Hi - If there is no error message in your scripts/trac-all.log file, that means
that it was able to read the information from the dicoms. You can double-check
if the gradient table was read correctly by inspecting the outputs of the
tensor fit with: freeview --dti dmri/dtifit_V1.nii.gz
Hello,
I chose comment out the set bvecfile, bvallist, bvalfile fromt the design
script.
>From my understanding those variable above are not needed if we have a
proper DICOM.
All my subjects ran without error, but,
How can I confirm that my DICOM version is compatible wtih tracula,
How do I
Dear FS experts,
I’m wondering whether the Monte-Carlo
simulation accountｓ for spatial or intensity thresholds (or both).
Thanks,
Yoichiro Takayanagi___
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I wouldn¹t trust resting state data that have not been properly denoised.
You should only need the structural and FIX cleaned packages for what you
are doing. The link that I put below explains how to get HCP data onto the
fsaverage4 surface. You will need FreeSurfer and Connectome Workbench for
Matt,
Thanks for the quick reply! I'll check out that Wiki document and the 2016
Nature paper first.
The reason I have the pre-processed (but not ICA-FIX'ed) rfMRI data is
because I would like to use the iterative parcellation algorithm from the
Liu Lab @Harvard (as described in Wang, D. et al.
You would be better off resampling the existing CIFTI data to the fsaverage4
surface rather than redoing the projection and smoothing in the volume.
Instructions for getting to fsaverage are available here:
https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFA
Dear LME developer and expert,
I am using LME recently, based on longitudinal brain structural data, but I
have two confusions in using it.
1) I followed the tutorial at:
https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels
However, I don't actually understand the Contrast
As a work-around to the above issue, I did the registrations directly in
FSL using FLIRT, and then converted the resultant fsl reg.mat files to
freesurfer reg.dat files (using tkregister2; they all look fine). Now, all
I need is to project these rfMRI data to fsaverage4, and I thought
mri_vol2surf
Is it possible to quit the freesurfer mailing list ?
Best regards,
Antoine
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the
Hello,
I am currently starting a project with the minimally pre-processed rfMRI
from the Human Connectome Project, but I need to do some additional
processing first. This includes smoothing at 6mm FWHM and projection onto
the fsaverage4 surface. I have smoothed the pre-processed rfMRI data using
Hi again,
I just wanted to revisit this thread to see if I had misunderstood
something or had done something incorrectly?
The commands I used for bert were as follows:
cd ${SUBJECTS_DIR}/bert
cd surf
mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right
rh.sphere.left_right
cd
Hi Martin,
I will have to defer to Bruce or Doug regarding the validity of analyzing
FreeSurfer output for your subject - although I would not recommend any
analysis on the current state of your subject's surfaces. After glancing at
your data, I have a few recommendations:
1. You seem
Thanks for replying me. But I still have two questions.
Firstly, when I try xhemi on pre-possessed longitudinal data, it showed
error like this:
Performing left-right swap of labels
TR=2300.00, TE=2.98, TI=900.00, flip angle=9.00
i_ras = (-1, 3.72529e-08, 3.35276e-08)
j_ras = (-2.6077e-08,
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