Try to use that
"gunzip path_to_nii.gz"
Jose
Mon, Mar 28, 2011 at 4:58 PM, Monica Giraldo
<[log in to unmask]>wrote:
> Sorry I have one last quesiton, is it possible to uncompress an image with
> FSL through the command line? Because I changed a little bit the script for
> generating the matrix and I need to introduce the images in .nii, because I
> got a problem when I tried to use .nii.gz
>
> Thanks,
>
>
> On Mon, Mar 28, 2011 at 4:29 PM, Jose Angel Pineda Pardo <
> [log in to unmask]> wrote:
>
>> Hi Monica,
>>
>> it seems you are just using two seed regions. So in that case it will be
>> correct.
>>
>> Cheers
>>
>> Jose
>>
>>
>> On Mon, Mar 28, 2011 at 4:10 PM, Monica Giraldo <
>> [log in to unmask]> wrote:
>>
>>> Hi Saad, thanks for your help. Well, my seeds are already in the DTI
>>> space. I did all the pre processing of the images with SPM before running
>>> anything in FSL and all the images used are in the same space as the DTI.
>>> That's why im not using the --xfm option in probtrackx.
>>>
>>> I tried anyway running your script and I did got a result but I don't
>>> know it it's correct. I got the following matrix:
>>> ConMat =
>>> 62470809 321160
>>> 461766 46066148
>>>
>>> but why the waytotal file shows the number 1.5015e+07? If it is not the
>>> sum of the numbers of the matrix?
>>>
>>> It may be something else wrong?
>>>
>>> Thankx,
>>>
>>> On Mon, Mar 28, 2011 at 2:15 PM, Saad Jbabdi <[log in to unmask]>wrote:
>>>
>>>>
>>>>
>>>>
>>>> sorry, I forgot another thing. and MATLAB doesn't recognize the command
>>>> read_avw, is there any chance that you wrote it wrong? Do I have to install
>>>> somehting in matlab to run that command?
>>>>
>>>>
>>>> that is why I've added the line "addpath([getenv('FSLDIR')
>>>> '/etc/matlab']);" in the script that I suggested to you. This tells matlab
>>>> to look for the appropriate directory where read_avw is coded.
>>>>
>>>>
>>>> Saad.
>>>>
>>>>
>>>>
>>>> On Mon, Mar 28, 2011 at 12:46 PM, Monica Giraldo <
>>>> [log in to unmask]> wrote:
>>>>
>>>>> Hello Saad, I just tryed doing what you told Jose. I executed first the
>>>>> following command for adding all the seed masks:
>>>>>
>>>>> fslmaths -dt double "mask1_path" -add "mask2_path" "resultImage_path"
>>>>>
>>>>> I put the type of the images as double because when I open them in
>>>>> MATLAB it says that they are double type.
>>>>>
>>>>> Then, I executed the probtrackx command with the following options:
>>>>>
>>>>> probtrackx --mode=seedmask -x "resultImage_path" -l -c 0.2 -S 2000
>>>>> --steplength=0.5 -P 5000 --forcedir --opd -s "bedpostDirectory+/merged" -m
>>>>> "nodif_brain_mask_path" --dir="output directory" --omatrix1
>>>>>
>>>>> Well, it did created the files it should have created: the
>>>>> coords_for_fdt_matrix1, fdt_matrix1, fdt_paths and waytotal. But there is
>>>>> something strange, although it does find tracks because in the waytotal file
>>>>> it appears the number 1.5015e+07 when I open the fdt_paths there is nothing!
>>>>> The other images dimensions are correct. And when I open the images I can
>>>>> visualize something.
>>>>>
>>>>> Other quesiton I have is, in your code when you write seeds =
>>>>> {'seed1','seed2',...}; 'seed1' and 'seed2' are the paths of the seed images
>>>>> or what?
>>>>>
>>>>> Thanks,
>>>>>
>>>>>
>>>>> --
>>>>> Monica Giraldo
>>>>> *Master student in Biomedical Engineering
>>>>> Universidad de Barcelona - Universidad Politécnica de Cataluña
>>>>> *
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Monica Giraldo
>>>> *Master student in Biomedical Engineering
>>>> Universidad de Barcelona - Universidad Politécnica de Cataluña
>>>> *
>>>>
>>>>
>>>> --
>>>> Saad Jbabdi
>>>> University of Oxford, FMRIB Centre
>>>>
>>>> JR Hospital, Headington, OX3 9DU, UK
>>>> (+44)1865-222466 (fax 717)
>>>> www.fmrib.ox.ac.uk/~saad <http://www.fmrib.ox.ac.uk/%7Esaad>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Monica Giraldo
>>> *Master student in Biomedical Engineering
>>> Universidad de Barcelona - Universidad Politécnica de Cataluña
>>> *
>>>
>>
>>
>
>
> --
> Monica Giraldo
> *Master student in Biomedical Engineering
> Universidad de Barcelona - Universidad Politécnica de Cataluña
> *
>
