Hi Paul and thank you for the replay, can you rewrite my code to work as
you said? Maybe I don't understand what do you mean.
Thank you very very much.
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.*
