2015-11-19 10:47 GMT+01:00 paul mccarthy <[log in to unmask]>:

Hi Carmine,

If you want to estimate the transformation in two steps, and then apply that transformation, you'll need three steps.

As Eelke suggested, drop the '-applyxfm' and '-out' options from the seccond step. Then add a third step which uses '-applyxfm' and '-init output_linear.mat' to produce a registered image.

Cheers,

Paul

On 18 November 2015 at 13:16, Carmine Pagliaro <[log in to unmask]> wrote:
yes, well I cannot use both?

2015-11-18 14:10 GMT+01:00 Eelke Visser <[log in to unmask]>:
Hi,

Are you trying to refine the registration from step 1 in step 2 by using weighting masks? In that case you should drop the -applyxfm.

Cheers,
Eelke

> On 18 Nov 2015, at 10:25, Carmine Pagliaro <[log in to unmask]> wrote:
>
> Hi Eelke,
> I would estimate a transformation starting from
>
> flirt -in moving_mask_roi.nii.gz -ref fixed_mask_roi.nii.gz -omat output_init_mask.nii.gz
>
> then use this matrix to
>
> flirt -in moving.nii.gz -ref fixed.nii.gz -inweight moving_mask_roi.nii.gz -refweight fixed_mask_roi.nii.gz -omat output_linear.mat -dof 9 -out output_mov_to_fix.nii.gz -init output_init_mask.nii.gz -applyxfm
>
> so I can improve my registration.
>
> 2015-11-18 11:13 GMT+01:00 Eelke Visser <[log in to unmask]>:
> Hi Carmine,
>
> That doesn’t look quite right, although I am not completely sure what your intended result is. Your step 2 will apply the registration produced by step 1, but none of the additional options will be used as it is just applying a transformation (rather than searching for an optimal one). Also note that output_init.nii.gz is a text file, not a nifti.
>
> Could you give some more details about what you want to do?
>
> Thanks,
> Eelke
>
>
>
> > On 17 Nov 2015, at 13:49, Carmine Pagliaro <[log in to unmask]> wrote:
> >
> > Can you check and give me a feedback for this code?
> > what a want do is, estimate a transformation matrix with the first step and then pass the transformation matrix to the second step.
> >
> > 1st step: flirt -ref fixed.nii.gz -in moving.nii.gz -dof 9 -omat output_init.nii.gz
> > 2nd step: flirt -in moving.nii.gz -ref fixed.nii.gz -refweight fixed_mask.nii.gz -inweight moving_mask.nii.gz -omat output_linear.mat -dof 9 -out output_mov_to_fix.nii.gz -init output_init.nii.gz -applyxfm
> >
> >
> > thank you
> >
> >
> > 2015-11-17 12:38 GMT+01:00 Carmine Pagliaro <[log in to unmask]>:
> > thank you very very much now its work.
> >
> > 2015-11-17 12:12 GMT+01:00 Matthew Webster <[log in to unmask]>:
> > Hello,
> > Does
> >
> > String cmd = "fslstats";
> > ProcessBuilder pb = new ProcessBuilder("bash","-c"," . /etc/fsl/fsl.sh;"+cmd);
> > Process p = pb.start();
> >
> > work on your system?
> >
> > Kind Regards
> > Matthew
> >
> >> Map<String, String> env;
> >> env = pb.environment();
> >> env.put("FSLDIR", "/usr/lib/fsl/5.0");
> >> env.put("PATH", "/usr/lib/fsl/5.0:$PATH");
> >> env.put("PATH", "$FSLDIR/bin:$PATH");
> >> Process p = pb.start();
> >> something like this?
> >>
> >> 2015-11-17 11:27 GMT+01:00 paul mccarthy <[log in to unmask]>:
> >> Hi Carmine,
> >>
> >> The exact list of variables and their values will differ on different platforms - it depends on your specific setup.
> >>
> >> Perhaps a better way would be to use an approach similar to what is suggested here:
> >>
> >> http://stackoverflow.com/a/18383904
> >>
> >> i.e. Set up your FSLDIR and PATH variables using the ProcessBuilder, and then source the fsl.sh script *and* run the command in a single line (and hence in the same shell).
> >>
> >> Cheers,
> >>
> >> Paul
> >>
> >> On 17 November 2015 at 10:18, Carmine Pagliaro <[log in to unmask]> wrote:
> >> Thank you Paul.
> >> there is a complete list of env that I must set?
> >>
> >> 2015-11-17 11:00 GMT+01:00 paul mccarthy <[log in to unmask]>:
> >> Hi Carmine,
> >>
> >> All of the FSL commands (with the exception of FSLView) must be run with a specific environment configuyation. For example. the PATH, FSLDIR, and FSLOUTPUTTYPE environment variables must be set to the correct value for the FSL commands to work. The FSL environment is typically configured from your ~/.bashrc, or ~/.profile script, with something like this:
> >>
> >> export FSLDIR=~/fsl_builds/fsl
> >> export PATH=$FSLDIR/bin:$PATH
> >> . $FSLDIR/etc/fslconf/fsl.sh
> >>
> >>
> >> Your java program is trying to run a FSL command in an environment that has not been configured to run FSL commands. You have three options:
> >>
> >> 1. Run your java program from within an environment that has already been configured to use FSL.
> >>
> >> 2. Get your java program to configure the environment before calling the FSL command (using e.g. the ProcessBuilder class)
> >>
> >> 3. Create a wrapper script which configures the FSL environment, and then calls the FSL command you wish to use.
> >>
> >> Cheers,
> >>
> >> Paul
> >>
> >> On 17 November 2015 at 08:29, Carmine Pagliaro <[log in to unmask]> wrote:
> >> I tried with this
> >> cmd2 = "fslinfo test.nii.gz"
> >> ProcessBuilder pb = new ProcessBuilder("bash","-l","-c",cmd2);
> >>
> >> and i obtained this
> >> bash: fslinfo: comando non trovato
> >>
> >> 2015-11-16 17:40 GMT+01:00 Matthew Webster <[log in to unmask]>:
> >> Hello,
> >> I think the best solution here is to call your fsl commands invoking bash as a login shell, this way your bash_profile should be sourced as normal, e.g. calls along the lines of:
> >>
> >> ProcessBuilder pb = new ProcessBuilder("bash","-l","-c","fslstats");
> >>
> >> Kind Regards
> >> Matthew
> >>
> >>> ok first solved. now i get this error:
> >>>
> >>> /usr/lib/fsl/5.0/fslinfo: 77: /usr/lib/fsl/5.0/fslinfo: /bin/fslhd: not found
> >>> /usr/lib/fsl/5.0/fslinfo: 77: /usr/lib/fsl/5.0/fslinfo: cat: not found
> >>> /usr/lib/fsl/5.0/fslinfo: 77: /usr/lib/fsl/5.0/fslinfo: egrep: not found
> >>>
> >>> 2015-11-16 17:01 GMT+01:00 Carmine Pagliaro <[log in to unmask]>:
> >>> thank Paul. in my case it look like this?
> >>>
> >>> env.put("PATH", env.get("PATH")+"/usr/lib/fsl/5.0");
> >>>
> >>>
> >>> 2015-11-16 16:52 GMT+01:00 Matthew Webster <[log in to unmask]>:
> >>> Hi Carmine,
> >>> Paul's email links to a pure-java solution - this should work without needing to modify .bashrc etc.
> >>> Kind Regards
> >>> Matthew
> >>>
> >>>> myabe i wrong something. env java command don't show fsl. i restart system too. nothing happens. what else i can do?
> >>>>
> >>>> 2015-11-16 16:26 GMT+01:00 Matthew Webster <[log in to unmask]>:
> >>>> Hello - that looks good, yes.
> >>>>
> >>>> Kind Regards
> >>>> Matthew
> >>>>
> >>>>
> >>>>> Hello Dr. Webster. I can confirm that fsl is not in the java env. so how can I add?
> >>>>> something like this:
> >>>>> export PATH="/usr/lib/fsl/5.0:$PATH"
> >>>>> ?
> >>>>>
> >>>>> 2015-11-16 16:12 GMT+01:00 Matthew Webster <[log in to unmask]>:
> >>>>> Hello,
> >>>>> Can you try execing env in your java program, and check to see if /usr/lib/fsl/5.0 is in the output? If not then you might want to add it to your PATH in .bashrc.
> >>>>> Kind Regards
> >>>>> Matthew
> >>>>>
> >>>>>
> >>>>>> carmine@HpCarmine:~$ which fslinfo
> >>>>>> /usr/lib/fsl/5.0/fslinfo
> >>>>>> carmine@HpCarmine:~$ which fslview
> >>>>>> /usr/bin/fslview
> >>>>>>
> >>>>>> fsl script are in the /usr/lib/fsl/5.0/ how can i link all the script. i think about a simbolic link it's the correct way?
> >>>>>>
> >>>>>> 2015-11-16 14:58 GMT+01:00 Matthew Webster <[log in to unmask]>:
> >>>>>> Hello Carmine,
> >>>>>> I think you need to check that your environment is set up correctly so that the FSL binaries can be located - the error is telling you that java cannot find the fslinfo script. You might want to run the command 'env' to check what environment java is using.
> >>>>>>
> >>>>>> Kind Regards
> >>>>>> Matthew
> >>>>>>
> >>>>>>> Sorry, i'm under debian 8.0
> >>>>>>>
> >>>>>>> 2015-11-16 14:26 GMT+01:00 Carmine Pagliaro <[log in to unmask]>:
> >>>>>>> this is the ccode that i use
> >>>>>>> String cmd2 = "fslinfo test.nii.gz";
> >>>>>>> Process p = Runtime.getRuntime().exec(cmd2);
> >>>>>>>
> >>>>>>> BufferedReader stdInput = new BufferedReader(new InputStreamReader(p.getInputStream()));
> >>>>>>>
> >>>>>>> BufferedReader stdError = new BufferedReader(new InputStreamReader(p.getErrorStream()));
> >>>>>>>
> >>>>>>> // read the output from the command
> >>>>>>> System.out.println("Here is the standard output of the command:\n");
> >>>>>>> while ((s = stdInput.readLine()) != null) {
> >>>>>>> System.out.println(s);
> >>>>>>> }
> >>>>>>>
> >>>>>>> // read any errors from the attempted command
> >>>>>>> System.out.println("Here is the standard error of the command (if any):\n");
> >>>>>>> while ((s = stdError.readLine()) != null) {
> >>>>>>> System.out.println(s);
> >>>>>>> }
> >>>>>>>
> >>>>>>> and thi is the error:
> >>>>>>>
> >>>>>>> java.io.IOException: Cannot run program "fslinfo": error=2, File o directory non esistente
> >>>>>>>
> >>>>>>> 2015-11-16 14:01 GMT+01:00 Matthew Webster <[log in to unmask]>:
> >>>>>>> Hi Carmine,
> >>>>>>> Can you provide a little more information on what is going wrong? Do you get any error messages?
> >>>>>>> Kind Regards
> >>>>>>> Matthew
> >>>>>>>
> >>>>>>>
> >>>>>>>> Hi FSL team,
> >>>>>>>> I would use FSL command like fslinfo, fslview flirt ecc. in java programm calling the java method:
> >>>>>>>> Process p = Runtime.getRuntime().exec("");
> >>>>>>>> this work fine only with fslview command, but with the others not.
> >>>>>>>> can anyone help me?
> >>>>>>>>
> >>>>>>>> thank you
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> --
> >>>>>>>> Carmine Pagliaro
> >>>>>>>> Research Fellow Neuroimaging Unit
> >>>>>>>> Institute of Bioimaging and Molecular Physiology-CNR
> >>>>>>>> Italy
> >>>>>>>> Life is for sharing.
> >>>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> --
> >>>>>>> Carmine Pagliaro
> >>>>>>> Research Fellow Neuroimaging Unit
> >>>>>>> Institute of Bioimaging and Molecular Physiology-CNR
> >>>>>>> Italy
> >>>>>>> Life is for sharing.
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> --
> >>>>>>> Carmine Pagliaro
> >>>>>>> Research Fellow Neuroimaging Unit
> >>>>>>> Institute of Bioimaging and Molecular Physiology-CNR
> >>>>>>> Italy
> >>>>>>> Life is for sharing.
> >>>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> --
> >>>>>> Carmine Pagliaro
> >>>>>> Research Fellow Neuroimaging Unit
> >>>>>> Institute of Bioimaging and Molecular Physiology-CNR
> >>>>>> Italy
> >>>>>> Life is for sharing.
> >>>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> --
> >>>>> Carmine Pagliaro
> >>>>> Research Fellow Neuroimaging Unit
> >>>>> Institute of Bioimaging and Molecular Physiology-CNR
> >>>>> Italy
> >>>>> Life is for sharing.
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> Carmine Pagliaro
> >>>> Research Fellow Neuroimaging Unit
> >>>> Institute of Bioimaging and Molecular Physiology-CNR
> >>>> Italy
> >>>> Life is for sharing.
> >>>>
> >>>
> >>>
> >>>
> >>>
> >>> --
> >>> Carmine Pagliaro
> >>> Research Fellow Neuroimaging Unit
> >>> Institute of Bioimaging and Molecular Physiology-CNR
> >>> Italy
> >>> Life is for sharing.
> >>>
> >>>
> >>>
> >>>
> >>> --
> >>> Carmine Pagliaro
> >>> Research Fellow Neuroimaging Unit
> >>> Institute of Bioimaging and Molecular Physiology-CNR
> >>> Italy
> >>> Life is for sharing.
> >>>
> >>
> >>
> >>
> >>
> >> --
> >> Carmine Pagliaro
> >> Research Fellow Neuroimaging Unit
> >> Institute of Bioimaging and Molecular Physiology-CNR
> >> Italy
> >> Life is for sharing.
> >>
> >>
> >>
> >>
> >>
> >> --
> >> Carmine Pagliaro
> >> Research Fellow Neuroimaging Unit
> >> Institute of Bioimaging and Molecular Physiology-CNR
> >> Italy
> >> Life is for sharing.
> >>
> >>
> >>
> >>
> >>
> >> --
> >> Carmine Pagliaro
> >> Research Fellow Neuroimaging Unit
> >> Institute of Bioimaging and Molecular Physiology-CNR
> >> Italy
> >> Life is for sharing.
> >>
> >
> >
> >
> >
> > --
> > Carmine Pagliaro
> > Research Fellow Neuroimaging Unit
> > Institute of Bioimaging and Molecular Physiology-CNR
> > Italy
> > Life is for sharing.
> >
> >
> >
> >
> > --
> > Carmine Pagliaro
> > Research Fellow Neuroimaging Unit
> > Institute of Bioimaging and Molecular Physiology-CNR
> > Italy
> > Life is for sharing.
> >
>
>
>
>
> --
> Carmine Pagliaro
> Research Fellow Neuroimaging Unit
> Institute of Bioimaging and Molecular Physiology-CNR
> Italy
> Life is for sharing.
>

--
Carmine Pagliaro
Research Fellow Neuroimaging Unit
Institute of Bioimaging and Molecular Physiology-CNR
Italy
Life is for sharing.

Carmine Pagliaro

Research Fellow Neuroimaging Unit
Institute of Bioimaging and Molecular Physiology-CNR
Italy

Life is for sharing.