Hi Cinzia
The file targetList.txt needs to be in ascii format (avoid using a "sophisticated" text editor to create it, or explicitly request it to save in ascii format).
It should contain a list of names of nifti volume files, including the path ( e.g. /home/cinzia/target1.nii.gz etc.)
Cheers,
Saad.
On 18 Apr 2011, at 09:08, Cinzia Cecchetto wrote:
>> Thanks again Saad
> I added --targetmasks=targetList.txt --os2t to my command line but it
> doesn't work.
> I read instructions and the explanation of the error and I concluded that
> if I want the output test file with the probability of connecting I need
> to prepare volume-like masks and then a txt file with the target masks
> list: is it true? If yes which file format do I have to use to write the
> masks? If I don't need masks what do I have to do?
>
> This is the output with the error
>
> Log directory is: /usr/local/freesurfer/subjects/ghidini/dti/test1
> 1_1
> 1_2
> 1_3
> 2_1
> 2_2
> 2_3
> 7
> Number of masks 11
> loading target masks - stage 1
> 1
> ** ERROR (nifti_image_read): failed to find header file for '75'
> ** ERROR: nifti_image_open(75): bad header info
> Error: failed to open file 75
> ERROR: Could not open image 75
> Image Exception : #22 :: Failed to read volume 75
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> Aborted
>
> Bests
> Cinzia
>
>
>
>
> Hi - that is because you need to add your target masks so probtrackx can
>> tell you how many samples went to each mask from each seed coordinate.
> Don't forget to add --os2t as well:
>>
>> probtrackx [the options you have used] --targetmasks=targetList.txt
> --os2t
>>
>>
>> Cheers,
>> Saad.
>>
>>
>> On 15 Apr 2011, at 16:31, Cinzia Cecchetto wrote:
>>
>>> Thanks Saad for your answer.
>>> We completed the first part and we obtained the nii.gz files with the
> images of fibers but it did not make the output test file with the
> probability of connecting (that is the important point). We don't
> understand how to use --s2tastext option.
>>> This is our command line:
>>> probtrackx --mode=simple
>>> --seedref=/usr/local/freesurfer/subjects/patient1/dti/DTI_BEDPOSTX.bedpostX/nodif_brain_mask
> -o test1.nii.gz -x
> /usr/local/freesurfer/subjects/patient1/dti/coord.txt
>>> -l -c 0.2 -S 2000 --steplength=0.5 -P 5000 --forcedir --opd -s
>>> /usr/local/freesurfer/subjects/patient1/dti/DTI_BEDPOSTX.bedpostX/merged
> -m
>>> /usr/local/freesurfer/subjects/patient1/dti/DTI_BEDPOSTX.bedpostX/nodif_brain_mask
> --dir=/usr/local/freesurfer/subjects/patient1/dti/test1 --s2tastext
> Where did we make the mistake?
>>> Bests
>>> Cinzia
>>>> Hi - if the idea is to use implant coordinates as seed points, then
> you
>>> do
>>>> not need to create for that, you can use probtrackx
>>>> in
>>> "simple" mode and input the coordinates as an ascii text file.
>>>> For example:
>>>> probtrackx -x coords.txt --mode=simple [other options]
>>>> where coords.txt looks like this:
>>>> x1 y1 z1
>>>> x2 y2 z2
>>>> ...
>>>> x,y,z being *voxel* coordinates in seed space (better to use
> structural
>>> space in your case i guess).
>>>> If you are interested in estimating the probability of connecting to a
>>> set
>>>> of targets (as in seed-to-target), then you can use the --s2tastext
>>> option. The output will be a text file that represents a matrix with size
>>>> (#seed coords)X(# targets).
>>>> Cheers,
>>>> Saad.
>>>> On 13 Apr 2011, at 12:18, Cinzia Cecchetto wrote:
>>>>> Dear FSL experts,
>>>>> I have to process a set of DTI images of patients. These patients
> have
>>> several implants in the deep brain and I want to know the fibers between
>>>>> these areas (I'm not interested about images of fiber but numbers,
>>> density, length ecc), I know everything about these points.
>>>>> I thought to use PROBTRACKX of FSL: I completed eddy current
>>>>> correction
>>> and bedpostx but I have some problems to insert multiple masks. Do I
> have to create a 3D images for each ROI? (there are about 100 ROI in
> each patients) or are there any methods to automatically insert the
> coordinates? Which is the better space (diffusion, structural or
> standard space) to create seed masks? Which file format do I have to
> use to write the masks?
>>>>> Bests
>>>>> Cinzia
>>>> --
>>>> Saad Jbabdi
>>>> University of Oxford, FMRIB Centre
>>>> JR Hospital, Headington, OX3 9DU, UK
>>>> (+44)1865-222466 (fax 717)
>>>> www.fmrib.ox.ac.uk/~saad
>>> ----------------------------------------------------------------
>>> SISSA Webmail https://webmail.sissa.it/
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>>> ----------------------------------------------------------------
>>> SISSA Webmail https://webmail.sissa.it/
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>>
>> --
>> Saad Jbabdi
>> University of Oxford, FMRIB Centre
>>
>> JR Hospital, Headington, OX3 9DU, UK
>> (+44)1865-222466 (fax 717)
>> www.fmrib.ox.ac.uk/~saad
>>
>
>
> ----------------------------------------------------------------
> SISSA Webmail https://webmail.sissa.it/
> Powered by SquirrelMail http://www.squirrelmail.org/
>
>
>
>
>
> ----------------------------------------------------------------
> SISSA Webmail https://webmail.sissa.it/
> Powered by SquirrelMail http://www.squirrelmail.org/
>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
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