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.giiAm I implementing the command incorrectly? I could not find any additional resources on how to convert between file types.Thank you again!LSOn 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.
CheersStam
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?
CheersStam
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
>
>
>