Hi Stam,

More specifically my question is whether I should I be converting the original dlabel file into gifti format and from there creating the rois or should I first be creating the rois with -cifti-convert-to-roi and then turning those into gifti files? 

If so, what is the best way to implement the command? 

Thank you again for all your help. 

Best,

LS 

On Tue, Nov 10, 2015 at 11:08 AM, LEVI SOLOMYAK <[log in to unmask]> wrote:

Hi Stam,

I had previously attempted to use -cifti-convert but kept getting an invalid structure message with a warning: label file contains data type other than int32. However, it is not clear how to indicatge a different data type. 

My command was wb_command -cifti-convert -to-giti-ext Networks.dlabel.nii rsn_netowrk.label.gii

Am I implementing the command incorrectly? I could not find any additional resources on how to convert between file types. 

Thank you again!

LS 

On Tue, Nov 10, 2015 at 10:32 AM, Stamatios Sotiropoulos <[log in to unmask]> wrote:

Yes, you should be able to convert using wb_command. See the -cifti-convert option.

Cheers

Stam

 

On 10 Nov 2015, at 15:30, LEVI SOLOMYAK <[log in to unmask]> wrote:

Hi Stam,

I was only provided with dlabel parcellation files. Is there any easy way to convert that to gifti format? I was working with -cifti-separate but having trouble getting it to work. 

Thank you so much for all your help,

LS 

On Tue, Nov 10, 2015 at 5:26 AM, Stamatios Sotiropoulos <[log in to unmask]> wrote:

Hi 

Yes, FSL does not currently support CIFTI. Why not using the respective GIFTI files and then follow the exact steps described in that practical (pages 13 & 14 in particular)?  I am not sure what Label_2.gii is in your case?

Cheers

Stam

On 9 Nov 2015, at 20:42, LEVI SOLOMYAK <[log in to unmask]> wrote:

Hi Stam,

The issue does not seem to reside in the surf2surf command but in the fact that I am working with a cifti files. I've looked through the tutorials/forums on how to turn those cifti files into actual rois that I can use as seeds but am not having any luck. I tried to run the wb_command to convert them into a different format but didn't have any luck (it created a .data file). 

Any suggestions for how to work with those files?

Thanks in advance!

LS 

On Sun, Nov 8, 2015 at 1:09 PM, LEVI SOLOMYAK <[log in to unmask]> wrote:

Hi Stam,

Thank you so much for this reference, it has been very useful for me. However, when I follow the tutorial and try to run surf2surf I continue to get the error:

 ** not well-formed (invalid token) at line 1, Segmentation fault (core dumped)

 My input is surf2surf -i 101006.R.white.32k_fs_LR.surf.gii -o label1.asc --outputtype=ASCII --values=Label_2.gii  

Do you happen to know what that could be?

Thank you so much,

LS 

On Sat, Nov 7, 2015 at 6:03 AM, Stamatios Sotiropoulos <[log in to unmask]> wrote:

Hi

Have a look at the HCP course tractography tutorial, when it comes to using workbench and surfaces:

http://www.humanconnectome.org/courses/2015/exploring-the-human-connectome.php
https://wustl.box.com/shared/static/n8pw64dba2tbiridhuzefxrhdmsabdr8.pdf

Cheers
Stam

On 6 Nov 2015, at 17:31, LS <[log in to unmask]> wrote:

> Dear FSL Experts,
>
> I am looking to run tractography using ROI's from a cortical parcellation using surface ROI's. I first converted the dlabel files from a network parcellation using workbench's wb_command -cifti-all-labels-to-rois command which turns the labels into gifti files. I now want to use those as seeds to run probtracx.
>
> The FDT tutorial describes how to use ROI's but only when it is specifically converted from free-surfer. If I used workbench on the dlabel file to produce my gifti files:
> 1) Do i still need to run surf2surf? If so what should -i and --values  be?
> 2) What should my --meshspace be?
>
>
> I tried running probtracx on those gii files directly just to see what would happen but I got an error:
>
> read scalar data that is a float 32
> read gifti
> segmentation fault (core dumped).
>
> Any help you could give would be much appreciated!
>
> Thank you!
> LS
>
>
>