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
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
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
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
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
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>
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
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
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
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
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
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 Shahar
Can you look at the input to that step? Usually it means something prior has
gone wrong (like the skull stripping remove the entire brain or something). And
maybe post a couple of images of the processing (the orig.mgz, the T1.mgz, the
brainmask.mgz, …)
Cheers
Bruce
From: freesurfer
: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Fischl, Bruce R.,PHD
Sent: Thursday, April 11, 2024 15:50
To: Freesurfer support list
Subject: Re: [Freesurfer] surface-based filtering
Hi Jiaen
I’m not sure what you mean by “stacked smoothing”. I think the N in nsmooth is
the number of
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: Thursday, April 11, 2024 14:24
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subjec
Yes, we support surface-based smoothing. Check out the help for mri_surf2surf
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Jiaen Liu
Sent: Thursday, April 11, 2024 2:14 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] surface-based filtering
Exter
issue, however, the same issue persisted. Thank
you for your help!
Best,
Salil
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,
Can you post some pictures? The norm.mgz, the wm.mgz, the lh.orig.nofix, the
aseg.mgz, that kind of thing? Something is badly wrong….
Bruce
On Apr 10, 2024, at 7:05 PM, Bhole, Salil wrote:
External Email - Use Caution
Hello,
I have tried to process this MRI a few times now and it a
What was your recon-all command line? You need to give it a directive (like
-all), otherwise it will just create a subject directory tree and put the
001.mgz in the orig dir
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Naama Zur
Sent: Sunday, March 17, 2024 5:13 PM
T
I guess if nothing else you can cite the 2012 FreeSurfer paper
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Shounak Nandi
Sent: Monday, March 4, 2024 2:50 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Citing the bert dataset
External Email - Use Caution
Hi,
gray matter ratio
: lh.w-g.pct and rh.w-g.pct and I have a file for the white matter so I think I
may be able to create a code to calculate the gray matter.
On Wed, Feb 21, 2024 at 7:21 PM Fischl, Bruce R.,PHD
mailto:bfis...@mgh.harvard.edu>> wrote:
I think that is exactly one of the outp
Of ERNEST KISSI
Sent: Wednesday, February 21, 2024 11:14 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Grey Matter Intensities
External Email - Use Caution
Yes, please
That's exactly what I mean.
On Wed, Feb 21, 2024, 6:44 PM Fischl, Bruce R.,PHD
mailto
Can you clarify what you mean by “measure the intensities for the grey matter
regions”? You could for example compute the mean gray matter intensity within
each cortical parcel and each subcortical structure. Is that what you want?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of ERNE
You can try
mri_compute_volume_fractions
USAGE: mri_compute_volume_fractions
--o outstem : output will be outstem.{cortex,subcort_gm,wm,csf}.mgz
--reg regfile : can be LTA or reg.dat (if reg.dat, then need template volume)
--regheader subject
.
.
.
Which should output a multi-frame MG
Hi Linn
The text you cite is how we measure it. It is the signed distance each points
moves to get from the white to the inflated surface, where outwards movement is
positive (along the surface normal direction) and inwards distance is negative.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.ha
Hi Melissa
mris_euler_number
writes out a bunch of stuff, including the Euler number:
mris_euler_number ~/links/subjects/bruce.dev/surf/lh.orig.nofix
euler # = v-e+f = 2g-2: 154526 - 463668 + 309112 = -30 --> 16 holes
F =2V-4: 309112 != 309052-4 (-64)
2E=3F:9273
d the command I copied in the last email, but we are not sure if
it was the right one, because we see the name Talairah (see screenshot, on the
right bottom).
I hope my explanation makes sense to you.
Best regards,
Anna
____
From: Fischl, Bruce R.,PHD
mailto:bfis...@
Hi Ernest
Take a look at mri_segstats. I think it should do what you want (and it has an
extensive help with examples, thanks to Doug)
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of ERNEST KISSI
Sent: Thursday, January 25, 2024 11:31 AM
To: Freesurfer support list
Sub
Hi Abeoseh
You need to take a look at the output and see what is causing the large defect.
It is usually something like a big piece of skull left around.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Flemister, Abeoseh B.
Sent: Thursday, January 25, 2024 10:33 AM
To:
It is whatever volume you gave as input to recon-all. If you tell us which
statistics you want to regenerate for another volume we can tell you know what
commands to run.
cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of ERNEST KISSI
Sent: Wednesday, January 24, 2024 9:05
with MRIread, regardless of
the orientation?
---
Thank you all again!
Best,
Panos
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
I agree with Eugenio - it doesn't do any resampling. Just reads in the data as
is
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Huang, Yujing
Sent: Tuesday, January 23, 2024 8:49 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] MRIread and RAS orientation
I'm
time series should be
pretty straightforward if that is what you want (although Doug will know the
commands better than I do)
Cheers
Bruce
From: Arkhipova Anna, MUDr.
Sent: Friday, January 19, 2024 10:08 AM
To: Fischl, Bruce R.,PHD ;
Freesurfer@nmr.mgh.harvard.edu; fischl
Cc: phlus...@up
A T1-weighted FLASH should work. When you say “it did not work” what do you
mean? Can you give us some details?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of ERNEST KISSI
Sent: Thursday, January 11, 2024 3:54 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer]
Do you acquire any other scans, like an mprage, in the same session? If so, the
easiest thing to do would be to push that through our recon-all pipeline, then
register your MPF images to either the mprage or to surfaces using bbregister
and you can transfer whatever parcellations/segmentations y
Hi Anna
Parcellation is more than just format conversion - you need to map it onto the
details of an individual subject's anatomy. In addition, the DKT atlas is only
cortical. If you want subcortical regions in addition you should run recon-all
as it will produce both.
Cheers
Bruce
From: Arkh
Hi Yunus
The ones with “pial” in them are from the pial surface for things like
curvature and surface area, the ones without are from the white surface. The
rest of the name indicates which cortical parcellation the statistics are
summarized in (e.g. the lh.aparc.pial.stats contains statistics
Hi Mudathir
No particular rationale. It is configurable if you want more/less
Cheers
Bruce
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of FMU
Sent: Thursday, December 14, 2023 5:25 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] The Corpus Call
to the subjects' native surfaces. This
should ensure that the parcellations for all subjects are generated in the same
way, right?
Many thanks again!
Best,
Leo
Em dom., 10 de set. de 2023 às 15:55, Fischl, Bruce R.,PHD
mailto:bfis...@mgh.harvard.edu>> escreveu:
External
ntion!
Best,
Leo
Em dom., 10 de set. de 2023 às 14:19, Fischl, Bruce R.,PHD
mailto:bfis...@mgh.harvard.edu>> escreveu:
External Email - Use Caution
Actually there is a whole Bayesian segmentation on the surface procedure that
generates the individual subject parcellation so it definite
External Email - Use Caution
Actually there is a whole Bayesian segmentation on the surface procedure that
generates the individual subject parcellation so it definitely won’t be the
same as just mapping fsaverage
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On B
External Email - Use Caution
Hi Sebastien
Do you know why they don't align in RAS coords? That seems a bit worrisome to
me. I think you can try what you are suggesting easily enough in matlab or
python. Read both in, replace the header in one with the header of the other
then s
External Email - Use Caution
This happens in one case or in all 292? You should follow the processing stream
backwards to see where things first went wrong. It could be the skull
stripping, but it might also be one of the inputs to it is already incorrect
like the T1.mgz or tra
External Email - Use Caution
Hi Haley
I'm not sure I understand how you ran SynthSeg in matlab, but we supply .m
files for reading/writing volumes (MRIread and MRIwrite). You probably want to
read in the existing aseg to get the header, then replace the data with the
segmentati
External Email - Use Caution
Hi Jason
There are morphological tools built into freeview, so you could select a single
vertex, make a label from it, then dilate it as many times as you want. That
will of course give you the graph distance not the actual surface geodesic, but
mig
External Email - Use Caution
Don’t you want a surface to print, not a volume? What would printing the
aseg/aparc mean?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Magang Visa
Sent: Tuesday, August 15, 2023 8:20 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Frees
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
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
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
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
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
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
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 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,
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
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 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
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 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
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
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
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
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
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
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
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
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
: 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>
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
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
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 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 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
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
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
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
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
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
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
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,
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
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
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
>
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
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
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
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
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
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
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 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_
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 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 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
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 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@
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 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 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 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.
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