[HCP-Users] Thalamic nuclei atlas
Could someone please point me at an MNI atlas for subthalamic nuclei. Thanks in advance, Heracles ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Fw:
Thank you very much, Tim, for the help. I think I ‘d like to try the
wb_command -volume-affine-resample approach. Could you please help me with a
complete command given a “mask.nii.gz” that needs to be transformed into a
“rfMRI.nii.gz” space.
Thanks,
-Heracles
From: Timothy Coalson
Sent: Monday, March 19, 2018 1:58 PM
To: HERACLES PANAGIOTIDES
Cc: Glasser, Matthew ; hcp-users
Subject: Re: [HCP-Users] Fw:
FSL's resampling does not truly respect the coordinates specified by the nifti
headers, which makes an FSL solution more complicated. FSLview also doesn't
respect those coordinates, and I am unsure whether its "alignment" is the same
as its resampling uses, or whether it is incorrect in a different way entirely.
FSL's newer viewer may display things correctly aligned, but their resampling
still doesn't respect that alignment. I don't know if FSL includes tools to
easily deal with these quirks.
Workbench does not have these quirks in its resampling, and if your volumes are
XYZ ordered and plumb, then what you see is what you get (and there is oblique
volume view for any strange volume files).
If you are committed to FSL-only solutions, then you may want to try the
FSL-specific support instead:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Support
Tim
On Sat, Mar 17, 2018 at 8:22 PM, HERACLES PANAGIOTIDES <he...@uw.edu> wrote:
Tim,
Thank you very much for taking the time to reply. I am hoping to be able to
resolve this issue with FSL. I have no experience with the Workbench platform.
I can look in that direction if I run out of FSL options. Do you know if
there is anyone who might be able to help with this?
Thanks again,
-hp
From: Timothy Coalson
Sent: Friday, March 16, 2018 2:15 PM
To: Glasser, Matthew
Cc: HERACLES PANAGIOTIDES ; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Fw:
Load both of the volumes into wb_view (high-res mask and low-res fMRI - you
may want to separate out a single frame from the fMRI to keep memory usage
down) and see if they align with each other (if they don't display correctly,
turn on oblique volume drawing mode). If they do align, the answer is trivial,
use wb_command -volume-affine-resample with the identity matrix as the
transform (for smoother edges, use trilinear interpolation of the mask, then
threshold it at 0.5 with -volume-math). If not, you will need a transform of
some kind, for instance, one that takes the fMRI into MNI space (which would
need to be inverted before using it for this).
workbench does not have the same issues as FSL with different FOV between
different volume files - all alignment is done by millimeters, not by corner of
FOV.
Tim
On Fri, Mar 16, 2018 at 12:58 PM, Glasser, Matthew <glass...@wustl.edu> wrote:
Perhaps if this were done with wb_command -volume-resample it would work
better, but Tim would have to comment on this.
Matt.
From: HERACLES PANAGIOTIDES <he...@uw.edu>
Date: Friday, March 16, 2018 at 12:11 PM
To: Matt Glasser <glass...@wustl.edu>
Subject: Re: [HCP-Users] Fw:
This is what I used:
applywarp -i left_Accumbens.nii.gz -r rfMRI_REST1_LR_hp2000_clean.nii.gz -o
left_Accumbens_in_FA.nii.gz
The position came our not in the right place.
-hp
From: Glasser, Matthew
Sent: Friday, March 16, 2018 9:39 AM
To: HERACLES PANAGIOTIDES
Subject: Re: [HCP-Users] Fw:
It should work if you use applywarp with no warp or affine.
Peace,
Matt.
From: HERACLES PANAGIOTIDES <he...@uw.edu>
Date: Friday, March 16, 2018 at 11:17 AM
To: Matt Glasser <glass...@wustl.edu>
Subject: Re: [HCP-Users] Fw:
Thanks for the reply, Matt. I did not define the problem properly. The
original mask is in MNI space (198 X 263 X 212) but does not have the same
number of voxels in each dimensions the rfMRI (91 X 109 X 91). Is it possible
to transform the the mask to have the same dimensionality (number of voxels in
each dimension) as the rfMRI?
Best,
-hp
From: Glasser, Matthew
Sent: Friday, March 16, 2018 7:22 AM
To: HERACLES PANAGIOTIDES ; HCP
Subject: Re: [HCP-Users] Fw:
Why can’t you use an MNI space accumbens mask?
Peace,
Matt.
From: <hcp-users-boun...@humanconnectome.org> on behalf of HERACLES
PANAGIOTIDES <he...@uw.edu>
Date: Friday, March 16, 2018 at 8:04 AM
To: HCP <hcp-users@humanconnectome.org>
Subject: [HCP-Users] Fw:
Could someone please help me warp a mask (left_Accumbens.nii) to an rfMRI
in MNI space.
I used the following FLIRT command:
flirt –in left_Accumbens.nii.gz -ref rfMRI_REST1_LR_hp2000_clean.nii.gz
-applyxfm -init MNI2FA.mat –out left_Accumbens_in_FA.nii.gz
I am attaching the input, output and mat files. the rfMRI is too big for
this email. I am also attaching an image that shows the original ROI (green)
Re: [HCP-Users] Fw:
Tim, Thank you very much for taking the time to reply. I am hoping to be able to resolve this issue with FSL. I have no experience with the Workbench platform. I can look in that direction if I run out of FSL options. Do you know if there is anyone who might be able to help with this? Thanks again, -hp From: Timothy Coalson Sent: Friday, March 16, 2018 2:15 PM To: Glasser, Matthew Cc: HERACLES PANAGIOTIDES ; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Fw: Load both of the volumes into wb_view (high-res mask and low-res fMRI - you may want to separate out a single frame from the fMRI to keep memory usage down) and see if they align with each other (if they don't display correctly, turn on oblique volume drawing mode). If they do align, the answer is trivial, use wb_command -volume-affine-resample with the identity matrix as the transform (for smoother edges, use trilinear interpolation of the mask, then threshold it at 0.5 with -volume-math). If not, you will need a transform of some kind, for instance, one that takes the fMRI into MNI space (which would need to be inverted before using it for this). workbench does not have the same issues as FSL with different FOV between different volume files - all alignment is done by millimeters, not by corner of FOV. Tim On Fri, Mar 16, 2018 at 12:58 PM, Glasser, Matthew <glass...@wustl.edu> wrote: Perhaps if this were done with wb_command -volume-resample it would work better, but Tim would have to comment on this. Matt. From: HERACLES PANAGIOTIDES <he...@uw.edu> Date: Friday, March 16, 2018 at 12:11 PM To: Matt Glasser <glass...@wustl.edu> Subject: Re: [HCP-Users] Fw: This is what I used: applywarp -i left_Accumbens.nii.gz -r rfMRI_REST1_LR_hp2000_clean.nii.gz -o left_Accumbens_in_FA.nii.gz The position came our not in the right place. -hp From: Glasser, Matthew Sent: Friday, March 16, 2018 9:39 AM To: HERACLES PANAGIOTIDES Subject: Re: [HCP-Users] Fw: It should work if you use applywarp with no warp or affine. Peace, Matt. From: HERACLES PANAGIOTIDES <he...@uw.edu> Date: Friday, March 16, 2018 at 11:17 AM To: Matt Glasser <glass...@wustl.edu> Subject: Re: [HCP-Users] Fw: Thanks for the reply, Matt. I did not define the problem properly. The original mask is in MNI space (198 X 263 X 212) but does not have the same number of voxels in each dimensions the rfMRI (91 X 109 X 91). Is it possible to transform the the mask to have the same dimensionality (number of voxels in each dimension) as the rfMRI? Best, -hp From: Glasser, Matthew Sent: Friday, March 16, 2018 7:22 AM To: HERACLES PANAGIOTIDES ; HCP Subject: Re: [HCP-Users] Fw: Why can’t you use an MNI space accumbens mask? Peace, Matt. From: <hcp-users-boun...@humanconnectome.org> on behalf of HERACLES PANAGIOTIDES <he...@uw.edu> Date: Friday, March 16, 2018 at 8:04 AM To: HCP <hcp-users@humanconnectome.org> Subject: [HCP-Users] Fw: Could someone please help me warp a mask (left_Accumbens.nii) to an rfMRI in MNI space. I used the following FLIRT command: flirt –in left_Accumbens.nii.gz -ref rfMRI_REST1_LR_hp2000_clean.nii.gz -applyxfm -init MNI2FA.mat –out left_Accumbens_in_FA.nii.gz I am attaching the input, output and mat files. the rfMRI is too big for this email. I am also attaching an image that shows the original ROI (green) and the transformed/output ROI (red). They are not registered correctly. Alternatively, I used the fnirt command with no better luck. fnirt --ref=rfMRI_REST1_LR_hp2000_clean.nii.gz --in=left_Accumbens.nii.gz -- inmask=left_Accumbens.nii.gz --aff=MNI2FA.mat --iout=left_Accumbens_in_FA.nii.gz Any ideas or suggestions? Thanks, -hp ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Fw:
I use Matlab to run my analyses. I prefer this to using the pipelines. I located a CIFTI reading function in Matlab authored by Matt. This is very useful. I also located files that appear to be CIFTI-formatted under the “rfMRI_REST_fix” category and was able to apply Matt’a CIFTI reading Matlab routine successfully. Am I on the right track? Thank you for any help you might be able to offer. HP From: Harms, Michael Sent: Thursday, January 04, 2018 4:12 PM To: HERACLES PANAGIOTIDES Cc: Elam, Jennifer Subject: Re: Hi, I think you’ll be able to get started if you review the Release Manual, and the HCP wiki pages. In the near future, the contents from the 2017 HCP Course will be available, and you can work through the tutorials. (Jenn can comment on the timing of that). Or, consider attending the 2018 HCP Course (dates/location not finalized yet, but we are planning on having one) ☺ Cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: HERACLES PANAGIOTIDES <he...@uw.edu> Date: Thursday, January 4, 2018 at 5:55 PM To: "Harms, Michael" <mha...@wustl.edu> Subject: Hello Mike, Jenn Elam suggested that you would be a good person to contact with questions. I am doing ROI analysis on the rfMRI data. Matt suggested that I use CIFTI files for the analysis. So here are my questions at this time: 1. Are there CIFTI files in the database; if so where are they, and how are they labeled? 2. I use Matlab for my analysis. Can I process those files in Matlab? I will wait for your answers before asking more questions. Best, Heracles The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
