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
boun...@nmr.mgh.harvard.edu
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Michelangelo
> Fabbrizzi mailto:michef...@gmail.com>>
> Sent: Saturday, August 5, 2023 11:33 AM
> To: Freesurfer support list <
External Email - Use Caution
I noticed all 292 images were processed in the same recon-all. I’m wondering if
they are from the same subject.
If they are data from longitudinal study, you can process them with
longitudinal pipeline -
https://secure-web.cisco.com/1DWOFf8HXjewTlD
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
I have to add a last question:
3- how can I generate the -head.fif file from the surfaces I have created
(brain_surface, inner_skull_surface corrected with 1mm, outer_skull_surface
corrected with -2mm, outer_skin_surface)? I should then use them in MN
External Email - Use Caution
there are not options to autorecon1 specifically. You can pass some
watershed args on the command line, but it is probably easier to use an
expert options file, eg, create a text file (eg, xopts.txt) with
something like
mri_watershed -less
then run r
External Email - Use Caution
Dear Yujing,
thanks again for your help, just a last question, how can give to autorecon1
the input to use certain options at the mri_watershed step (for instance a
certain preflood height (-h 5) or use of the atlas option (-atlas))?
recon-all -s su
External Email - Use Caution
I'm not sure how to force mri_watershed command to use the brainmask.mgz
already created.
Recon-all '-gcut' is achieved by running mri_gcut after mri_watershed.
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Mi
External Email - Use Caution
You don’t need ‘-careg’ if you just run autorecon3.
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Michelangelo Fabbrizzi
Sent: Monday, July 31, 2023 8:55 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_watershed and
adding ‘-careg’ at the end of command line.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Michelangelo Fabbrizzi
Sent: Sunday, July 30, 2023 11:34 AM
To: freesurfer@nmr.mgh.harvard.edu; fsbuild ; freesurfer-ow...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer
arvard.edu
On Behalf Of Michelangelo Fabbrizzi
Sent: Sunday, July 30, 2023 11:34 AM
To: freesurfer@nmr.mgh.harvard.edu; fsbuild ;
freesurfer-ow...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_watershed and improvements of skullstripping
External Email - Use Caution
Dear All,
an
External Email - Use Caution
Dear All,
another question: after the below if I use the command to run autorecon2:
recon-all -s sub-01_recon -autorecon2
I get the following error:
ERROR: cannot find or read transforms/talairach.m3z
Can you help me please?
Thanks, regards,
Michel
: freesurfer-boun...@nmr.mgh.harvard.edu
Date: Friday, 4 December 2020 at 4:54 am
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_watershed error: problem in the COG calcuation
Make sure it looks reasonable (that there is a brain in there, and the
intensities look ok). You can send it to
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
Date: Thursday, 3 December 2020 at 12:39 pm
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mri_wat
Have you looked at the T1.mgz?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Julia Yang
Sent: Wednesday, December 2, 2020 8:37 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_watershed error: problem in the COG calcuation
External Email - Use Caution
Hi,
Wh
External Email - Use Caution
Is there a way to pass an already corrected brainmask file or force the
function to do that so all the subsequent surf are created accordingly
without using after mri_binarize?
On Fri, 5 Jun 2020, 7:52 p.m. Douglas N. Greve,
wrote:
> mri_watershe
mri_watershed creates brainmask.mgz, and the inner_skull should fit
around that.
On 6/3/2020 9:36 AM, Edoardo Pinzuti wrote:
External Email - Use Caution
Dear Freesurfer community,
I have a question regarding the mri_watershed. Is the inner_skull
extracted from the brain.mgz which
Hi Abby
can you check the T1.mgz and see if it was normalized properly? Most of
the WM should have an intensity around 110. If it doesn't, adding a couple
of control points and rerunning may do the trick.
If you can't figure it out feel free to ftp us the tarred and gzipped
subject dir.
ch
External Email - Use Caution
It would be great if you can have a look at the nu.mgz and talairach.xmf but
unfortunately I´m not able to provide it in the mailing list.
Is there another way to send you the files?
Thanks,
Boris
> Am 11.10.2018 um 22:04 schrieb Bruce Fischl :
>
>
Hi Boris
the input to that watershed call is the T1.mgz, but it is already
problematic as you can see from the log. You should take a look at the
nu.mgz and make sure it is correct. You can also email me the nu.mgz and
the talairach.xfm (in the mri/transforms dir) if you want and I'll take a
External Email - Use Caution
Hi again,
sorry. Please find attached the recon-all.log. I´m not sure how to check the
input to watershed.
recon-all.log
Description: Binary data
Thanks,
Boris
> Am 11.10.2018 um 18:55 schrieb Bruce Fischl :
>
> Hi Boris
>
> can you check to m
Hi Boris
can you check to make sure that the input to the watershed looks ok? Also,
in general it is a lot easier for us to help if you send us the full
command line and screeen output and attach the recon-all.log
cheers
Bruce
On Thu, 11 Oct
2018, Boris Rauchmann wrote:
Externa
can you send the recon-all log file?
On 10/11/2018 11:22 AM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> When I run recon-all i get the follwing error message:
>
> mri_watershed Error:
> GLOBAL region of the brain empty !
> Linux 02f92500bcfb 4.15.0-36-generic #39~16.04.1
I think so. Or apply it with mri_convert -at
On Fri, 27 Apr 2018, miracle
ozzoude wrote:
External Email - Use Caution
Hello Bruce,
Thanks. Can I use tkregisterfv to visualize it?
Best,
Paul
On Fri, Apr 27, 2018 at 11:37 AM, Bruce Fischl
wrote:
Hi Paul
that
External Email - Use Caution
Hello Bruce,
Thanks. Can I use tkregisterfv to visualize it?
Best,
Paul
On Fri, Apr 27, 2018 at 11:37 AM, Bruce Fischl
wrote:
> Hi Paul
>
> that usually means something went wrong before the watershed. Check the
> input image to make sure that it
Hi Paul
that usually means something went wrong before the watershed. Check the
input image to make sure that it and the talairach_with_skull.lta are ok
cheers
Bruce
On Fri, 27 Apr 2018, miracle
ozzoude wrote:
External Email - Use Caution
Hello FreeSurfer,
While runnin
Can you send us the recon-all.log?
> On Mar 30, 2018, at 11:32 AM, Darko Komnenić wrote:
>
> Dear experts,
> while running recon-all on FreeSurfer 5.1.0 I encountered the following error:
> mri_watershed Error: indices out of bounds
>
> I searched the email archive and found this thread:
> http
Dear Kristen,
looking at the source code of mri_watershed, the seed point has to be specified
in the format:
-s i j k
and the option can be specified more than once when you want to add more seed
points (30 seed points is maximum).
i.e., when you want to input seed points in coordinates 50,60,
Hi Sam
if you want us to help you, you need to provide us with the full
command line and screen output (at least!)
cheers
Bruce
On Tue, 21 Jul 2015, Sam Zorowitz
wrote:
Hi all,
I am using mri_watershed to create skull surfaces for a cohort of subjects
for whom we were unable to collect a F
Hello Edgar,
We think we were able to isolate the problem. Version 5.1 is failing to
apply the talairach transform to the nu.mgz. It gets computed and
applied to the orig.mgz but then not transferred during the next step.
When mri_normalize tries to run without this information, it fails, and
Hello Edgar,
I am going to be looking at your case and seeing if I can replicate the
error. I have your .nii file and will run it through our processing
stream here, but could you send me your subject folder so that I can
look through your files/logs to give me some more information?
You can
Hello Bruce,
I just wanted to touch base regarding the "Indices_oob.nii" subject I had
sent to MGH. Were you by any chance able to detect the issue with running
recon-all on this subject. Thanks in advance for taking a look at this.
Best regards,
Edgar Busovaca
_
Hello Edgar,
Could you upload the whole subject folder? I could try to run it through
recon all here and see if I can reproduce the error. It would also allow
me to look through your log files to see if I can spot anything that
could be causing this issue.
You can use FileDrop2.0 if the dire
Hello Bruce,
I took a look at the file with freeview and I can't identify anything
peculiar about the data. The file is named Indices_oob.nii and has been
uploaded to /transfer/incoming on the FTP file exchange server. Thank you
for your swift reply and in advance for your time.
Best regards,
E
Hi Edgar
the LINE SEARCH thing is not a real problem. I've never seen "indices out
of bounds" before though. Is there anything strange about your dataset?
Does freeview display it properly (that is, are what freeview thinks the
RAS dirs the correct anatomical ones)? If you upload the dataset w
Hi Tom
I'll cc Flo who wrote this code (a long time ago!). I think the
-brain_atlas flag takes a gca atlas and uses it to avoid large-scale
errors, while -atlas uses some built-in statistics about the shape and size
of e.g. the cerebellum to avoid erasing it accidentally. Flo can correct me
if
ntation is inadequate: central segmentation is
missing.
Cheers,
Úrsula
Date: Fri, 29 Aug 2014 11:48:51 -0400
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_watershed: really bad skull stripping
you can give any format we support to recon-all as
-0400
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_watershed: really bad skull stripping
you can give any format we support to recon-all as the input, including
.mgz
cheers
Bruce
On Fri, 29 Aug 2014, Úrsula Pérez Ramírez wrote:
> Hi Bruce,
&g
e the options for
recon-all if I have already the .mgz file?, I'm getting errors, appart from
the warning for updating tcsh.
Cheers,
Ursula
Date: Fri, 29 Aug 2014 11:23:06 -0400
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_watershed: really
Date: Fri, 29 Aug 2014 11:23:06 -0400
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_watershed: really bad skull stripping
Hi Arsula
are you running this through recon-all or outside of it? The skull
stripping works better after the intensity nor
Hi Arsula
are you running this through recon-all or outside of it? The skull
stripping works better after the intensity normalization that is part of
recon-all
cheers
Bruce
On Fri, 29 Aug 2014, Úrsula Pérez Ramírez wrote:
Hello,
I’m new with FreeSurfer and I’m getting a really bad sku
OK. So do you have any other suggestions? Is there some minor difference
between my version and yours that would explain this behavior. Other
settings to try?
Darren
On Wed, Sep 5, 2012 at 4:28 PM, Bruce Fischl wrote:
> our internal development version.
> On Wed, 5 Sep 2012, Darren Gitelman
> wr
our internal development version.
On Wed, 5 Sep 2012, Darren Gitelman
wrote:
Bruce
I used the following
version: freesurfer-x86_64-redhat-linux-gnu-stable5-20110522
Is that the same as the one you are using or are you referring to an
internal development version?
I will try Nick's suggestion
Nick
I ran: recon-all -skullstrip -no-wsgcaatlas -clean-bm -s 3157
and got the exact same problem with brainmask.mgz
Darren
On Wed, Sep 5, 2012 at 3:37 PM, Nick Schmansky wrote:
> Darren,
>
> I forgot to mention that you'll need to add
>
> -clean-bm
>
> after the -no-wsgcaatlas flag, otherwis
Bruce
I used the following
version: freesurfer-x86_64-redhat-linux-gnu-stable5-20110522
Is that the same as the one you are using or are you referring to an
internal development version?
I will try Nick's suggestion as well.
Darren
On Wed, Sep 5, 2012 at 4:05 PM, Bruce Fischl wrote:
> I'm run
I'm running it now with the current dev version and it's passed the skull
stripping stage and it seems to have worked fine...
On Wed,
5 Sep 2012, Nick Schmansky wrote:
> Darren,
>
> I forgot to mention that you'll need to add
>
> -clean-bm
>
> after the -no-wsgcaatlas flag, otherwise the prior
Darren,
I forgot to mention that you'll need to add
-clean-bm
after the -no-wsgcaatlas flag, otherwise the prior brainmask.mgz will be
retained and the new one will be saved as brainmask.auto.mgz.
Nick
On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote:
> Nick, List:
>
>
>
> Still
Bruce:
Thank you for looking. I have uploaded the files:
I uploaded them in Dicom Format.
This is a T1, MPRAGE, image, acquired with GRAPPA, resolution 1x1x1.
Name: 3157.tar.gz
Darren
On Wed, Sep 5, 2012 at 11:27 AM, Bruce Fischl wrote:
> Hi Darren
>
> can you describe your input data? What f
Hi Darren
can you describe your input data? What format, resolution, etc... is it?
If you upload it we'll take a look
cheers
Bruce
On Wed, 5 Sep 2012, Darren Gitelman
wrote:
Nick, List:
Still no luck with this data. See attached as an example.
To get to this point I had run:
r
Nick, List:
Still no luck with this data. See attached as an example.
To get to this point I had run:
recon-all -all
This ran to the error: mri_watershed Error: GLOBAL region of the brain
empty !
Then I followed your recommendation below
recon-all -s -skullstrip -no-wsgcaatlas
try running:
recon-all -s -skullstrip -no-wsgcaatlas
if that works, continue the rest with:
recon-all -s -autorecon2 -autorecon3
n.
On Wed, 2012-08-29 at 17:01 +, Darren R Gitelman wrote:
> Hi
>
> I am having a problem getting recon-all to finish on 1 subject.
>
> The first time I r
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_watershed for inner_skull_surface question
Matti Hamalainen (ccd) might have some thoughts. Do you have T2 or PD images?
cheers
Bruce
On Tue, 20 Sep 2011, Roderick McColl wrote:
> Hi all,
>
> Trying to get mri_watershe
Matti Hamalainen (ccd) might have some thoughts. Do you have T2 or PD
images?
cheers
Bruce
On Tue, 20 Sep 2011, Roderick McColl wrote:
Hi all,
Trying to get mri_watershed to give me a good inner_skull_surface, which I want
to combine with the pial surface to estimate sulcal CSF, as I don't
You can try using mkheadsurf. Run it with --help to get more info.
doug
Vema Krishnamurthy, Santosh wrote:
> Hello Everyone,
>
> I have an application outside freesurfer where I need the scalp/face
> surface from the MRI file so I'm trying to use mri_watershed algorithm
> to generate the scalp
you could also try adding the -no-wsgcaatlas flag to the end of
recon-all. but also make sure that the T1.mgz is not junk.
n.
On Thu, 2010-09-23 at 12:06 -0400, Bruce Fischl wrote:
> can you check the talairach xform and see if it's ok?
> On Thu, 23 Sep 2010,
> Shugao Xia wrote:
>
> > Hi,
> >
can you check the talairach xform and see if it's ok?
On Thu, 23 Sep 2010,
Shugao Xia wrote:
> Hi,
>
> I ran recon-all on one subject, and exited with errors:
>
> mri_watershed Error: GLOBAL region of the brain empty!
>
> what is the reason which caused this error? Thank you in advance
>
> Best
Hi Toh,
did you check the talairach transform? If it's ok, try either running the
watershed skull stripping with a different preflooding height or without
the atlas.
cheers
Bruce
On Sat, 17 Jul 2010, Toh Hock Wong wrote:
> Dear freesurfer experts,
>I need your help on recon. I tried to p
Hi Andres,
those errors are probably not related (tkmedit tries to read an array of
cortical surfaces that don't exist for the BEM analysis). I'm not sure what
BEM mesh editing tools exist - maybe Matti knows?
cheers,
Bruce
On Wed, 3 Mar 2010, Andres Felipe Salazar Gomez wrote:
Hello Fre
it's in the same coordinates as all the other conformed volumes
doug
s...@nmr.mgh.harvard.edu wrote:
Hi,
I used mri_watershed to get volume segmenstation with -LABEL option.
mri_watershed -atlas -LABEL $SUBJECTS_DIR/test/mri/T1.mgz
$SUBJECTS_DIR/test/tmp/
What coordinate system is used for t
Kathy,
Can you send me the 001.mgz file for one of these subjects? Send it via
the filedrop:
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
The 001.mgz file is in the /mri/orig directory (and you might have
a 002.mgz file as well, if you had two structurals for this subject).
Nic
Hi Ian,
does this mess up the ?h.white or ?h.pial surfaces? Or the aseg.mgz? If
not, I wouldn't worry about it.
cheers,
Bruce
On Tue, 5 Aug 2008, Ian Malone wrote:
To illustrate the issue, this is a slice from one of the problematic volumes.
The blue outlines surround non-zero voxels, the re
It's not terrible; it can be worked around. But it does feel more like
a bug than a feature, as these voxels are un-connected with any in the
brain. It looks a bit like the edge of a bounding box.
Thanks,
Ian
Bruce Fischl wrote:
Hi Ian,
mri_watershed minimizes a risk functional in which we
Hi Ian,
mri_watershed minimizes a risk functional in which we weigh the cost of
leaving non-brain voxels to be much less than stripping true brain ones,
so it does sometimes leave stuff around. Is this causing any problems?
Bruce
On
Wed, 30 Jul 2008, Ian Malone wrote:
Hi,
Has anyone enco
matlab's reducepatch
Date: Thu, 10 Apr 2008 10:39:37 -0700
From: [EMAIL PROTECTED]
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_watershed -> BEM surfaces problem
P.S. Also, I was wondering if there is a utility to reduce the number
of vertices of a given surface (i.e. to make a le
Hi Ozlem,
if it's the talairach_with_skull.lta as described previously. I have a fix
for it that will be in the upcoming stable. In the interim you could try
running watershed without the talaiarch_with_skull.lta
cheers,
Bruce
Hello,
I have the same error (mri_watershed Error: GLOBAL regi
Nima,
There is no flag to mri_watershed to allow this, but you can trick it by
doing the following:
cd $FREESURFER_HOME/lib/bem
mv ic5.tri ic5.bak
ln -s ic4.tri ic5.tri
This will force usage of ic4.tri, which has 5120 triangles.
Nick
On Wed, 2007-08-08 at 17:46 -0400, [EMAIL PROTECTED] w
Hi Avram,
not sure if it will work, but it certainly shouldn't crash. If you put
the data somewhere I can get it (e.g. on our filedrop) I'll take a look.
cheers,
Bruce
On
Wed, 2 Aug 2006, Avram Holmes wrote:
All,
I am interested in using mri_watershed to remove the skull from an inplane
l
Oh, don't do that! recon-all will compare the auto with the non-auto.
If they are the same then it will re-compute the auto and simply copy
to the non-auto, and your changes will be lost. If they are different,
then it will recompute the auto but will not propagate it to the
non-auto. Make sen
or in your case dave, just:
cp brainmask.mgz brainmask.auto.mgz
since you manually edited brainmask.mgz
On Thu, 2006-06-29 at 14:18 -0400, Doug Greve wrote:
>
> I'm not sure what will happen. Safest to just recreate it:
>
> cd subject/mri
> mri_watershed T1.mgz brainmask.auto.mgz
>
>
> [E
I'm not sure what will happen. Safest to just recreate it:
cd subject/mri
mri_watershed T1.mgz brainmask.auto.mgz
[EMAIL PROTECTED] wrote:
Alright I converted the COR files to mgz fine, and saved the volume as
brainmask.mgz. All looks good. But before I run -autorecon2, am I
going to r
Alright I converted the COR files to mgz fine, and saved the volume as
brainmask.mgz. All looks good. But before I run -autorecon2, am I
going to run into problems because I only have a brainmask.mgz and not a
brainmask.auto.mgz? (I deleted the old brainmask.auto.mgz because it
was the old volum
but you'll need to convert the COR file you saved to brainmask.mgz if you
want to recover your edits (4 hours of manual editing!).
Bruce
On Wed, 28 Jun
2006, Nick Schmansky wrote:
The brainmask.mgz file is the one that should be edited (and saved), so
select that filename to save. Then jus
sounds like you saved it in COR format, which is what will happen if you
specify a destination folder instead of a file name (e.g. brainmask.mgz).
Try loading that in tkmedit to make sure it's got your edits, then you can
convert it to .mgz with mri_convert.
On Wed, 28 Jun 2006 [EMAIL PROTECTE
The brainmask.mgz file is the one that should be edited (and saved), so
select that filename to save. Then just continue with autorecon2 (and
it will use your brainmask.mgz). It will not overwrite your
brainmask.mgz unless you specify the aptly named '-clean-bm' flag to
recon-all.
On Wed, 2006-
I just finished my 4 hour manual editing...went to file>save volume
as...then saved it to where it defaulted me, which was the mri folder of
this subject. When i pull up my brainmask, it is giving me the same one
that it had before i made any changes. I hope i didnt do something
wrong and lost al
it helps detect cases in which the deformation is too big (e.g. when the
surface deforms all the way into the cerebellum), and can thus recover from
e.g. cerebellum chopping.
On
Wed, 28 Jun 2006 [EMAIL PROTECTED] wrote:
I am currently in the process of manual editing...just curious though,
I am currently in the process of manual editing...just curious though,
what exatly does adding an atlas do to the skullstrip process?
Quoting Nick Schmansky <[EMAIL PROTECTED]>:
> First have a look at the troubleshooting wiki pages at:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tro
First have a look at the troubleshooting wiki pages at:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData
In particular, Subject 1 has a skull strip problem, and the fix info is
here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix
I'm guessing you have
Xander,
I'm glad its working for you. I'm not sure why it did not work as-is,
because the GSL library is included with the distribution (in
$FREESURFER_HOME/lib/gsl) and the DYLD_LIBRARY_PATH is setup to point to
it. I do need to figure-out why the hard-coded path
'/usr/pubsw/packages' is shown
Hi Nick,
Just wanted to let you know that Anthony has tried mri_watershed and after installing the gsl binary everything seems to work fine. Thank you for everything.
>Xander
On Apr 4, 2006, at 4:25 PM, Xander Meadow wrote:
Hi Nick,
I tried running mri_watershed on Anthony's computer today an
Hi Nick,
I tried running mri_watershed on Anthony's computer today and got a different error from last time. I got the following error:
% freesurfer/bin/mri_watershed
dyld: freesurfer/bin/mri_watershed can't open library: /usr/pubsw/packages/gsl/current/lib/libgsl.0.dylib (No such file or dire
Hi Nick--
I'm responding on behalf of Xander (our computer tech):
[serge:NL-GCS/subjects/freesurfer_3.0.1] adick% otool -L `which
mri_watershed`
/Applications/freesurfer/bin//mri_watershed:
/usr/pubsw/packages/gsl/current/lib/libgsl.0.dylib (compatibility
version 8.0.0, current versio
Can you send me the output of:
otool -L `which mri_watershed`
On Mon, 2006-04-03 at 13:34 -0500, [EMAIL PROTECTED] wrote:
> Hi,
>
> I just downloaded and installed from:
>
> http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer-Darwin-panther-
> stable-pub-v3.0.1-full.dmg
>
> And installed
Hi Dan,
the watershed core dump is a known bug that I think will be fixed in
tomorrow's dev version (not positive though).
Looking at recon-all I think it runs it without any # of iterations on the
command. Not sure what the default is for it in terms of # of iters.
cheers,
Bruce
On Wed, 1
Sasha Wolosin
Research Assistant
Developmental Cognitive Neurology
Kennedy Krieger Institute
707 N. Broadway
Baltimore, MD 21205
ph: (443) 923-9270--- Begin Message ---
Hi Xiao,
That seems to be it, thanks. The actual values are the same. I looked at
the brightness/contrast settings for the sk
Alternatively, depending on what version of tkmedit you have, you can use
the -mm-main option to specify an out-of-range min and max
visible value on the command line. As Xiao said, normally the min and max
visible values that determine the color scale are preset to the actual min
and max v
no, it should just strip. Is that not happening? If not, you can always
use mri_mask to use the skull stripped volume as a mask to apply to
whatever volume (in register with the orig) you want.
cheers,
Bruce
On Fri, 19 Aug 2005,
Sasha Wolosin wrote:
We use an anatomical analysis program cal
Hi Sasha,
If you use tkmedit to visualize the results, then the contrast change you
saw may be just due to the display problem (not exactly a problem) of
tkmedit.
You can move the mouse around the image to actually see whether the image
intensity values were changed or not.
I used mri_waters
Dear Sasha,
mri_watershed was initially designed to skull strip orig images, without
any preprocessing step, such as intensity normalization or contrast
modification. So, This certainly seems like a reasonable thing to do.
However, mri_watershed might normalize intensities during the
process
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