Hi Saad
Thanks for the answer and the tool
Cheers
Jürgen
On [DATE], "Saad Jbabdi" <[ADDRESS]> wrote:
> Hi Jürgen
>
> You can load the matrix1 output in matlab using the read_avw command form
> $FSLDIR/etc/matlab and then save it as ascii if you want.
> Alternatively, you can use probtrackx2 (which has been pre-released on this
> list) which saves the matrix directly in ascii
>
> Saad
>
>
>
> On 16 Feb 2012, at 11:30, Jürgen Hänggi wrote:
>
>> Dear FSL experts
>>
>> I have run probtrackx with the --omatrix1 option, but the output file
>> fdt_matrix1 is a .nii file and not an ASCII file.
>>
>> I used following command:
>>
>> rm -rf
>> /Users/juergenhaenggi/Desktop/Collaboration_LTHV/LTHV_Pat05_TP1/DTI.bedpostX
>> /whole_fa_map
>> mkdir -p
>> /Users/juergenhaenggi/Desktop/Collaboration_LTHV/LTHV_Pat05_TP1/DTI.bedpostX
>> /whole_fa_map
>> /Applications/fsl/bin/probtrackx --mode=seedmask -x
>> /Users/juergenhaenggi/Desktop/Collaboration_LTHV/LTHV_Pat05_TP1/DTI/dti_FA_4
>> .nii.gz -l -f -c 0.2 -S 2000 --steplength=0.5 -P 1000 --forcedir --opd -s
>> /Users/juergenhaenggi/Desktop/Collaboration_LTHV/LTHV_Pat05_TP1/DTI.bedpostX
>> /merged -m
>> /Users/juergenhaenggi/Desktop/Collaboration_LTHV/LTHV_Pat05_TP1/DTI.bedpostX
>> /nodif_brain_mask
>> --dir=/Users/juergenhaenggi/Desktop/Collaboration_LTHV/LTHV_Pat05_TP1/DTI.be
>> dpostX/whole_fa_map --omatrix1
>>
>> Does I have to use another option to get a matrix and instead of an image?
>>
>> Thanks in advance
>> Regards
>> Jürgen Hänggi
>>
>> ----------------------------------------------------------------------------
>> Jürgen Hänggi, Ph.D.
>> Division Neuropsychology
>> Institute of Psychology
>> University of Zurich
>> Binzmuehlestrasse 14, PO Box 25
>> 8050 Zurich, Switzerland
>> 0041 44 635 73 97 (phone office)
>> 0041 76 445 86 84 (phone mobile)
>> 0041 44 635 74 09 (fax office)
>> BIN 4.D.04 (office room number)
>> j.haenggi[at]psychologie.uzh.ch (email)
>> http://www.psychologie.uzh.ch/neuropsy/ (website)
>> http://www.juergenhaenggi.ch (private website)
>>
>> This e-mail (and any attachment/s) contains confidential and/or privileged
>> information. If you are not the intended recipient (or have received this
>> e-mail in error) please notify the sender immediately and destroy this
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>> material in this e-mail is strictly forbidden.
>> ----------------------------------------------------------------------------
>>
>
> --
> Saad Jbabdi
> University of Oxford, FMRIB Centre
>
> JR Hospital, Headington, OX3 9DU, UK
> (+44)1865-222466 (fax 717)
> www.fmrib.ox.ac.uk/~saad
----------------------------------------------------------------------------
Jürgen Hänggi, Ph.D.
Division Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)
j.haenggi[at]psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged
information. If you are not the intended recipient (or have received this
e-mail in error) please notify the sender immediately and destroy this
e-mail. Any unauthorised copying, disclosure or distribution of the
material in this e-mail is strictly forbidden.
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