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DSI Studio Workshop - Shared screen with speaker view
Zeke Gleichgerrcht
01:40
The hands-on identifying sampling schemes were not working for me, FYI
Rebecca Wilkes Roth
02:13
They aren’t working for me either.
Anupa
05:18
A silly question- ARe DWI and DTI, both the same?
Mengfei Cai
07:05
DTI can be taken as the down-stream branch of DWI~~
Anupa
08:14
Thank you.
Yasaman Baghezadeh
15:09
Why sometimes we have several B0?
Anupa
24:31
What's the difference between single and multi-shell data?
Anupa
31:33
Does multishell data have a balance between high and low sensitivity to diffusion? Means, better SNR than single shell data?
Anupa
36:02
Will do, thanks.
Iyad Ba Gari
40:57
Does DSI support GPU for Eddy correction?
Yasaman Baghezadeh
41:40
Eddy Current correction with DSI studio is very fast on my computer (labout one minute). Dose it mean it is not performed correctly?
Mengfei Cai
42:54
do we always need to correct for head motion followed by eddy correction, or the other way around ?
Zeke Gleichgerrcht
43:12
Do I install FSL separately to be able to Eddy correct in DSI?
Zeke Gleichgerrcht
43:50
Ah in Mac it's saying i don't have FSL
Anupa
44:28
I'm sorry if I missed it. What's the difference between top-up eddy and normal eddy? And when to use TOPUP eddy?
Mengfei Cai
45:03
also: my Q: do we always need to correct for head motion followed by eddy correction, or the other way around ?
Smitha
46:24
Do we need to do top up eddy and again Eddy for AP and PA images
Hengenius, James B
54:04
What if we have full AP and PA data (each with all diffusion directions) rather than a PA file that is only a b0 image for correction. Can we correct each with topup using the opposite PE file?
Smitha
54:19
Thanks
Jing Xu
54:38
So this step also doesn't work on Mac, or if we download FSL, it'll work?
Smitha
55:37
can you demonstrate DWI with reverse-PE (full DWI)
Jing Xu
57:27
Also, does this mean that we should always acquire the reverse PE images?
Smitha
57:46
Thanks Frank
Smitha
59:57
After Top up Eddy and Run reconstruction, Do we get only one image named rsrc.gz
Hengenius, James B
01:00:43
In the case of full data in both PE directions, can both src files be merged in the fib file after distortion correction? For example, aligning both to MNI template with QSDR?
Iyad Ba Gari
01:01:08
Can we use acquisition parameters as txt file such astopup --imain=all_my_b0_images.nii --datain=acquisition_parameters.txt --config=b02b0.cnf --out=my_output
Zeke Gleichgerrcht
01:01:19
Hi Frank- I sent a forum entry with a Dropbox file on Sept 19th, could we look at why the tractography is not looking correct perhaps?
Iyad Ba Gari
01:01:20
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/TopupUsersGuide#A--datain
Hengenius, James B
01:01:46
Ah, got it - thanks!
Linda Robayo
01:01:55
I tried to run the eddy correction but there was an error that says " cublas64_11.dll was not found"
Zeke Gleichgerrcht
01:03:26
Sorry lost power due to Hurricane Ian, landed in CHarleston not sure if you called out my question yet
Ricardo Morais
01:03:33
using a t1 does it help to correct top up correction?
Anupa
01:04:17
I have a question regarding the DTI metric, QA. I have been using single shell data (bval of 1000 s/mm2) for analysis and I saw significant quantitative anisotropy reductions in white matter tracts. Can I confidently say that QA reductions are due to axonal damage/degeneration or should I be careful with my interpretations as it is a single shell data?
Iyad Ba Gari
01:04:21
Got it, Thank you
Jing Xu
01:05:20
Thank you, Frank! See you next week!
Linda Robayo
01:10:41
thank you!
Iyad Ba Gari
01:11:37
Can we take screenshots using the vis command in the cluster, if we have lots of subjects or do we have to use desktop/laptop?
Ricardo Morais
01:11:41
thanks
Anupa
01:13:58
Yes, you did. Thanks.
Anupa
01:15:01
Looking forward to your class on tensor model and model free DTI metrics. Thanks.
Mengfei Cai
01:15:09
can I share my screen to fix the issue on fiber tracking: from precisely starting thalamus to cortex ?
Iyad Ba Gari
01:15:22
Thanks
Hengenius, James B
01:17:04
Have to run - see you next week. Thanks!
Anupa
01:19:58
Sorry if you already answered this. But just to understand: the order of preprocessing steps is motion correction followed by eddy current correction, isn't it?
Smitha
01:24:33
Can you check our data. We just started working on DWI. We haven't checked for quality control of this data. it has two phase encoding. So we done Topup eddy. We have the src file and fib file.
Anupa
01:25:08
I see, thanks. Cool!
Smitha
01:25:56
ok I will send the data. Thanks
Linda Robayo
01:26:12
Thank you Frank see you next week!
anshul kishore
01:26:30
Thank you Frank
Smitha
01:28:22
i can share the screen
Mengfei Cai
01:33:53
*tt.nii —> *nii.gz
Anupa
01:35:35
Bye, thank you.