I can't tell from those pics what is happening. Does it look like an
imaging artifact? You can try putting control points
On 2/26/2024 12:58 PM, lejia2011411409 wrote:
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Hi,
I used command: recon-all -s subject1 -i subject1.nii -all -sd
/home/t1. I t
External Email - Use Caution
Hi,
I used command: recon-all -s subject1 -i subject1.nii -all -sd
/home/t1. I think it is FrreSurfer default method to segementation.
Lejia
At 2024-02-27 01:24:00, "Douglas N. Greve" wrote:
what did you use the do the segmentation?
what did you use the do the segmentation? Include command line and
terminal output
On 2/26/2024 10:46 AM, lejia2011411409 wrote:
External Email - Use Caution
Dear freesurfer experts,
A large amount of subjects got segmentation white matter bad (some
dark white matter cannot be recog
Hi Jakob,
I believe we fixed the bug in FS 7.4 release. Can you give it a try?
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Litsch, Jakob Benjamin
Sent: Wednesday, December 6, 2023 10:40 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Segmentation error w
n.edu<mailto:joshua.pas...@northwestern.edu>
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Iglesias Gonzalez, Juan
E.
Date: Friday, November 17, 2023 at 2:48 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Segmentation of hippocampal subfields and nuclei of
the am
Dear Joshua,
This is a bit of an empirical question. I’d totally run both on a few subjects
and compare the results.
If you do so: I would selfishly/greatly appreciate it if you shared your
impressions with me :-)
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
http://www.jeiglesias.com
From: freesur
External Email - Use Caution
As Yujing said, the 5.1.0 release is quite old (dating back to CentOS4) and
binary backwards compatibility cannot be expected to work indefinitely going
forwards to newer versions of the OS. I ran a simple mri_surf2surf
command from 5.1.0 on CentOS7
Hi Tracy,
I’m wondering if you have any success with other subjects. Can you attach the
failed recon-all.log?
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Tracy Riggins
Sent: Sunday, March 5, 2023 1:22 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Segm
Hello,
If you have T1 images that have been processed with FreeSurfer, you can use the
script 'segmentHA_T1.sh' to automatically segment hippocampal subfields.
Best,
Jackson
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of PRASAD D
Sent: Monday, Octo
Try running recon-all on the unskull stripped data. Alternatively, if
you just want hippo you can run mri_synthseg or samseg
On 10/31/2022 5:32 AM, PRASAD D wrote:
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Hello everyone. I’m new to FREESURFER
I would like to segment the sMRI images.
I have ext
External Email - Use Caution
Hello Joann,
If I read correctly, you are doing a remote mount of a shared network
drive to your Mac to store/read/write the subject files but running the
recon-all using your Mac processors.
You might want to check the directory for the last subject
External Email - Use Caution
Hello Priya,
It could help to know,- the version of freesurfer you installed, e.g., the
latest 7.3.2 release
from https://secure-web.cisco.com/1zdcvVhqKzcbDdvruGd5f9eNe1UebLwxcHQNPPf-imCCfHdpe0i9n7VbHnkOmApVqwXLBFsNTr00VNAx6komIIAOhuIRk6xXYWHGaglPYJch
It really can be anything. Hard to say
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Ruifeng Dong
Sent: Tuesday, August 30, 2022 3:01 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Segmentation protocol used by Freesurfer
External Email - Use Caution
Thanks. I
in a structure can change (e.g.
> is the fimbria part of the hippocampal label?)
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Ruifeng Dong
> *Sent:* Tuesday, August 30, 2022 2:34 PM
> *To:* Free
...@nmr.mgh.harvard.edu
On Behalf Of Ruifeng Dong
Sent: Tuesday, August 30, 2022 2:34 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Segmentation protocol used by Freesurfer
External Email - Use Caution
Thanks, Bruce.
Actually, I am comparing the volume computations between
External Email - Use Caution
Thanks, Bruce.
Actually, I am comparing the volume computations between different
segmentation tools. In some software's paper, they mentioned there is a
slight difference in protocol from Freesurfer and thus not easy to compare.
I am wondering what th
Hi Ruifeng
I think they are similar, but you would have to ask Neuromorphometrics about
the differences. Our protocol was published in the Neuron 2002 paper and the
papers it cites, which I think is also where the Neuromorphometrics’ protocol
came from
Cheers
Bruce
From: freesurfer-boun...@nm
Hi Lauren - What you want is to replace the thalamus labels in aparc+aseg.mgz
with the thalamic nuclei labels. This is a bit less straightforward than it may
first seem because the outer boundaries of the thalamus in the two
segmentations are not necessarily the same. However, we've implemented
what are you using as input? I can't tell from the image you sent, but
it looks pretty blurry. What is the resolution? What kind of acquistion?
On 6/28/2022 11:38 PM, Wang, Yu wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I used the _recon-all -s c1NT816 -i smwrc1N
Sure, just run your subject through recon-all, then use mri_binarize or
mri_extract_label to pull the cc labels out of the aseg.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Mostafa Fakhri
Sent: Sunday, July 3, 2022 1:31 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject:
I'm not sure that will work. You should use mri_sclimbic_seg
https://surfer.nmr.mgh.harvard.edu/fswiki/ScLimbic
On 6/27/2022 3:31 AM, Mostafa Fakhri wrote:
External Email - Use Caution
Hello to all of you
I ran recon-all:
$ recon-all -sd /share/users/mfakhri/FS/subjects -subject 1021
Hi Katie,
This is weird. Does /home/bdl/freesurfer/subjects/SD027/scripts/ exist?
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
On 16 Nov 2021, at 17:19, Katherine Andrade
mailto:kandrade8...@sdsu.edu>> wrote:
Dear Edyta,
The smaller nuclei are definitely less accurate than the bigger ones in the
atlas.
Is it only the VM giving you trouble? Is it in every case, or only on this case?
Cheers,
Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeigle
External Email - Use Caution
Hello Yuhui,
Did you try something like the following (from
https://secure-web.cisco.com/1hub7Psr57JCR6YgoGWEJLmEuz6voF9O_4wwW1Ngq-Krek8hQagKNFY9pH9jg_UzrEMFBjBl1Lo36JvBnp02E7HopuMgcNTaG0pTRx-2PR61unk8dCsv-4Gp50vSlBbeEJzjsRZGWS1jqAp0pVmSzDy9Ob23Rg1PB3s
Thanks, Marco.
The volume of the LGN in our atlas is ~215mm3. Volume discrepancies with other
atlases or manual tracing are common, particularly for such small nuclei with
faint contrast (and also due to discrepancies in criteria eg to determine the
posterior / medial boundary with the rest of
External Email - Use Caution
Dear Eugenio,
Thank you.
I've uploaded via FTP a zip file (g1120_5.zip) containing a recon-all
folder of a subject, including thalamic nuclei segmentation.
Best,
Marco
Il giorno lun 30 ago 2021 alle ore 10:17 Marco Aiello <
marcoaiello1...@gmail.c
Hi Marco,
Would you mind sharing a representative case with us, please?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
On Aug 30, 2021, at 04:17, Marco Aiello
mailto:marcoaiello1...@gmail.com>> wrote:
Ext
External Email - Use Caution
Thanks!!!
Kind regards,
Rosie
El mié., 7 jul. 2021 21:32, Paul Wighton escribió:
> External Email - Use Caution
>
> Hi Rosie,
>
> In that case, you can try running the v6 version of hippocampal subfields,
> e.g:
>
> recon-all -s sub-002_ses-
External Email - Use Caution
Hi Rosie,
In that case, you can try running the v6 version of hippocampal subfields,
e.g:
recon-all -s sub-002_ses-BSL -hippocampal-subfields-T1
-Paul
On Wed, Jul 7, 2021 at 3:21 PM Rosalia Dacosta Aguayo
wrote:
> External Email - Use Caut
External Email - Use Caution
Hi Paul,
Thank you.
The think is that I already run recon-all in all the participants and I
made some corrections (control points,...). I just want the hipocampal
subfields...What should I do in this case scenario?
El mié., 7 jul. 2021 21:03, Paul
External Email - Use Caution
Thanks Rosie, that explains it.
You are using version 6.0.0 of FreeSurfer. The script segmentHA_T1.sh is
not in this version.
There are two options. If you want to continue using v6.0.0, you can
refer to the instructions here:
https://secure-web.cis
External Email - Use Caution
Here it is:
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ ls -la
$FREESURFER_HOME/bin/segmentHA_T1.sh
ls: cannot access '/usr/local/freesurfer/bin/segmentHA_T1.sh': No such file
or directory
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ cat $FREESURFER_HOME/build-st
External Email - Use Caution
Ok, it looks like the file $FREESURFER_HOME/bin/segmentHA_T1.sh doesn't
exist for some reason.
You should be able to confirm that by running:
ls -la $FREESURFER_HOME/bin/segmentHA_T1.sh
Does it say something like?
ls: cannot access '/usr/local/frees
External Email - Use Caution
Hi Nayan,
Do you mean this?
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ sh
$ segmentHA_T1.sh
sh: 1: segmentHA_T1.sh: not found
$
On Wed, Jul 7, 2021 at 7:04 PM nayan wadhwani wrote:
> External Email - Use Caution
>
> Dear Rosalia,
>
> Once y
External Email - Use Caution
Dear Rosalia,
Once you export and source freesurfer with the following commands
export FREESURFER_HOME=/usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
type sh
after sourcing and then try running it(without closing the terminal)
hopef
External Email - Use Caution
Hi Paul,
I did it:
# FREESURFER
export FREESURFER_HOME=/usr/local/freesurfer
export PATH=${FREESURFER_HOME}/bin:${PATH}
export SUBJECTS_DIR=/home/rosalia/Desktop/CAN_RUTI
source $FREESURFER_HOME/SetUpFreeSurfer.sh
And I even re-started the computer b
External Email - Use Caution
Sure Rosie, no worries.
Try adding the following line to the end of your ~/.bashrc (it must come
after the line 'export FREESURFER_HOME=/usr/local/freesurfer'):
export PATH=${FREESURFER_HOME}/bin:${PATH}
After saving, close all your terminal windows,
External Email - Use Caution
Hi Paul,
Thank you very much for answering my question. I set the subjects_dir in a
way I can run freesufer in CAN_RUTI folder.
When I do what you ask me to do:
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ echo $FREESURFER_HOME
/usr/local/freesurfer
rosali
External Email - Use Caution
Hi Rosie,
The segmentHA_T1.sh script is located in the $FREESURFER_HOME/bin
directory. It looks like your PATH environment variable does not include
this directory.
If the $FREESURFER_HOME variable is set (you can check by running `echo
$FREESURFER_H
External Email - Use Caution
Following this more actualized link:
https://secure-web.cisco.com/1ozTwtUw1KSbQpdNIwz2_3DPsUQKXTak4jBUzEnwIwEGF0QA7dU_-WV0knTWg34z8sLPS4TLvOowD6YEHvTPyuu1COU4jC563p9sON2p14wsI0mWSVnMilPCEFBKfXGbJmDCkIIe9mDAmujVdwFROi8q9itBngp6RN-ghAwNGf8tT3Vb_bKoCj-_QoT
behalf of Roman Fleysher
Sent: Tuesday, February 23, 2021 12:59 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] segmentation is shifted with respect to NIFTI T1W
CAUTION: This email comes from an external source; the attachments and/or links
may compromise our secure environment. Do
do not know
details.
Thank you,
Roman
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Roman Fleysher
Sent: Tuesday, February 23, 2021 10:54 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] segmentation is shifted with respect to
) have the same issue. Looking into these.
Roman
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Tuesday, February 23, 2021 10:04 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] segmentation is shifted with respect
Those commands look right
On 2/23/2021 9:27 AM, Roman Fleysher wrote:
External Email - Use Caution
Dear FreeSurfers,
I am working with version 6, starting point is T1W image in NIFTI
format. I typically transform segmentations back to native space in
NIFTI format to be able to use o
,
Kevin
Date: Tue, 12 Jan 2021 15:45:37 +
From: "Greve, Douglas N.,Ph.D."
mailto:dgr...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] Segmentation Fault During mri_convert
running FS 5.0
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesu
+
From: "Greve, Douglas N.,Ph.D."
mailto:dgr...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] Segmentation Fault During mri_convert
running FS 5.0
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>"
mailto:freesurf
For some reason, it is not capturing the terminal output in the log files. Can
you just run
mri_convert
/autofs/cluster/deplin/chris/data/Selected_Scans/3800033/MPRAGE/003/MEMPRAGE.nii
deleteme.mgz
and send me the terminal output?
On 1/2/2021 2:23 PM, Dowling, Kevin Francis wrote:
Hello FreeSur
Please send the recon-all.log file
On 12/25/2020 8:42 PM, Wei Koo wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to run recon2 for a number of subjects, but one of my subjects I
get the following error when I run the mri_tesellate command:
Removing int
External Email - Use Caution
Thank you for your advice!
Best regards,
Sunah.
2020년 9월 14일 (월) 오후 9:50, Iglesias Gonzalez, Juan E. <
jiglesiasgonza...@mgh.harvard.edu>님이 작성:
> Dear Sunah,
>
> I would use the T1 alone.
>
> Cheers,
>
> /E
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senio
Dear Sunah,
I would use the T1 alone.
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of 최선아 / 학생 / 뇌인지과학과
Reply-To: Freesurfer support list
Date: Monday, September 14, 2020 at 03:16
To: "freesurfer@nm
You can try running samseg on it (in version 7.1.1), eg
samseg --i ct.nii.gz --o samseg
Then look at samseg/seg.mgz
I have no Idea what will happen, but samseg is pretty robust, so it
might work
On 8/27/2020 4:53 AM, mudassar liaq wrote:
External Email - Use Caution
Hi,
As far as I
I don't. My guess is that there is a tolpolgical default there that is
not fixed correctly in 7.1. Sometimes these things are on the edge and
slight changes will affect them.
On 7/13/2020 4:22 AM, Sara PONTICORVO wrote:
External Email - Use Caution
Dear FreeSurfer experts,
we are pe
Hi Harriet
it's tough to diagnose from just this, but that is pretty bad! Can you give
us some details about the editing? Or tar/gzip the whole subject dir and
upload it and we will take a look
cheers
Bruce
On Tue, 24 Mar 2020, Harriet Cornwell
wrote:
External Email - Use Cautio
It is seg faulting at the defect correction stage which is before the FLAIR
would be used. At this point it should be identical to the T1-only analysis.
Check your commands to make sure they are the same except for the FLAIR part
On 1/16/2020 9:55 AM, Swanson,Clayton wrote:
External Ema
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
Did you check the talairach transform? See
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview
On 10/4/2019 1:37 PM, Backhausen, Lea wrote:
External Email - Use Caution
Dear FreeSurfer experts,
when running the recon -all –all command (I included the -3T flag) with
recon-all does not do so well with data at 0.5mm. I created a high-res
patch for version 6.0 as part of my support fo r the HCP. You can get it
here https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp
this shold work much better.
On 8/27/19 10:15 AM, Giovana dos Santos Cover w
External Email - Use Caution
Yes! The changes will probably be tiny, though.
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Boris Rauchmann
Reply-To: Freesurfer support list
namens Greve, Douglas N.,Ph.D.
Verzonden: donderdag 14 maart 2019 17:17:54
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] Segmentation fault
Can you send the command line with out variables and the full terminal
output?
On 3/14/19 8:48 AM, Donatienne Van Weehaeghe wrote
t;
> --no-rescale --threads 8
>
> Kind regards
>
> Donatienne
>
>
> //
>
>
> *Van:* freesurfer-boun...@nmr.mgh.harvard.edu
> namens Tim Schäfer
>
> *Verzonden:* woensdag 13 maart 2019 23:22:07
> *Aan:* Frees
/gtmpvc.output.suvrcerebellum.spmreg
--no-rescale --threads 8
Kind regards
Donatienne
Van: freesurfer-boun...@nmr.mgh.harvard.edu
namens Tim Schäfer
Verzonden: woensdag 13 maart 2019 23:22:07
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer
External Email - Use Caution
> On March 13, 2019 at 9:18 PM Donatienne Van Weehaeghe
> wrote:
> The code I tried to run:
>
> #mri_gtmpvc --i SUVR_cerebellum.nii.gz --reg suv.reg.lta --psf 5 --seg
> /gtmseg.mgz --default-seg-merge --auto-mask 5 0.01 --rbv --o
> gtmpvc.output.su
External Email - Use Caution
Hi there,
Just want to check if you get the recon-all files that I sent for an entire
subject?!
I am also wondering if the problem with the segmentation can be related to
the small size of aged Portuguese brains considering the expected size
based for
Hi Manuela
you can certainly do manual editing in freeview
cheers
Bruce
On Thu, 10 Jan 2019, Manuela
Costa wrote:
External Email - Use Caution
Dear all,
We have a subject for whom we would like to do hippocampal subfield and
amygdalar nuclei
segmentation. Unfortunately,
Hi Fariha
The number of regions is based on the anatomy. You can combine them if
you like. The volume to use is probably the aparc+aseg.mgz, which is
easily convertible to .nii with mri_convert.
Also, you should use freeview not tkmedit (tkmedit has been deprecated
for many years)
cheers
B
External Email - Use Caution
Hi Bruce
I am working on segmentation of brain regions. I wanted to know:
1. If it is possible that I could get brain segmented into 8 regions or
maybe 20, because when I segmented using recon-all command, I got
segmentation of 45 regions ?
2. I was loo
Hi Fariha
can give us more details? How would you like to customize them? I think the
answer is probably no, but I'm not sure I understand what you are trying to
do
cheers
Bruce
On Wed,
12 Dec 2018, Fariha Muazzam wrote:
External Email - Use Caution
Hi
I am working in
External Email - Use Caution
Nope, please don't rerun the recon-all with dev. Just run the hippo+amyg module
on the 6.0-reconned data.
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London, and
External Email - Use Caution
Update - Segmentation fault
I think I have finally found the issue. The bvec files I uploaded actually
contained only zeroes for each bvec value, and that made it impossible for
Tracula to function properly. This was a result of the original files w
External Email - Use Caution
I probably deleted the log file prior to running the path step so I could
focus on what was going on. I'll re-run it and give you the results when
it finishes.
Thanks!
--
Notice: This e-mail message, together with any attachments, contains
informat
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, October 31, 2018 at 9:57 AM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>"
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Segmentation fault
External Email - Use Caution
Hi HSK
We use it in the model fitting but do not segment it due to the absolute lack
of contrast with the white matter.
Kind regards,
Eugenio
--
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
Department of Medical Physics and Biomedic
External Email - Use Caution
Hello Jon,
Since trac-all is a tcsh script, you could try prefacing it with "tcsh -x" to
get extra output about what it is doing, i.e.,
$ tcsh -x trac-all rest of args...
- and then look thru the trac-all output to see where it actually runs a bi
External Email - Use Caution
Hello Jon,
Looks like you are already running with -debug and -allowcoredump option, and
the shell limits do not look like they are too small to allow the coredump to
be written. I don't know offhand if that coredump option causes a file to
be wri
External Email - Use Caution
Hello Jon,
Can you get any stack or backtrace information after the segfault occurs ?,
e.g., Mac OS has the option to display the crash report with a trace. On
Linux you could run thru gdb and get a back trace. This would help
us to see where the
Hi Cody
yes, it could be due to poor contrast. The watershed isn't the issue
though, it is mri_segment and mris_make_surfaces. You can try changing
the wm/gm limits, or upload the subject and we will take a look
cheers
Bruce
On Tue, 24
Apr 2018, Barlow, Cody wrote:
External Email
Hi Antonin
unfortunately the atlas subjects were not collected with an IRB that
allows us to distribute them. We are working to update the atlas with
data we can distribute, but that is not a short-term solution. You second
proposal would work I imagine
cheers
Bruce
On Sat, 14 Apr 2018, Antoni
Great! Thanks!
2018-01-08 16:44 GMT+01:00 Hoopes, Andrew :
> Hi Carme,
>
> segmentHA_T1.sh is available in the fs dev version: ftp://surfer.nmr.mgh.
> harvard.edu/pub/dist/freesurfer/dev
>
> best,
> Andrew
>
>
> On Jan 4, 2018, at 9:17 AM, Carme Uribe Codesal
> wrote:
>
> Dear FreeSurfer users,
Hi Carme,
segmentHA_T1.sh is available in the fs dev version:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev
best,
Andrew
On Jan 4, 2018, at 9:17 AM, Carme Uribe Codesal
mailto:carme.ur...@gmail.com>> wrote:
Dear FreeSurfer users,
I wanted to run the new script that segments the h
N Greve
>
> *Sent:* Monday, December 18, 2017 5:09:25 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Segmentation fault (core dumped)
>
> We need more details. Try looking at this web site
>
>
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
We need more details. Try looking at this web site
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
On 12/18/2017 04:08 PM, Uquillas, Federico D'Oleire wrote:
>
> Dear FreeSurfer experts,
>
>
> I am unable to run the qcache procedure and was wondering if anybody
> could help me find what is goi
Dear FreeSurfer experts,
I am unable to run the qcache procedure and was wondering if anybody could help
me find what is going on.
I've tried running qcache with several versions of the fsaverage (e.g.,
fsaverage5, fsaverage6, fsaverage), and have also tried running it in a variety
of subjec
try mris_seg2annot Run it with --help to get examples
On 11/13/17 3:06 PM, Hengda He wrote:
Hi Freesurfer Developers,
I have a manually edited segmentation of the brain cortical regions,
and I want to map it to cortical parcellation labels on both white
matter surface and pial surface. So I
Hi Hengda
yes, I think you can either use mri_vol2surf or mris_sample_parc to get
your segmentation onto the surface
cheers
Bruce
On Mon, 13 Nov 2017, Hengda He wrote:
> Hi Freesurfer Developers,
>
> I have a manually edited segmentation of the brain cortical regions, and I
> want to map it t
help,
> Idil
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
> [gr...@nmr.mgh.harvard.edu]
> Sent: Tuesday, July 25, 2017 11:00 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Su
]
Sent: Tuesday, July 25, 2017 11:00 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
what is your command line?
On 07/25/2017 03:52 PM, Yagmur Ozdemir 19 wrote:
> When I do either of the conversions with mris_convert, the system gi
...@nmr.mgh.harvard.edu]
Sent: Tuesday, July 25, 2017 11:00 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
what is your command line?
On 07/25/2017 03:52 PM, Yagmur Ozdemir 19 wrote:
> When I do either of the conversions with mris_convert, the sys
t; Best,
> Idil
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Tuesday, July 25, 2017 10:21 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Segmenta
...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Tuesday, July 25, 2017 10:21 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
you can convert the overlays directly to nifti, but they aren't surfaces
- they are scalar f
r-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Tuesday, July 25, 2017 7:47 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
>
> Hi Idil
>
> I'm not sure what you m
Sent: Tuesday, July 25, 2017 7:47 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
Hi Idil
I'm not sure what you mean. If you give us a better idea of your overall
goal we can give you more helpful answers I expect
Bruce
On Tue, 25 Jul 20
rvard.edu]
> Sent: Monday, July 24, 2017 10:36 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
>
> Hi Idil,
>
> we only store surface overlays in .mgz not surfaces themselves. Try loading
> a surface (like lh.infl
-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, July 24, 2017 10:36 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
Hi Idil,
we only store surface overlays in .mgz not surfaces themselves. Try loading
a su
Hi Idil,
we only store surface overlays in .mgz not surfaces themselves. Try loading
a surface (like lh.inflated) then load whatever you were looking at as an
overlay on the surface
cheers
Bruce
On Mon, 24 Jul 2017, Yagmur Ozdemir 19 wrote:
> Hello freesurfer experts,
>
> I am trying to use
I see. Yes, that kind of thing is hard. YOu can try the gcuts
skullstripping, which is more aggressive and can sometimes get rid of
this kind of thing, but it also is more likely to strip brain. Or
manually remove those voxels in the brainmask.mgz
cheers
Bruce
On Thu, 22 Jun 2017, Lisa
Delal
Hi Bruce,
Thank you very much for your mail. I am going to specify my question.
In fact, we saw a problem after the recon-all step. The dura was included
in the lh.pial and rh.pial. Indeed, the red demarcation included the
meninges.
I send you an attachment
Cheers
Marine
2017-06-21 18:51
Hi Marine
the brainmask is just a rough estimate of what is brain and what is not.
You don't need to worry if it is not accurate *unless* the lh.pial and/or
rh.pial surfaces end up not being accurate because of dura left in the
brainmask.
cheers
Bruce
On Wed, 21 Jun 2017, Lisa Delalande wrot
to the files
listed in the folder "mri". Maybe the problem is caused here?
I will try to rerun the recon-all analysis of this subject.
Thank you very much for your help!
Regards,
Jens
Gesendet: Montag, 29. Mai 2017 um 16:32 Uhr
Von: "Bruce Fischl"
An: "Freesurfer
matic section. I will report,
if the issue appears there, too.
Regards,
Jens
Gesendet: Montag, 29. Mai 2017 um 07:41 Uhr
Von: "Jens Offenbach"
An: freesurfer@nmr.mgh.harvard.edu
Cc: "Freesurfer support list"
Betreff: Re: [Freesurfer] Segmentation fault (core dumped) error
I
An: freesurfer@nmr.mgh.harvard.edu
Cc: "Freesurfer support list"
Betreff: Re: [Freesurfer] Segmentation fault (core dumped) error
I am facing a similar issue with recon-all in FreeSurfer 6.0.0. on two subjects
from OASIS-Brains.
I will retry the run.
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