005
/usr/local/freesurfer/trctrain/trc006 /usr/local/freesurfer/trctrain/trc007
/usr/local/freesurfer/trctrain/trc008 /usr/local/freesurfer/trctrain/trc009
/usr/local/freesurfer/trctrain/trc010 /usr/local/freesurfer/trctrain/trc011
/usr/local/freesurfer/trctrain/trc012 /usr/local/freesurfer/trctrain/trc013
/usr/local/freesurfer/trctrain/trc014 /usr/local/freesurfer/trctrain/trc015
/usr/local/freesurfer/trctrain/trc016 /usr/local/freesurfer/trctrain/trc017
/usr/local/freesurfer/trctrain/trc018 /usr/local/freesurfer/trctrain/trc019
/usr/local/freesurfer/trctrain/trc020 /usr/local/freesurfer/trctrain/trc021
/usr/local/freesurfer/trctrain/trc022 /usr/local/freesurfer/trctrain/trc023
/usr/local/freesurfer/trctrain/trc024 /usr/local/freesurfer/trctrain/trc025
/usr/local/freesurfer/trctrain/trc026 /usr/local/freesurfer/trctrain/trc027
/usr/local/freesurfer/trctrain/trc028 /usr/local/freesurfer/trctrain/trc029
/usr/local/freesurfer/trctrain/trc030 /usr/local/freesurfer/trctrain/trc031
/usr/local/freesurfer/trctrain/trc032 /usr/local/freesurfer/trctrain/trc033)
set ntrainlist = (33)
set avgname = (avg)
set reinit = (0)
set usetrunc = (0)
set doprior = (0)
set dosegprior = (1)
set dopathsubdirs = (0)
set fmin = (0.05)
set nburnin = (200)
set nsample = (5000)
set nupdate = (0)
set nkeep = (5)
set doinitprop = (0)
set trcdir = (/usr/local/freesurfer/bin)
On Fri, Sep 16, 2011 at 8:29 AM, Priti Srinivasan <
rspr...@nmr.mgh.harvard.edu> wrote:
> Hi Ansgar,
>
> If you have your own bvals and bvecs, you should add the following extra
> lines to your dmrirc file.
>
> set bvalfile = /path/to/bvals.txt
> set bvecfile = /path/to/bvecs.txt
> set nb0 = *No. of low-b images* (In your case you can set nb0 to 5 and
> tracula will use the first 5 images to get an average lowb image.)
>
> set dcmroot = /path/to/diffusion_data
> set dcmlist = Diffusion file (relative to dcmroot) //you can specify any
> image format if you have given th bvals,bvecs info from the paragraph
> above.
>
>
> The training dataset that is distributed as a part of freesurfer consists
> of 33 subjects. For the purposes of the tutorial we used the first 10
> subjects for demonstration and hence used the remaining 23 as training
> subjects.
>
> Hope that helps,
>
> Please let us know if you have any questions,
> Priti
>
> > Dear Anastasia and Team FreeSurfer,
> > First of all thanks so much for developing TRACULA. I think it has a lot
> > of
> > potential!
> > Here is my question: I'm trying to modify "dmrirc_single_subject" file in
> > order to reflect our local sequence and wondered how you are dealing with
> > DTI repeat sequences for the same subject.
> > We acquire 5 B0s and 30 directional scans twice in a row. So our
> > *Diffusion
> > bvalue Table would look like this:
> > ==================================================================
> > * 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000
> > 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000
> > 1000
> > 1000 1000 1000 1000 1000 1000 1000 1000 0 0 0 0 0 1000 1000
> > 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000
> > 1000
> > 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000
> > 1000
> > 1000 1000
> > Now I wonder how I would modify the below default settings from the
> > tutorial
> > data to reflect this:
> > =====================================================================
> > set subjlist = (Diff001)
> >
> > set runlist = (1)
> >
> > # Input diffusion DICOMs (file names relative to dcmroot)
> >
> > set dcmroot = /usr/local/freesurfer/TUTORIAL_DATA/diffusion_tutorial/
> >
> > set dcmlist = (Diff001/orig/6-1.dcm)
> >
> > =====================================================================
> >
> > Oh also, I noticed that in the wiki you have the following settings:
> > =======================================================================
> >
> > set trainfile =
> > $TUTORIAL_DATA/diffusion_tutorial/subj,train,difftutorial23.txt
> >
> >
> ===============================================================================================
> > In the latest version of the freesurfer distribution I counted 33
> > subjects for the training algorithm and therefore use:
> >
> > "subj,train,difftutorial33.txt" pointing to
> >
> > /usr/local/freesurfer/trctrain/trc001
> > /usr/local/freesurfer/trctrain/trc002
> > /usr/local/freesurfer/trctrain/trc003
> > /usr/local/freesurfer/trctrain/trc004
> > /usr/local/freesurfer/trctrain/trc005
> > /usr/local/freesurfer/trctrain/trc006
> > /usr/local/freesurfer/trctrain/trc007
> > /usr/local/freesurfer/trctrain/trc008
> > /usr/local/freesurfer/trctrain/trc009
> > /usr/local/freesurfer/trctrain/trc010
> > /usr/local/freesurfer/trctrain/trc011
> > /usr/local/freesurfer/trctrain/trc012
> > /usr/local/freesurfer/trctrain/trc013
> > /usr/local/freesurfer/trctrain/trc014
> > /usr/local/freesurfer/trctrain/trc015
> > /usr/local/freesurfer/trctrain/trc016
> > /usr/local/freesurfer/trctrain/trc017
> > /usr/local/freesurfer/trctrain/trc018
> > /usr/local/freesurfer/trctrain/trc019
> > /usr/local/freesurfer/trctrain/trc020
> > /usr/local/freesurfer/trctrain/trc021
> > /usr/local/freesurfer/trctrain/trc022
> > /usr/local/freesurfer/trctrain/trc023
> > /usr/local/freesurfer/trctrain/trc024
> > /usr/local/freesurfer/trctrain/trc025
> > /usr/local/freesurfer/trctrain/trc026
> > /usr/local/freesurfer/trctrain/trc027
> > /usr/local/freesurfer/trctrain/trc028
> > /usr/local/freesurfer/trctrain/trc029
> > /usr/local/freesurfer/trctrain/trc030
> > /usr/local/freesurfer/trctrain/trc031
> > /usr/local/freesurfer/trctrain/trc032
> > /usr/local/freesurfer/trctrain/trc033
> >
> > Does that make sense?
> >
> > Thanks so much for your help!
> >
> > Ansgar
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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