Hi, Tim and Matt
Thank you for your suggestions! I will try matlab method first, as I can expect
there will be some math to parcellate the results. The workbench commands sound
great too and I didn't know that I can directly create cifti file from texts.
Thanks againLongchuan
On Thursday, June 23, 2016 7:48 PM, Timothy Coalson <[email protected]> wrote:
So it isn't parcels by parcels, it is dense, but within an ROI only? If I
understand the format correctly, you could use -cifti-create-dense-scalar to
make a template cifti, then use that in -cifti-convert -from-text, if the text
format is simple enough. If you want to expand it to the standard
grayordinates, you can then do -cifti-create-dense-from-template.
Tim
On Thu, Jun 23, 2016 at 6:12 PM, Glasser, Matthew <[email protected]> wrote:
Hi Longchuan,
I think you will need to use matlab for this. You can make a dscalar that
contains the PFC_L ROI as ones. Then you can map the vertices in that ROI to
the rows? in the asc file and put the values in the appropriate locations.
Then save the file back out and view it in Connectome Workbench. We will think
about whether we cn make this easier in wb_command.
Peace,
Matt.
From: Longchuan Li <[email protected]>
Reply-To: Longchuan Li <[email protected]>
Date: Thursday, June 23, 2016 at 4:54 PM
To: Matt Glasser <[email protected]>, HCP Users <[email protected]>
Subject: Re: [HCP-Users] Visualize outputs of seeds to targets classification
in workbench
Hi, all
Sorry for sending several identical emails, as I repeatedly got replies saying
my emails are waiting to be approved.
So, basically I have four ROIs: PFC_L.border, ATC_L.border; IPL_L.border and
OC_L.border. I want to parcellate PFC_L, according to the connectivity inputs
from the other three ROIs. So, I run 'probtrackx2', with PFC_L as the seed and
other three as the targets. As all files are surface files, after the run, I
get several files like below: seeds_to_ATC.gii.ascseeds_to_IPL.gii.asc...
However, I find that workbench cannot read these standard ASCII files. So my
question is how I can read these surface files from FSL in workbench?
I kind of figured out a workaround after I posted the question: it seems that a
file called "matrix_seeds_to_all_targets" contains N*P matrix, with N being the
number of vertex in the seed mask and P being the number of target masks. The
values seem to be the number of connected streamlines. So, I may write a simple
matlab script to parcellate the seed mask myself by using "winner-take-all"
strategy, based on the matrix and their corersponding vertex on the surface.
If you know any better ways, please let me know.
Many thanksLongchuan
On Thursday, June 23, 2016 5:32 PM, "Glasser, Matthew" <[email protected]>
wrote:
Hi Longchuan,
Can you give some details on what the seeds and targets are?
Peace,
Matt.
From: <[email protected]> on behalf of Longchuan Li
<[email protected]>
Reply-To: Longchuan Li <[email protected]>
Date: Thursday, June 23, 2016 at 9:31 AM
To: HCP Users <[email protected]>, "[email protected]"
<[email protected]>
Subject: [HCP-Users] Visualize outputs of seeds to targets classification in
workbench
Hi, HCP experts
I searched this topic in the mailing list for a while and seem not have found
the answer: after I performed seed-to-target analyses in probtrackx2 using
surface-based ROIs, how can I convert the results "seed_to_target_ROIs.asc" to
a format that is supported by Workbench and could be loaded and visualized in
WB?
Thank you in advance!Longchuan
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