...@nmr.mgh.harvard.edu
On Behalf Of Rosalia Dacosta Aguayo
Sent: Wednesday, July 21, 2021 10:49 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Control points and white matter segmentation
External Email - Use Caution
Hi Bruce,
Thank you for answering my question.
But the
; Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Rosalia Dacosta
> Aguayo
> *Sent:* Wednesday, July 21, 2021 5:10 AM
> *To:* Freesurfer support list
> *Subject:* [Freesurfer] Control points and
21, 2021 5:10 AM
To: Freesurfer support list
Subject: [Freesurfer] Control points and white matter segmentation
External Email - Use Caution
Dear Freesurfer team,
Sorry for this basic question.
I wonder if once I have edited the white matter (topological defects), I can
run control
External Email - Use Caution
Dear Freesurfer team,
Sorry for this basic question.
I wonder if once I have edited the white matter (topological defects), I
can run control points without deleting what I have done to white matter
segmentation.
Kind regards,
Rosie
_
Hi Doro
it's hard to tell from your image, but it looks like at least one of your
cps is not in wm but in the gm. This will mess everything up. Make sure
that they are in unpartial-volumed wm
cheers
Bruce
On Tue, 3 Mar 2020, Meike Hettwer
wrote:
>External Email - Use Caution
>
> Dear
External Email - Use Caution
Dear Freesurfer Team,
I am currently performing manual edits using freesurfer v. 6.0.1. (on
Debian /Linux 7). While brainmask edits work perfectly, the control
points i set (mainly in temporal and frontopolar regions, running
recon-all -autorecon2-c
Instead of putting control points, you should edit the wm.mgz. BTW, it
looks like some of the control points were not fully in white matter,
which can be problematic.
On 5/14/19 2:27 PM, Rachel Hoel wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer Developers,
>
> We're still s
Hi Rachel
hmmm, what does the wm.mgz look like there? And the orig? If the wm.mgz
includes those voxels but the orig does not it is likely a topological
defect that was fixed incorrectly. If you can't find it, you can upload the
subject and we can take a look
cheers
Bruce
On Sat, 23 Feb
20
https://gate.nmr.mgh.harvard.edu/filedrop2/
Thanks,
Emma
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Arsenije Subotic
Sent: Thursday, February 1, 2018 5:54:20 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Control Points Not Working
Dear ex
Dear experts,
I’m currently performing quality control for my data, and most of my issues so
far have been that in many cases adding control points has not been able to
extend the white surface. I’ve also noticed that most of the regions where I
have needed to add CPs are in the parietal region
Hi Andrea
1. the control points don't need to go into locations that are
misclassified, just ones that the intensity is signifantly different from
(and usually less than) 110. They can be correctly segmented as WM.
2. Each control point changes things in a region so they can have a global
ef
Hi FreeSurfer experts,
I have some questions (maybe trivial) about Control Points editing.
1) Following the guide in your website and exploring your tutorial subject
"cp_before" I understood that a Control Point has to be placed in a region
that is definitely white matter but the standard recon-all
Hello Freesurfer, I played around with mri_normalize for control point section by changing the parameters using -b 20 or 23 and writing it in an expert file. However, when I ran recon-all -autorecon2-cp -autorecon3 -expert expert.opts, the command showed "mri_normalize - mprage -noconform ) se
Hi Andrea
our coordinate systems are documented here:
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
the control points are stored in RAS (either "surface ras" or "scanner ras"
depending on the header). By default it is "surface ras" (if not otherwise
specified at the top of the
Hi Freesurfer users!
We are performing such analysis on Matlab using cartesian coordinates of
the control points for the study of cortical thickness.
We have some problems to exactly localize control points from matlab
viewing to freview or tkmedit: if the localization in Matlab is fine, in
freevie
Hi Kiersten
at its heart it is a region-growing algorithm followed by soap bubble
smoothing. That is, the detected control points become fixed points in the
soap bubble (which amounts to iterative averaging of all the non-fixed
points). We use a Voronoi diagram to initialize the soap bubble fo
Hello,
I am new to using Freesurfer and am currently using it for a biomedical
image processing class. I am working on a project and would like to know
the image processing technique behind the Control Points function. Is it
region growing, or what other process?
Thanks for the help!
Kiersten
___
Hi P,
if you want to investigate the control.dat file you can do so with freeview
(File-> Load Point Set and choose the control.dat file). In the dev version of
Freeview there is an option to select a cp number or move through the list with
arrows. In the stable version, there is no box, but y
In the dev version of freeview, you can go to File ->Load Point set, and choose
the control point file (shoulb be /tmp/control.dat)
This allows you to flip through the points by entering the control point
number or using an arrow to go to the next/previous control point in the file.
This move
Hi,
On this page https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits it
mentions "it is recommended to check if all CPs are accurately placed in the
long."
I was wondering what is the best way to do this?
I know I can type in the RAS coordinates from the control.dat file and check
Hi Elissa
the control point can still have an effect if the brainmask.mgz intensity
is not 110. Please make sure that you aren't adding control points to gray
matter though - that will mess everything up!
Bruce
On Wed, 25 Jun 2014, Elissa McIntosh wrote:
> Hello freesurfer experts,
>
> I ha
Hi Victor
If you upload the subject we will take a look
Bruce
> On Jun 19, 2014, at 1:59 PM, Victor Kovac wrote:
>
> Hello,
>
> I have run recon-all on two timepoints of a subject (MPS1011-4 and
> MPS1011-5). I added control points to MPS1011-4 after the initial recon-all
> processing becaus
and how many do you see in the control.dat file? Sounds like they aren't
getting saved to disk somehow
On Mon, 7 Oct 2013, Francesco Siciliano
wrote:
> I counted at least 28 control points on the brainmask when I loaded the set
> and my log indicates that freesurfer read 22 control points.
I counted at least 28 control points on the brainmask when I loaded the set and
my log indicates that freesurfer read 22 control points. I've attached part of
the log below.
#@# Intensity Normalization2 Mon Sep 16 19:44:17 EDT 2013
/Users/jonathanposner/Desktop/AdultControls/diffusion_recon/615
>
> -Francesco
>
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, October 07, 2013 12:47 PM
> To: Francesco Siciliano
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] [FreeSurfer] control points
>
> Hi Francesc
urfer] control points
Hi Francesco
where do you save the file control.dat? It must be in the directory
$SUBJECTS_DIR/$subject/tmp/control.dat
otherwise recon-all won't find it
cheers
Bruce
On Mon, 7 Oct 2013, Francesco
Siciliano wrote:
> Hello,
> I am still having issues getting all of m
Hi Francesco
where do you save the file control.dat? It must be in the directory
$SUBJECTS_DIR/$subject/tmp/control.dat
otherwise recon-all won't find it
cheers
Bruce
On Mon, 7 Oct 2013, Francesco
Siciliano wrote:
> Hello,
> I am still having issues getting all of my control points to be ef
Hello,
I am still having issues getting all of my control points to be effective. When
I load my original point set (control.dat) and add control points to the set
(using the control points edit tool), the new control points are visible but
are not taken into account when I re-run recon-all (re
Uploaded look for CPsDon'tMatch. It's the subject directory so surfaces,
volumes, tmp folder with control.dat
jon
On Sep 25, 2013, at 2:34 PM, Jonathan Holt wrote:
> Yep, I'll upload to the ftp server.
> On Sep 25, 2013, at 2:28 PM, Ruopeng Wang wrote:
>
>> Would it be possible to send us th
Yep, I'll upload to the ftp server.
On Sep 25, 2013, at 2:28 PM, Ruopeng Wang wrote:
> Would it be possible to send us the volume and control point files?
>
> Thanks,
> Ruopeng
>
> On 09/25/2013 02:09 PM, Jonathan Holt wrote:
>> I've read in the mailing list archives people have had issues wit
Would it be possible to send us the volume and control point files?
Thanks,
Ruopeng
On 09/25/2013 02:09 PM, Jonathan Holt wrote:
> I've read in the mailing list archives people have had issues with tkmedit
> and free view displaying control points differently. For me the first brain
> I've load
I've read in the mailing list archives people have had issues with tkmedit and
free view displaying control points differently. For me the first brain I've
loaded up has a single control point in free view that does not show in
tkmedit. Others have complained of free view showing points seemingl
Hi list,
I've been creating control points and I got the following error:
MRIwriteControlPoints(/home/glerma/freesurfer/subjects/TNT/TNT_solosubs/S_11/tmp/control.dat):
could not open file
No such file or directory
I created the /tmp/ folder by hand and then it created the control.dat file
prope
Hello Bruce,
By creating new errors after adding cp, it usually leaves out a large
portion of cortex (and its white matter) that was originally correctly
identified in the first attempt. I have tried to add cp in areas that are
not in partial volume voxels. The version command says I am using:
$I
Hi Megan
it's hard for us to diagnose without seeing the details. In general
though you have to be careful to make sure that you aren't putting control
points in partial volumed voxels. When you say it creates new errors, can
you give us some details? Is the wm too bright in those regions? Wha
Hi,
I have been using freesurfer on a large dataset and I am having some trouble.
Sometimes the temporal lobes are not fully covered, so I will go back to add a
few control points based on the recommendations of freesurfer (voxels that are
<110 and not next to a gray matter voxel) and send it t
Hi Bruce,
Sorry for the multitude emails. I have attempted to upload via both FTP and
Martinos file drop. The martinos site keeps dropping out, and FTP is giving the
following error:
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd transfer/incoming
Great, thanks. Do you need the brainmask plus surf ?h orig and/or aparc/aseg?
Alana
On 17/01/2012, at 2:09 PM, Bruce Fischl wrote:
> Hmmm. If you upload the subject we will take a look
> Bruce
>
>
>
> On Jan 16, 2012, at 9:53 PM, Alana Shepherd
> wrote:
>
>> On the brainmask the intensity
Hmmm. If you upload the subject we will take a look
Bruce
On Jan 16, 2012, at 9:53 PM, Alana Shepherd wrote:
> On the brainmask the intensity within the STG wm is either slightly lower
> than 110 or slightly higher, though at the exact location of the control
> points it is 110. Similarly on
Hi Alana
Have you tried changing the skull strip parameters?
Cheers
Bruce
On Jan 16, 2012, at 6:33 PM, Alana Shepherd wrote:
> Hello,
> I am running version 5.0, and am finding in a few cases that some areas (most
> commonly STG) are missing from the original brainmask - after adding contro
Hello,
I am running version 5.0, and am finding in a few cases that some areas (most
commonly STG) are missing from the original brainmask - after adding control
points and re-running the pipeline, these regions are still not being picked up
in the surfs or in the aseg.
Can you suggest any other
Hi Tanja,
if you upload the subject we can take a look. Does the aseg look ok in
those regions?
cheers
Bruce
On Mon, 21 Nov 2011, Tetiana Dadakova wrote:
> Dear FreeSurfer list,
>
> I was trying to edit wm surface by adding control points. After saving
> them and re-running recon-all -autorecon
Dear FreeSurfer list,
I was trying to edit wm surface by adding control points. After saving
them and re-running recon-all -autorecon2-cp -autorecon3, the control
points are still there, but wm is not edited (although cp worked in
other places for the same brain). The intensity there is around 95-
You want to make sure you are placing the control points only on wm voxels
that are < 110 and wm voxels that are at least 1 voxel away from a gm
voxel in all directions.
If you'd like, you could send me a snapshot of where you placed the
control points and I can give you feedback on that. You a
Hello,
I have about 10 subjects that I am trying to obtain cortical
segmentations. In some of the cases parts of the temporal lobes are
not included in the segmentation due to low intensity (or RF bias).
I tried adding control points as described in the tutorial
(http://surfer.nmr.mgh.harvard.edu
gt;
> Many thanks
> Ali
>
> -Original Message-
> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> Sent: Tuesday, September 07, 2010 2:22 AM
> To: Ali Radaideh
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] control points
>
> you need to visualiz
:22 AM
To: Ali Radaideh
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] control points
you need to visualize it in tkmedit. As for the control points, we
haven't seen that happen. Can you try saving a couple and seeing if the
file changes?
cheers
Bruce
On Tue, 7 Sep 2010
t; Sent: Tuesday, September 07, 2010 1:30 AM
> To: Ali Radaideh
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] control points
>
> Hi Ali,
>
> that means that there are 0 control points stored in the file. For the
> 2nd
> error have you checked the talairach.xfm?
&
07, 2010 1:30 AM
To: Ali Radaideh
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] control points
Hi Ali,
that means that there are 0 control points stored in the file. For the
2nd
error have you checked the talairach.xfm?
cheers
Bruce
On Tue, 7 Sep
2010, Ali Radaideh wrote:
> Hi
t;
>
> Thanks
> Ali
>
>
>
>
>
> -Original Message-----
> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> Sent: Monday, September 06, 2010 3:30 PM
> To: Ali Radaideh
> Subject: RE: [Freesurfer] control points
>
> Hi Ali,
>
> can you post y
ischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Monday, September 06, 2010 3:30 PM
To: Ali Radaideh
Subject: RE: [Freesurfer] control points
Hi Ali,
can you post your responses to the list? Try catting that file to see
what's in it. Also, what version are you running?
cheers
Bruce
On
Hi Ali,
the control points are saved in the subject's directory under
/tmp/control.dat
does that file exist? It also looks like you hadn't finished running this
subject previously. Try running -make all in recon-alll which will rerun
only what it needs to.
cheers
Bruce
On Mon, 6 Sep
2010,
Dear Freesurfer experts,
One more question for today please. I have edited the wm in tkmedit and
saved the control points then ran
Recon-all -autorecon2-cp -autorecon3 -s mySubjectName
But unfortunately I got the following message after 5min of running. I
tried to use a different subjec
can you do that copy by hand?
Muhammad Ayaz wrote:
Yes i do have read and write permissios to these data set.
I just ran another subject from the data set and it ended at different
stage but again says permission denied.
#...@# Fix Topology lh Thu Feb 19 11:14:14 EST 2009
cp ../surf/lh.orig.
Yes i do have read and write permissios to these data set.
I just ran another subject from the data set and it ended at different
stage but again says permission denied.
#...@# Fix Topology lh Thu Feb 19 11:14:14 EST 2009
cp ../surf/lh.orig.nofix ../surf/lh.orig
cp ../surf/lh.inflated.nofix
Do you have read and write permissions to that file?
Muhammad Ayaz wrote:
Dear All,
I am in phase of learning freesurfer. I added control points using tkmedit
and ran recon-all -autorecon2-cp and i get the following error.
"
Total Number of Modified Voxels = 854 (out of 716825: 0.119136)
sh: w
Dear All,
I am in phase of learning freesurfer. I added control points using tkmedit
and ran recon-all -autorecon2-cp and i get the following error.
"
Total Number of Modified Voxels = 854 (out of 716825: 0.119136)
sh: wm.mgz: Permission denied
Broken pipe
Linux eesmith 2.6.9-67.ELsmp #1 SMP Fri
Hello,
I have a subject with substantial cortex in the temporal lobe that is
labelled in the aseg volumes, but not included in the surfaces. As well
there is a bit of cortex that is neither labelled or included in the
surfaces. (It is all included in the brainmask.mgz volume, though)
I used
with control points, it would be beneficial to
start again at the mri_normalize step?
From: Nick Schmansky <[EMAIL PROTECTED]>
To: Bruce Fischl <[EMAIL PROTECTED]>
CC: Freesurfer Mailing List ,Don
Hagler <[EMAIL PROTECTED]>
Subject: Re: [Freesurfer] control points
Date: Th
t: Re: [Freesurfer] control points
Date: Thu, 12 Jul 2007 15:51:17 -0400
Don,
If the file $subjdir/tmp/control.dat exists, then it is automatically
added to the mri_normalize and mri_ca_normalize steps. An explicit flag
is not needed.
Nick
On Wed, 2007-07-11 at 21:27 -0400, Bruce Fischl wrote:
Don,
If the file $subjdir/tmp/control.dat exists, then it is automatically
added to the mri_normalize and mri_ca_normalize steps. An explicit flag
is not needed.
Nick
On Wed, 2007-07-11 at 21:27 -0400, Bruce Fischl wrote:
> Hi Don,
>
> Nick actually just recently included something to allow yo
Hi Don,
Nick actually just recently included something to allow you to pass the
control points to mri_ca_normalize, so it can help the subcortical
segmentation. Nick: what is the new flag?
cheers,
Bruce
On Wed, 11 Jul 2007, Don Hagler
wrote:
In recon-all, it says you are supposed to use -
In recon-all, it says you are supposed to use -autorecon2-cp if you use
control points. So I wonder why earlier normalization steps also use
control points, such as Norm1 and CANormalize. What effect do the control
points have in those steps?
_
How often do you use control points to fix white matter? Because I do
not have clear when I have to use it, despite I have read the example
in the website.
Thanks
Best Regards
Leticia Gutierrez
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harva
Hi Trina,
not really. Is this the aseg.mgz of the wm.mgz that you are talking about?
Bruce
On Fri, 30 Mar 2007, Trina Kok wrote:
Hi,
I understand that it is possible to use control points to fix intensity
normalization, so that volumes which were not selected as white matter can be
manual
Hi,
I understand that it is possible to use control points to fix intensity
normalization, so that volumes which were not selected as white matter
can be manually selected as white matter. Is it possible to
"de-select" volumes which were determined as white matter in freesurfer,
even though i
y in those areas.
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Thursday, January 18, 2007 9:58 AM
To: Tanji, Kazuyo (NIH/NIMH) [F]
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] control points and white matter edits
is the wm properly labeled th
Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] control points and white matter edits
>
> is the wm properly labeled there in the wm.mgz?
>
> On Thu, 18 Jan 2007, Tanji, Kazuyo (NIH/NIMH) [F] wrote:
>
> > There is no apparent topological wm or gm defect in those are
Fischl [mailto:[EMAIL PROTECTED]
Sent: Thursday, January 18, 2007 9:33 AM
To: Tanji, Kazuyo (NIH/NIMH) [F]
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] control points and white matter edits
yes, they won't do anything if the wm is already 110. Check
to see if there is a topolo
yo (NIH/NIMH) [F]
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] control points and white matter edits
>
> yes, they won't do anything if the wm is already 110. Check
> to see if there is a topological defect there.
>
> On Thu, 18 Jan 2007, Tanji, Kazu
h I will be out of town all next week so it might take me a
while to get to it.
Jenni
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Paul Greenberg
Sent: Friday, January 05, 2007 7:04 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] control p
>
> Jenni
>
>
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Paul Greenberg
> Sent: Friday, January 05, 2007 7:04 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] control points and white matter edits
&g
D]
[mailto:[EMAIL PROTECTED] On Behalf Of Paul Greenberg
Sent: Friday, January 05, 2007 7:04 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] control points and white matter edits
Hi all,
I'm having trouble getting accurate white and pial surfaces in inferior
temporal regions on a fe
Hi all,
I'm having trouble getting accurate white and pial surfaces in inferior
temporal regions on a few lower quality scans with significant intensity
variation. I've added hundreds of control points and drawn in white
matter in these regions when control points failed to recover unlabeled
can you send an image showing what you mean?
On Wed, 1 Feb 2006, Fornito,
Alexander wrote:
Hi,
I've generally been successful in using control points to get the white
surfaces into darker areas, where the white matter appears similar to grey
matter. I'm wandering if it's possible to use cont
Hi,
I've generally been successful in using control points to get the white
surfaces into darker areas, where the white matter appears similar to grey
matter. I'm wandering if it's possible to use control points (or any other
remedy) to get make the white matter segmentation less 'harsh', i.e.,
Hi Martin,
the control points won't hurt the aseg unless you actually put them in the
basal ganglia or thalamus. As long as they are clearly in wm you should be
fine.
Bruce
On Mon, 5 Dec 2005,
Martin Ystad wrote:
Hi, I'm using a lot of control-points (typically 200-500) to compensate for
Hi, I'm using a lot of control-points (typically 200-500) to compensate
for intensity inhomogeneities in my images.
This tends to create a rather uniformly looking white matter without any
clearly discernible anatomical landmarks, such as the basal ganglia,
etc. Does this mean that the subcortic
Hi Alex,
it depends on your images. What kind of coil were they acquired with? In
general if a volume coil then placing control points in the wm at the base
of the strand at least 1-2mm from the gray/white junction will fix this
without eating into the gray. If you have a surface coil/phased a
Hi,
I was just after some more pointers on using control points. Some gyri are
missed in some of my images, and using control points recovers them, but it
also tends to make the wm surface eat into the grey matter in some regions.
Just wandering if there's anyway to prevent this from happening?
Hi Sasha,
you want to pick them in a region where the wm intensity is lower than it
should be. That is, less than 110. In general, they can help recover thin
wm strands that are dark by putting some at the base of the strand. Note
that they will only have an effect if you put them at points th
Dear all,
I am trying to add control points for a subject in order to improve
normalization and skull stripping, but I found that the control points I added
did not have much effect on the end result. I know control points should be
added at points that the user feels sure are inside the wh
Hi Peggy,
Your control points file might not be saving. Make sure there is a tmp
directory in the directory for each subject. Inside this directory should
be a file called control.dat. If that file isn't there, you need to modify
the COR-.info file in the $SUBJECTS_DIR/$SUBJECT/mri/T1 directo
Hey everyone,
Someone has given me a monkey volume (it's actually the average of 4
volumes and the gray-white matter contrast is pretty good) and I need to
make a surface from it. I've never dealt with non-human datasets, but I
did read in the freesurfer mailing archives that control points m
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