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Thanks so much for the quick and clear reply Bruce. I'll look into doing that.
Cheers,
Joel
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Bruce Fischl
Sent: 27 September 2019 12:52:47
To: Freesurfer s
Hello everyone,
I've been using mri_vol2surf to move some activation data in MNI space to the
fsaverage surface with the following command:
mri_vol2surf --mov MNIvol.nii --projfrac-max 0 1 0.1 --hemi rh --o rh.out.mgz
--mni152reg
This works well, but I'm losing a small temporal gyrus cluster t
Hi Joel
I believe they are stored in "tkreg ras" by default. In any case,
mri_label2label should let you map them to pretty much any space you
like.
cheers
Bruce
On Fri, 27 Sep 2019, Berger, Joel wrote:
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Hi friendly Freesurfers,
I have seen th
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Hi friendly Freesurfers,
I have seen this question asked, but can't find the answer. When exporting a
label from tksurfer for a particular ROI for a subject, the coordinates in the
.label document don't match up with any of the coordinates I can vie
Nifti files don't store that info. You'd have to get the gradient table and
b-values either from the dicom header or from the scanner.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Daniel Callow
Sent: Friday, September 27, 2019 11:32 AM
To: Freesurf
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Gotcha. I was wondering if it would be possible to extract the bvecs and
bval files directly from the Nifti file, however, it seems like based on
the documentation that this is not possible and I will have to specify the
bvals and bvecs and make sure th
Yes. Please check out the instructions in the tutorial on how to specify your
input DWIs and let us know if you have any questions:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Daniel Call
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Dear Freesurfer experts,
May I ask what's the difference between FSFAST and SPM in the 1st level
GLM? Now I use fsfast to pre-process my task-based imaging data, then model
the data with FSFAST and SPM respectively. I expected to get very similar
resul
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Hello I was given a dataset already in Nifti format that I would like to
run Tracula on. Is it possible to input Nifti files in the config file
instead of DICOMs? How would this work?
Best,
Daniel Callow
--
*Daniel Callow*
*PhD Student, Neuroscience a
Hi Tim
you probably also want to do the files in the orig dir (like
orig/001.mgz).
cheers
Bruce
On Fri, 27 Sep 2019, Tim Schäfer wrote:
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Dear FS experts,
I want to upload neuroimaging data pre-processed by FreeSurfer's recon-all
pipeline to a consortium
ok, we'll see if we can replicate it.
On Fri, 27 Sep 2019, Троицкий Антон
Александрович wrote:
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Dear Bruce,
I don't’ know exactly what happened during the processing.
I have 8 Gb of RAM of my Mac. When the freesurfer is working there is
approxima
Hi,
if you upload this entire subject to our ftp site we will take a look
cheers
Bruce
On
Fri, 27 Sep 2019, Троицкий Антон Александрович wrote:
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Hello FreeSurfer Developers,
during the processing of patient data an error occurred. I don’t clearl
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prl.saheli...@gmail.com
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Dear FS experts,
I want to upload neuroimaging data pre-processed by FreeSurfer's recon-all
pipeline to a consortium server, and they require all data to be anonymized.
I found mri_deface [1] and wondered which files I would have to apply it to,
and
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