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Hi Experts,
This question may have been addressed elsewhere on the list, but I can’t find a
response.
I want to smooth BOLD data on the surface. First, I pre-processed the data in
FEAT with no smoothing applied. Then I registered the filtered_func d
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Hi experts,
I am trying to resample some surface overlays from fsaverage to fsaverage_sym
surface. I have used the following command:
mri_surf2surf --srcsubject fsaverage --srcsurfreg fsaverage_sym.sphere.reg
--trgsubject fsaverage_sym --trgsurfreg
t of bbregister (might also be a
.dat file). If the output is on fsaverage, then you can use nifit as output. FV
will read mgh, mgz, nii, nii.gz, as well as dicom
On 4/19/2021 10:26 AM, Mason Wells wrote:
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Hi Doug,
I
the syntax for doing this in one step I defer to Doug. Doing it in 2
steps I would use the white or pial surface to go vol->surf, then the
sphere.reg to go surf->surf
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Mason Wells
Sent: Monday, April 19, 2021 12:16 PM
To: Frees
his advise over mine. In general the
native->average surface transform is stored in the ?h.sphere.reg files
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Mason Wells
Sent: Monday, April 19, 2021 11:50 AM
To: Freesurfer support list
Subject: Re: [Freesur
u
On Behalf Of Mason Wells
Sent: Monday, April 19, 2021 5:45 AM
To: Freesurfer support list ;
freesurfer-boun...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Native volume to fs_average surface
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HI Matt,
Thanks for the
yw hwn - Cymerwch ofal wrth ateb/agor
atodiadau neu ddolenni.
If you have the data in the native functional space, then just
mri_vol2surf --mov func.nii --hemi rh --reg reg.lta --trgsubject fsaverage
--projfrac 0.5 --o rh.func.fsa.mgz
On 4/19/2021 5:23 AM, Mason Wells wrote:
MzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C2000%26sdata%3DonZCSJ%252BqbbMwKvfa8vc8su1R8GtPpJOz3DGYrWoB7CU%253D%26reserved%3D0>).
Matt.
From: on behalf of Mason Wells
Reply-To: Freesurfer support list
Date: Monday, April 19, 2021 at 4:45 AM
To: Freesurfer support list ,
"freesurfer-bo
ymerwch ofal wrth ateb/agor
atodiadau neu ddolenni.
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You would do that through the subject’s own surface. It does not work very
well to map data directly from the volume onto group average surfaces (see e.g.
Coalson et al., 2018 PNAS).
Matt.
From
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Hi experts,
I have some fMRI data that I have pre-processed in Feat. I want to resample a
single subject's data to the fs_average surface but unsure of the most optimal
way of doing this. At present I am warping the functional data to the MNI brain
Caerdydd yw hwn - Cymerwch ofal wrth ateb/agor
atodiadau neu ddolenni.
I don't know, that msg probably comes from the gifti code we link to. It looks
like it is just a warning. Do the output waveforms look ok?
On 12/9/2020 6:05 AM, Mason Wells wrote:
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Hi Experts,
I have pre-processed some resting-state date using fMRI prep. I have the
functional data on the fs_native surface in bold.func.gii format for each
hemisphere. I have created some FS labels and I would like to extract the mean
time course
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Monday, September 21, 2020 3:34 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Masking surface overlays and spatial correlations
On 9/19/2020 10:31 AM, Mason Wells
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Hi Experts,
I wonder if anyone can give me any advice on a couple of things.
1) I have some ICA spatial maps which I have resampled to the surface using
bbregister and vol2surf. I can load this data in Freeview as a generic overlay
(see attched). I a
- the inner surface of the ribbon
- the outer surface of the ribbon
Which can be a repeat of one of the other surfaces I think, though we typically
use the midthickness surface here.
Matt.
From: on behalf of Mason Wells
Reply-To: Freesurfer support list
Date: Monday, Jun
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Dear experts,
I posted a message last week about converting NIFTI files into GIFTI format,
then GIFTI to CIFTI, whilst keeping these functional data in the same space as
the subjects FS surface. I got some information RE usign the HCP workbench, but
purpose and I don’t know
what level of compatibility there is with CIFTI in FreeSurfer currently.
Perhaps one of the FreeSurfer developers can comment more on that.
Matt.
From: on behalf of Mason Wells
Reply-To: Freesurfer support list
Date: Wednesday, June 24, 2020 at 12:07 PM
To
rdydd
CF24 4HQ
DU
E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628
From: on behalf of Mason Wells
Reply to: Freesurfer support list
Date: Wednesday, 24 June 2020 at 15:46
To: Freesurfer support list ,
"freesurfer-boun...@nmr.mgh.harvard.edu"
Doing sICA on that
will potentially be more computationally intensive than on the original volume
given the upsampling; however. I wonder if it would be better to resample the
sICA maps computed in CIFTI standard space back to the native FreeSurfer mesh
based on the ciftify output?
Mat
independent of each other, and one can have standard meshes in subject’s
physical space and FreeSurfer original meshes in MNI space.
Matt.
From: on behalf of Mason Wells
Reply-To: Freesurfer support list
Date: Wednesday, June 24, 2020 at 8:27 AM
To: Freesurfer support list ,
"freesurfer-bo
684856bdbf06759778fcbc%7C1%7C0%7C637286004836544062&sdata=aQvX1V%2FJTKoPBFy0mCmduWA6ZuDNfcwjjFYQgIhuFJ8%3D&reserved=0>)
might be a good choice if you have already done your preprocessing, or you
could use the HCP Pipelines to do all of your preprocessing.
Matt.
From: on behalf of Mason W
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Hi Experts,
I have a set of resting state data in nifti format. I want to get these data
into gifti format, so I can then convert them into cifti format and run melodic
ICA. I suspect using mri_vol2surf would do the trick, but I know you need to
spe
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Hi Expets,
I am trying to work with the Ciftify package, a great tool for converting
non-HCP data into cifti format. I am running the following docker command.
However, I get an error with the return code 255
sudo docker run --entrypoint ciftify_rec
hat do you mean you “just get a series of letters/symbols”? Can you send us
the commands you ran and the screen output?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Mason Wells
Sent: Monday, June 15, 2020 6:15 AM
To: Freesurfer support list
Subject: Re: [Freesurfer]
label"?
Or just the indices of the vertices which are part of the label?
What software should be able to read the file?
Tim
> On June 15, 2020 at 12:15 PM Mason Wells wrote:
>
>
> External Email - Use Caution
>
> Hi B
eful about the one-based indexing in matlab. That is, if your ROI is in a
label file and you read the vertex indices from it, you need to add 1 to the
index that point into the overlay.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Mason Wells
Sent: Friday, June 12, 2020
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Hi Experts,
Apologies if this is a rather simple question. Is there a FreeSurfer equivalent
of fslmaths? I have an atlas overlay that has 25 visual areas in a single .mgz
file. I want to separate each atlas region into a different file, so that I end
t will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.
On 6/2/2020 9:14 AM, Mason Wells wrote:
.uk>
Ffôn: 02920 879628
From: on behalf of Mason Wells
Reply to: Freesurfer support list
Date: Tuesday, 2 June 2020 at 14:06
To: Freesurfer support list
Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}
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Hi Doug,
I have FS v6.0 and t
g to your VM
and see if it works.
On 6/2/2020 6:40 AM, Mason Wells wrote:
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I am using version 5.3, this is the version on the virtual machine I am working
from. I can ask about an updated version, but is there a way to fix this on
v5.3 in the meantime?
ag was introduced with v6
On 6/1/2020 12:57 PM, Mason Wells wrote:
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Hi Doug,
That flag isn’t recognised in the terminal? Have I placed the flag in the wrong
place? I tried it between the –feat and the directory, same outcome.
bbregister --s PPT_001 --feat
r missing your first email. Can you try adding --init-coreg to your
first bbregister command? Make sure to add it AFTER --feat
On 6/1/2020 12:06 PM, Mason Wells wrote:
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Hi Experts,
I posted earlier, but I believe my message has not been posted due to the size
of
6 May 2020 at 23:11
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] Recon-all exited WITH errors
It looks like that command finished without error. Have you tried running it in
recon-all again to see if it fails again? You can just run that command with
-parc
: 02920 879628
From: on behalf of Mason Wells
Reply to: Freesurfer support list
Date: Monday, 4 May 2020 at 20:01
To: Freesurfer support list
Subject: Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}
External Email - Use Caution
Ah yes. I just set the SUBJECTS_DIR cor
sarmed}
Something else has gone wrong. wm.mgz should have been there in order to get as
far as it did. Is your SUBJECTS_DIR set properly?
On 5/4/2020 2:49 PM, Mason Wells wrote:
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Hi,
Terminal output is below:
/Documents/Analysis/Data/freesurfer/subjects/PPT_00
.cortex.label -f
../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c
../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white
On 5/4/2020 1:34 PM, Mason Wells wrote:
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Hi Experts,
I appear to be having some issues with recon-all. I ran
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Hi Experts,
I want to take an ROI label that I have drawn on the surface and transform this
into the volume. I have drawn the label in the T1 anatomical space and I want
to keep the label in this space during the conversion. I am currently using
thi
2, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Mason Wells" wrote:
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Sorry, just to follow up on this. The surface based analysis needs the
outputs in the format of MGH. I fear I may have missed a step here. Any advice
wo
Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU
E-bost: wells...@caerdydd.ac.uk
Ffôn: 02920 879628
On 17/04/2020, 21:41, "
The only thing to change is to specify the projection
fraction for vol2surf to --projfrac 0.5 (so that it samples in the
middle of the cortical ribbon rather than at the white/gray boundary)
On 4/17/2020 1:36 PM, Mason Wells wrote:
> External Email -
s%3D&reserved=0
On 4/17/2020 10:43 AM, Mason Wells wrote:
> External Email - Use Caution
>
> Great, thanks again Bruce.
> Doug, can you confirm this is the process for taking a filtered_func file
and getting it onto the freesurfer surface re
.mgh.harvard.edu on behalf of
Bruce Fischl" wrote:
oh, then you probably want to use bbreg to register it and mri_vol2surf
to sample it onto the surface. Doug is the expert on this and can
add/correct if this is not the whole story :)
cheers
Bruce
On Fri, 17 Apr 2020
8
On 17/04/2020, 15:11, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Bruce Fischl" wrote:
Hi Mason
is your filtered_func file already sampled onto the surface or is it a
volume?
cheers
Bruce
On Fri, 17 Apr
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Hi all,
I am trying to use an analysis package that works on surface based data
(SamSrf). I have ran Feat and have a filtered_func file which is of course the
motion corrected/unwarped version of my EPI. However, I need some advice on how
to get the
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Hi all,
I apologise for cross-posting to both FSL and Freesurfer lists.
I am trying to use an analysis package that works on surface based data
(SamSrf). I have ran Feat and have a filtered_func file which is of course the
motion corrected/unwarped
03/2020, 18:38, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Mason Wells" wrote:
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HI Bruce,
Ok, great. I just thought some sections of white matter had not been traced
in their entirety (see red crosshair in attached image
: 02920 879628
On 25/03/2020, 16:19, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Bruce Fischl" wrote:
something like
freeview -v $SUBJECTS_DIR//mri/norm.mgz \
-f $SUBJECTS_DIR//surf/?h.white
cheers
Bruce
On Wed, 25 Mar
uot;freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Bruce Fischl" wrote:
Hi Mason
can you confirm that things look ok within FreeSurfer if you look at the
surface over the volume in freeview?
cheers
Bruce
On Wed, 25 Mar 2020, Mason Wells wrote:
>
>
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Hello FreeSurfer Developers,
I'm attempting to run the recon-all command on a Linux machine but it appears
to be falling at one of the first hurdles.
INFO: extension is mgz
#
#@# Talairach Wed Mar 18 15:30
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