Hi Sanna
They were kind of hand tuned ages ago, but I'm pretty sure that they get
re-estimated by a procedure that adapts to the intensities in the input images.
They were probably tuned for a specific class of T1-weighted scans (like
FLASH), but the adaptive estimation usually works well on a
Hi Yunus
I think typically you would normalize by eTIV^(2/3), which would result in a
dimensionless scaling
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of yunus soleymani
Sent: Friday, May 3, 2024 3:31 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] surface
Mostly these:
https://pubmed.ncbi.nlm.nih.gov/15501102/
https://doi.org/10.1016/S0896-6273(02)00569-X
cheers
Bruce
From: Ahsan Ali
Sent: Wednesday, May 22, 2024 4:31 AM
To: Freesurfer support list ; Huang, Yujing
; Fischl, Bruce R.,PHD
Subject: Atlas Used in FreeSurfer for Segmentation of
In freeview I believe you can right click on a given label in the list in the
left-hand pane and “go to centroid” or something is an option
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Douglas N. Greve
Sent: Friday, June 28, 2024 9:22 AM
To: freesurfer@nmr.mgh.harvard
Hi Patricio
No, none of the stats are from normalized data. They all represent the results
for that individual.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of PATRICIO FELIPE RIQUELME
Sent: Wednesday, July 3, 2024 1:11 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Fr
Hi Nys
.gcs is a different format for storing different information (surface-based
parcellation) than .gca, so mri_convert won't be able to read it. There might
be matlab code for loading .gcs files if you want. Or maybe mris_convert? I'm
not sure, possibly someone else can take a look?
Cheers
from
the .gcs file, I would gladly take it.
Best regards and much appreciation for your help,
Nys Tjade
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
Can you check the earlier volumes? And maybe post an image of the orig and/or
T1.mgz?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of ???
Sent: Saturday, August 10, 2024 9:05 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_watershed Error: GLOBAL region of the brain em
Hi Tania
I believe those are parcels in Christophe Destrieux's parcellation. We generate
them automatically for every subject. You can view them via:
cd $SUBJECTS_DIR//surf
freeview -f lh.inflated:aparc=../label/lh.aparc.a2009s.annot
for the left hemi (or rh for the right)
cheers
Bruce
From: f
Hi JamesB
there is T2/FLAIR normalization in recon-all if you process it through there.
You can look for "nonmax_suppress" if you want to find the command line
cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of James Brown
Sent: Friday, Se
I think you need to add something like -FLAIRpial or -T2pial so it uses it (in
which case it will first normalize it), but hopefully someone else can confirm
cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of James Brown
Sent: Friday, Septe
Hi Caspar
Usually that means the lh.smoothwm and the lh.sphere.reg don't have the same
topology (number of vertices,edges and triangles), frequently caused by one of
them having been recreated and the other not. Run mris_info on them and see if
they match
Cheers
Bruce
From: freesurfer-boun...
r
just white matter normalization within a mask.
Thank you very much for all that you do.
James
it looks like you are using v6. In v6, the flair might not have been normalized
On 9/23/2022 3:53 PM, Fischl, Bruce R.,PHD wrote:
I think you need to add something like -FLAIRpial or -T2pial so it uses i
Have you tried changing the window levels (contrast and brightness)?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Wighton, Paul
Sent: Friday, September 30, 2022 10:17 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found
Hi Ju
Hi Eszter
We provide estimates of architectonic boundaries like 1, 3a, 3b, 2 etc… as
label maps in each subject’s label dir. They are either unthresholded (and have
the estimated probability of being in that area for all vertices with p>0) or
thresholded so that the label has the average surfac
It looks like you have a space between “/usr/local/freesurfer/subjects/1268”
and “/label/lh.BN_Atlas.annot”
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of ???
Sent: Saturday, October 22, 2022 11:06 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mris_ca_label -l can not
Hi James
It really depends on your sequence. Some sequences, like mprage, trade off SNR
for CNR, so the distance between gray and white is larger, but the noise in
each is also larger. In that case white might end up brighter because of the
noise. There are also inflow effects where you get non
What was your mri_cnr command line? I’m not really sure I understand all your
questions. It might be helpful if you told us what you are trying to achieve,
as the different algorithms you reference below do somewhat different things
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Jam
I would check your results to see if it is doing the right thing. I also think
that the input to mri_segment is not the norm.mgz, but rather the brain.mgz,
which is more aggressively normalized
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of James Brown
Sent: Monday, October 24, 2022
Hi Sarah
Sorry, I’m not sure we have much to add. We don’t flatten much any longer, and
the cuts are kind of ad hoc – the one around the medial wall to get rid of
non-cortical stuff, then the radial ones from there to remove particularly the
curvature from the 3 poles. Mostly we just follow wha
Yes, that should be fine
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Ryosuke Hayashi
Sent: Monday, October 31, 2022 6:31 PM
To: freesurfer
Subject: [Freesurfer] About recon-all -i option
External Email - Use Caution
Dear All,
Hi. I hav
Hi Daniel
Can you clarify what you mean? The surfaces don't have any values/vertex (e.g.
scalar fields over the surface like thickness). Those are typically stored in
separate files. What are you trying to display on the surface vertices?
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On
reesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Fischl, Bruce R.,PHD
mailto:bfis...@mgh.harvard.edu>>
Sent: Tuesday, November 1, 2022 11:49:23 AM
To: Freesurfer support list
Subject: [EXTERNAL] Re: [Freesurfer] Freesurfer labels vertices and not
Hi Sarah
It is something like:
100 * (mean(abs(distance error)) / mean(original_distances))
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Sarah Lavelle
Sent: Tuesday, November 8, 2022 12:20 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Calculating Disto
Hi Haiyun
We reslice everything to coronal as part of the recon process. If you want to
map it back to the original orientation I think something like this should work:
mri_convert -rt nearest -rl rawavg.mgz aseg.mgz aseg.original_orientation.mgz
cheers
Bruce
From: freesurfer-boun...@nmr.mgh.
Hi Sarah
I think you didn't give it any flags other than the subject and input. You need
to specify -all if you want it to run all the steps it knows how to
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of O'Dor, Sarah,PhD
Sent: Tuesday, November 15, 2022 9:31 AM
To: fre
Hi Tommi
If you point us at the location of the data (and we have access) we will take a
look
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Raij, Tommi A.
Sent: Monday, November 14, 2022 11:14 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Pial surfaces i
Hi Rachel
Is RGB the correct type for the file? What kind of data do you expect it to be?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Rachel Wagner
Sent: Wednesday, November 16, 2022 1:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Unsupported Datatype
Hi Greta
Make sure you are in the "3D" view (the icon that looks like a little head next
to the coronal/axial/sagittal ones)
Cheers
Bruce
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Greta Tuckute
Sent: Thursday, December 1, 2022 6:19 PM
To: freesurfer@
I think mri_convert can take a frame number. Something like:
mri_convert -nth 0 image.nii frame0.mgz
mri_convert -nth 1 image.nii frame1.mgz
.
.
.
Although that means you have to know how many frames are in the original file
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Wighton, Pa
Hi Nazanin
What is your recon-all command line? Usually people create a SUBJECTS_DIR
somewhere other than in the freesurfer install directory. You can do this
either by setting the env variable or specifying -sd on the command
line
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
Hi Rakshathi
I don’t think this is the right recon-all.log. It seems to have finished with
no error:
Started at Sun Jan 15 04:38:40 IST 2023
Ended at Sun Jan 15 06:00:56 IST 2023
#@#%# recon-all-run-time-hours 1.371
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Ra
Hi Steven
Why wouldn’t they be the same size? The qcache files have all been mapped to an
fs average icosahedral space, so they all have the same number of vertices (and
hence the same size)
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Steven Meisler
Sent: Monday, F
Hi Sebastien
I believe that Doug has had success using bbregister for this. You might give
it a try
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Reuter, Martin,Ph.D.
Sent: Thursday, February 23, 2023 4:19 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_
You can try mris_transform, although you might need to convert the nonlinear
warp to our format. I’m pretty sure others have done this, so maybe someone
else can comment?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Aaron Tanenbaum
Sent: Friday, March 3, 2023 9:59 PM
Hi Sarah
You can use read_annotation.m to load an annotation into matlab, which should
give you the info you are after.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Sarah Lavelle
Sent: Sunday, March 5, 2023 12:09 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesu
Hi Chris
It sounds like a topological defect, but hard to say without seeing it. Can you
post some images? Or follow Doug’s instructions about visualizing the defects
and see if there is one in the sulcus you mention below?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf
No worries. I’m glad it worked out
Bruce
On Mar 15, 2023, at 10:52 PM, Chris Adamson wrote:
External Email - Use Caution
Hi Bruce,
It was a topological defect. I found it after looking harder. My bad.
Hi Chris
It sounds like a topological defect, but hard to say without seeing it
I think it usually means it ran out of memory
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Gonzalo Rojas Costa
Sent: Thursday, March 16, 2023 2:01 PM
To: Iglesias Gonzalez, Juan E.
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] CT and mri_synthsr
External Email
Hi Rob
Can you run mri_info on that volume? And just ls -l to see if it is a
reasonable size?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Bartlett, Rob
Sent: Tuesday, March 21, 2023 6:50 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] FreeSurfer Segmenta
>
On Behalf Of Fischl, Bruce R.,PHD
Sent: Tuesday, March 21, 2023 1:58 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] FreeSurfer Segmentation Fault
CAUTION: This email originated from outside of the organisation. Do not click
links or ope
Oh, sorry, should have read to the end of my inbox before responding. What
does ls -l show for that file?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Bartlett, Rob
Sent: Tuesday, March 21, 2023 12:18 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] FreeSurfer Segmentatio
That is what mri_synthsr does (which is part of the FS distribution)
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Glasser, Matt
Sent: Friday, March 31, 2023 7:48 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Is it possible to add additional T1 scans to impr
Hmmm, trying mri_convert file.nii.gz file.mgz
Then give file.mgz to synthstrip. I thought it would work with nifty, but maybe
not?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Salil Soman
Sent: Wednesday, April 5, 2023 8:11 PM
To: free surfer
Subject: [Freesurfer] synthstrip erro
External Email - Use Caution
Hi Shahin
What is your command line? mris_flatten does some random sampling of distances
since the whole N^2 distance matrix is too big. You can remove the randomness
by either specifying -norand or using a specific seed like -seed 1234.
That said,
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Fischl, Bruce R.,PHD
mailto:bfis...@mgh.harvard.edu>>
Sent: Friday, April 7, 2023 5:11:49 PM
To: Freesurfer support
External Email - Use Caution
Can you try running it with -distances 20 20 added to the command line?
From: Nasr, Shahin,Ph.D.
Sent: Saturday, April 8, 2023 8:59 AM
To: Freesurfer support list
Cc: Fischl, Bruce R.,PHD
Subject: Re: mris_flatten Version 6 vs. 7
Dear Bruce
p.s. adding -norand won’t fix the failed flattening, it will just make it
repeatable. In my experience (admittedly a long time ago now), adding more
distances and longer ranges fixes this problem
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Fischl, Bruce R.,PHD
Sent: Saturday
neighbor)
From: Nasr, Shahin,Ph.D.
Sent: Saturday, April 8, 2023 11:47 AM
To: Fischl, Bruce R.,PHD ; Freesurfer support list
Subject: Re: mris_flatten Version 6 vs. 7
Hi Bruce,
Adding -distance 20 20 definitely helped (see the attached file). Even
though, the outcome is still different than
External Email - Use Caution
Moving the thread back to the list as I don’t know, but maybe someone else does?
From: Nasr, Shahin,Ph.D.
Sent: Saturday, April 8, 2023 4:10 PM
To: Fischl, Bruce R.,PHD
Subject: Re: mris_flatten Version 6 vs. 7
it doesn't exist in the cut, and
a path, the path would curve around instead of
cutting straight across.
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Fischl, Bruce R.,PHD
mailto:bfis...@mgh.harvar
External Email - Use Caution
Hi John
1. We empirically set it at 2, but that was a long time ago, but the optimal
number is dependent on a lot of things, mostly image CNR. If the gray/white
contrast is good enough you can run it for more, but you have to make sure that
the
External Email - Use Caution
Hi Jan
If you create a family template you will only be able to compare within family,
unless you also align the templates I guess?
-nonorm will disable z-normalization of curv and sulc. We typically start with
a single subject atlas, do a nonlinear
External Email - Use Caution
Hi Sofia
Unfortunately that doesn't really work as the most time-intensive steps are
required. We are working on replacing some of these with deep-learning
equivalents, but it will be some months before that is available.
Sorry
Bruce
From: freesurf
External Email - Use Caution
Hi Hengameh
By far the most common reason for this is running out of disk space.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of hmarz...@student.ubc.ca
Sent: Monday, May 15, 2023 1:02 PM
To: freesurfer@nmr.mgh.harvard.edu
S
again for your assistance.
Best regards,
Hengameh
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Fischl, Bruce R.,PHD
mailto:bfis...@mgh.harvar
: fread failed" error.
Regards
Hengameh
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Fischl, Bruce R.,PHD
mailto:bfis...@mgh.harvard.edu>
External Email - Use Caution
Hi Jenna
It is pretty straightforward. Just give it a surface as input (see below)
Cheers
Bruce
mris_euler_number
Help
NAME
mris_euler_number
SYNOPSIS
mr
External Email - Use Caution
Hi Yang
The input to recon-all should be a T1-weighted MRI volume. I think what you are
giving it instead is a label volume
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Man YANG
Sent: Wednesday, June 14, 2023 6:52 AM
To:
External Email - Use Caution
Yes, they are the intensity statistics of different structures in the norm.mgz
volume
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Michael Mc Laughlin
Sent: Thursday, June 22, 2023 6:10 AM
To: Freesurfer support list
Subj
External Email - Use Caution
FYI
Subject: MICCAI Workshop on Machine Learning in Clinical NeuroImaging: Paper
Submissions & Talent Award
Dear Researchers!
We are excited to announce that the paper submissions for the #MICCAI Workshop
on Machine Learning in Clinical NeuroImagin
pecific
than "Re: Contents of Freesurfer digest..."
Today's Topics:
1. Re: Size of overlap between a label and a volume (John Anderson)
2. Freeview: data not displayed (Haley O Higginbotham)
3. Re: Freevie
External Email - Use Caution
Hi Pavlina
Every FreeSurfer list email comes with a header that has this link:
https://secure-web.cisco.com/14Jga6NsMm6yzyJonL9J1u2FbtbRKLO2bgfBWh3q0JJ-HebL9PoPZKxoDbm5IGqbD8QmRFQ4jgococz-6q1aXzxtZOOHMSlC5n36_MClIJzpBie4_x2Fxm0IDm50NUsZHEWdpizn7IrGTm1
External Email - Use Caution
you can also use our longitudinal stream that improves sensitivity and
reliability. Run it after you have run the cross-sectional - it will improve
your results considerably
cheers
Bruce
From: freesurfer-boun...@nmr.m
do I find out how to run the longitudinal stream, please?
Best wishes,
Hamied
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Fischl, Bruce R.,PHD
Sent: Tuesday, June 27, 202
External Email - Use Caution
Hi Parsa
The parcellations are done on the cortical surface which exists in the
individual subject "conformed" space. What do you mean by "original T1w space
coordinates"?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of par
External Email - Use Caution
Hi Rosie
Sorry but I don’t think we localize V3d yet
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of ???
Sent: Thursday, July 13, 2023 4:02 AM
To: freesurfer
Subject: [Freesurfer] How to segment the visual cortex?
External
External Email - Use Caution
Hi Amir
The brain.mgz isn’t used for subcortical segmentation so this may not matter.
Check the aseg.mgz over the norm.mgz and see if it retrains the contrast and
has the correct boundaries. The intensity normalization in the brain.mgz is
much more
External Email - Use Caution
Can you try it on a computer with more ram?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Matthew Lynch
Sent: Thursday, July 13, 2023 1:55 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all-clinical out of memory error
External Email - Use Caution
Hi Andy
The zigzag comes because the lines have to connect vertices on the surface. How
big is your rectangle? If it is pretty big I would think the zigzags would be
relatively small (although still high-frequency since the vertices are about
1mm apa
External Email - Use Caution
Hi Jiayue
At the bottom of every email to the list there is a link to listinfo management
that should let you unsubscribe yourself
Cheers
Bruce
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of ???
Sent: Sunday,
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Fischl, Bruce R.,PHD
mailto:bfis...@mgh.harvard.edu>>
Sent: 03 August 2023 11:23:42
To: Freesurfer su
External Email - Use Caution
Hi Phillip
The flattening preserves vertex correspondence between the flat maps and all
our surfaces (for that hemisphere). So if you can map data onto the flattened
patches, you should be able to look up the vertex index and use that to go
from fl
External Email - Use Caution
Hi Cain
Have you tried using mri_synthstrip instead?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of DS
Sent: Sunday, August 6, 2023 3:34 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Bad skull stripping
Cain
At 2023-08-07 05:22:33, "Fischl, Bruce R.,PHD"
mailto:bfis...@mgh.harvard.edu>> wrote:
External Email - Use Caution
Hi Cain
Have you tried using mri_synthstrip instead?
Cheers
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-bou
External Email - Use Caution
What is your freeview command line/
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of DS
Sent: Monday, August 7, 2023 2:51 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Use freeview to visualize white and pial surface
of
Freeview. But, both approaches do not work. The first image it loads just
flashed, and then it's closed when it started to load the second image. But, I
tried some images from another subject, then it works.
Best,
Cain
At 2023-08-08 03:13:52, "Fischl, Bruce R.,PHD&quo
mages larger than
the image that it fails to load, it also works. So, I guess it might be related
to other issues.
PS. the current free RAM is 6GB.
Best,
Cain
At 2023-08-08 03:49:29, "Fischl, Bruce R.,PHD"
mailto:bfis...@mgh.harvard.edu>> wrote:
External Email - Use
Hi Thomas
Can you check the input images? I’ve seen this happen when e.g. the skull
stripping failed and the images are blank
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Thomas Kaufmann
Sent: Wednesday, October 9, 2024 1:37 PM
To: Freesurfer@nmr.mgh.harvard.edu
Subj
Hi Bronwyn
Hard to say without seeing the data, but I would guess that there are
topological defects causing these issues. You can overlay the locations of the
defects in freeview and see if that explains things.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Bronwyn
Hi Francesco
Tkmedit has been deprecated for a *long* time. Can you try FreeView instead?
Cheers
Bruce
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Francesco Lomi
Sent: Monday, October 7, 2024 6:50 AM
To: Freesurfer support list
Subject: [Freesurfer] tkm
Hi Yujia
Have you tried using mris_expand instead? That is what I wrote it for.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Yujia Huang
Sent: Friday, October 18, 2024 12:11 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] lost volume geometry information u
Caution
Works like a charm. Thank you, Bruce!
Best,
Yujia
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Fischl, Bruce R.,PHD
mailto:bfis...@mgh.harvard.edu>>
Date:
ura.edu.au%2Fhelp-research%2Fsubscribe>
________
From: "Fischl, Bruce R.,PHD"
mailto:bfis...@mgh.harvard.edu>>
To: "Freesurfer support list"
mailto:freesurfer@nmr.mgh.harvard.edu>>
Sent: Saturday, 12 October, 2024 12:42:03 AM
Subject:
You could try synthstrip, it might work
Cheers
Bruce
On Sep 29, 2024, at 7:38 AM, William Baare wrote:
External Email - Use Caution
Hi Sara,
You need to denoise the background.
Here are some links that might be of help. Always check the quality of the
output :-)
https://github.com
Outlook per iOS<https://aka.ms/o0ukef>
Da: freesurfer-boun...@nmr.mgh.harvard.edu
per conto di Fischl, Bruce R.,PHD
Inviato: Sunday, September 29, 2024 4:20:00 AM
A: Freesurfer support list
Oggetto: Re: [Freesurfer] Freesurfer - skull stripping error
You
Hi Alex
I think the area of a vertex is the average area of the triangles it is
attached to. It isn’t a point measure so it is a bit hard to interpret on an
individual basis, particularly since the individual triangle areas reflect the
white/pial surface deformation dynamics. Probably makes mor
freeview. The lh.orig.nofix loads okay, but I was wondering if it was a problem
that this file is even called "nofix", does that mean it was not able to
correct for defects?
On Sun, Dec 1, 2024 at 5:49 PM Fischl, Bruce R.,PHD
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Chemda
Us
Hi Chemda
Usually that means something big has gone wrong in the segmentation or skull
stripping (like the cerebellum is still attached to a cortical hemisphere in
the wm.mgz or the skull is or something like that). More generally this happens
when there is a topological defect that is too big
Hi Tamir
I guess a quick and dirty way to do it would be to use mris_expand to create a
surface 1mm out from the white, then fill that with mris_ribbon (or maybe
mris_fill?). That would probably leave small holes. An alternative would be to
use some kind of non-maximum suppression, but I'm not
Bbregister is rigid by default (since it is within subject), so you would need
a rigid/affine version of synthmorph
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Hoffmann, Malte,PhD
Sent: Friday, December 13, 2024 7:47 AM
To: Freesurfer support list
Subje
Hi John
It is mostly for background and other stuff outside of the brain
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Barsotti, Ercole
Sent: Friday, December 13, 2024 5:17 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] FreeSurfer Labels Question
Hi Allison
The parameter you give the -i flag is the file name for a single slice in the
correct dicom series (the t1-weighted scan).
Cheers
Bruce
On Jan 11, 2025, at 3:51 PM, allio34...@aol.com wrote:
External Email - Use Caution
Hi,
I'm following the tutorial for dcmunpack, b
Hi Gonzalo
Can you clarify what you mean? People use ssh all the time to log into remote
machines and run recon-all (and freeview)
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Gonzalo Rojas Costa
Sent: Monday, January 20, 2025 7:12 AM
To: freesurfer@nmr.mgh.harvard.e
Hi Tania
I believe (Benjamin can confirm) that the SynthSeg label outputs are the same
as the aparc+aseg.mgz that recon-all creates. This is the combination of the
whole brain segmentation labels in aseg.mgz with the parcellation labels in the
aparc.annot file (the Desikan-Killiany atlas)
Chee
Hi Allison
No, we generate individual level subject statistics but don’t have a normative
database to compare to (since it would depend on your acquisition type and what
pathology you were interested in)
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of allio34...@aol.co
...@hms.harvard.edu<mailto:elisabetta_de...@hms.harvard.edu>
...e il mio cuore rise...
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Fi
Hello FS List
I'm sending the following letter:
https://docs.google.com/document/d/1pie-bVZHm_iQneZrfkGKX8hiRXLuIJy6CvuXjcnQJJE/edit?usp=sharing
to the Boston Globe. Anyone in the US that wants to sign it is welcome to paste
their signature in at the end. IMO if your immigration status is vulne
Hi Hengameh
What does the pial surface look like in the volume? If it is grabbing dura you
would erase it and rerun part of recon-all.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of hmarz...@student.ubc.ca
Sent: Thursday, March 13, 2025 7:47 PM
To: freesurfer@nmr.mgh.h
subjects
with this issue), do you think adding T2w to recon-all might help resolve it?
Thank you!
Hengameh
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Fischl, Bruce R.,PHD
Sent: March 13, 2025 4:49 PM
To: Freesurfer support list
Subject: Re
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