Hi Barbara,
Yes, you can use recon-all-clinical for the enhanced T1. But, the surface
reconstruction might fail and in that case, you might have to try running
SynthSR + recon-all.
Thank you,
Karthik
On Jun 13, 2024, at 1:30 AM, Barbara Bellenberg
wrote:
External Email - Use Caution
n case of any clue? Thank you so much!
>
> Best,
> Chen
>
>
>
> - Original Message -
>> From: "Douglas N. Greve"
>> To: "freesurfer"
>> Sent: Wednesday, 29 May, 2024 15:26:25
>> Subject: Re: [Freesurfer] Recon-all for a common temp
sounds like something is wrong with the image. Did you look at
ANTS_QS_... ? Is it oriented correctly? Does it look like a brain in a
head?
On 5/28/2024 6:07 AM, Chen Yang wrote:
> External Email - Use Caution
>
> Hi everyone,
>
> I tried to run the reconstruction with the command
External Email - Use Caution
Hi everyone,
I tried to run the reconstruction with the command line: recon-all -i
ANTS_QS_template_MNI.nii.gz -subject CGBT -all
then I got the error message:
talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
talairach_avi log
,
Yilei
*From:* Dong, Yilei
*Sent:* Tuesday, April 23, 2024 3:34 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] recon-all process still not finishing
properly
Hi Freesurfer support,
I have several
or it's more
of a cluster issue I have to talk with the staff that manage it?
Sincerely,
Yilei
From: Dong, Yilei
Sent: Tuesday, April 23, 2024 3:34 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all process still not finishing properly
Hi
on behalf of Douglas N. Greve
Sent: Thursday, April 18, 2024 2:57 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all process still not finishing properly
not sure what is happening. You can run recon-all with -debug and capture the
output (both stdout and stderr
not sure what is happening. You can run recon-all with -debug and
capture the output (both stdout and stderr) into a file. This will cause
it to print out huge amounts of text specifying what it is doing on each
line. You should also see if there is some stderr output that is not
being caught.
support list
Subject: Re: [Freesurfer] Recon-all stuck at topology fix
External Email - Use Caution
Here are some images from the patient. I also have the recon-all log posted
here is well. This is the same patient but taken from a file where I tried to
manually skull strip to fix
Can you post some pictures? The norm.mgz, the wm.mgz, the lh.orig.nofix, the
aseg.mgz, that kind of thing? Something is badly wrong….
Bruce
On Apr 10, 2024, at 7:05 PM, Bhole, Salil wrote:
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Hello,
I have tried to process this MRI a few times now and it
External Email - Use Caution
Hello,
I have tried to process this MRI a few times now and it always seems to get
stuck on the step I have pasted below here. I have tried to fix the defect
myself by editing the voxels manually, but that has also not seemed to help.
I've looked
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That worked beautifully. Thank you Yujing!
Best,
Will
On Apr 8, 2024, at 8:58 AM, Huang, Yujing wrote:
It looks like mris_fix_topology for lh hemisphere core dumped. This is from
your recon-all.log:
“
An extra large defect has been detected...
It looks like mris_fix_topology for lh hemisphere core dumped. This is from
your recon-all.log:
“
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see
Dear Sam,
The native images live in one space (typically anisotropic), whereas the
recon-all-clinical files always live in their own 1x1x1mm isotropic grid (which
is the whole point!). I am not familiar with the Enigma QC procedure but I
wouldn’t be surprised if it’s not compatible with these
You have a space in your current path (between severe and similar). That
is causing the problem
On 4/1/2024 8:26 AM, Huang, Yujing wrote:
There is a space in your path
‘/home/pengcuiyi/Desktop/QinLab/MRI_human_brain/severe
similar/first_sT1W_3D_TFE_tra_MR350895.nii’.
Rename the directory
There is a space in your path
‘/home/pengcuiyi/Desktop/QinLab/MRI_human_brain/severe
similar/first_sT1W_3D_TFE_tra_MR350895.nii’.
Rename the directory name and try again.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of ???
Sent: Sunday, March 31, 2024 11:18 PM
To:
pport list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all nu_correct error
Hi Yilei,
I think "nu_correct: Command not found. FREESURFER: Undefined variable." is
unrelated to your recon-all didn’t finish. That error happens in the beginning
of recon-all and rec
Hi Yilei,
I think "nu_correct: Command not found. FREESURFER: Undefined variable." is
unrelated to your recon-all didn't finish. That error happens in the beginning
of recon-all and recon-all uses ANTS N4BiasFieldCorrection for nu correct
instead. We have addressed this error in our dev
External Email - Use Caution
Thanks Yujing,
I realized that was likely the issue after sending my message. Indeed,
removing the -qcache option for this longitudinal processing step resolved
my issue.
Thanks for the clarification.
Dan
On Mon, Mar 25, 2024 at 9:37 AM Huang,
The recon-all ‘WM/GM Contrast’ step is skipped for longitudinal base
processing. So, I’m not sure that ‘-qcache’ option can be used in base
processing.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Dan Levitas
Sent: Thursday, March 21, 2024 11:56 AM
To:
What was your recon-all command line? You need to give it a directive (like
-all), otherwise it will just create a subject directory tree and put the
001.mgz in the orig dir
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Naama Zur
Sent: Sunday, March 17, 2024 5:13 PM
Hi Taylor,
I don't understand how you could get that error. It seems to me that
read_signa() is for reading .signa files.
Can you try 'mris_calc -o rh.area.mid rh.area add rh.area.pial' directly? Pass
full path to your rh.area and rh.area.pial.
What does 'mri_info rh.area' report?
Best,
External Email - Use Caution
Hi!
I've managed to debug the problem and it turns out that it was generated by
the mri_convert function - it produced a corrupted native.mgz image that
synthseg couldn't correctly read. I encounter this problem when pulling the
freesurfer:7.4.1 from
: [Freesurfer] recon all with optiBET brain mask
This is from Freesurfer wiki - MailScanner has detected a possible fraud
attempt from "secure-web. cisco. com" claiming to be https: //surfer. nmr. mgh.
harvard. edu/fswiki/UserContributions/FAQ Q. I have already skull-stripped
data. Can
Th
External Email - Use Caution
Hi!
Thanks for getting back to me. I'm running it on CentOS Linux 7 in a
singularity container. What I did is to pull the freesurfer container from
the DockerHub
External Email - Use Caution
It could help to know what OS version and what Freesurfer version you are
running. From your path /usr/local/freesurfer it looks like you are
running a Freesurfer release, e.g., 7.4.1.
- R.
On Feb 25, 2024, at 21:45, Agata Wolna awo...@mit.edu
Can you send the recon-all.log file that contains the error?
On 1/24/2024 4:01 AM, Kapteijns, Kirsten wrote:
External Email - Use Caution
Dear all,
I have run recon-all successfully on multiple subjects on multiple
timepoints. If I open the mri folder, it shows the correct talairach
Your recon-all command doesn't have the directive to tell it what to run - add
option '-all' to your command.
See this wiki page for detail
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Weisholtz, Daniel S.,MD
External Email - Use Caution
I don’t see what FREESURFER _HOME is set to, but if you used the .deb package
installer, it would be /usr/local/freesurfer/7.4.0, i.e.
$ wget
er support list
Subject: Re: [Freesurfer] recon-all cannot execute: required file not found
I’m wondering how you ran recon-all. Do you see the error even running it w/o
any arguments?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Peled, Noam,PhD
Sent: Friday, January 19, 20
I'm wondering how you ran recon-all. Do you see the error even running it w/o
any arguments?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Peled, Noam,PhD
Sent: Friday, January 19, 2024 2:59 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all cannot execute
, 2024 2:54 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all cannot execute: required file not found
After sourcing Freesurfer, $FREESURFER_HOME is added to the front of your $PATH.
1. ‘ls -l $FREESURFER_HOME/bin/recon-all’ to check if your recon-all has the
execute permissions
After sourcing Freesurfer, $FREESURFER_HOME is added to the front of your $PATH.
1. 'ls -l $FREESURFER_HOME/bin/recon-all' to check if your recon-all has the
execute permissions?
2. use 'chmod +x $FREESURFER_HOME/bin/recon-all' to grant the permission
Best,
Yujing
From:
7 (UTC+09:00)Subject: Re: [Freesurfer] recon-all errors
(cannot execute binary file
+External Email - Use
Caution
do not wish to continue communication over unencrypted e-mail
-Original Message-From: "윤혜정" hyejung7...@amc.seoul.krTo:
"Freesurfer support list&
External Email - Use Caution
do not wish to continue communication over unencrypted e-mail
-Original Message-From: "윤혜정" hyejung7...@amc.seoul.krTo:
"Freesurfer support list" freesurfer@nmr.mgh.harvard.edu; Cc:Sent:
2024-01-17 (수) 10:49:56
External Email - Use Caution
It looks like you did not use the .pkg file installer to install Freesurfer on
the Mac, otherwise you would have a path like /Applications/freesurfer/7.4.1 to
use as FREESURFER_HOME. The installer should ensure the privileges should
be correct to
Dear Francesca,
Our method cannot reliably segment these thin/faint structures from clinical
scans of arbitrary resolution and contrast, which is why they don’t get
segmented.
If you want to segment the choroid plexus, you could take then intensities
under the ventricles and split them into
Abeoseh B. flemist...@missouri.edu
Sent: Saturday, January 6, 2024 12:24:40 PM
To: fsbuild fsbu...@contbay.com; freesurfer@nmr.mgh.harvard.edu
freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS
No, I installed using tar.gz
freesu
External Email - Use Caution
I’m using Ubuntu.
Abeoseh Flemister
From: Flemister, Abeoseh B.
Sent: Saturday, January 6, 2024 12:24:40 PM
To: fsbuild ; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited
nux-ubuntu22_amd64-7.4.1.tar.gz>
Abeoseh Flemister
From: fsbuild
Sent: Friday, January 5, 2024 9:35 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Flemister, Abeoseh B.
Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS
Did you install Freesurfer 7.4.1
External Email - Use Caution
Did you install Freesurfer 7.4.1 using the Debian installer package
@nmr.mgh.harvard.edu
Cc: Flemister, Abeoseh B.
Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS
For issues with Freeview displaying graphics when running via Linux on a
Windows host thru WSL, you could look at the recent thread with the subject
"Re: [Freesurfer] Fre
External Email - Use Caution
For issues with Freeview displaying graphics when running via Linux on a
Windows host thru WSL, you could look at the recent thread with the subject
"Re: [Freesurfer] Freeview not showing output",
beoseh Flemister
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Huang, Yujing
Sent: Friday, January 5, 2024 3:05 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS
WARNING: This message has originated from an External
This is from your recon-all.log
"
mri_convert /home/abeoseh/Downloads/OneDrive_1_1-4-2024/Subject
6/Baseline/3D_T1_MPRAGE_PRE_MPR_AX.nii.gz
/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz
mri_convert: extra argument
This is from Freesurfer wiki - MailScanner has detected a possible fraud
attempt from "secure-web.cisco.com" claiming to be
External Email - Use Caution
Thanks for pointing that out! That seems to be working. Jim
On Thu, Dec 28, 2023 at 6:53 PM Huang, Yujing
wrote:
> This is from Freesurfer wiki -
>
This is from Freesurfer wiki -
https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ
Q. I have already skull-stripped data. Can I submit it to recon-all?
A: If your skull-stripped volume does not have the cerebellum, then no. If it
does, then yes, however you will have to run the data
yes, sending the full log file will be helpful. My guess is that the
surfaces got out of synch (eg, if you had done edits).
On 11/21/2023 8:15 PM, Mark Wagshul wrote:
External Email - Use Caution
Dear Freesurfer experts,
Hi. Hoping someone can give me some guidance in how to proceed
NaNs are in your original input image. They are replaced with 0 in the output
mri/orig/001.mgz.
Doug mentioned “Sometimes SPM will put NaNs in the image to indicate a mask.”.
Is that your case?
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Carlos Alcocer
Sent: Tuesday,
And how did you create 001.mgz? Sometimes SPM will put NaNs in the
image to indicate a mask.
On 11/17/2023 10:12 AM, Huang, Yujing wrote:
Hi Carlos,
Can you attach recon-all.log?
Best,
Yujing
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
*On Behalf Of *Carlos Alcocer
*Sent:*
Hi Carlos,
Can you attach recon-all.log?
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Carlos Alcocer
Sent: Thursday, November 16, 2023 4:57 PM
To: Freesurfer support list
Subject: [Freesurfer] recon-all error
External Email - Use Caution
Hi,
For some of
Dear Pauline,
Thanks for the interest in our new pipeline!
You can only run one scan at the time (but that scan may be of any resolution /
contrast).
Cheers,
/E
--
Juan Eugenio Iglesias
http://www.jeiglesias.com
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Lieshout, P.B. van
tember 2023 um 00:55
An: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
Cc: "Conrad, Julian" julian.con...@medma.uni-heidelberg.de
Betreff: Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error
in SynthSeg
Besides
patching the python di
External Email - Use Caution
Besides patching the python distribution, another option available now is
the development arm64 build for silicon Macs with an M1, M2 processor.
But this is not a release build and so has not been tested like a stable
release. The dev builds are
2. Hope
this works!
Annabel
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Iglesias Gonzalez, Juan
E.
Date: Tuesday, 26 September 2023 at 17:35
To: Freesurfer support list
Subject: Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error
in SynthSeg
Exter
External Email - Use Caution
Dear Julian,
I believe this is a problem with SynthSeg not being compatible with the new
microprocessor in MAC computers. Our software engineers are looking into
solutions to this.
Sorry for the inconvenience,
Eugenio
--
Juan Eugenio Iglesias
External Email - Use Caution
Hello Lauren:
Open the sR0391178-0002-1-000208-01.nii.gz file using freeview and see
if the whole 3D brain is in place. This should give you a clue as to why
this occurred.
best,
Alan
On Wed, Sep 13, 2023 at 1:02 PM Lauren Stephens
wrote:
>
Wednesday, September 13, 2023 2:11 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Recon-all completed without error in 10 seconds
External Email - Use Caution
Hi Yujing,
Thank you, that did work!
Follow up question: Why would the code I used above, successfully generate the
recon-a
External Email - Use Caution
I think you need to pass the flag ‘-all’ in the command line.
recon-all -s 967 -i
/Users/corpuscallosum/Desktop/subjects/sR0391178-0002-1-000208-01.nii.gz
-all
Nárlon Cássio
Nárlon Cássio Boa Sorte Silva PhD (He, Him, His)
CIHR and MSHR
support list
Subject: Re: [Freesurfer] Recon-all completed without error in 10 seconds
External Email - Use Caution
Hi Lauren,
You will also need to specify ‘-all’ to recon-all.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Lauren Stephens
Sent
External Email - Use Caution
Hi Lauren,
You will also need to specify '-all' to recon-all.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Lauren Stephens
Sent: Wednesday, September 13, 2023 2:02 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject:
External Email - Use Caution
Recon-all-clinical worked consistently with 32 Gb RAM. I used WSL Ubuntu
with 26Gb allocated to WSL before it would use swap. I watched one run,
and it used total physical and swap memory of about 28 Gb.
With 16Gb RAM it worked on about 75% of
External Email - Use Caution
Thanks for the updates. Not that it will likely help with the
memory underrun, but it should be straightforward to update Freesurfer from
7.2.0 to 7.4.1 in the VM from the command line.
You can use the Firefox browser in the VM to download the 7.4.1
External Email - Use Caution
Thank you fsbuild for the suggestions. Unfortunately it still does not
work. I did not try the virtual machine, because I could only find version
7.2.0 ova file on the freesurfer website. It appears the 7.4.0 version
does not yet have a virtual
External Email - Use Caution
The method I mentioned before does not always work. It worked for all but
about 3 scans out of approximately 30. There are some scans for which the
"committed memory" caps at about 23 Gb in the task manager and then either
the out of memory error
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Hello Matthew,
Thanks for this info.
If it is not too much work, just wondering if you could make a rough estimate
or compute an average for the *total*memory* in use = (size of physical RAM in
use by synthseg + size of all swap files resident on
External Email - Use Caution
Here is some additional follow up. I was able to get recon-all-clinical
working in Ubuntu in WSL on a 16 Gb machine by increasing the swap and
memory allowed in WSL. This is done through the .wslconfig file which is
located in the %USERPROFILE%
External Email - Use Caution
I was able to get recon-all-clinical working with 16 Gb computer.
I thought the problem might be Windows hogging memory, so I created a live
persistent USB install of lubuntu, using lubuntu 22 as a low resource
distro in order to minimize memory
External Email - Use Caution
I do not have access to a computer with more RAM. I can run recon-all with
1mm T1 images without any problems. How much RAM would recon-all-clinical
be expected to need? Does it require less RAM if it uses the GPU instead
of CPU?
On Thu, Jul 13,
External Email - Use Caution
Can you try it on a computer with more ram?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Matthew Lynch
Sent: Thursday, July 13, 2023 1:55 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all-clinical out of memory error
External Email - Use Caution
It looks like you started recon-all by copying in mri/orig/001.mgz. I saw
multiple runs of recon-all that were run on top of each other.
Can you try to restart clean by providing the input on the command line
‘recon-all -s -I -all’?
Best,
Yujing
External Email - Use Caution
So when I fixed those two _thresh errors in
External Email - Use Caution
Actually, that is not the problem at all.
I have found two errors in your script (the one on Github)
There are two lines which refer to colortable_BA_thresh.txt that should say
/colortable_BA.txt
The script gets further when I fix those but I still
External Email - Use Caution
I found the problem. Your script has the following lines :
You need to delete the fsaverage from the $SUBJECTS_DIR definition because
the lines following it put it in also.
ln -s $FREESURFER_HOME/subjects/fsaverage $SUBJECTS_DIR/
cd ../label
# labels
: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Date: Tuesday, June 20, 2023 at 9:32 AM
To: freesurfer@nmr.mgh.harvard.edu , Iglesias
Gonzalez, Eugenio , Gopinath, Karthik
Subject: Re: [Freesurfer] recon-all-clinical
External Email - Use Caution
On 5/26/2023 5:39 PM
External Email - Use Caution
On 5/26/2023 5:39 PM, Andrew Dedinas Geoly wrote:
External Email - Use Caution
Hello Freesurfer experts!
I am conducting a longitudinal GMV and CT analysis of mTBI
participants who received an experimental single-dose pharmacological
External Email - Use Caution
I think your SUBJECTS_DIR environment variable is still set to the default
spath to ubject data that is set by default in the 7.2.0 release. It is
not intended that you add your own subjects in the freesurfer distribution as
those are examples (and
External Email - Use Caution
We should have an update for this installed there soon.
- R.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this
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Hi Sofia
Unfortunately that doesn't really work as the most time-intensive steps are
required. We are working on replacing some of these with deep-learning
equivalents, but it will be some months before that is available.
Sorry
Bruce
From:
Carlos,
I’m not sure what happened. There are no errors reported in recon-all.log. Can you try running it again without ‘-parallel’?
Best,
Yujing
From: Carlos Estévez Fraga
Sent: Friday, March 10, 2023 7:39 AM
To: Freesurfer support list ; Huang, Yujing
Subject: Re: [Freesurfer] recon-all
Hi Carlos,
I’m not sure what happened. There are no errors reported in recon-all.log. Can
you try running it again without ‘-parallel’?
Best,
Yujing
From: Carlos Estévez Fraga
Sent: Friday, March 10, 2023 7:39 AM
To: Freesurfer support list ; Huang, Yujing
Subject: Re: [Freesurfer] recon
External Email - Use CautionSorry just wanted to follow up on this as not sure the email was receivedMany thanks Best regards CarlosEnviado desde mi iPhoneEl 9 mar 2023, a la(s) 17:32, Carlos Estévez Fraga escribió:Sure I am attaching the recon-all file. Below is the output I get
Hi Carlos,
Can you send recon-all.log as attachment? So, we can have a better
understanding of what happened.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Carlos Estévez Fraga
Sent: Thursday, March 9, 2023 9:33 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject:
help!
*Bryna Goeckner* (she/her)
Graduate Student
Meier Lab
Medical College of Wisconsin
Neuroscience Doctoral Program
Date: Fri, 10 Feb 2023 20:48:26 +
From: "Huang, Yujing"
Subject: Re: [Freesurfer] Recon-all exited with errors
To: Freesurfer support list
Message-ID:
Co
You can find information about recon-all process here
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all
Add '-finalsurfs' to you recon-all command line options.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Faraz
Yazdanibanafshedaragh
Sent: Wednesday, February
for your help!
Bryna Goeckner (she/her)
Graduate Student
Meier Lab
Medical College of Wisconsin
Neuroscience Doctoral Program
Date: Fri, 10 Feb 2023 20:48:26 +
From: "Huang, Yujing"
Subject: Re: [Freesurfer] Recon-all exited with errors
To: Freesurfer support list
Message-ID:
Hi Bryna,
In this tutorial, it talks about how to fix bad output from the talairach
registration:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Goeckner, Bryna
Sent: Friday, February 10, 2023 3:35 PM
-boun...@nmr.mgh.harvard.edu
On Behalf Of MANSON ERIC NAAB
Sent: Friday, January 6, 2023 12:37 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all terminates with error
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Thank you for your quick response. Please, can you kindly assist me
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Thank you for your quick response. Please, can you kindly assist me with
freesurfer input image template for sT1-weighted? How do I solve this
orientation problem?
Thank you.
On Fri, 6 Jan 2023, 14:34 Huang, Yujing, wrote:
> It looks like there is
It looks like there is a problem with your input dicom file - image orientation
tag is missing.
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of MANSON ERIC NAAB
Sent: Thursday, January 5, 2023 11:15 PM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all terminates
Hi Christopher,
I noticed that you were only running 'recon-all -autorecon1 -autorecon2'. I
don't think ?h.white surface are generated for the command combinations.
'recon-all -all' will run all recon steps and generate ?h.white.
Here is a description of recon-all process and flags:
please send the recon-all.log file
On 11/23/2022 5:10 PM, Christopher Mcnorgan wrote:
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A student and I have independently been trying to reconstruct a
dataset. We've tried it a couple different ways using either an
additional FLAIR or a T2 image and
Hi Christopher,
I noticed that you were only running 'recon-all -autorecon1 -autorecon2'. I
don't think ?h.white surface are generated for the command combinations.
'recon-all -all' will run all recon steps and generate ?h.white.
Here is a description of recon-all process and flags:
Hi Andrew,
1. The recon-all output is in the subject's native space.
2. So, registration of the volume (MNI) and surfaces (fsaverage) happens as
part of the recon-all process, but they're not resampled automatically i.e.
kept in the subject's native space. You can use mri_vol2vol command
Sometimes the stroke will mess up the analysis in the undamaged hemi. A
lot of times people will make a mask of the stroke area, left-right
reverse the brain and register it to itself, then map the contralateral
hemi into the voxels of the stroke, then run recon-all on this modified
image.
Hi Steve,
You can use ‘-hemi ’ to select which hemisphere to process. If you are
interested in right hemisphere only, pass ‘-hemi rh’ to recon-all along with
other flags.
I don’t have answers to your first question.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of
It is not clear what is going wrong as there is not really an error
message.Was there anything printed to the terminal that is not in the
log file? The last thing it did was to write out
mri/aparc.DKTatlas+aseg.mgz. Can you check that and see if it looks ok?
Did you run out of space on the
There might be some issues with jpeg compressed dicom files in 7.2 and
before. Can you try using 7.3 to do the conversion with mri_convert or
dcmunpack (add -dcm2niix to either one to get the new, better code).
On 9/5/2022 10:53 PM, Beatrice Everall wrote:
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I'm not sure what is going wrong with that. Can you look at the data?
Particilarly the norm.mgz
On 7/26/2022 9:53 AM, gianrocco wrote:
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Hi,
I attache hereby my email, as it was rejected — since I was not
registered yet to the list
Thanks again
Kind
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