The following nodes do not have any streamlines assigned

Vaasudev · July 30, 2019, 1:09pm

Dear all,

When i am trying to assign a stream line for the nodes, i am unable to obtain any stream lines, could you please let me know why is it happening

tck2connectome: [WARNING] The following nodes do not have any streamlines assigned:
tck2connectome: [WARNING] 1, 2, 3, 4, 5, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 54, 55, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 75, 76, 77, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 102, 104, 111, 112, 114, 115, 116, 117, 119, 120, 121, 126, 140, 141, 142, 143, 144, 145, 146, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 168, 169, 170, 171, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 362, 363, 364, 365, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379
tck2connectome: [WARNING] (This may indicate a poor registration)

Thanks
Vasudev

mblesac · July 30, 2019, 1:31pm

Hi Vaasudev,

How is the alignment between the T1w and the diffusion image? and the alignment between the labels and the diffusion image?

Two things come to my mind that could be causing this:

The registration between the T1w and the diffusion is very poor, only overlapping certain areas.
For the label propagation, the interpolation used was not a nearest neighboor, so the labels are wrongly propagated.

If you post a couple of images, we should be able to inspect better whats’s the cause.

I hope this helps.

Best regards,

Manuel

vanlam2308 · July 30, 2019, 1:35pm

Hi Vaasudev,

I think this issue is also caused from your applied atlas/regions file whose regions were not assigned correctly. In mrtrix3, it is necessary to have all the regions (in your atlas file) be labeled in a continuous order, starting from 1. Most atlas contain regions which are labeled randomly. You can try labelconvert . In my case, I used DSI studio instead since it was very easy. I just needed to load my atlas file in DSI studio and saved it as another file. All regions were then labeled in order.
Hope this helps,

Jane

Vaasudev · July 30, 2019, 2:15pm

I am attaching the registration between T1w and Diffusion file, please see

and the alignment between labels and diffusion file

and for label propagation i have used following method

labelconvert hcpmmp1.mif hcpmmp1_original.txt hcpmmp1_ordered.txt hcpmmp1_parcels_nocoreg.mif

is this wrong ?

Vaasudev · July 30, 2019, 2:26pm

I have used label convert,kindly see the update, i am still incurring the same error.

mblesac · July 30, 2019, 2:35pm

Hi,

The first figure is the diffusion data or the 5TT overlaid to the T1w? you could play a little bit with the opacity to see what’s going on.

In the second figure and the command line there is something that I don’t understand:
You seem to use Glasser’s parcellation in the command line, but the figure looks like the Dsikan-Killany with 84 ROIs. Also note that with labelconvert you are not doing label propagation, you simple are changing the values of you ROIs. You need to align your T1w to the diffusion data first, and then apply the same transformation to the labels.

I hope this helps.

Best regards,

Manuel

Vaasudev · July 30, 2019, 2:41pm

Dear ,

I have changed the reply , i am sorry for my mistake, now i have overlaid the glasser atlas.

Yes first figure is 5tt overlaid on diffusion data.

I have transformed the Glasser labels into T1w space using

mrtransform hcpmmp1_parcels_nocoreg.mif -linear diff2struct_mrtrix.txt -
inverse -datatype uint32 hcpmmp1_parcels_coreg.mif

this is how i have generated diff2struct_matrix.txt

flirt -in myprefix0000.nii.gz -ref 5tt_nocoreg.nii.gz -interp nearestneighbour -dof 6 -omat diff2struct_fsl.mat

transformconvert diff2struct_fsl.mat mean_b0_preprocessed.nii.gz 5tt_nocoreg.nii.gz flirt_import diff2struct_mrtrix.txt

mblesac · July 30, 2019, 2:48pm

Hi,

Could you display together the 5TT and the label map? If indeed the two files are aligned between them and with the diffusion, I’m running out of ideas.

How many streamlines are you generating?

Best regards,

Manuel

Vaasudev · July 30, 2019, 2:52pm

Dear ,

Labels overlaid on 5TT , i am generating 1 million streamlines.

Thanks
Vasudev

mblesac · July 30, 2019, 2:56pm

Hi,

I can not see if they overlay or not, could play a little bit with the opacity to be able to see the two images superposed?

Also my feeling is that 1 million streamlines is a very low number for this parcellation, try to increase that to 10 or 100 and see what happens.

Best regards,

Manuel

Vaasudev · July 30, 2019, 3:09pm

Indeed there is an overlay problem

I dont know what i have done wrong in this case, i have tried to overlay 5TT image on label map.

Could you please let me know how to resolve this issue.

mblesac · July 30, 2019, 3:16pm

Hi,

By the coreg, at the end of the 5TT name, I assume that the 5TT is aligned to the diffusion.

Then, I can think of two possibilities:

the transformation was not applied to the labels
the T1w used for the 5TT and the parcellation are with different orientations

For the first case, you said that the transformation was applied to the labels. What about the second possibility? are you using the raw T1w for the 5TT? I’m not familiar with freesurfer, maybe they perform an internal reorientation of the data?

Best regards,

Manuel

Vaasudev · July 30, 2019, 3:19pm

5TT is aligned with the diffusion file

this is the procedure i have used

flirt -in myprefix0000.nii.gz -ref 5tt_nocoreg.nii.gz -interp nearestneighbour -dof 6 -omat diff2struct_fsl.mat

transformconvert diff2struct_fsl.mat mean_b0_preprocessed.nii.gz 5tt_nocoreg.nii.gz flirt_import diff2struct_mrtrix.txt

mrtransform 5tt_nocoreg.mif -linear diff2struct_mrtrix.txt -inverse 5tt_coreg.mif

I have got myprefix0000.nii.gz by using fslsplit and i used b0 from dwi file and registered it to 5tt_nocoreg.nii.gz

mblesac · July 30, 2019, 3:29pm

Hi,

flirt -in myprefix0000.nii.gz -ref 5tt_nocoreg.nii.gz -interp nearestneighbour -dof 6 -omat diff2struct_fsl.mat

You should use the T1w to guide the registration, not the 5TT. It would be something like:

flirt -in myprefix0000.nii.gz -ref T1w.nii.gz -dof 6 -omat diff2struct_fsl.mat
transformconvert diff2struct_fsl.mat mean_b0_preprocessed.nii.gz T1w.nii.gz flirt_import diff2struct_mrtrix.txt

You can also play with other cost functions like bbr, please see here

And then, if your parcellation is already aligned with your T1w data, you only need to do:

mrtransform labels_nocoreg.mif -linear diff2struct_mrtrix.txt -inverse labels_coreg.mif

If is not, the first try to find the cause for this miss-alignment. The you have two options, or repeat the process with the other T1w, or align the two T1ws

Best regards,

Manuel

Vaasudev · July 30, 2019, 3:46pm

it did not change a bit, i am still getting the same error

mblesac · July 30, 2019, 3:54pm

Could you overlay the 5tt_nocoreg.mif and the hcpmmp1_parcels_nocoreg.mif? In the overlay image could you setup the lower threshold for display at 0.7 or something similar?

Vaasudev · July 30, 2019, 4:04pm

I have changed the threshold and there seems to registration problem :overlay 5tt_nocoreg.mif and the hcpmmp1_parcels_nocoreg.mif

mblesac · July 30, 2019, 8:15pm

Hi,

I think that the T1w output of freesurfer and the T1w used for 5TT are in different spaces. Registering the output of freesurfer to the other, and applying the transformation to the labels should do the trick. Then you only have to apply the transformation you calculated before to both.

Best regards,

Manuel

Vaasudev · July 31, 2019, 2:57pm

This is the registration procedure that i have applied to register Freesurfer labels to DWI space

mri_aparc2aseg --old-ribbon --s KON11 --annot hcpmmp1 --o hcpmmp1.mgz

mrconvert –datatype uint32 hcpmmp1.mgz hcpmmp1.mif

labelconvert hcpmmp1.mif hcpmmp1_original.txt hcpmmp1_ordered.txt hcpmmp1_parcels_nocoreg.mif

mrtransform hcpmmp1_parcels_nocoreg.mif -linear diff2struct_mrtrix.txt -inverse -datatype uint32 hcpmmp1_parcels_coreg.mif

Is there anything wrong that i have done here ?.

mblesac · July 31, 2019, 3:13pm

Hi,

I’m no familiar with freesurfer commands, but it looks like the transformation you are applying (diff2struct_mrtrix.txt) is not defined in the same space than the hcpmmp1.mgz, I could try to open the T1w image you are using to generate the 5TT and overlay the norm.mgz generated by freesurfer.

If you see a miss-alignment something like this should work:

mrconvert –datatype uint32 norm.mgz norm.nii.gz
flirt -in norm.nii.gz -ref T1w.nii.gz -omat norm_2_t1w -dof 6 -out norm_2_t1w.nii.gz

Then you apply this transformation to your labels befor applying the other transformation (or you can concatenate them)

Best regards,

Manuel