u>
Subject: [EXTERNAL] Re: [Freesurfer] Recon-all error - release
8.0.0-betaThe new version will be announced in the next couple of
days. From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf
Of Yanez-Ramos, Lupita
Sent: Tuesday, February 1
There are no details of the error message in the log.
Does your error look something like this?
(0) INVALID_ARGUMENT: input must be 4-dimensional[1,72,72,72,24]
[[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]]
[[unet/unet_merge_4/concat/_64]]
(1) INVALID_ARGUM
It says that it cannot find /run/media/user/2TB/freesurfer/ASegStatsLUT.txt
does that file exist on your system?
On 1/16/2025 6:20 PM, 박경일 wrote:
External Email - Use Caution
Dear FS Development Team,
I recently encountered an error while running the recon-all process.
This is the
That recon-all.log file says it returned without error:
"recon-all -s E0001 finished without error at Mon Dec 23 12:20:40 KST 2024"
what's the problem?
On 1/13/2025 10:26 PM, 박경일 wrote:
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Dear FS Development Team,
I recently encountered an error while runn
External Email - Use Caution
Hello Pei-Ying,
It does not work to run freesurfer/recon-all command(s) on subject data that
lives on a Windows formatted drive (in your case visible from inside the Linux
VM via the mount point to drive d, /mnt/d). The SUBJECTS_DIR needs to
poin
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
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, Nov
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:* Thursday,
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 m
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 e-ma
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 disk
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:
External Email - Use Caution
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:
External Email - Use Caution
Dear FreeSurfer developers,
I’m attempting to run recon-all with t
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 et
: 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
r his help 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 li
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?
Hi Joanna,
Is it possible you've run out of disk space? What's the output of `df --si`?
-Paul
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Joanna L Eckhardt
Sent: Friday, May 6, 2022 12:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurf
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 wit
@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
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 variable. You
should be able to do that with these 2 commands:
```
mkdir -p /home/developer/guest_shared/
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
il 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 dcm2n
eesurfer-boun...@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:
cooper
rom: coope...@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> &g
, 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 individu
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 to
Hi Rebecca,
I’m trying to get more information to determine how it core dumped.
1. Can you confirm that you are running Freesurfer 6.0?
2. From which directory, did you run recon-all and dcmunpack?
3. Can you try dcmunpack by passing it full path to dicom directory?
Thanks.
Yujing
-
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 u
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, an
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 for
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 Cau
Hi Travis
It is because you have a space “ “ in your path:
Processed Data
If you rename the path to
Processed_Data
It should work fine
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of William McCuddy AZ-Phoenix
Sent: Saturday, December 11, 2021 3:13 PM
To: freesurfer@nmr.mgh.h
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
ADNI_002_S_6652_MR_Ac
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:
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Hello freesurfers,
I’m new to freesurfer and I can’t fix a har
External Email - Use Caution
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. T
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:
External Email - Use Caution
External Email - Use Caution
Hi,
I have a pro
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 (core dumped)
Not sure, can you try this
cd /home/liubing/FreeSurfer/data/test_recon/ANDI1/
;
*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 Cauti
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,
>
>
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:
External Email - Use Caution
Running the command in another directory I got another error:
(base) eduardo@eduardo-X55
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):
Hi Dimitri,
Could you indicate the recon command that you ran? You could try rerunning the
recon-all command in the directory with one of the dicom files for the T1 image.
I’ve posted an example command below:
recon-all -all -i I50 -s Subj001
• The file after the “-i” flag indicates your inpu
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 ha
External Email - Use Caution
Thanks Andrew!
Nárlon Cássio
Nárlon Cássio Boa Sorte Silva, PhD
CIHR/MSFHR Postdoctoral Research Fellow
Aging, Mobility, and Cognitive Neuroscience Lab
Djavad Mowafaghian Centre for Brain Health
University of British Columbia
Twitter: @BoaNarlon
On D
Hi Nárlon,
Unfortunately, this is a known bug with parallel processing in FS 7.1.1. A fix
will make it into the next v7 patch. As you mentioned, this error occurs at
random, so in the meantime, you can mitigate this by either:
- Rerunning recons until they don’t fail (not recommended)
-
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,
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 Email
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, Septe
n-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 erro
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, and it
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
ew 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
. Thanks
Best,
Jie
> -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 freevie
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
>
ing)
-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 tr
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 sugg
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,
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
orms/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-
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 som
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 PAT
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
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: freesurfer-boun
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:
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**
Dear Freesurfer experts,
I ran Recon-all on a batch of subject. Only one Recon-all error
results were ge
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-al
@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
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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:
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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. Th
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 brainmask.auto.m
It is not clear what is failing. Can you check two things?
1. Check the talairach.lta with
cd $SUBJECTS_DIR/subject/mri/transforms
tkregisterfv --mov ../orig.mgz --reg talairach.lta --targ
$FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca
This does not have to be perfect, but it sh
.harvard.edu
on behalf of Meena M. Makary
Sent: Thursday, November 21, 2019 2:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Recon-all Error
External Email - Use Caution
Thank you, Doug! So here's what I've tried now.
I want to confirm first that this is the only
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> On November 21, 2019 at 7:56 PM "Greve, Douglas N.,Ph.D."
> wrote:
> [...]
> But the error you are
> seeing appears to be that the mritotal program cannot be found (not a
> computational problem or problem with your data). But it is strange that
I don't generally discourage it, but I don't think many people use it,
and so it might not be maintained that well. But the error you are
seeing appears to be that the mritotal program cannot be found (not a
computational problem or problem with your data). But it is strange that
you could run
External Email - Use Caution
Thank you, Douglas, for your fast reply. I have used -3T option for all my
dataset (>80 subject so far) and it worked well for all except for this
subject. Do you generally discourage using this option? I thought it does
some normalization/denoising for
This is something that is being triggered by use -3T. Is there a reason
you are using that option?
On 11/19/19 5:15 PM, Meena M. Makary wrote:
>
> External Email - Use Caution
>
> Hi,
>
> I have been getting this error with one of my subjects Recon-all. I am
> attaching the recon-all log
can you give more info on the error? Eg, command line, terminal output, log file
On 7/31/2019 6:55 PM, Gregory Mierzwinski wrote:
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Hello,
Even though this is an old post, the entire solution to this has not been
posted and I couldn’t find it anywhere.
I hit
External Email - Use Caution
Hello,
Even though this is an old post, the entire solution to this has not been
posted and I couldn’t find it anywhere.
I hit this error, and I had to (1) make sure the SUBJECT_DIR environment
variable was pointing to a directory
that is not on the
spital
> 149 13th Street
> Charlestown, MA 02129
> (p): 617-726-6598
>
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas
> Fernández
> Sent: Wednesday, June 26, 2019
vas
Fernández
Sent: Wednesday, June 26, 2019 11:37 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all error: Correcting defect
External Email - Use Caution
Hello Bruce,
Ok, I have sent to you the subject via FileDrop if you want to take a look.
Thanks.
Best regards,
E
I think the dicom series that 1.DCM is part of is not a 3D T1-weighted
structural. Can you run mri_info on it, or dcmdump (or both)?
On Sat, 6 Jul
2019, Yueming wrote:
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My command: recon-all -all -i /usr/local/110/UN18/1.DCM -s 18p
I DON'T KNOW,W
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My command: recon-all -all -i /usr/local/110/UN18/1.DCM -s 18p
I DON'T KNOW,WHAT KIND OF frames will be considered unmultiple?
My inputs' format is dicom,when it is about 200kB,the software can run and has
no such error.but when the dicom is more than
External Email - Use Caution
Hello Bruce,
Ok, I have sent to you the subject via FileDrop if you want to take a look.
Thanks.
Best regards,
El mié., 26 jun. 2019 a las 17:04, Bruce Fischl ()
escribió:
> Hi Miguel
>
> depending on the lesions it may not be fixable (since they ma
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