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I installed freesurfer 7.4.1 on Debian 12 (using the Ubuntu 22 .tar.gz).
Some programs run fine, but some do not.
When running recon-all, I get the following error:
-bash: /opt/freesurfer/freesurfer-7.4.1/bin/recon-all: cannot execute:
required file
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:
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Dear Freesurfer experts,
Hi. Hoping someone can give me some guidance in how to proceed
External Email - Use Caution
Dear Freesurfer experts,
Hi. Hoping someone can give me some guidance in how to proceed with this error
in recon-all (at the moment, was running autorecon-wm, but not sure that's
relevant). Just pasting the last few commands which were successfully
, November 21, 2023 10:59 AM
To: Freesurfer support list
Subject: [Freesurfer] recon-all error
External Email - Use Caution
Reposting due to issue with email bouncing. I am receiving following error on
my subjects. Recon-all still continues after error and finishes "without error&quo
, November 16, 2023 4:57 PM
*To:* Freesurfer support list
*Subject:* [Freesurfer] recon-all error
*External Email - Use Caution *
Hi,
For some of my subjects I get the following error at the beginning of
recon-all:
mri_convert /path/to/inputt1.nii /path/to/mri/orig/001.mgz
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
External Email - Use Caution
Hi,
For some of my subjects I get the following error at the beginning of
recon-all:
mri_convert /path/to/inputt1.nii /path/to/mri/orig/001.mgz
mri_convert /path/to/anat_t1.nii /path/to/mri/orig/001.mgz
reading from /path/to/anat_t1.nii...
NaN
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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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Hello Everyone,
due to new hardware my old freesurfer did not work anymore,
so I have new UBUNTU 22.04
and
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
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
Not sure what is happening. Does it work if you restart the long time
point from scratch (ie, remove the folder that is there)?
On 6/29/2022 5:49 PM, coope...@student.unimelb.edu.au wrote:
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Dear FreeSurfer developers,
I’m attempting to run recon-all with
External Email - Use Caution
Dear FreeSurfer developers,
I'm attempting to run recon-all with the longitudinal stream, but one
subject (out of >500) fails recon-all (I've re-started many times). The
cross-sectional and base (i.e. steps 1 and 2 of the longitudinal processing)
External Email - Use Caution
Hello Mouna,
You should not need to set FREESURFER_HOME in the terminal window or source the
setup script as that is already set in the environment to the pre-installed
7.2.0 release of freesurfer. if the setup information listing
FREESURFER_HOME
To: Freesurfer support list
Subject: Re: [Freesurfer] Recon-all Error: "ln: failed to create symbolic link
'lh.white.H': Operation not permitted"
Hmm, ok that's not the issue. You have plenty of free disk space (185Gb)
Is the folder /home/developer/guest_shared shared with the host O
diagnosing this issue!
-Paul
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Joanna L Eckhardt
Sent: Friday, May 6, 2022 2:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Recon-all Error: "ln: failed to create symbolic link
'lh.wh
on behalf of Wighton, Paul
Sent: Friday, May 6, 2022 10:55 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all Error: "ln: failed to create symbolic link
'lh.white.H': Operation not permitted"
Hi Joanna,
Is it possible you've run out of disk space? What's the output o
: [Freesurfer] Recon-all Error: "ln: failed to create symbolic link
'lh.white.H': Operation not permitted"
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Dear FreeSurfer Team,
I am attempting to run Recon-all on practice cannabis data on the tutorial,
using Ubuntu18 VM for Windows os (also I comp
External Email - Use Caution
Dear FreeSurfer Team,
I am attempting to run Recon-all on practice cannabis data on the tutorial,
using Ubuntu18 VM for Windows os (also I completely new to coding and Ubuntu).
On my first attempt to run Recon-all, I got the error shown below: "ln:
Thanks Joanna, that's great to hear!
-Paul
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Joanna L Eckhardt
Sent: Thursday, May 5, 2022 8:30 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Recon-All Error: "Command exited with non
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-All Error: "Command exited with non-zero status"
Hi Joana,
There are a few things going on here.
First, you should create a subjects directory for FreeSurfer recons and tell
FreeSurfer where it is by setting the SUBJECTS_DIR environment vari
of Joanna L Eckhardt
Sent: Thursday, May 5, 2022 3:37 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Recon-All Error: "Command exited with non-zero status"
External Email - Use Caution
Hi FreeSurfer Team,
I am trying to run Recon-all on the cannabis
External Email - Use Caution
Hi FreeSurfer Team,
I am trying to run Recon-all on the cannabis test data on the freesurfer
tutorial (I am running Ubuntu 18 VM on Windows os).
When I try to use the Recon-all command, I get the error "Command exited with
non-zero status" and
April 2022 2:26 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all error
Hi Rebecca,
I was able to access and download the data. But they don’t look like dicom
files. They don’t have the prefix ‘DICM’ in them. Dcm2niix that I mentioned
before doesn’t recognize them either
Elizabeth Cooper
Sent: Tuesday, April 26, 2022 5:59 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all error
External Email - Use Caution
Dear Yujing,
My apologies! Hopefully you can access this now.
Kind regards,
Rebecca
On Tue, Apr 26, 2022 at 11:29 PM Huang, Yujing
rmission to access it.
>
>
>
> Yujing
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Rebecca Elizabeth
> Cooper
> *Sent:* Monday, April 25, 2022 7:12 PM
> *To:* Freesurfer
April 2022 8:34 AM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all error
Hi Rebecca,
We would like to understand why those dicom files are not recognized by
Freesurfer. If it is possible, can you provide us some of those dicom files to
F1l-ZiyouIRcvEgR258PYb5B90P2b3EFDg%2Fview%3Fusp%3Ddrive_web>
*From:* freesurfer-boun...@nmr.mgh.harvard.edu <
freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Huang, Yujing
*Sent:* Tuesday, 26 April 2022 8:34 AM
*To:* Freesurfer support list
*Subject:* Re: [Freesurfer] recon-all error
Hi Rebecca,
:50 PM
To: 'Freesurfer support list'
Subject: Re: [Freesurfer] recon-all error
Hi Rebecca,
Thank you for the information.
I'm wondering if you would like to try converting those dicom using dcm2niix to
.nii, and then feed .nii to recon-all pipeline.
You can download dcm2niix here:
https
oun...@nmr.mgh.harvard.edu
on behalf of
coope...@student.unimelb.edu.au
Sent: Saturday, April 23, 2022 2:44 AM
To: 'Freesurfer support list'
Subject: Re: [Freesurfer] recon-all error
External Email - Use Caution
Hi Yujing,
I guess not. This is the output:
cooperr@marge:/data/netapp01/wo
...@student.unimelb.edu.au <mailto:coope...@student.unimelb.edu.au>
mailto:coope...@student.unimelb.edu.au> >
Sent: Friday, April 22, 2022 1:34 AM
To: Huang, Yujing mailto:yhuan...@mgh.harvard.edu>
>; 'Freesurfer support list' mailto:freesurfer@nmr.mgh.harvard.edu> >
Subject: RE: [Fre
, 2022 1:34 AM
To: Huang, Yujing ; 'Freesurfer support list'
Subject: RE: [Freesurfer] recon-all error
External Email - Use Caution
Dear Yujing,
Thank you for your reply.
1. Confirmed I am running Freesurfer 6.0.
2. I am running both commands from within the individual subject
unique series:
Patient: Undefined variable.
With thanks,
Rebecca
From: Huang, Yujing
Sent: Friday, 22 April 2022 4:19 AM
To: Freesurfer support list
Cc: coope...@student.unimelb.edu.au
Subject: RE: [Freesurfer] recon-all error
Hi Rebecca,
I’m trying to get more information
Forwarded Message
Subject:
[Freesurfer] recon-all error
Date:
Sun, 10 Apr 2022 07:01:30 +1000
From:
coope...@student.unimelb.edu.au<mailto:coope...@student.unimelb.edu.au>
Reply-To:
Freesurfer support list
<mailto:freesurfer@nmr.mgh.harvard.edu>
To:
freesurfer@nmr.mgh
External Email - Use Caution
Dear FreeSurfer developers,
I'm attempting to run recon-all on a set of T1-weighted images acquired in
the 1980s-1990s and am having trouble with the recon-all pipeline. I have
used the original dicom files in the recon-all using the command below.
Did you check the transform? It was the automatic failure detection that
threw the error. This can sometimes happen when the head is at a "funny"
orientation in the scanner, but at 7T there might be some bias fields
having an effect. Also, see if it works when you sample it at 1mm (just
don't
I'm not sure what is happening or why the tal reg is apparently failing.
My guess is that it is something non-standard about the image. The first
thing to try is to run it at 1mm (without the -hires). At some point,
you may have to send us the volume (or at least some pictures in axial,
sag,
Thanks, Tim,
The lh.white.K and lh.white.H were created.
Thanks,
Noam
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Tim Schäfer
Sent: Friday, January 14, 2022 11:18 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all: error in creating
External Email - Use Caution
Can you check whether any of the .H/.K files were created? They contain the
per-vertex mean/Gaussian curvature for the respective surface, but what's more
important is that they are symbolic links.
If you try to save recon-all output onto a drive
Glad to hear it
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of William McCuddy AZ-Phoenix
Sent: Saturday, December 11, 2021 3:44 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer recon-all error “mri_convert: extra
argument”
External Email - Use
@nmr.mgh.harvard.edu
Subject: [Freesurfer] Freesurfer recon-all error “mri_convert: extra argument”
External Email - Use Caution
Hello Freesurfer Community,
I'm new to freesurfer and could use some help with recon-all on a single
subject. The input file is a 3D T1 WAND from a Philips scanner. I
it is not clear why it failed. Can you look at nu.mgz to see if
anything looks weird about it?
On 11/18/2021 1:43 AM, Wei Shao wrote:
External Email - Use Caution
Hi, Dear Freesurfer experts
I'm have met a recon-all errors with data collected recently like this
External Email - Use Caution
Hi, Dear Freesurfer experts
I'm have met a recon-all errors with data collected recently like this
ADNI_002_S_6652_MR_Accelerated_Sagittal_MPRAGE__br_raw_20190122095958285_147_S786989_I1118713.dcm
The attachments are the recon-all script and the
wow, that is weird. The RH extends far into the LH. What does the
aseg.presurf.mgz look like? Are the cortices and WM properly separated
left-right?
On 11/15/2021 4:33 AM, Alec Süwolto wrote:
External Email - Use Caution
Hello freesurfers,
I’m new to freesurfer and I can’t fix a
External Email - Use Caution Hello freesurfers, I’m new to freesurfer and I can’t fix a hard failure of recon-all.The error message is: CORRECTING DEFECT 0 (vertices=94923, convex hull=13109, v0=0)error: Cannot allocate memoryerror: Excessive topologic defect encountered: could not
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Hi,
I’m using macOS big sur 11.5.2. The file did exist and I do have read
permissions; I also did resolve the problem eventually :) - I had a backup of
fs and replaced the whole subject directory with it and now recon-all seems to
be working fine.
What platform are you using (eg, mac?). Can you send the recon-all.log
file? Can you verify that the file actually exists and that you have
read permissions?
On 9/3/2021 4:52 AM, Szulia Agata wrote:
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Hi,
I have a
抄送:
主题: Re: [Freesurfer] Recon-all error :Segmentation fault (core dumped)
Actually, I think I see what the problem is. You apparently have a command
called "bc" in your path. mri_nu_correct.mni is trying to use the linux-native
bc command (a simple calculator usually located in /bin). What do y
;
*发送时间:*2021-06-01 08:35:38 (星期二)
*收件人:* freesurfer@nmr.mgh.harvard.edu
*抄送:*
*主题:* Re: [Freesurfer] Recon-all error :Segmentation fault (core
dumped)
Not sure, can you try this
cd /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri
mri_nu_correct.mni --debug --i
transforms/talairach.xfm --n 2 --ants-n4 >& nucor.log
and got the nucor.log.
-原始邮件-
*发件人:*"Douglas N. Greve"
*发送时间:*2021-06-01 08:35:38 (星期二)
*收件人:* freesurfer@nmr.mgh.harvard.edu
*抄送:*
*主题:* Re: [Freesurfer] Recon-all error :Segmentation fault (cor
ot;
发送时间:2021-06-01 08:35:38 (星期二)
收件人: freesurfer@nmr.mgh.harvard.edu
抄送:
主题: Re: [Freesurfer] Recon-all error :Segmentation fault (core dumped)
Not sure, can you try this
cd /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri
mri_nu_correct.mni --debug --i orig.mgz --o nu.mgz --uchar
transforms/
Not sure, can you try this
cd /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri
mri_nu_correct.mni --debug --i orig.mgz --o nu.mgz --uchar
transforms/talairach.xfm --n 2 --ants-n4 >& nucor.log
and send the file nucor.log
On 5/28/2021 7:51 AM, liub wrote:
External Email - Use
External Email - Use Caution
Hello,
please ignore my message below: the problem was in the name of the folder
"Group 0".
Please do excuse me for bothering you,
best,
GT
> Il 24/05/2021 17:57 g.ton...@libero.it ha scritto:
>
>
> Hello FreeSurfer Developers,
>
>
External Email - Use Caution
Hello FreeSurfer Developers,
Thank you for your work ! I am new to Freesurfer and I apologize if my question
is naive but I cannot find a solution in any of the online resources.
I successfully set up Freesurfer and I am now attempting to run
My guess is that the problem is the spaces in the folder name. Try
removing those spaces and see if it works
On 2/18/2021 7:29 PM, Eduardo Bergonzoni Junqueira wrote:
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Running the command in another directory I got another error:
(base)
External Email - Use Caution
Running the command in another directory I got another error:
(base) eduardo@eduardo-X555UB:/usr/local/freesurfer/subjects$ recon-all -i
/home/eduardo/Área\ de\ Trabalho/Grant_Tractography/t1.nii.gz -s Grant_sub
-all
Traceback (most recent call last):
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to preprocesss a t1.nii.gz image in freesurfer with
recon-all. I'm following the tutorial for linux in
on the
Freesurfer
wiki
Let me know if you have more questions.
Best regards,
Ren
From: freesurfer-boun...@nmr.mgh.harvard.edu
Date: Wednesday, January 6, 2021 at 21:34
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Recon-all Error
External Email - Use Caution
Hello! I’m
External Email - Use Caution
Hello! I'm experiencing an error while I try to use recon-all in a T1 MRI
image, the following error message appears:
"[...]
using segmentation for initial intensity normalization
using MR volume brainmask.mgz to mask input volume...
reading mri_src
Hard to say without the recon-all.log file, but my guess is that something is
wrong with one of your surfaces. Load the surfaces in freeview and see how they
look
On 12/14/2020 7:30 PM, Boa Sorte Silva, Narlon wrote:
External Email - Use Caution
Hi there,
Hope this finds you well
I
.mgh.harvard.edu>>
Date: Monday, December 14, 2020 at 7:31 PM
To: FS Help
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Recon-all error: MatrixMultiply: m1 is null!
External Email - Use Caution
Hi there,
Hope this finds you well
I have noticed the following erro
rew
From: on behalf of "Boa Sorte Silva,
Narlon"
Reply-To: FS Help
Date: Monday, December 14, 2020 at 7:31 PM
To: FS Help
Subject: [Freesurfer] Recon-all error: MatrixMultiply: m1 is null!
External Email - Use Caution
Hi there,
Hope this finds you well
I have noticed the fo
External Email - Use Caution
Hi there,
Hope this finds you well
I have noticed the following error for some of my runs:
@# Cortical ribbon mask Mon Dec 14 15:43:24 PST 2020
/Applications/freesurfer/7.1.1/subjects/BT_long/BT_055_base/mri
\n mris_volmask --aseg_name aseg.presurf
Does it work on other subjects? I'm guessing this has to do with having the MNI
tools properly installed. For testing purposes, can you download and run
version 7 to see if it works?
On 12/8/2020 12:40 PM, Devanshi jain wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to convert my .nii files (taken from ADNI dataset) to
subject files (like bert). For the same I'm following this website :
Hi Courtney
Can you send us your command line and a recon-all.log?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Courtney Haswell
Sent: Wednesday, December 2, 2020 9:24 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Recon-all error
External
External Email - Use Caution
I am trying to debug why all of our T1's are failing Freesurfer recon-all.
It seems that most of the files are being created but it isn't getting to
the stats steps to output those files. In the recon-all log it does say
"recon-all -s 13265 exited with
期五)
收件人: "Freesurfer support list"
抄送:
主题: Re: [Freesurfer] recon-all error
Oh. Talairach is a human atlas - you won't be able to register a macaque to it
Sorry
Bruce
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Jie Zhao
Sent: Friday, September
error
External Email - Use Caution
Yes , It is the macaque subject from Siemens 7T MRI
> -原始邮件-
> 发件人: "Fischl, Bruce"
> 发送时间: 2020-09-04 00:18:53 (星期五)
> 收件人: "Freesurfer support list"
> 抄送:
> 主题: Re: [Freesurfer] recon-all error
>
External Email - Use Caution
Yes , It is the macaque subject from Siemens 7T MRI
> -原始邮件-
> 发件人: "Fischl, Bruce"
> 发送时间: 2020-09-04 00:18:53 (星期五)
> 收件人: "Freesurfer support list"
> 抄送:
> 主题: Re: [Freesurfer] recon-all error
>
Hi Jie,
Is this a scan of a non-human primate?
Cheers
Bruce
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Jie Zhao
Sent: Thursday, September 3, 2020 9:34 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all error
External Email
/lh.white
Best,
Jie
-Original Messages-
*From:*"Douglas N. Greve"
*Sent Time:*2020-08-29 23:31:44 (Saturday)
*To:* freesurfer@nmr.mgh.harvard.edu
*Cc:*
*Subject:* Re: [Freesurfer] recon-all error
What is the error? tkregister2 is an old program, an
08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all error
External Email - Use Caution
Here is the snapshot of my freeview window attached.
-Original Messages-
From: "Fischl, Bruce" Sent Time: 2020-08-30
02:07:50 (Sunday)
To: "Freesurfer support
n freeview before we will be able to process it.
Cheers
Bruce
-
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Jie Zhao
Sent: Saturday, August 29, 2020 10:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all error
External
: [Freesurfer] recon-all error
External Email - Use Caution
Hi Bruce
Thank you for quick answer。
I tryrd the freeview -v /usr/local/freesurfer/subjecs/2018MPRAGE_p4iso.nii, my
freeview orienatation is RAS. could you tell me how to change it from RAS to
(ASL)anterior/superior/left
las N. Greve"
Sent Time:2020-08-29 23:31:44 (Saturday)
To: freesurfer@nmr.mgh.harvard.edu
Cc:
Subject: Re: [Freesurfer] recon-all error
What is the error? tkregister2 is an old program, and it might not work on all
systems. You can try using tkregisterfv instead, available
> -原始邮件-
> 发件人: "Fischl, Bruce"
> 发送时间: 2020-08-27 23:39:20 (星期四)
> 收件人: "Freesurfer support list"
> 抄送:
> 主题: Re: [Freesurfer] recon-all error
>
> Hi Jie
>
> I would start by looking at your input volume in freeview, my orientation on
>
---Original Messages-
From:"Douglas N. Greve"
Sent Time:2020-08-29 23:31:44 (Saturday)
To: freesurfer@nmr.mgh.harvard.edu
Cc:
Subject: Re: [Freesurfer] recon-all error
What is the error? tkregister2 is an old program, and it might not work on all
systems. You can try using tk
regards,
Jie
-Original Messages-
From: "Douglas N. Greve"
Sent Time: 2020-08-28 00:06:31 (Friday)
To: freesurfer@nmr.mgh.harvard.edu
Cc:
Subject: Re: [Freesurfer] recon-all error
This is the automatic failure detection raising a warning flag. Did you
notice that the output
it.Thanks.
Please check the error log file attached.
King regards,
Jie
> -Original Messages-
> From: "Douglas N. Greve"
> Sent Time: 2020-08-28 00:06:31 (Friday)
> To: freesurfer@nmr.mgh.harvard.edu
> Cc:
> Subject: Re: [Freesurfer] recon-all error
>
sday, August 27, 2020 11:21 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] recon-all error
>
> External Email - Use Caution
>
> Hi, Andrew
>
> Attached is the right recon-all.log file, please check it.
> I am new to the freesurfer,
On Behalf Of Jie Zhao
Sent: Thursday, August 27, 2020 11:21 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all error
External Email - Use Caution
Hi, Andrew
Attached is the right recon-all.log file, please check it.
I am new to the freesurfer, so really need you
2020-08-26 10:17:00 (Wednesday)
> To: "Freesurfer support list"
> Cc:
> Subject: Re: [Freesurfer] recon-all error
>
> Hi Jie, this appears to be the log for your original issue, and not the
> talairach registration failure.
> Andrew
>
> On 8/25/20, 9:23 AM, &qu
t list"
> Cc:
> Subject: Re: [Freesurfer] recon-all error
>
> Hi Jie,
>
> Can you send the subject's full recon-all.log file to provide some more
context for this failure? Usually this error is due to a poor registration, but
there might be someth
esurfer support list"
> Cc:
> Subject: Re: [Freesurfer] recon-all error
>
> Hi Jie,
>
> Can you send the subject's full recon-all.log file to provide some more
> context for this failure? Usually this error is due to a poor registration,
> but there might be somethin
"Freesurfer support list"
> 抄送:
> 主题: Re: [Freesurfer] recon-all error
>
> External Email - Use Caution
>
> What happems if you type 'mri_ca_label' in your shell?
>
> Did you setup your PATH environment v
rach.xfm
> ***FAILED*** (p=0., pval=0. < threshold=0.0050
>
> How can solve this error?
>
> Regards,
> Jie
>
>> -原始邮件-
>> 发件人: "Tim Schäfer"
>> 发送时间: 2020-08-23 16:24:28 (星期日)
>> 收件人: "Freesurfer support list&qu
/talairach.xfm
***FAILED*** (p=0., pval=0. < threshold=0.0050
How can solve this error?
Regards,
Jie
> -原始邮件-
> 发件人: "Tim Schäfer"
> 发送时间: 2020-08-23 16:24:28 (星期日)
> 收件人: "Freesurfer support list"
> 抄送:
> 主题: Re: [Freesurfer] recon-all error
External Email - Use Caution
What happems if you type 'mri_ca_label' in your shell?
Did you setup your PATH environment variable to include the Freesurfer binary
directory?
Tim
> On August 23, 2020 at 9:34 AM Jie Zhao wrote:
>
>
> External Email - Use Caution
External Email - Use Caution
Dear freesurfer developer:
I am using Freesurfer 7.1.1 and encounter an error like this when using
recon-all :
zhao@zhao-VirtualBox:~$ export SUBJECTS_DIR=/usr/local/freesurfer/subjects
zhao@zhao-VirtualBox:~$ recon-all -s test4 -i
Hi Nina,
The recon all pipeline uses an adult atlas. We have had collaborators
successfully using it with subjects all the way down to age 4.5yrs, but under
that it would not be recommended. Have you looked at the infant pipeline?
Best, Lilla
From:
Can you send the subject to us? See below for instructions
From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous"
If you look at the recon-all.log file, you will see
Include the flag -cw256 with recon-all
So try that
On 6/22/2020 10:03 AM, Frank Chau wrote:
External Email - Use Caution
**
Dear Freesurfer experts,
I ran Recon-all on a batch of subject. Only one Recon-all error
results were
External Email - Use Caution
Dear Freesurfer experts,
I ran Recon-all on a batch of subject. Only one Recon-all error results were
generated which the process just last for few minutes. There just 2 mgz file in
mri folder of the subject output directory were generated. I
if someone wants it?
Best,
René
*Von:*freesurfer-boun...@nmr.mgh.harvard.edu
*Im Auftrag von *Douglas N. Greve
*Gesendet:* Donnerstag, 28. Mai 2020 17:47
*An:* freesurfer@nmr.mgh.harvard.edu
*Betreff:* Re: [Freesurfer] Recon-all error in CA Normalize
(FreeSurfer V 7.1)
You can use it with al
t a better bias correction?
And is it possible to use ANTsN3 instead of ANTsN4, if someone wants it?
Best,
René
Von: freesurfer-boun...@nmr.mgh.harvard.edu
Im Auftrag von Douglas N. Greve
Gesendet: Donnerstag, 28. Mai 2020 17:47
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Recon
@nmr.mgh.harvard.edu
*Betreff:* Re: [Freesurfer] Recon-all error in CA Normalize
(FreeSurfer V 7.1)
Are all your subjects skull stripped or just this one?
On 5/24/2020 9:08 AM, Schranzer René wrote:
*External Email - Use Caution *
Hi Douglas,
First of all, thank you for your
External Email - Use Caution
All subjects.
Best,
René
Von: freesurfer-boun...@nmr.mgh.harvard.edu
Im Auftrag von Douglas N. Greve
Gesendet: Mittwoch, 27. Mai 2020 18:37
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V
Are all your subjects skull stripped or just this one?
On 5/24/2020 9:08 AM, Schranzer René wrote:
External Email - Use Caution
Hi Douglas,
First of all, thank you for your help.
I forgot to mention that I am already using skull-stripped data for
the recon-all processing stream.
External Email - Use Caution
Hi Douglas,
First of all, thank you for your help.
I forgot to mention that I am already using skull-stripped data for the
recon-all processing stream. Therefore, I stopped after -autorecon1 and copied
the T1.mgz to brainmask.mgz and
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