Hi,

I've created a mask and tried to run ProbtackX on it. However this time the tracts did not load into fslview, and I'm not sure why even though I have tried numerous times. Can you tell me what I am doing wrong? Also, I did not get the fat_paths files which I did before. Thanks.

By the way, these are the files I obtained after running ProbtrackX:

file://localhost/Users/neuro/Desktop/PD_PATIENTS/60-70yrs/16/NPW_DTIb70032d/NPW/23644/P16.bedpostX/P16strPPNR2Putamen/fdt_coordinates.txt
file://localhost/Users/neuro/Desktop/PD_PATIENTS/60-70yrs/16/NPW_DTIb70032d/NPW/23644/P16.bedpostX/P16strPPNR2Putamen/fdt.log
file://localhost/Users/neuro/Desktop/PD_PATIENTS/60-70yrs/16/NPW_DTIb70032d/NPW/23644/P16.bedpostX/P16strPPNR2Putamen/P16strPPNR2Putamen_246_231_96.nii.gz
file://localhost/Users/neuro/Desktop/PD_PATIENTS/60-70yrs/16/NPW_DTIb70032d/NPW/23644/P16.bedpostX/P16strPPNR2Putamen/probtrackx.log
file://localhost/Users/neuro/Desktop/PD_PATIENTS/60-70yrs/16/NPW_DTIb70032d/NPW/23644/P16.bedpostX/P16strPPNR2Putamen/waypoints.txt

Best regards,

Isobel French

Researcher and Coordinator
Neurosurgery Research Unit, Division of Neurosurgery
Department of Surgery, Faculty of Medicine
University Malaya

Suite 15 T8-4a 
Level 4, Menara Timur
University of Malaya Medical Center

016-7937605
03-79493138

On Tue, Jan 17, 2017 at 5:31 PM, Moises Hernandez <[log in to unmask]> wrote:
probtrackx2 --help

Moises

On 17 January 2017 at 02:52, Isobel French <[log in to unmask]> wrote:
Hi Moises,

What is the command line utility which I will need to use here?

Thanks.


Best regards,

Isobel French

On Tue, Jan 17, 2017 at 10:08 AM, Isobel French <[log in to unmask]> wrote:
Hi Moises,

Will try this thanks!


Best regards,

Isobel French

Researcher and Coordinator
Neurosurgery Research Unit, Division of Neurosurgery
Department of Surgery, Faculty of Medicine
University Malaya

Suite 15 T8-4a 
Level 4, Menara Timur
University of Malaya Medical Center

016-7937605
03-79493138

On Mon, Jan 16, 2017 at 4:45 PM, Moises Hernandez <[log in to unmask]> wrote:
Hi Isobel. 

There are 3 compulsory arguments 

Compulsory arguments (You MUST set one or more of):

-s,--samples Basename for samples files - e.g. 'merged'

-m,--mask Bet binary mask file in diffusion space

-x,--seed Seed volume or list (ascii text file) of volumes and/or surfaces


If you want to obtain fdt_paths, you need to use the argument --opd

--opd Output path distribution


Moises.

On 16 January 2017 at 08:23, Isobel French <[log in to unmask]> wrote:
Sorry for the typo error, I meant an fdt_paths file

Best regards,

Isobel French

I would just like to confirm, is it absolutely compulsory that i will need to specify a mask during tractography in order for me to obtain an fat_paths file? 

Thanks.

Best regards,

Isobel French

Researcher and Coordinator
Neurosurgery Research Unit, Division of Neurosurgery
Department of Surgery, Faculty of Medicine
University Malaya

Suite 15 T8-4a 
Level 4, Menara Timur
University of Malaya Medical Center

016-7937605
03-79493138

On Thu, Jan 12, 2017 at 10:08 AM, Isobel French <[log in to unmask]> wrote:
Allright thanks

Best regards,

Isobel French

Researcher and Coordinator
Neurosurgery Research Unit, Division of Neurosurgery
Department of Surgery, Faculty of Medicine
University Malaya

Suite 15 T8-4a 
Level 4, Menara Timur
University of Malaya Medical Center

016-7937605
03-79493138

On Wed, Jan 11, 2017 at 7:10 PM, Saad Jbabdi <[log in to unmask]> wrote:
Hi - please try to go through the relevant FSL course practicals, which is a step by step introduction to all of this.

Cheers,
Saad






On 11 Jan 2017, at 02:56, Isobel French <[log in to unmask]> wrote:

Hi Saad,

in the fslwiki is says:

The output directory will contain: 

  • probtrackx.log - a text record of the command that was run. 
  • fdt.log - a log of the setup of the FDT GUI when the analysis was run. To recover this GUI setup, type Fdt fdt.log
  • fdt_paths - a 3D image file containing the output connectivity distribution. 
  • waytotal - a text file containing one number per seed mask (in the order that has been specified when listing them). These numbers correspond to the total number of generated tracts from each seed mask that have reached at least one of the other masks and have not been rejected by inclusion/exclusion mask criteria.

    However, I do not seem to get all the files. I only have:

    probackx.log
    fdt_coordinates.txt
    fdt_log
    nii.gz

    Is it because I am running probtackx in a different (structural) space? Because I am using structural space to obtain my tracts after registering it to the diffusion space.

    Thanks.

Best regards,

Isobel French

Researcher and Coordinator
Neurosurgery Research Unit, Division of Neurosurgery
Department of Surgery, Faculty of Medicine
University Malaya

Suite 15 T8-4a 
Level 4, Menara Timur
University of Malaya Medical Center

016-7937605
03-79493138

On Wed, Jan 11, 2017 at 10:41 AM, Isobel French <[log in to unmask]> wrote:
Hi Saad,

in the fslwiki is says:

The output directory will contain: 

  • probtrackx.log - a text record of the command that was run. 
  • fdt.log - a log of the setup of the FDT GUI when the analysis was run. To recover this GUI setup, type Fdt fdt.log
  • fdt_paths - a 3D image file containing the output connectivity distribution. 
  • waytotal - a text file containing one number per seed mask (in the order that has been specified when listing them). These numbers correspond to the total number of generated tracts from each seed mask that have reached at least one of the other masks and have not been rejected by inclusion/exclusion mask criteria.

    However, I do not seem to get all the files. Is it because I am running probtackx in a different (structural) space? Because I am using structural space to obtain my tracts after registering it to the diffusion space.

    Thanks.


Best regards,

Isobel French

Researcher and Coordinator
Neurosurgery Research Unit, Division of Neurosurgery
Department of Surgery, Faculty of Medicine
University Malaya

Suite 15 T8-4a 
Level 4, Menara Timur
University of Malaya Medical Center

016-7937605
03-79493138
On Wed, Jan 11, 2017 at 10:20 AM, Isobel French <[log in to unmask]> wrote:
Hi,

I see. Allright thanks

Best regards,

Isobel French

Researcher and Coordinator
Neurosurgery Research Unit, Division of Neurosurgery
Department of Surgery, Faculty of Medicine
University Malaya

Suite 15 T8-4a 
Level 4, Menara Timur
University of Malaya Medical Center

016-7937605
03-79493138
On Tue, Jan 10, 2017 at 7:40 PM, Saad Jbabdi <[log in to unmask]> wrote:
Hi - Once you run probtrackx to get your tracts, these are save in a file called fdt_paths.nii.gz.  

If you are unsure how to do that I would recommend going through the FDT practical on the FSL wiki.

Cheers,
Saad






On 10 Jan 2017, at 03:37, Isobel French <[log in to unmask]> wrote:

Hi Saad,

Where do I locate the file? Also what would be the command line that i would need to use to measure tract volume? Also are there procedures i need to do to prepare my data before I  am able to carry out the measuring the tract volume?

Thanks.

On Sat, Jan 7, 2017 at 7:21 PM, Saad Jbabdi <[log in to unmask]> wrote:
Hi - not sure what you mean exactly.  If you mean tract volume, you can use fslstats on the fdt_paths file.

Cheers,
Saad





On 6 Jan 2017, at 07:05, Isobel French <[log in to unmask]> wrote:

Dear experts,

Is there a way to measure the diversity/ "spreadness" of tracts in DTI?

Tqvm.

Best regards,

Isobel French