HI Stef
defect_labels is not a surface, it’s a scalar overlay over a surface. You can
load it via:
-surf lh.orig.nofix:overlay=lh.defect_labels
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Stef Meliss
Sent: Wednesday, March 24, 2021 10:04 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Some brain area missing after running recon-all
External Email - Use Caution
External Email - Use Caution
Hi Bruce,
I tried to load the ?h.defect_labels, but am getting error messages (“Failed to
load Surface PATH_TO_SUBJ/surf/?h.defect_labels”). This is true when using the
GUI and terminal, please see below for the code:
freeview -v mri/brainmask.mgz \
-f surf/rh.orig.nofix \
surf/lh.orig.nofix \
surf/rh.defect_labels \
surf/lh.defect_labels
RROR: MRISread: file
'/storage/shared/research/cinn/2018/MAGMOT/derivatives/FreeSurfer/sub-control035/surf/rh.defect_labels'
has many more faces than vertices!
Probably trying to use a scalar data file as a surface!
The same error message occurs for both hemispheres and also if I try to load
?h.inflated.nofix instead of ?h.orig.nofix first.
Do I need to convert the /?h.defect_labels first? If so, how? I tried running
mris_convert -c lh.defect_labels lh.defect_labels.asc from the surf directory,
but it just prints the help message.
Stef
From:
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Fischl, Bruce"
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>>
Reply to: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, 23 March 2021 at 15:45
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Some brain area missing after running recon-all
Hi Stef
It’s really hard to say without seeing the data. We do have a topology fixing
tutorial you can go through. If most of the wm.mgz is correct you likely need
to find the source of the defect and correct it. You can load the
?h.defect_labels onto the ?h.orig.nofix and/or ?h.inflated.nofix to see where
the defective vertices are. Make sure to set the overlay thresholds to 0 so you
can see all of them!
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Stef Meliss
Sent: Tuesday, March 23, 2021 9:38 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Some brain area missing after running recon-all
External Email - Use Caution
External Email - Use Caution
Hi Bruce,
Thanks so much for your quick reply. Indeed, the area is still present in the
?h.orig.nofix but not in the ?h.orig. Most of the wm.mgz voxels that are
included in ?h.orig.nofix, but not in ?h.orig have intensities above 100, but
some are as low as 86. Additionally, it also looks to me as if wm.mgz is also
missing some voxels. What kind of intervention would you recommend?
Many thanks,
Stef
From:
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Fischl, Bruce"
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>>
Reply to: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, 22 March 2021 at 17:16
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>"
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Some brain area missing after running recon-all
Hi Stef
This is usually the result of a incorrectly fixed topological defect. You can
confirm this if the area is present in the ?h.orig.nofix and not in the
?h.orig. The fix depends on the source of the defect. It might be as simple as
drawing a single voxel back into the wm.mgz, but might need more. Look at the
wm and see if it is mostly accurate or not and whether the intensities in the
white matter are near where they should be (target is 110, so ideally mostly
above 100)
Cheers
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Stef Meliss
Sent: Monday, March 22, 2021 10:37 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Some brain area missing after running recon-all
External Email - Use Caution
External Email - Use Caution
Dear FreeSurfer Experts
I am using FreeSurfer on my anatomical data to use segmentations and
parcellations in my fMRI analyses in AFNI. After reviewing the output from
recon-all -all (FreeSurfer version 6.0.0), I noticed that one subject is
missing some occipital areas in the output (e.g. aparc+aseg.mgz). Please see
attached for a screenshot of the output from
freeview -v mri/brainmask.mgz \
mri/wm.mgz:colormap=heat:opacity=0.4 \
-f surf/lh.white:edgecolor=yellow \
surf/lh.pial:edgecolor=red \
surf/rh.white:edgecolor=yellow \
surf/rh.pial:edgecolor=red \
surf/rh.inflated:visible=0 \
surf/lh.inflated:visible=0
From what I read in the information on troubleshooting the output, I understand
that manual editing is necessary to fix this – is this correct? I have verified
that the missing areas are included in the brainmask as well as aseg.presurf. I
am not sure though how to determine whether I am dealing with a segmentation
error or a normalization error or maybe even a combination of both.
If you could give me some pointers on which steps to take, that would be highly
appreciated.
Many thanks in advance for your help.
Best regards,
Stef
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