Hi Rohin
Can you send us your command line and full screen output? Probably you need to
include th e-all directive to recon-all
Cheers
Bruce
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Rohin Singh
Sent: Friday, August 7, 2020 10:11 PM
To: freesurfer@nm
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Hello,
I am a student at the Mayo Clinic trying to do a project with fresurfer. When I
run recon-all, it only creates one file “001.mgz” in the MRI directory and the
rest of the folders are blank. I am not sure why this is as it completes the
proces
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Hi all,
Does this command calculate the Cortical Surface Area without the non-cortical
Medial Wall??
mris_calc --label ../label/lh.cortex.label lh.area stats
Jim
The materials in this message are private and may
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Regarding alternatives: you could run something like mriqc
(https://pypi.org/project/mriqc/) on the source nifti/dicom files. It includes
SNR measures if I remember correctly.
Tim
> On August 7, 2020 at 4:22 PM "Douglas N. Greve"
> wrote:
>
>
>
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Dear Douglas,Thank you for the reply,The MDROI.nii is a set of ROIs, which I
want to transform in separate labels. So how can I extract the ROIs?? I already
tried:
mri_extract_label MDROI.nii 1 label1.mgz
but it extracts the labels according to the in
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How is lh.lgi.mgz created?
The output files from running localGI is:
lh.pial-outer-smoothed
lh.pial_lgi
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Douglas N. Greve
Sent: Monday, June 29, 2020 9:47 AM
To: freesurfer@nmr.mgh.harvard.ed
Could you please explain how you came up with “0.0625 Hz”?
You mentioned in your first email: “With a block length of 16 sec, you will
have frequencies at 0.0625Hz and multiples thereof.”
Thanks
Mona
> On Aug 7, 2020, at 10:42 AM, Douglas N. Greve wrote:
>
> Sorry, I don't have a paper on it
>
Can you upload an example dataset? It looked like an intensity normalization
failure that probably caused a topological defect
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Elana Sarabin
Sent: Friday, August 7, 2020 11:08 AM
To: Freesurfer support list
Subject: Re: [F
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More so that the brainmask.mgz is missing a lot of both grey and white matter.
For some the area cut out in brainmask is much smaller and for others it is
large just like the photo I sent. I am wondering if there is a way to fix this
since 50% of my
Your mri_vol2label command is fine (since these are surfaces)
On 8/7/2020 10:52 AM, Eleni Nikalexi wrote:
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Dear Douglas,
Thank you for the reply,
The MDROI.nii is a set of ROIs, which I want to transform in separate
labels. So how can I extract the ROIs??
Sorry, I don't have a paper on it
On 8/7/2020 10:27 AM, Nasiriavanaki, Zahra wrote:
> Hi Doug
>
> Thanks so much for your reply. This is a question that a reviewer has pointed
> out. They were concerned that with the stimuli duration of 16 sec, maybe I am
> not using the correct hpf cutoff.
> Co
Hi Doug
Thanks so much for your reply. This is a question that a reviewer has pointed
out. They were concerned that with the stimuli duration of 16 sec, maybe I am
not using the correct hpf cutoff.
Could you please refer me a paper about this?
Thanks
Mona
> On Aug 7, 2020, at 10:15 AM, Dougla
It should be related to the SNR, but including it as a noise measure
regressor in a GLM sounds dicey to me.
On 8/6/2020 5:02 AM, Scheffler, F, Mev [fre...@sun.ac.za] wrote:
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Dear FreeSurfer Devs
I got a comment about including a SNR variable in my main
There is not a hard and fast formula. With a block length of 16 sec, you
will have frequencies at 0.0625Hz and multiples thereof. The closer you
are to 0.625, the more signal you are going to lose. Also, if you don't
remove the whitening, then FSFAST will compute a highpass filter for
you. I th
The hemi just refers to either lh or rh to load the proper surface. The
command have no idea what you are transferring to the surface.
Before the mri_vol2label stage, try loading surf.MDROI onto the surface
as an overlay and see if the ROIs are showing up in the right place
On 8/6/2020 11:4
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