Thanks a lot, Matt! I just saw Stam's email and responded as well.
Regards,
Karthik
From: Glasser, Matthew
Sent: Friday, September 1, 2017 5:07:25 PM
To: Gopalakrishnan, Karthik; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users]
Hi Stam,
Thanks for the suggestion! Is this only for the network mode call (corrected
call pasted below)?
probtrackx2 --network --omatrix1 --loopcheck -x white-masks.txt -l
--onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01
--distthresh=0.0 --sampvox=0.0 --forcedir
Well the good news is that all of that looks correct and Stam made some
concrete suggestions as to your probtrackx command.
Peace,
Matt.
From: "Gopalakrishnan, Karthik"
>
Date: Friday, September 1, 2017 at 4:04 PM
To: Matt Glasser
S.O.S diffusion guys, poor and highly stressed Computer Science grad student
here, trying to break into the neuroscience community! :)
Matt, in case this helps, here are the commands I used to go from the released
ROI files to the subject ROIs, in order:
1) Create .label.gii files from both
Hi Karthik
You need to run —network —omatrix1, and I would add —loopcheck.
Have a look at the HCP course tractography practical for the different options
in getting connectomes.
Cheers
Stam
On 1 Sep 2017, at 21:30, Glasser, Matthew
> wrote:
I
Yes, both surface files I mentioned previously are the ones that are provided
in the following directory:
${Subject}/T1w/fsaverage_LR32k
Thanks!
Karthik
From: Glasser, Matthew
Sent: Friday, September 1, 2017 4:21:43 PM
To: Gopalakrishnan,
Are all of these files in ${StudyFolder}/${Subject}/T1w?
Matt.
From: "Gopalakrishnan, Karthik"
>
Date: Friday, September 1, 2017 at 3:19 PM
To: Matt Glasser >,
Yes, I used the released bedpostX data.
The white matter surfaces used were:
100206.L.white_MSMAll.32k_fs_LR.surf.gii
100206.R.white_MSMAll.32k_fs_LR.surf.gii
Thanks!
Karthik
From: Glasser, Matthew
Sent: Friday, September 1, 2017
Which white matter surface are those on? I assume the bedpostX data are what
we released?
Peace,
Matt.
From: "Gopalakrishnan, Karthik"
>
Date: Friday, September 1, 2017 at 3:11 PM
To: Matt Glasser
Well, if they want to get to cifti starting from the volume data, I still
wouldn't suggest -volume-parcel-resampling. Instead, just use the
subject's subcortical label volume when making the initial flipped or not
flipped cifti files, and use -cifti-resample to get them into a shared
grayordinate
The file white-masks.txt and the file targets.txt contain newline-separated
paths to each of the 360 ROIs (.gii files).
Thanks!
Karthik
From: Glasser, Matthew
Sent: Friday, September 1, 2017 4:06:15 PM
To: Gopalakrishnan, Karthik;
What is in the .txt?
Peace,
Matt.
From: "Gopalakrishnan, Karthik"
>
Date: Friday, September 1, 2017 at 3:04 PM
To: Matt Glasser >,
Mike was talking about the effect of using some within parcel smoothing and
some between parcel smoothing so I suggested he make the data from scratch if
he wants to do all between parcel smoothing. I think they should just smooth
within parcels and only add the needed smoothing to get things
Hi Matt,
Here's the probtrackx calls:
For network mode:
probtrackx2 --network -x white-masks.txt -l --onewaycondition -c 0.2 -S 2000
--steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0
--forcedir --opd -s Diffusion.bedpostX/merged -m
Using that transform that flips X around the origin should put left on
right and right on left, yes. Note, however, that the left and right
parcel ROIs are not the same, so you will have to figure out how to handle
the mismatched edges.
I would not suggest -volume-parcel-resampling. If you want
I guess I don’t know why one would want to smooth across the known boundaries,
but the option is available in wb_command -cifti-smoothing. One could instead
redo the volume mapping to CIFTI with wb_command -volume-parcel-resampling
using a very small number for the kernel, and then apply the
@Matt: The minimally preprocessed subcortical data in the CIFTI was smoothed
with a 2 mm FWHM “parcel-constrained” kernel, right? (i.e, the smoothing does
not cross boundaries of subcortical structures). In that case, if they were to
then further smooth the subcortical data, but smooth
1. That command for the surface is not quite what you are looking for. For
the surface, the left and right hemisphere vertices are already in register
(meaning that vertices with the same number will be in the anatomically
corresponding location). You would need to translate between the
Hi Claude,
Sorry that some of the variables don't have more logical scoring. The up to
date HCP data dictionary with the following clarifications is available for
download on the HCP wiki: https://wiki.humanconnectome.org/x/N4AvAw
SSAGA_Agoraphobia is scored 1 = No agorophobia experienced
Dear HCP list,
We’re interested in clustering of subcortical structures in the HCP
resting-state fMRI data and have two questions regarding the pre-processing:
1. We’re looking for a way to flip the data of the two hemispheres, including
subcortical structures, It seems that an option exist
Can you post your probtrackx call?
Peace,
Matt.
From:
>
on behalf of "Gopalakrishnan, Karthik"
>
Date: Thursday, August 31, 2017 at 9:27 PM
To:
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