Hi Bruno
it looks to me like there is very little gray/white contrast, which is
the root of your problem. YOu could try limiting the intensity ranges in
the segmentation and surface deformation steps using expert options (e.g.
-wlo for mri_segment). We can also help improve the acquisition. If
Hi Adam
the most common metric would involve doing a manual stripping, usually of
a T2. Note that in FS we designed it using a risk-minimization approach
that weighs removing brain as much more costly (~10x I think) then leaving
around skull.
cheers
Bruce
On Mon, 17 Feb 2020, Adam Rytina wr
Hi Kirill
I think this is a question for Matti (now ccd)
cheers
Bruce
On Fri, 14 Feb 2020, Kirill
Elin wrote:
External Email - Use Caution
Hallo everybody,
I am not entirely sure whether this is FreeSurfer error actually.
I am doing first recon all which completes without e
Hi Ben
you need to rerun autorecon3 also otherwise some of the results will be
new and some old and the surfaces/overlays (like thickness) will be
inconsistent
cheers
Bruce
On Wed, 12 Feb 2020, Benjamin Ineichen wrote:
External Email - Use Caution
Dear Freesurfer experts,
Hi Adam
yes, mri_robust_register should do the trick. You will need to specify
--affine as rigid is the default
cheers
Bruce
On Fri, 7 Feb 2020, Adam Rytina
wrote:
External Email - Use Caution
Hello all, I need to perform an affine registration between two input
images. P
Hi Tim
if you upload the input files to mri_deface and the full command line
I'll take a look. Is this the dev version you are using?
cheers
Bruce
On Mon, 3 Feb 2020,
Tim Schäfer wrote:
External Email - Use Caution
Dear FreeSurfer experts,
I am running mri_deface for all relevant
Hi Monica
sure, if you tar and gzip the entire subject dir and ftp it to us, then
send us a description that includes the voxel coords of where you think
things should be more accurate we will take a look
cheers
Bruce
On Fri, 31 Jan 2020,
Monica Bondy wrote:
External Email - Use
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Bruce Fischl
Sent: Tuesday, January 28, 2020 3:37 PM
To: Freesurfer support list
Cc: Greve, Douglas N.,Ph.D.
Subject: Re: [Freesurfer] recon-all errors - mri_segstats and
mri_relabel_hypointensities
Hi Devika
these types of huge defects usually mean something dramatic has gone
wrong with e.g. the skull stripping. Even if it completes it is unlikely
to generate accurate surfaces. Check the ?h.inflated.nofix and
?h.orig.nofix over the wm.mgz and you will likely find the issue quicky
cheers
Hi Paul
yes, the -mprage flag could definitely cause what you are seeing. It
assume higher CNR and lower SNR in the images (hence bigger class
separation between gray and white), and if used on SPGR it could
definitely erode boundaries like this.
cheers
Bruce
On Fri, 31 Jan 2020, Wright, Pau
Hi Philipp
does this happen for all the FS executables? What kind of machine are you
trying it from and who installed it? Sounds like you are on a mac and
maybe trying to use a version installed for a different kind of computer
cheers
Bruce
On Thu, 30 Jan 2020, Philipp Barzyk
wrote:
Hi Devika
the very large defects can take a very long time to fix, and probably
won't produce good results. They are typically caused by something
significant going wrong - large portions of the skull left behind and
connected to the surface, an incorrect aseg, that kind of thing. You should
Hi Laurel
if a subject dir already exists recon-all will exit unless you specify
-force. Alternatively you can try using the -make all flag, which should
rerun only the steps that are needed (assuming the reboot didn't happen
e.g. in the middle of writing a file)
cheers
Bruce
On Tue, 28 Jan
Hi Louise
1. All the spatial, distributional and markov info we detailed in our
methods paper (priors at each point, markov priors in principal directions
and means and variances of geometry, all stored per label
2. It is on the surface/sphere.
3. Not trivially, but the code is open source
, so this is very helpful.
All the best,
Tim
--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
On January 21, 2020 at 11:02 PM Bruce
Hi Antonin and Tim
you should be able to do:
setenv FS_SKIP_TAGS 1
mri_convert vol_with_tags.mgz vol_without_tags.mgz
and verify it worked with mri_info
cheers
Bruce
On Tue, 21 Jan 2020, Antonin Skoch wrote:
External Email - Use Caution
Hi, Tim,
the subject ID can be also c
Hi Rafael
the ?h.curv files are spatially smoothed mean curvature
cheers
Bruce
On Tue, 21 Jan
2020, Raffaele Dubbioso wrote:
External Email - Use Caution
Hello FS team,
can you please tell me what is the measurement scale of the curv.mg file?
Is it a mean curvature (mm-1)
2. registration of dwi images (Sam W)
3. Re: registration of dwi images (Yendiki, Anastasia)
4. Project hippocampus to inflated 3D model? (Mohammad
Rashid)
5. Re: aparcstats2table error (Devika K)
6. Re: Project hippocampus to inflated 3D model? (Bruce
Hi Devika
In the future can you include the text of the command and the output in
your email instead of a screenshot? That will make our job easier.
Try specifying which subjects you want processed explicitly with
--subjects
cheers
Bruce
On Sun, 19 Jan
2020, Devika K wrote:
Ex
Hi Mohammad
you can use mri_tessellate or mri_mc to build a mesh model of the
hippocampus from the aseg if you want, then use mris_inflate on it. You
will lose internal structure though.
cheers
Bruce
On Sun, 19 Jan 2020, Mohammad Rashid
wrote:
External Email - Use Caution
Hi Marina
how did you create your average inflated surface? mris_inflate typically
normalizes the scale of the inflated surface to have the same total
surface area as the input surface (so for the less-folded inflated
surface it has to become bigger). I guess you could try running it
directly
Hi Karel
you can specify a label to mris_anatomical_stats with the -l option
cheers
Bruce
On Fri,
17 Jan 2020, Karel Mauricio Lopez Vilaret wrote:
External Email - Use Caution
Dear Freesurfer team,
I would like to get the thickness values of a specific ROI (volume mask).
Hi Marina
for the lower res fsaverage subjects you probably want to decrease the
number of iterations of the inflation. For fsaverage6 you could try:
mris_inflate -n 5 lh.smoothwm lh.inflated.new
it should be just a min or two so you can try different values for the -n
switch
cheers
Bruce
if the gray matter you are interested looks ok then you should be fine
Bruce
On
Tue, 14 Jan 2020, Rachel Hoel wrote:
External Email - Use Caution
Thank you, I am still checking in with my supervisors about sending the
subject. For now, if we are only interested in looking at
set of bias corrected images
(probably using ANTs). The plan is to extract regional and whole brain
volumes for these T1-weighted images.
Regards
Patrick
On Tuesday, January 14, 2020, 6:45:20 AM GMT+5:30, Bruce Fischl
wrote:
I agree with Matt. We do multiple stages of bias correection to
I agree with Matt. We do multiple stages of bias correection to flatten
things out as much as possible. Can you give us an idea of what you are
trying to achieve?
On Mon, 13 Jan 2020, Glasser, Matthew wrote:
External Email - Use Caution
Why do you want to do that? FreeSurfe
Hi Meike
can you send us some images? And what volume are the intensity values
around 73 for white matter? That is way to low for the norm.mgz or the
brain*.mgz
cheers
Bruce
On Fri, 10 Jan 2020, Meike Hettwer wrote:
>External Email - Use Caution
>
> Hi everyone,
>
> I am currently work
Hi Laurel
yes, I think that is the way to go, but it's hard to tell for sure only
looking at one slice.
cheers
Bruce
On Thu, 9 Jan 2020, Laurel Quinlan wrote:
External Email - Use Caution
Hi FS Support,
I am working on manual edits to a brain with a suspected cyst. Attache
Hi Marina
how do you project to fsaverage5?
cheers
Bruce
On Wed, 8 Jan 2020, Marina Fernández wrote:
External Email - Use Caution
Dear Freesurfer experts,
I would like to convert the individual preprocessed EPI volume (that it is
normalized to MNI152 space and without smoothin
Hi Joe
do you know what the forward model for VIBE is? mri_ms_fitparms uses the
FLASH forward model of image formation then does a max likelihood
estimation of the T1/T2*/PD using that model. If VIBE is a different model
then it certainly won't work.
cheers
Bruce
On Sun, 5 Jan 2020, joe va
no, and it isn't inflation, strictly speaking. The spherical mapping
minimizes metric distortion, which to us is more neuroscientifically
plausible. The conformal maps minimize (local) angular distortion and
push all the distortion into area compression and expansion. Metric
distortion minimize
Hi Sudhakar
if you want us to help you we will need a lot more information. What
exact command did you run? What was the entire screen output? What kind
of computer are you running it on? That kind of thing
cheers
Bruce
On Sat, 4 Jan 2020,
sudhakar Mishra wrote:
External Email -
on-all -s {.} -i {} -all -qcache", after installing Xcode and
Homebrew.) But I couldn't find any similar information on the Linux
platform.
Regards
Frank
On Jan 3, 2020 11:15 PM, Bruce Fischl wrote:
Hi Frank
do you mean completing a single recon faster? The easiest way to
Hi Frank
do you mean completing a single recon faster? The easiest way to do that
is to use the -openmp flag, and set to the number of
threads/cores you want to use. Alternatively if you have enough RAM you
can just run multiple recon-alls at the same time (which will give you a
bigger effe
no, sorry, it is not
cheers
Bruce
On Thu, 2 Jan 2020, Fatemeh Ahmadi wrote:
External Email - Use Caution
Dear all,
I'm working on brain surface with conformal geometry algorithms, I need to
know whether triangular mesh that gets from "recon-all" in Freesurfer is a
Delaunay tria
using Winrar and renamed it subject-0001.mgh and this time it showed this
>> error:
>> ERROR: could not open C:\Users\home\Desktop\Project
>> code\QuickNATv2\SampleDatasample-0001.mgh for reading
>> ERROR: loading C:\Users\home\Desktop\Project
>> code\QuickNATv2\Sampl
Hi Mahdi
can you run mri_info in a Linux shell on that file and send us the entire
screen output?
cheers
Bruce
On Sun, 29 Dec 2019, mahdi mahdavi wrote:
External Email - Use Caution
Hi. I'm a medical student and I'm trying to use the QuickNATv2 MATLAB code for
structural MR
Hi Zhang
1. the aseg.stats should contains statistics on intensities in various
structures.
2. Do you want a surface or a measurement at each point? If you want a
surface use mris_expand, if just a measure use mri_vol2surf with a
projfrac of 0.5
cheers
Bruce
On Sun, 29 Dec 2019, a Chines
Hi Tamir
you can use mri_binarize --match or mri_extract_labels.
cheers
Bruce
On Fri, 27 Dec 2019,
Tamir Eisenstein wrote:
External Email - Use Caution
Dear FS experts,
How can I create a binary mask of the lateral ventricles based on the ASEG
output?
Thanks!
Tamir
___
Hi Sarah
I'm not sure I understand. The smoothing doesn't really matter as the BAs
reflect the location along the cortical sheet in spherical coordinates
cheers
Bruce
On
Sun, 29 Dec 2019, sarah.kloep...@web.de wrote:
External Email - Use Caution
Hi,
Do the Brodmann par
gards
Nader
Neuroimaging phd student
On 21 Dec 2019 18:36, "Bruce Fischl" wrote:
sorry, can you clarify what you mean? Isn't the attachment
already a
saved output of freeview? I don't understand what you are trying
to do
cheers
Bruce
sorry, can you clarify what you mean? Isn't the attachment already a
saved output of freeview? I don't understand what you are trying to do
cheers
Bruce
On
Sat, 21 Dec 2019, Nader Razmara wrote:
External Email - Use Caution
Dear I want to save output of freeview as attach f
Bruce,
Thanks for the info. Can the tool display the vertexes with low G/W
contrast? I would like to use those vertexes as a guide for visual
evaluation.
Cheers,
Yawu
Bruce Fischl 于 2019年12月19日周四 16:52写道:
Hi Yawu
we have tools for mapping G/W contrast and CNR, but of course
that
Hi Yawu
we have tools for mapping G/W contrast and CNR, but of course that
presupposes that our surfaces are in the correct location (more or less).
You can for example use vol2surf to sample at negative and positive
proj_dist and compute this kind of thing, or I believe Doug has some
binarie
Hi Cody
not sure we have a binary for this, but it would be about 5 lines of
matlab code
cheers
Bruce
On Thu, 19 Dec 2019, cody samth wrote:
External Email - Use Caution
Hi,
I was wondering if there is any automated command/method to create a new
label that consists of the
Hi Marina
yes, mri_vol2surf will sample volumes onto the surface. You will need to
register them first (we typically use Doug Greve's bbregister for this).
What preprocessing did you do? For cortical data we don't recommend
smoothing in the volume - you are much better off sampling to the surf
sorry, my fault. That was for someone else
On Mon, 16 Dec 2019, Boris
Rauchmann wrote:
External Email - Use Caution
This is the log when I´m creating this file:
Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_ca_label
$SUBJECTS_DIR/1122/mri/brain.mgz
$SUBJECTS_DIR/1122/mri
to summarize, I want a warp that:
foreach subject
compute warp based on curvature
apply warp to a functional overlay
add that functional overlay to avg
return (tf.reduce_mean(tf.square(avg)))
make sense? So maximizing the mean squared average acivation
On Mon, 16 Dec 2019, Boris Rau
Hi Yuanyuan
this is really more of a batch processing/shell scripting question than a
FreeSurfer one. Something like (in tcsh)
set SUBJECTS = (N001 N002...)
foreach s ($SUBJECTS)
mris_anatomical_stats -l lh.precentral.label -t lh.thickness -b \
-f $s/stats/lh.precentra
Hi Monica
hmmm, hard to say without seeing the dataset. You could try using expert
options to change some of the intensity thresholds if this is something
specific to your acquiisition. If you upload the gzipped subject dir we
will take a look
cheers
Bruce
On Fri, 13 Dec 2019, Monica Bondy
Hi Sparsh
probably easiest to do with a surface, but I defer to Ruopeng
cheers
Bruce
On Fri, 13 Dec
2019, Sparsh Jain wrote:
External Email - Use Caution
Hi!
Can I create a brain volume with about 40% opacity and save it as a matlab
figure? The volume may not be
very accur
Hi Ricardo
hmmm, the fact that it says "MRImaskDifferentGeometry" suggests that your
skull stripping didn't end up "conforming", which is probably the error.
Try something like:
cp brainmask.mgz brainmask.bet.mgz
mri_convert -rl orig.mgz brainmask.bet.mgz brainmask.mgz
then rerun and see if
Hi Tim
mris_expand -thickness ...
should do the trick. If you specify -thickness it will read in the
?h.thickness file and interpret the argument as a percentage of
thickness, which is what you want I think
cheers
Bruce
On Thu, 12 Dec 2019, Tim Schäfer wrote:
External Email - Us
Hi Boris
can you send us the full command line and screen output of the commands
that are failing?
cheers
Bruce
On Thu, 12 Dec
2019, Boris Rauchmann wrote:
External Email - Use Caution
Thanks. unfortunately I get an error message when I use the --aseg flag for
BN_Atlas_s
AM Bruce Fischl wrote:
Does your 3D model need to be topologically correct? What are you trying
to achieve? And are the holes/handles due to the tumor? Can you send us
some images?
cheers
Bruce
On Tue, 10 Dec 2019, Kong Chuizheng wrote
ill in the tumor do you mean adding the hollow part of the
brain in wm.mgz?
Best,
Chuizheng Kong
On Dec 10, 2019, at 12:07 PM, Bruce Fischl
wrote:
have you looked at our tutorial on topology fixing? I would try that
first. You might need
to fill in the tumor in the wm.mgz.
n Tue, Dec 10, 2019 at 8:58 AM Bruce Fischl wrote:
Does your 3D model need to be topologically correct? What are you trying
to achieve? And are the holes/handles due to the tumor? Can you send us
some images?
cheers
Bruce
On Tue, 10 Dec 2019, Kong Chuizheng
Does your 3D model need to be topologically correct? What are you trying
to achieve? And are the holes/handles due to the tumor? Can you send us
some images?
cheers
Bruce
On Tue, 10 Dec 2019, Kong Chuizheng wrote:
External Email - Use Caution
Hello Freesurfer Developers,
Hi Fredrik
yes, the subcortical segmentation can still be ok when the cortical
stream results are not that good
cheers
Bruce
On Tue, 10 Dec 2019, Fredrik wrote:
External Email - Use Caution
Hi FreeSurfer experts,
In our data, we have a sample of older people with brain
Hi Zhang
look at the docs for mri_vol2surf. In particular, check out the various
--proj* options like projfrac and projdist
cheers
Bruce
On Tue, 10 Dec 2019, a Chinese
reader wrote:
External Email - Use Caution
Dear Freesurfer experts,
I have some questions about intensit
can you check to see if there is a large defect that is too big to fix? You
should be able to see this in the log file or by checking the output of the
job it is waiting for (PID 175414)
On Tue, 10 Dec 2019, Gwang-Won Kim wrote:
External Email - Use Caution
Hi there,
I tr
s gray/white
matter that should be
> included in the pial line?
>
> Thanks!
>
> -Laurel
>
>
>___
_
> From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of
Bruce
> Fi
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Bruce
Fischl
Sent: Tuesday, December 3, 2019 11:57 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] topological defect error
it might also be the hemispheres not being separated, hard to tell
(although that almost never happens)
Hi Laurel
yes, the lh.orig.nofix is created using the control points and other
things, and so the number of holes in it will definitely change if the
placement of control points changes
cheers
Bruce
On Thu, 5 Dec 2019, Laurel Quinlan
wrote:
External Email - Use Caution
H
it might also be the hemispheres not being separated, hard to tell
(although that almost never happens). You can look at the filled.mgz to
check this (the hemis should have different labels)
On Tue, 3 Dec 2019,
Greve, Douglas N.,Ph.D. wrote:
Look at the lh.orig.nofix and see if you can find t
Hi Jordi
yes, this should be possible. You might need to run recon-all in stages
though. Although if you set the wm.mgz values from SPM to 255 and 1 (not 0)
recon-all should detect them as "edits" and retain them
cheers
Bruce
On Tue, 26 Nov 2019, Jordi Huguet wrote:
External Emai
Hi Tashrif
yes, because then you can just run it by itself (as opposed to part of one
of the -autorecon targets)
cheers
Bruce
On Mon, 25 Nov 2019, Billah, Tashrif wrote:
> Hi Bruce,
>
> Thanks for your reply. But then we wouldn't need a -skullstrip option again
> given it's on my
> default,
Hi Tashrif
in case you have data in which the skull has already been stripped. Yes,
it is on by default
cheers
Bruce
On Mon, 25 Nov 2019, Billah, Tashrif wrote:
>
> With recon-all, is
> [-skullstrip](https://surfer.nmr.mgh.harvard.edu/fswiki/skullstrip) option
> set by
> default?
>
> I am t
it's not delicate - it's just confusing for us when you use it as it
refers to a specific dataset
cheers
Bruce
On Mon, 18 Nov 2019, An wrote:
External Email - Use Caution
Sorry for the confusion, I don't know it has a delicated meaning. I just
followed the steps on the
frees
sorry, I don't understand what your question is. What are you trying to do?
Convert every dicom series in the directory? Convert a single series?
On Sun, 17 Nov 2019,
sudhakar Mishra wrote:
External Email - Use Caution
Hi,
Sorry for the late reply.
As I was asked the questi
Hi Adam
we do multiple different bias corrections - nu_correct, plus two of our
own (mri_ca_normalize and mri_normalize). Is there a reason you don't
want to just let recon-all run them in the way it usually does?
cheers
Bruce
On Fri, 15
Nov 2019, Adam Rytina wrote:
External Emai
Hi Yang
the size of the smoothing kernel depends on the size of the effect you are
looking for (this is called the matched filter theorem), so there is no
general smoothing size that is appropriate. We smooth a bit by default for
visualization purposes, but you can pick any smoothing size you
Hi Dalton
you need to give us a lot more information. What command did you run?
What was the full output?
cheers
Bruce
On Wed, 13 Nov 2019, Dalton Bermudez wrote:
External Email - Use Caution
-- Forwarded message -
From: Dalton Bermudez
Date: Wed, Nov 13,
mer
>
>
> From: "Greve, Douglas N.,Ph.D."
> To: "freesurfer"
> Sent: Tuesday, November 12, 2019 4:46:49 PM
> Subject: Re: [Freesurfer] Recon all hard failure,
>
> And before that you should check the orig and white surfaces
>
> On 11/12/
Hi Vicente
I'm not sure what the images are showing - maybe the inflated surface?
That isn't useful to look at in the volume. You should check the
inflated.nofix surface and see if something big is wrong (cerebellum or
skull attached, that kind of thing). There is a tutorial on our wiki for
co
Hi Larissa
I think we need more details. What do you mean you used 6 for anatomical
ROI analysis? On the same subjects? Did you rerun them?
Sorry, I can't figure out exactly what you are doing
cheers
Bruce
On Fri, 8
Nov 2019, Larissa Bechtle wrote:
>External Email - Use Caution
>
> He
or start by sending us the recon-all.log from the two runs
On Fri, 8 Nov
2019, Chen, Christine wrote:
External Email - Use Caution
Hello,
My lab has been running T1 (MPRAGE) data through run_subject (uses recon-all,
autorecon, mris_volume
and mris_wm_volume) then through
Hi Christine
maybe you can tar and gzip a subject that has been run twice with
different results and file drop it or ftp it to us?
cheers
Bruce
On Fri, 8 Nov 2019,
Chen, Christine wrote:
External Email - Use Caution
Hello,
My lab has been running T1 (MPRAGE) data thro
Hi Mona
that is pretty strange looking. Is the data somewhere local that we can
take a look at it? I would guess that one of the cuts left a connection
around, but would need to look at it to tell. Have you flattened other
subjects successfully?
cheers
Bruce
On Fri, 8 Nov 2019, Nasiriavana
>> On Thu, Nov 7, 2019 at 4:41 PM Bruce Fischl
>> wrote:
>> hmmm, does it always happen for this subject? What if you don't use
>> -parallel?
>> On Thu, 7 Nov 2019, Emanuel Alvaredo wrote:
>>
>> >
>> > External Email - Use Caution
know why.
Thanks in advance
Emanuel
On Wed, Oct 30, 2019 at 10:51 AM Bruce Fischl
wrote:
Hi Emanuel
can you give us more details. What was your command line? What was the
full job output? What is in the recon-all.log? Does this happen if you
run directly instead of th
Hi Fernando
it is a volume after resampling to 1mm isotropic, 8 bits/voxel and 256^3
cheers
Bruce
On
Thu, 7 Nov 2019, Fernando Castellano wrote:
External Email - Use Caution
good afternoon,
I am using freesurfer for my thesis in image technician.
I would like to know specif
Hi Mike
our license lets you do pretty much whatever you want :). That said, the
recon pipeline is complex and it isn't so easy to pick and choose steps,
although I guess if you are just processing already datasets that have
already been run through recon-all it should be pretty straightforwar
Hi Emanuel
can you give us more details. What was your command line? What was the
full job output? What is in the recon-all.log? Does this happen if you
run directly instead of through some type of batch server?
cheers
Bruce
On Wed, 30 Oct
2019, Emanuel Alvaredo wrote:
External E
fer.
Thanks,
Vinny
On Sat, Oct 19, 2019 at 12:16 PM Bruce Fischl
wrote:
Hi Vinny
why do you need to brain structures from MNI space? Isn't the
aseg
sufficient? Or are there structures that are not in the aseg?
cheers
Bruce
On Sat, 19 Oct
Hi Vinny
why do you need to brain structures from MNI space? Isn't the aseg
sufficient? Or are there structures that are not in the aseg?
cheers
Bruce
On Sat, 19 Oct
2019, Vinny K wrote:
External Email - Use Caution
Hi,
FreeSurfer does a great job in registering atlas str
Hi Asim
can you give us a bit more information? Where does the brainmask come
from? I believe we should detect the fact that the brainmask.mgz is
different than the automatically created one (brainmask.auto.mgz) and use
it instead. Note that the recon editing mode in freeview sets erased voxel
or pretty much any mailing list email - they should all come with an
"unsubscribe" link
On Thu, 17 Oct 2019, Damion V Demeter wrote:
External Email - Use Caution
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Check the bottom of the page you used to sign up. :)
Da: freesurfer-boun...@nmr.mgh.harvard.edu
per conto di Bruce Fischl
Inviato: mercoledì 16 ottobre 2019 17:58
A: Freesurfer support list
Oggetto: Re: [Freesurfer] R: R: R: recon-all skull stripping
Hi Marianna
I think you can just run recon-all -s -skullstrip and it will
question is: does
recon-all add optional flagged arguments to this function while running
recon-all? and which of them?
Thank you.
BW
Marianna
Da: freesurfer-boun...@nmr.mgh.harvard.edu
per conto di Bruce Fischl
Inviato
...@nmr.mgh.harvard.edu
On Behalf Of Bruce Fischl
Sent: Wednesday, October 16, 2019 12:48 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] R: R: recon-all skull stripping
oh, sure, you can just run that part of recon-all. You don't need to rerun the
whole thing cheers Bruce On Wed, 1
ianna
Da: freesurfer-boun...@nmr.mgh.harvard.edu
per conto di Bruce Fischl
Inviato: mercoledì 16 ottobre 2019 17:40
A: Freesurfer support list
Oggetto: Re: [Freesurfer] R: recon-all skull stripping
Hi Marianna
I'm not sure wha
s recon-all.
BW
Marianna
Da: freesurfer-boun...@nmr.mgh.harvard.edu
per conto di Bruce Fischl
Inviato: mercoledì 16 ottobre 2019 17:23
A: Freesurfer support list
Oggetto: Re: [Freesurfer] recon-all skull stripping
Hi Marianna
the skull stripping is a hybrid procedure that uses both
Hi Marianna
the skull stripping is a hybrid procedure that uses both a watershed
algorithm and a deformable surface. There is no single intensity threshold
in it. Maybe I'm misunderstanding your question? There are parameters you
can change (for example the preflooding height), but there is no
Hi Xiaoqian
it's pretty hard to tell what's going on from these images. If you tar/gzip
your whole subject dir and upload it with an email telling us the specific
voxel coords that you want us to examine
cheers
Bruce
On Wed, 16 Oct 2019, Xiaoqian Yan wrote:
External Email - Use C
Hi Asim
if you edited the brainmask in recon-mode in freeview the edits will be
detected and retained.
cheers
Bruce
On Mon, 14 Oct 2019, Asim Hassan wrote:
External Email - Use Caution
Good afternoon,
I would like to know is there a way to run recon-all on subjects in whi
Hi Sara
we will need to know the actual commands and the screen output from them
that you ran
cheers
Bruce
On Mon, 14 Oct 2019, Sims, Sara A (Campus) wrote:
External Email - Use Caution
Freesurfers,
I am trying to use mri_mask using surface overlays. I made a label into a
Hi Ezequiel
-noscale 1 works in most cases, but here the analyze file itself specifies
a scalling that is done as part of the reading process. If you want to
disable it try (in tcsh):
setenv FS_ANALYZE_NO_RESCALE 1
then run mri_convert as before. You should see an addition printout in the
o
Hi James
I think the -lh/-rh flags are for processing single (ex vivo) hemis, not
for only processing one hemi in a whole-brain image. If you want to erase
the hemi with the tumor it will probably work
cheers
Bruce
On Wed, 9 Oct 2019, 王子谦
wrote:
External Email - Use Caution
meaning you have to give recon-all the -all switch so it can create
things like the lh.white surface
cheers
Bruce
On Mon, 7 Oct 2019, Greve, Douglas N.,Ph.D.
wrote:
You can to run the full recon-all on a given subject's data, and it will
create the broadmann areas
On 10/5/2019 1:31 AM, sang
101 - 200 of 9695 matches
Mail list logo