[Freesurfer] recon-all error

[Gregory Book]

External Email - Use Caution

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 not found

It does have execute permissions.

What might be happening?
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Re: [Freesurfer] recon-all error - MRISlabel2Mask()

[Douglas N. Greve]

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 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 run, can send the whole recon-all.log file if 
needed. Nothing obvious in terms of the T1 or T2 images. Thanks!


#===

mri_surf2surf --s sub-XXX --hemi rh --sval-xyz woT2.pial.rawavg 
--surfreg woT2.pial.rawavg --reg transforms/conf2rawavg.dat orig.mgz 
--tval-xyz orig.mgz --tval woT2.pial.rawavg.conf


Reading header for orig.mgz

Source registration surface changed to woT2.pial.rawavg

Target registration surface changed to woT2.pial.rawavg

7.3.2

setenv SUBJECTS_DIR 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w


cd 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri


mri_surf2surf --s sub-XXX --hemi rh --sval-xyz woT2.pial.rawavg 
--surfreg woT2.pial.rawavg --reg transforms/conf2rawavg.dat orig.mgz 
--tval-xyz orig.mgz --tval woT2.pial.rawavg.conf


sysname  Linux

hostname cpu-771.cluster.local

machine  x86_64

user mwagshul

srcsubject = sub-XXX

srcval = (null)

srctype    =

trgsubject = sub-XXX

trgval = woT2.pial.rawavg.conf

trgtype    =

srcsurfreg = woT2.pial.rawavg

trgsurfreg = woT2.pial.rawavg

srchemi    = rh

trghemi    = rh

frame  = 0

fwhm-in    = 0

fwhm-out   = 0

label-src  = (null)

label-trg  = (null)

OKToRevFaceOrder = 1

UseDualHemi = 0

Reading source surface reg 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/surf/rh.woT2.pial.rawavg


Loading source data

Reading surface file 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/surf/rh.woT2.pial.rawavg


Applying linear registration transform

1.0 0.0   0.0  -0.4;

0.0 1.0   0.0   0.0;

0.0 0.0   1.0   0.3;

0.0 0.0   0.0   1.0;

INFO: trgsubject = srcsubject

Saving target data

/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/surf 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri 



/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri 



Tue Nov 21 17:49:18 EST 2023

#===

bbregister --s sub-XXX --mov orig/T2raw.mgz --lta 
transforms/T2raw.auto.lta --init-coreg --t2 --surf white.preaparc 
--proj-abs 1.5 --threads 1


tmp transforms/tmp.bbregister.3166191

Log file is transforms/T2raw.auto.log

Tue Nov 21 17:49:18 EST 2023

setenv SUBJECTS_DIR 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w


cd 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri


/public/apps/freesurfer/7.3.2/bin/bbregister --s sub-XXX --mov 
orig/T2raw.mgz --lta transforms/T2raw.auto.lta --init-coreg --t2 
--surf white.preaparc --proj-abs 1.5 --threads 1


bbregister 7.3.2

Linux cpu-771.cluster.local 4.18.0-477.13.1.el8_8.x86_64 #1 SMP Thu 
May 18 10:27:05 EDT 2023 x86_64 x86_64 x86_64 GNU/Linux


FREESURFER_HOME /public/apps/freesurfer/7.3.2

mri_convert orig/T2raw.mgz transforms/tmp.bbregister.3166191/template.nii

mri_convert orig/T2raw.mgz transforms/tmp.bbregister.3166191/template.nii

reading from orig/T2raw.mgz...

TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 1, 0)

k_ras = (0, 0, 1)

writing to transforms/tmp.bbregister.3166191/template.nii...

mri_coreg --s sub-XXX --mov 
transforms/tmp.bbregister.3166191/template.nii --regdat 
transforms/tmp.bbregister.3166191/reg.init.dat --reg 
transforms/tmp.bbregister.3166191/mri_coreg.lta --nthreads 1 --dof 6 
--sep 4 --ftol .0001 --linmintol .01


$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $

cwd 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri


cmdline mri_coreg --s sub-XXX --mov 
transforms/tmp.bbregister.3166191/template.nii --regdat 
transforms/tmp.bbregister.3166191/reg.init.dat --reg 
transforms/tmp.bbregister.3166191/mri_coreg.lta --nthreads 1 --dof 6 
--sep 4 --ftol .0001 --linmintol .01


sysname  Linux

hostname cpu-771.cluster.local

machine  x86_64

user mwagshul

dof    6

nsep    1

cras0    1

ftol    0.000100

linmintol 0.01

bf   1

bflim 30.00

bfnsamp    30

SmoothRef 0

SatPct 99.99

MovOOB 0

optschema 1

Seed 53

Reading in mov transforms/tmp.bbregister.3166191/template.nii

Reading in ref brainmask.mgz

Reading in and applying refmask aparc+aseg.mgz

Setting cras translation parameters to align volume centers

Creating random numbers for coordinate dithering

Performing intensity 

[Freesurfer] recon-all error - MRISlabel2Mask()

[Mark Wagshul]

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 run, can 
send the whole recon-all.log file if needed. Nothing obvious in terms of the T1 
or T2 images. Thanks!

#===
mri_surf2surf --s sub-XXX --hemi rh --sval-xyz woT2.pial.rawavg --surfreg 
woT2.pial.rawavg --reg transforms/conf2rawavg.dat orig.mgz --tval-xyz orig.mgz 
--tval woT2.pial.rawavg.conf
Reading header for orig.mgz
Source registration surface changed to woT2.pial.rawavg
Target registration surface changed to woT2.pial.rawavg

7.3.2

setenv SUBJECTS_DIR 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w
cd 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri
mri_surf2surf --s sub-XXX --hemi rh --sval-xyz woT2.pial.rawavg --surfreg 
woT2.pial.rawavg --reg transforms/conf2rawavg.dat orig.mgz --tval-xyz orig.mgz 
--tval woT2.pial.rawavg.conf

sysname  Linux
hostname cpu-771.cluster.local
machine  x86_64
user mwagshul
srcsubject = sub-XXX
srcval = (null)
srctype=
trgsubject = sub-XXX
trgval = woT2.pial.rawavg.conf
trgtype=
srcsurfreg = woT2.pial.rawavg
trgsurfreg = woT2.pial.rawavg
srchemi= rh
trghemi= rh
frame  = 0
fwhm-in= 0
fwhm-out   = 0
label-src  = (null)
label-trg  = (null)
OKToRevFaceOrder  = 1
UseDualHemi = 0
Reading source surface reg 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/surf/rh.woT2.pial.rawavg
Loading source data
Reading surface file 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/surf/rh.woT2.pial.rawavg
Applying linear registration transform
1.0   0.0   0.0  -0.4;
0.0   1.0   0.0   0.0;
0.0   0.0   1.0   0.3;
0.0   0.0   0.0   1.0;
INFO: trgsubject = srcsubject
Saving target data
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/surf
 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri
Tue Nov 21 17:49:18 EST 2023

#===
bbregister --s sub-XXX --mov orig/T2raw.mgz --lta transforms/T2raw.auto.lta 
--init-coreg --t2 --surf white.preaparc --proj-abs 1.5 --threads 1
tmp transforms/tmp.bbregister.3166191
Log file is transforms/T2raw.auto.log
Tue Nov 21 17:49:18 EST 2023

setenv SUBJECTS_DIR 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w
cd 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri
/public/apps/freesurfer/7.3.2/bin/bbregister --s sub-XXX --mov orig/T2raw.mgz 
--lta transforms/T2raw.auto.lta --init-coreg --t2 --surf white.preaparc 
--proj-abs 1.5 --threads 1

bbregister 7.3.2
Linux cpu-771.cluster.local 4.18.0-477.13.1.el8_8.x86_64 #1 SMP Thu May 18 
10:27:05 EDT 2023 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /public/apps/freesurfer/7.3.2
mri_convert orig/T2raw.mgz transforms/tmp.bbregister.3166191/template.nii
mri_convert orig/T2raw.mgz transforms/tmp.bbregister.3166191/template.nii
reading from orig/T2raw.mgz...
TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to transforms/tmp.bbregister.3166191/template.nii...
mri_coreg --s sub-XXX --mov transforms/tmp.bbregister.3166191/template.nii 
--regdat transforms/tmp.bbregister.3166191/reg.init.dat --reg 
transforms/tmp.bbregister.3166191/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 
--ftol .0001 --linmintol .01

$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $
cwd 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri
cmdline mri_coreg --s sub-XXX --mov 
transforms/tmp.bbregister.3166191/template.nii --regdat 
transforms/tmp.bbregister.3166191/reg.init.dat --reg 
transforms/tmp.bbregister.3166191/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 
--ftol .0001 --linmintol .01
sysname  Linux
hostname cpu-771.cluster.local
machine  x86_64
user mwagshul
dof6
nsep1
cras01
ftol0.000100
linmintol0.01
bf   1
bflim30.00
bfnsamp30
SmoothRef 0
SatPct99.99
MovOOB 0
optschema 1
Seed 53
Reading in mov transforms/tmp.bbregister.3166191/template.nii
Reading in ref brainmask.mgz
Reading in and applying refmask aparc+aseg.mgz
Setting cras translation parameters to align volume centers
Creating random numbers for coordinate dithering
Performing intensity dithering
Performing intensity dithering on mov with computed dither
Init matrix params -0.1000  0.1000 -0.9000  0.  0.  0.  1.  
1.  1.  0.  0.  0.
Initial parameters to be opt -0.1000  0.1000 -0.9000  0.  

Re: [Freesurfer] recon-all error

[Huang, Yujing]

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, 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" 
I have attached the recon-all log as well.

 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 found at voxel (0, 0, 244, 0)
error: No such file or directory
error: WARNING: 319676 NaNs found in volume /path/to/anat_t1.nii...

Thank you,

Carlos


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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
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Re: [Freesurfer] recon-all error

[Douglas N. Greve]

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, 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


mri_convert /path/to/anat_t1.nii /path/to/mri/orig/001.mgz
reading from /path/to/anat_t1.nii...
NaN found at voxel (0, 0, 244, 0)
error: No such file or directory
error: WARNING: 319676 NaNs found in volume /path/to/anat_t1.nii...

However, recon-all will keep running and then later finish without 
error. What exactly is going on? This is only happens on some subjects.


Thank you,

Carlos


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___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] recon-all error

[Huang, Yujing]

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 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 found at voxel (0, 0, 244, 0)
error: No such file or directory
error: WARNING: 319676 NaNs found in volume /path/to/anat_t1.nii...

However, recon-all will keep running and then later finish without error. What 
exactly is going on? This is only happens on some subjects.

Thank you,

Carlos
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] recon-all error

[Carlos Alcocer]

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 found at voxel (0, 0, 244, 0)
error: No such file or directory
error: WARNING: 319676 NaNs found in volume /path/to/anat_t1.nii...

However, recon-all will keep running and then later finish without error.
What exactly is going on? This is only happens on some subjects.

Thank you,

Carlos
___
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] recon-all error: cannot find or read colortable_BARe: recon-all error: cannot find or read colortable_BA_thresh.txt_thresh.txt

[fsbuild]

External Email - Use Caution

We should have an update for this installed there soon.
- R.
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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] recon-all ERROR on new installation UBUNTU 22.04 Ubuntu 22 amd64 (64b) DEB installer 7.3.2 release

[Steinbacher Jürgen]

External Email - Use Caution

Hello Everyone,

due to new hardware my old freesurfer did not work anymore,
so I have new UBUNTU 22.04
and 
freesurfer_ubuntu22-7.3.2_amd64.deb
 istalled..

machine is Intel i7-4790
28 GB
+
GeForce GTX 1650 4 GB



I tried just to run one job,
autorecon1
"finished without error"

and autorecon2  stops with
ERROR: cannot find or read transforms/talairach.m3z

I have seen this error in other cases here, but I did not calculate multiple 
patients.. and have more memory..

Do you have an idea?

Many thanks
 jürgen

(I wanted to try the Virtual Box version too, but the download file from here 
can not be unzipped because of broken header??
Downloaded it twice.. )










Thu Oct 20 09:47:31 CEST 2022
cd /usr/local/freesurfer/7.3.2/subjects/Wen.23.9.21
setenv SUBJECTS_DIR /usr/local/freesurfer/7.3.2/subjects
/usr/local/freesurfer/7.3.2/bin/recon-all -s Wen.23.9.21 -autorecon2

subjid Wen.23.9.21
setenv SUBJECTS_DIR /usr/local/freesurfer/7.3.2/subjects
FREESURFER_HOME /usr/local/freesurfer/7.3.2
Actual FREESURFER_HOME /usr/local/freesurfer/7.3.2
build-stamp.txt: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275
Linux ph 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 2022 x86_64 
x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024
memorylocked 3579276 kbytes
maxproc  111576
maxlocks unlimited
maxsignal111576
maxmessage   819200
maxnice  0
maxrtprio0
maxrttimeunlimited

   totalusedfree  shared  buff/cache   available
Mem:27Gi   2.7Gi12Gi46Mi12Gi24Gi
Swap:  2.0Gi   3.0Mi   2.0Gi


program versions used
7.3.2 (freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275)
7.3.2

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  
ProgramVersion: 7.3.2  TimeStamp: 2022/10/20-07:47:31-GMT  BuildTime: Aug  4 
2022 06:17:15  BuildStamp: 
freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275  User: jstein  Machine: 
ph  Platform: Linux  PlatformVersion: 5.15.0-47-generic  CompilerName: GCC  
CompilerVersion: 8.4.0
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 
7.3.2  TimeStamp: 2022/10/20-07:47:31-GMT  BuildTime: Aug  4 2022 06:17:15  
BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275  User: 
jstein  Machine: ph  Platform: Linux  PlatformVersion: 5.15.0-47-generic  
CompilerName: GCC  CompilerVersion: 8.4.0
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label 
-all-info  ProgramVersion: 7.3.2  TimeStamp: 2022/10/20-07:47:31-GMT  
BuildTime: Aug  4 2022 06:17:15  BuildStamp: 
freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275  User: jstein  Machine: 
ph  Platform: Linux  PlatformVersion: 5.15.0-47-generic  CompilerName: GCC  
CompilerVersion: 8.4.0
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  
ProgramVersion: 7.3.2  TimeStamp: 2022/10/20-07:47:31-GMT  BuildTime: Aug  4 
2022 06:17:15  BuildStamp: 
freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275  User: jstein  Machine: 
ph  Platform: Linux  PlatformVersion: 5.15.0-47-generic  CompilerName: GCC  
CompilerVersion: 8.4.0
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  
ProgramVersion: 7.3.2  TimeStamp: 2022/10/20-07:47:31-GMT  BuildTime: Aug  4 
2022 06:17:15  BuildStamp: 
freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275  User: jstein  Machine: 
ph  Platform: Linux  PlatformVersion: 5.15.0-47-generic  CompilerName: GCC  
CompilerVersion: 8.4.0
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  
ProgramVersion: 7.3.2  TimeStamp: 2022/10/20-07:47:31-GMT  BuildTime: Aug  4 
2022 06:17:15  BuildStamp: 
freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275  User: jstein  Machine: 
ph  Platform: Linux  PlatformVersion: 5.15.0-47-generic  CompilerName: GCC  
CompilerVersion: 8.4.0
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  
ProgramVersion: 7.3.2  TimeStamp: 2022/10/20-07:47:31-GMT  BuildTime: Aug  4 
2022 06:17:15  BuildStamp: 
freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275  User: jstein  Machine: 
ph  Platform: Linux  PlatformVersion: 5.15.0-47-generic  CompilerName: GCC  
CompilerVersion: 8.4.0
ProgramName: mri_ca_normalize  ProgramArguments: 

Re: [Freesurfer] recon-all error: ERROR: recon-all command failed with return_code: 1

[Douglas N. Greve]

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?


On 9/10/2022 4:06 PM, Estephan Moana Filho wrote:


External Email - Use Caution

Hello, I am using QuNex to process MRI data with the HCP pipelines. I 
was able to complete the hcp_pre_freesurfer without problems, but I am 
having trouble completing the hcp_freesurfer step. I tried processing 
10 participants, and they all fail after several hours of processing. 
The qunex log reports the error "ERROR: recon-all command failed with 
return_code: 1". The recon-all.log is not clear about what went wrong 
(at least to me). See attached the log file.


Please let me know your thoughts on this. Thank you.

Estephan

--
Estephan J. Moana-Filho, DDS, MS, PhD
Assistant Professor
Division of TMD, Orofacial Pain and Dental Sleep Medicine
Graduate Faculty in Oral Biology
Department of Diagnostic and Biological Sciences
UMN School of Dentistry
moana...@umn.edu

6-320d Moos Tower
515 Delaware St. SE
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Graduate Faculty in Oral Biology
Department of Diagnostic and Biological Sciences
UMN School of Dentistry
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Re: [Freesurfer] Recon-all Error

[Douglas N. Greve]

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 regards,
Gianrocco Lazzari, PhD
Data Scientist

Bottneuro AG
Novartis Campus
Lichtstrasse 35
CH-4056 Basel

*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* www.bottneuro.ch 



On 26 Jul 2022, at 14:52, gianrocco  
wrote:


Dear FreeSurfer support,


I am trying to test free surfer, via simNIBS , following this tutorial

*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://simnibs.github.io/simnibs/build/html/documentation/command_line/mri2mesh.html#mri2mesh-docs 
 




It gets stuck at recon-all — please, find attached the relevant logs 
files


Thanks for your support

Ps: On Ubuntu 20.04.4 LTS and FS 6.0






Kind regards,
Gianrocco Lazzari, PhD
Data Scientist

Bottneuro AG
Novartis Campus
Lichtstrasse 35
CH-4056 Basel

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Re: [Freesurfer] recon-all error: mri_cc

[Douglas N. Greve]

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 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) have completed successfully; it’s this final step that has 
the error. It appears that the error lies in mri_cc.


The final lines of the recon-all.log are below:

#--

#@# CC Seg Wed Jun 29 14:56:47 AEST 2022

mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta 
/data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-baselineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/transforms/cc_up.lta 
sub-NDARINVL8EJK2VY_ses-baselineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY


will read input aseg from aseg.auto_noCCseg.mgz

writing aseg with cc labels to aseg.auto.mgz

will write lta as 
/data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-baselineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/transforms/cc_up.lta


reading aseg from 
/data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-baselineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/aseg.auto_noCCseg.mgz


error: No such file or directory

error: mri_cc: volume 
/data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-baselineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/aseg.auto_noCCseg.mgz 
already has CC in it.


Run with -force to reprocess (not recommended)

@#@FSTIME  2022:06:29:14:56:47 mri_cc N 7 e 0.39 S 0.00 U 0.38 P 99% M 
21240 F 0 R 1813 W 0 c 6 w 5 I 0 O 0 L 64.77 63.93 63.78


@#@FSLOADPOST 2022:06:29:14:56:47 mri_cc N 7 64.77 63.93 63.78

Linux spartan-bm112.hpc.unimelb.edu.au 3.10.0-1160.36.2.el7.x86_64 #1 
SMP Thu Jul 8 02:53:40 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux


recon-all -s 
sub-NDARINVL8EJK2VY_ses-baselineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY 
exited with ERRORS at Wed Jun 29 14:56:47 AEST 2022


Freesurfer version: 
freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b (I have also 
attempted with version 7.1.0 with identical results)


Platform: centos7_x86_64

Recon-all.log: attached.

With thanks,

Rebecca


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[Freesurfer] recon-all error: mri_cc

[cooperr1]

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)
have completed successfully; it's this final step that has the error. It
appears that the error lies in mri_cc.

The final lines of the recon-all.log are below:

 

#--

#@# CC Seg Wed Jun 29 14:56:47 AEST 2022

 

mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta
/data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-bas
elineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/transforms/cc_up.lta
sub-NDARINVL8EJK2VY_ses-baselineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2V
Y

 

will read input aseg from aseg.auto_noCCseg.mgz

writing aseg with cc labels to aseg.auto.mgz

will write lta as
/data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-bas
elineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/transforms/cc_up.lta

reading aseg from
/data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-bas
elineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/aseg.auto_noCCseg.mgz

error: No such file or directory

error: mri_cc: volume
/data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-bas
elineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/aseg.auto_noCCseg.mgz
already has CC in it.

Run with -force to reprocess (not recommended)

 

@#@FSTIME  2022:06:29:14:56:47 mri_cc N 7 e 0.39 S 0.00 U 0.38 P 99% M 21240
F 0 R 1813 W 0 c 6 w 5 I 0 O 0 L 64.77 63.93 63.78

@#@FSLOADPOST 2022:06:29:14:56:47 mri_cc N 7 64.77 63.93 63.78

Linux spartan-bm112.hpc.unimelb.edu.au 3.10.0-1160.36.2.el7.x86_64 #1 SMP
Thu Jul 8 02:53:40 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

 

recon-all -s
sub-NDARINVL8EJK2VY_ses-baselineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2V
Y exited with ERRORS at Wed Jun 29 14:56:47 AEST 2022

 

 

Freesurfer version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b
(I have also attempted with version 7.1.0 with identical results)

Platform: centos7_x86_64

Recon-all.log: attached.

 

With thanks,

 

Rebecca

 



recon-all.log
Description: Binary data
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Re: [Freesurfer] Recon-all Error

[fsbuild]

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 etc. is not automatically displayed when you open a new 
terminal window, then something is not right with your current VM setup.

Please see the online 
documentationhttps://secure-web.cisco.com/1gznVcTKDzEuwdybT3u9uoWvv2vyQ2VyjeZSC33cwgqeQTC4qk9L5J4P27HNxNCAs6qCyHEbSSzRM_XH7JBBoErvzNhXGKU4G5KnpirwfiHBLPriRyxWwEeSaWo61d9AULl3_TMM_sQjK8fiS9PoWKl6FO8q0nbYLsLtpQLJA1JXHuExQHxte2c5I7X_ndk-1vm3CSUaPUML4NblYdKytD09t2fBIXL7oUgJ1k6KPzdz_F48yNKbmObMp2-KCO29mHSGL8HJUsADvhMhgc3ql3g2qvlaw9Xt_RwukxXnBajJe5a49tTWa2svfe9QQwxdDI1lJSfGtd52B0Am2XjFLsw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67%26nbsp;which
 contains a link to the documentVbox_load_image showing how to setup the 
VM, i.e., page 12 says you can go 
tohttp://secure-web.cisco.com/1q0X87yBimuGRycgbM3K-M42AWFTRmdTzLmdSTPgHTTkSPNYpXfDaU6VxcwCs75gxfN-y_hit_8ZaZjCNI3_jcOJUCNarj7VfTLSbgbmDXiNzRW2tiaMbkWllr8rh8ljN4YYYJQ7I0Mkp0FfsEQVatzjG5vTQ8m7D1Hy3IdMj2sd3vl9cH5JXr9_rstJZbpOl6rqf4h9vDFkHHLW1cJb4hRhzVj8dUFR9uxU5rHKPjcf9r1rx1DlUrZaRhuTEeLiYKXkXhPoXEeHcHczUVeCBFut8Q11D19-7GRkWd9GSrq8TcdvE_qCYBFINpxbywmuh9ZHm-Ir1NJV7UHGfZTV-PQ/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer%26nbsp;to
 obtain a license and how to use it in the terminal window.

- R.
On May 9, 2022, at 10:01, Mouna JABEUR mouna.jab...@enetcom.u-sfax.tn 
wrote:External Email - Use 
CautionHi,how can i solve this 
please ?Capture d’écran 2022-05-09 145325.pngCapture d’écran 
2022-05-09 145137.pngCapture d’écran 2022-05-09 
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 .
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Re: [Freesurfer] Recon-all Error: "ln: failed to create symbolic link 'lh.white.H': Operation not permitted"

[Joanna L Eckhardt]

External Email - Use Caution

Hi Paul,

That was definitely the issue! I had originally shared that folder between 
Windows and Ubuntu because it was in the tutorial for setting up VM, but I 
changed the directory to a non-shared folder, and recon-all finished without 
error.

Thank you Paul and R for all of your help!

All my best,
Joanna

--

Joanna Eckhardt

Neurosciences Graduate Program

University of California, San Diego


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Wighton, Paul 

Sent: Friday, May 6, 2022 11:59 AM
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 OS (windows)? 
That could be the issue as windows does not support symbolic links.  Could you 
try changing the subject's directory to something that is not shared with the 
host OS?

e.g:
```
mkdir -p /home/developer/fs-subjects
export SUBJECTS_DIR=/home/developer/fs-subjects
```

And then try running recon-all again?

My apologies.  This is my fault as I originally suggested that location for the 
subjects directory. Also, thanks to R. for 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 link 
'lh.white.H': Operation not permitted"


External Email - Use Caution

Hi Paul,

I have everything on my Data (D:) drive because my OS (C:) drive was already 
nearly full when I began this process of downloading FreeSurfer and knew it 
wouldn't have enough space. Is that a problem that I am using the D: drive? (I 
am not too familiar with the differences between the two).

Pasted below is the output of df --si.

Thank you for your help!
Joanna

developer@developer-VirtualBox:~/guest_shared/fs-subjects$ df --si
Filesystem  Size  Used Avail Use% Mounted on
udev4.2G 0  4.2G   0% /dev
tmpfs   835M  1.6M  833M   1% /run
/dev/sda1   216G   21G  185G  10% /
tmpfs   4.2G 0  4.2G   0% /dev/shm
tmpfs   5.3M  4.1k  5.3M   1% /run/lock
tmpfs   4.2G 0  4.2G   0% /sys/fs/cgroup
/dev/loop0   69M   69M 0 100% /snap/gtk-common-themes/1519
/dev/loop1  230M  230M 0 100% /snap/gnome-3-34-1804/72
/dev/loop3   47M   47M 0 100% /snap/snapd/15534
/dev/loop2   46M   46M 0 100% /snap/snapd/15177
/dev/loop6  787k  787k 0 100% /snap/gnome-characters/726
/dev/loop5  2.8M  2.8M 0 100% /snap/gnome-calculator/920
/dev/loop4  787k  787k 0 100% /snap/gnome-characters/741
/dev/loop7  230M  230M 0 100% /snap/gnome-3-34-1804/77
/dev/loop9  254M  254M 0 100% /snap/gnome-3-38-2004/70
/dev/loop8  2.8M  2.8M 0 100% /snap/gnome-system-monitor/174
/dev/loop10  66M   66M 0 100% /snap/core20/1434
/dev/loop11 132k  132k 0 100% /snap/bare/5
/dev/loop12  69M   69M 0 100% /snap/gtk-common-themes/1515
/dev/loop13 656k  656k 0 100% /snap/gnome-logs/106
/dev/loop15  59M   59M 0 100% /snap/core18/2128
/dev/loop14 2.7M  2.7M 0 100% /snap/gnome-system-monitor/163
/dev/loop16 261M  261M 0 100% /snap/gnome-3-38-2004/99
/dev/loop17  59M   59M 0 100% /snap/core18/2344
/dev/loop18 2.7M  2.7M 0 100% /snap/gnome-calculator/884
/dev/loop19  66M   66M 0 100% /snap/core20/1376
tmpfs   835M   17k  835M   1% /run/user/121
tmpfs   835M   46k  835M   1% /run/user/1000
shared  1.1T   48G  953G   5% /home/developer/guest_shared




--

Joanna Eckhardt

Neurosciences Graduate Program

University of California, San Diego


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 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 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: [Freesurfer] Recon-all Error: "ln: failed to create symbolic link 
'lh.white.H': Operation not permitted"


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

Re: [Freesurfer] Recon-all Error: "ln: failed to create symbolic link 'lh.white.H': Operation not permitted"

[Wighton, Paul]

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 OS (windows)? 
That could be the issue as windows does not support symbolic links.  Could you 
try changing the subject's directory to something that is not shared with the 
host OS?

e.g:
```
mkdir -p /home/developer/fs-subjects
export SUBJECTS_DIR=/home/developer/fs-subjects
```

And then try running recon-all again?

My apologies.  This is my fault as I originally suggested that location for the 
subjects directory. Also, thanks to R. for 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 link 
'lh.white.H': Operation not permitted"


External Email - Use Caution

Hi Paul,

I have everything on my Data (D:) drive because my OS (C:) drive was already 
nearly full when I began this process of downloading FreeSurfer and knew it 
wouldn't have enough space. Is that a problem that I am using the D: drive? (I 
am not too familiar with the differences between the two).

Pasted below is the output of df --si.

Thank you for your help!
Joanna

developer@developer-VirtualBox:~/guest_shared/fs-subjects$ df --si
Filesystem  Size  Used Avail Use% Mounted on
udev4.2G 0  4.2G   0% /dev
tmpfs   835M  1.6M  833M   1% /run
/dev/sda1   216G   21G  185G  10% /
tmpfs   4.2G 0  4.2G   0% /dev/shm
tmpfs   5.3M  4.1k  5.3M   1% /run/lock
tmpfs   4.2G 0  4.2G   0% /sys/fs/cgroup
/dev/loop0   69M   69M 0 100% /snap/gtk-common-themes/1519
/dev/loop1  230M  230M 0 100% /snap/gnome-3-34-1804/72
/dev/loop3   47M   47M 0 100% /snap/snapd/15534
/dev/loop2   46M   46M 0 100% /snap/snapd/15177
/dev/loop6  787k  787k 0 100% /snap/gnome-characters/726
/dev/loop5  2.8M  2.8M 0 100% /snap/gnome-calculator/920
/dev/loop4  787k  787k 0 100% /snap/gnome-characters/741
/dev/loop7  230M  230M 0 100% /snap/gnome-3-34-1804/77
/dev/loop9  254M  254M 0 100% /snap/gnome-3-38-2004/70
/dev/loop8  2.8M  2.8M 0 100% /snap/gnome-system-monitor/174
/dev/loop10  66M   66M 0 100% /snap/core20/1434
/dev/loop11 132k  132k 0 100% /snap/bare/5
/dev/loop12  69M   69M 0 100% /snap/gtk-common-themes/1515
/dev/loop13 656k  656k 0 100% /snap/gnome-logs/106
/dev/loop15  59M   59M 0 100% /snap/core18/2128
/dev/loop14 2.7M  2.7M 0 100% /snap/gnome-system-monitor/163
/dev/loop16 261M  261M 0 100% /snap/gnome-3-38-2004/99
/dev/loop17  59M   59M 0 100% /snap/core18/2344
/dev/loop18 2.7M  2.7M 0 100% /snap/gnome-calculator/884
/dev/loop19  66M   66M 0 100% /snap/core20/1376
tmpfs   835M   17k  835M   1% /run/user/121
tmpfs   835M   46k  835M   1% /run/user/1000
shared  1.1T   48G  953G   5% /home/developer/guest_shared




--

Joanna Eckhardt

Neurosciences Graduate Program

University of California, San Diego


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 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 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: [Freesurfer] Recon-all Error: "ln: failed to create symbolic link 
'lh.white.H': Operation not permitted"


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: failed 
to create symbolic link 'lh.white.H': Operation not permitted."

 mris_curvature -w -seed 1234 lh.white.preaparc

setting seed for random number generator to 1234
total integrated curvature = 25.993*4pi (326.639) --> -25 handles
ICI = 146.8, FI = 1524.9, variation=23628.367
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...done.
@#@FSTIME  2022:05:05:23:34:15 mris_curvature N 4 e 1.66 S 0.10 U 1.30 P 84% M 
144988 F 3 R 39631 W 0 c 13 w 718 I 616 O 0 L 1.08 1.11 1.08
@#@FSLOADPOST 2022:05:05:23:34:17 mris_curvature N 4 1.08 1.11 1.08
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
ln: failed to create symbolic link 'lh.white.H': Operation not permitted
Linux 

Re: [Freesurfer] Recon-all Error: "ln: failed to create symbolic link 'lh.white.H': Operation not permitted"

[Joanna L Eckhardt]

External Email - Use Caution

Hi Paul,

I have everything on my Data (D:) drive because my OS (C:) drive was already 
nearly full when I began this process of downloading FreeSurfer and knew it 
wouldn't have enough space. Is that a problem that I am using the D: drive? (I 
am not too familiar with the differences between the two).

Pasted below is the output of df --si.

Thank you for your help!
Joanna


developer@developer-VirtualBox:~/guest_shared/fs-subjects$ df --si
Filesystem  Size  Used Avail Use% Mounted on
udev4.2G 0  4.2G   0% /dev
tmpfs   835M  1.6M  833M   1% /run
/dev/sda1   216G   21G  185G  10% /
tmpfs   4.2G 0  4.2G   0% /dev/shm
tmpfs   5.3M  4.1k  5.3M   1% /run/lock
tmpfs   4.2G 0  4.2G   0% /sys/fs/cgroup
/dev/loop0   69M   69M 0 100% /snap/gtk-common-themes/1519
/dev/loop1  230M  230M 0 100% /snap/gnome-3-34-1804/72
/dev/loop3   47M   47M 0 100% /snap/snapd/15534
/dev/loop2   46M   46M 0 100% /snap/snapd/15177
/dev/loop6  787k  787k 0 100% /snap/gnome-characters/726
/dev/loop5  2.8M  2.8M 0 100% /snap/gnome-calculator/920
/dev/loop4  787k  787k 0 100% /snap/gnome-characters/741
/dev/loop7  230M  230M 0 100% /snap/gnome-3-34-1804/77
/dev/loop9  254M  254M 0 100% /snap/gnome-3-38-2004/70
/dev/loop8  2.8M  2.8M 0 100% /snap/gnome-system-monitor/174
/dev/loop10  66M   66M 0 100% /snap/core20/1434
/dev/loop11 132k  132k 0 100% /snap/bare/5
/dev/loop12  69M   69M 0 100% /snap/gtk-common-themes/1515
/dev/loop13 656k  656k 0 100% /snap/gnome-logs/106
/dev/loop15  59M   59M 0 100% /snap/core18/2128
/dev/loop14 2.7M  2.7M 0 100% /snap/gnome-system-monitor/163
/dev/loop16 261M  261M 0 100% /snap/gnome-3-38-2004/99
/dev/loop17  59M   59M 0 100% /snap/core18/2344
/dev/loop18 2.7M  2.7M 0 100% /snap/gnome-calculator/884
/dev/loop19  66M   66M 0 100% /snap/core20/1376
tmpfs   835M   17k  835M   1% /run/user/121
tmpfs   835M   46k  835M   1% /run/user/1000
shared  1.1T   48G  953G   5% /home/developer/guest_shared




--

Joanna Eckhardt

Neurosciences Graduate Program

University of California, San Diego


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 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 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: [Freesurfer] Recon-all Error: "ln: failed to create symbolic link 
'lh.white.H': Operation not permitted"


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: failed 
to create symbolic link 'lh.white.H': Operation not permitted."

 mris_curvature -w -seed 1234 lh.white.preaparc

setting seed for random number generator to 1234
total integrated curvature = 25.993*4pi (326.639) --> -25 handles
ICI = 146.8, FI = 1524.9, variation=23628.367
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...done.
@#@FSTIME  2022:05:05:23:34:15 mris_curvature N 4 e 1.66 S 0.10 U 1.30 P 84% M 
144988 F 3 R 39631 W 0 c 13 w 718 I 616 O 0 L 1.08 1.11 1.08
@#@FSLOADPOST 2022:05:05:23:34:17 mris_curvature N 4 1.08 1.11 1.08
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
ln: failed to create symbolic link 'lh.white.H': Operation not permitted
Linux developer-VirtualBox 5.4.0-109-generic #123~18.04.1-Ubuntu SMP Fri Apr 8 
09:48:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub101-sesBL exited with ERRORS at Thu May  5 23:34:17 EDT 2022

For more details, see the log file 
/home/developer/guest_shared/fs-subjects/sub101-sesBL/scripts/recon-all.log
To report a problem, see MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://secure-web.cisco.com/14hambhZcwlHm-TUI0wi8GmzTNRhNjDTjrHO81ZQzO0DprnW0ojx5KD-LTyISI4jeDK03AwgiBl28UP0y9ABz9oQu4W7oS_NXfwjPp6LAouUz1f4eSYthZ_hC_Xe6Ssi4Jbhohpaz2cc4oBujQeDBrB7o9HpBeXAJV9SzelG8_1cSCHJ_xDzXjoivdxgRhqq_UPMkj0_euOS5YUjLZnbqxrX5JdxoaKJ9H8_hEnI86Itt0-mKyyac6YBC_6s2dtm9erpXBai63ObIhSxSauL2NgayuNw4CWfUE9yEZNy-Ilh16UGedwBKUUuMLrwJ259C/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting<https://secure-we

Re: [Freesurfer] Recon-all Error: "ln: failed to create symbolic link 'lh.white.H': Operation not permitted"

[Wighton, Paul]

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: [Freesurfer] Recon-all Error: "ln: failed to create symbolic link 
'lh.white.H': Operation not permitted"


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: failed 
to create symbolic link 'lh.white.H': Operation not permitted."

 mris_curvature -w -seed 1234 lh.white.preaparc

setting seed for random number generator to 1234
total integrated curvature = 25.993*4pi (326.639) --> -25 handles
ICI = 146.8, FI = 1524.9, variation=23628.367
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...done.
@#@FSTIME  2022:05:05:23:34:15 mris_curvature N 4 e 1.66 S 0.10 U 1.30 P 84% M 
144988 F 3 R 39631 W 0 c 13 w 718 I 616 O 0 L 1.08 1.11 1.08
@#@FSLOADPOST 2022:05:05:23:34:17 mris_curvature N 4 1.08 1.11 1.08
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
ln: failed to create symbolic link 'lh.white.H': Operation not permitted
Linux developer-VirtualBox 5.4.0-109-generic #123~18.04.1-Ubuntu SMP Fri Apr 8 
09:48:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub101-sesBL exited with ERRORS at Thu May  5 23:34:17 EDT 2022

For more details, see the log file 
/home/developer/guest_shared/fs-subjects/sub101-sesBL/scripts/recon-all.log
To report a problem, see MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://secure-web.cisco.com/1qOeaquoMOTkikWpYGZ4Zmm7T4aU7IdoLWz_R7WjwgxWoQGxY3cPBUDVV4WjL1HTzvXW83WzudLxHfUxd3VMjIW_onAfNPXVndE-taWDHNlTvxXSVt2XAWWGqV2_tqFc6xj1PgghG-vQD5NzYL7fMWU0fWUyVO3gu-hnNg-Nlw0SYtMFHU1Mpf_ezbHxFnHKFMhZR7-V9ztKJPq48qnxSxdaYp3f90UN5PtdDDL_YToCmUoLNZzThrPogT-MkRuyqenk7hzKn-vnr1u89-jcjkzLqvD1Zlp4rCTKFLJ1mv-WZ7GImSBJ-q_-ejSRyOeOLlCao4_RYJXLprXzFkq51bQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>




After searching through the archives, I see that other people have had the same 
problem in that their os is not able to create a symbolic link.  I tried 
following one of the archives and did:



developer@developer-VirtualBox:~/guest_shared/mv-ds000174-1.0.1-Cannabis/sub-101/ses-BL/anat$
 cd /home/developer/guest_shared/fs-subjects
developer@developer-VirtualBox:~/guest_shared/fs-subjects$ ln -s 
/home/developer/guest_shared/fs-subjects/fsaverage
ln: failed to create symbolic link './fsaverage': Operation not permitted

But I again received the "failed to create symbolic link. How can I allow 
symbolic links? Also, I was generally wondering how do you rerun recon-all 
starting from a specific step once I get this working? Does one have to rerun 
all of recon-all each time there is an error or can I start from where I left 
off?

Thank you so much for your help!

Best wishes,
Joanna

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] Recon-all Error: "ln: failed to create symbolic link 'lh.white.H': Operation not permitted"

[Joanna L Eckhardt]

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: failed 
to create symbolic link 'lh.white.H': Operation not permitted."

 mris_curvature -w -seed 1234 lh.white.preaparc

setting seed for random number generator to 1234
total integrated curvature = 25.993*4pi (326.639) --> -25 handles
ICI = 146.8, FI = 1524.9, variation=23628.367
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...done.
@#@FSTIME  2022:05:05:23:34:15 mris_curvature N 4 e 1.66 S 0.10 U 1.30 P 84% M 
144988 F 3 R 39631 W 0 c 13 w 718 I 616 O 0 L 1.08 1.11 1.08
@#@FSLOADPOST 2022:05:05:23:34:17 mris_curvature N 4 1.08 1.11 1.08
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
ln: failed to create symbolic link 'lh.white.H': Operation not permitted
Linux developer-VirtualBox 5.4.0-109-generic #123~18.04.1-Ubuntu SMP Fri Apr 8 
09:48:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub101-sesBL exited with ERRORS at Thu May  5 23:34:17 EDT 2022

For more details, see the log file 
/home/developer/guest_shared/fs-subjects/sub101-sesBL/scripts/recon-all.log
To report a problem, see 
http://secure-web.cisco.com/1qOeaquoMOTkikWpYGZ4Zmm7T4aU7IdoLWz_R7WjwgxWoQGxY3cPBUDVV4WjL1HTzvXW83WzudLxHfUxd3VMjIW_onAfNPXVndE-taWDHNlTvxXSVt2XAWWGqV2_tqFc6xj1PgghG-vQD5NzYL7fMWU0fWUyVO3gu-hnNg-Nlw0SYtMFHU1Mpf_ezbHxFnHKFMhZR7-V9ztKJPq48qnxSxdaYp3f90UN5PtdDDL_YToCmUoLNZzThrPogT-MkRuyqenk7hzKn-vnr1u89-jcjkzLqvD1Zlp4rCTKFLJ1mv-WZ7GImSBJ-q_-ejSRyOeOLlCao4_RYJXLprXzFkq51bQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting




After searching through the archives, I see that other people have had the same 
problem in that their os is not able to create a symbolic link.  I tried 
following one of the archives and did:



developer@developer-VirtualBox:~/guest_shared/mv-ds000174-1.0.1-Cannabis/sub-101/ses-BL/anat$
 cd /home/developer/guest_shared/fs-subjects
developer@developer-VirtualBox:~/guest_shared/fs-subjects$ ln -s 
/home/developer/guest_shared/fs-subjects/fsaverage
ln: failed to create symbolic link './fsaverage': Operation not permitted

But I again received the "failed to create symbolic link. How can I allow 
symbolic links? Also, I was generally wondering how do you rerun recon-all 
starting from a specific step once I get this working? Does one have to rerun 
all of recon-all each time there is an error or can I start from where I left 
off?

Thank you so much for your help!

Best wishes,
Joanna

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Recon-All Error: "Command exited with non-zero status"

[Wighton, Paul]

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-zero status"


External Email - Use Caution

Hi Paul,

Thank you so much for the timely response and the easy-to-follow explanation 
(and especially for the little tips on naming/spacing, which are helpful for a 
new coder). I did all these steps and everything worked great - the recon-all 
is running fine now.

Thank you!
Joanna


--

Joanna Eckhardt

Neurosciences Graduate Program

University of California, San Diego


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Wighton, Paul 

Sent: Thursday, May 5, 2022 1:26 PM
To: freesurfer@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 variable.  You 
should be able to do that with these 2 commands:

```
mkdir -p /home/developer/guest_shared/fs-subjects
export SUBJECTS_DIR=/home/developer/guest_shared/fs-subjects
```

Next, it looks like you've downloaded the dataset to a folder called 
`/home/developer/guest_shared/mv ds000174-1.0.1 Cannabis/` and the spaces in 
the folder name are confusing recon-all.  Can you rename that directory and 
remove the spaces?  You should be able to do that in the file explorer, but 
this should also work:

```
mv '/home/developer/guest_shared/mv ds000174-1.0.1 Cannabis/' 
/home/developer/guest_shared/mv-ds000174-1.0.1-Cannabis/
```

You should then be able to run the recon-all command.  However, when running 
recon-all, you might want to rename the subject from 'sub101' to 'sub101-sesBL' 
(recon-all -s sub101-sesBL) so that you don't confuse it with the follow-up 
session (ses-FU) in the dataset.

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf 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 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 "recon-all -s sub101 exited with ERRORS." Can you help me 
solve this?

I am completely new to coding/Ubuntu so I am also confused about the 
SUBJECTS_DIR. Where can I find that folder? I do not see 
/usr/local/freesurfer/7.2.0/subjects anywhere in the VM.

Also, if there is a better way to export and present my code to you other than 
copy-pasting it as I have done below, please let me know so I can do that with 
future emails.


developer@developer-VirtualBox:~/guest_shared/mv ds000174-1.0.1 
Cannabis/sub-101/ses-BL/anat$ recon-all -s sub101 -i sub-101_ses-BL_T1w.nii.gz 
-all
Subject Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
Current Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
INFO: SUBJECTS_DIR is /usr/local/freesurfer/7.2.0/subjects
Actual FREESURFER_HOME /usr/local/freesurfer/7.2.0
Linux developer-VirtualBox 5.4.0-109-generic #123~18.04.1-Ubuntu SMP Fri Apr 8 
09:48:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
/usr/local/freesurfer/7.2.0/subjects/sub101

 mri_convert /home/developer/guest_shared/mv ds000174-1.0.1 
Cannabis/sub-101/ses-BL/anat/sub-101_ses-BL_T1w.nii.gz 
/usr/local/freesurfer/7.2.0/subjects/sub101/mri/orig/001.mgz

mri_convert /home/developer/guest_shared/mv ds000174-1.0.1 
Cannabis/sub-101/ses-BL/anat/sub-101_ses-BL_T1w.nii.gz 
/usr/local/freesurfer/7.2.0/subjects/sub101/mri/orig/001.mgz

mri_convert: extra arguments 
("Cannabis/sub-101/ses-BL/anat/sub-101_ses-BL_T1w.nii.gz" and following)

type mri_convert -u for usage

Command exited with non-zero status 1
@#@FSTIME  2022:05:05:15:24:40 mri_convert N 4 e 0.00 S 0.00 U 0.00 P 100% M 
6204 F 0 R 242 W 0 c 0 w 1 I 0 O 0 L 0.19 0.11 0.04
@#@FSLOADPOST 2022:05:05:15:24:40 mri_convert N 4 0.19 0.11 0.04
Linux developer-VirtualBox 5.4.0-109-generic #123~18.04.1-Ubuntu SMP Fri Apr 8 
09:48:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub101 exited with ERRORS at Thu May  5 15:24:40 EDT 2022

For more details, see the log file 
/usr/local/freesurfer/7.2.0/subjects/sub101/scripts/recon-all.log
To report a problem, see MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://surfe

Re: [Freesurfer] Recon-All Error: "Command exited with non-zero status"

[Joanna L Eckhardt]

External Email - Use Caution

Hi Paul,

Thank you so much for the timely response and the easy-to-follow explanation 
(and especially for the little tips on naming/spacing, which are helpful for a 
new coder). I did all these steps and everything worked great - the recon-all 
is running fine now.

Thank you!
Joanna


--

Joanna Eckhardt

Neurosciences Graduate Program

University of California, San Diego


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Wighton, Paul 

Sent: Thursday, May 5, 2022 1:26 PM
To: freesurfer@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 variable.  You 
should be able to do that with these 2 commands:

```
mkdir -p /home/developer/guest_shared/fs-subjects
export SUBJECTS_DIR=/home/developer/guest_shared/fs-subjects
```

Next, it looks like you've downloaded the dataset to a folder called 
`/home/developer/guest_shared/mv ds000174-1.0.1 Cannabis/` and the spaces in 
the folder name are confusing recon-all.  Can you rename that directory and 
remove the spaces?  You should be able to do that in the file explorer, but 
this should also work:

```
mv '/home/developer/guest_shared/mv ds000174-1.0.1 Cannabis/' 
/home/developer/guest_shared/mv-ds000174-1.0.1-Cannabis/
```

You should then be able to run the recon-all command.  However, when running 
recon-all, you might want to rename the subject from 'sub101' to 'sub101-sesBL' 
(recon-all -s sub101-sesBL) so that you don't confuse it with the follow-up 
session (ses-FU) in the dataset.

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf 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 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 "recon-all -s sub101 exited with ERRORS." Can you help me 
solve this?

I am completely new to coding/Ubuntu so I am also confused about the 
SUBJECTS_DIR. Where can I find that folder? I do not see 
/usr/local/freesurfer/7.2.0/subjects anywhere in the VM.

Also, if there is a better way to export and present my code to you other than 
copy-pasting it as I have done below, please let me know so I can do that with 
future emails.


developer@developer-VirtualBox:~/guest_shared/mv ds000174-1.0.1 
Cannabis/sub-101/ses-BL/anat$ recon-all -s sub101 -i sub-101_ses-BL_T1w.nii.gz 
-all
Subject Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
Current Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
INFO: SUBJECTS_DIR is /usr/local/freesurfer/7.2.0/subjects
Actual FREESURFER_HOME /usr/local/freesurfer/7.2.0
Linux developer-VirtualBox 5.4.0-109-generic #123~18.04.1-Ubuntu SMP Fri Apr 8 
09:48:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
/usr/local/freesurfer/7.2.0/subjects/sub101

 mri_convert /home/developer/guest_shared/mv ds000174-1.0.1 
Cannabis/sub-101/ses-BL/anat/sub-101_ses-BL_T1w.nii.gz 
/usr/local/freesurfer/7.2.0/subjects/sub101/mri/orig/001.mgz

mri_convert /home/developer/guest_shared/mv ds000174-1.0.1 
Cannabis/sub-101/ses-BL/anat/sub-101_ses-BL_T1w.nii.gz 
/usr/local/freesurfer/7.2.0/subjects/sub101/mri/orig/001.mgz

mri_convert: extra arguments 
("Cannabis/sub-101/ses-BL/anat/sub-101_ses-BL_T1w.nii.gz" and following)

type mri_convert -u for usage

Command exited with non-zero status 1
@#@FSTIME  2022:05:05:15:24:40 mri_convert N 4 e 0.00 S 0.00 U 0.00 P 100% M 
6204 F 0 R 242 W 0 c 0 w 1 I 0 O 0 L 0.19 0.11 0.04
@#@FSLOADPOST 2022:05:05:15:24:40 mri_convert N 4 0.19 0.11 0.04
Linux developer-VirtualBox 5.4.0-109-generic #123~18.04.1-Ubuntu SMP Fri Apr 8 
09:48:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub101 exited with ERRORS at Thu May  5 15:24:40 EDT 2022

For more details, see the log file 
/usr/local/freesurfer/7.2.0/subjects/sub101/scripts/recon-all.log
To report a problem, see 
http://secure-web.cisco.com/1Y7KxvLmbdY8baQtI8r8UC0Z8yYcBNKe9xZsDQ2R-daiTkblulhENlIdYpZF14tH6ZoZ3LyaKXPAX5yR_dq1GywPmMNNc7nVYyvnYZl01yb74Bk1oCbrddqv7hssK9YPzX5-axqIh-62IltCuOqnQNjH1kIuabyu4q8JnSzx6rOmnMLIuyg6mDTbTHrJyU45S8f5mJh-fxGiy_q3-g5UGheGf66xJg8uF2jdLsqGrE9_nMzXn4wbrPZGn1VzqkBJPxubtdpQpO-EBLqTB1xoV-sZLFjncq-qDeN3F69akam63pBz9rSSSOcqciu4riSyj/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting<https://secure-web.cisco.com/171g7W4aWq3g90gDYi_bDLIcS8Y5d6ZDSv8P1BtEB0c8Ly1DMxcJKeele5KmRxWCr7JKNdg8_cR8p

Re: [Freesurfer] Recon-All Error: "Command exited with non-zero status"

[Wighton, Paul]

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/fs-subjects
export SUBJECTS_DIR=/home/developer/guest_shared/fs-subjects
```

Next, it looks like you've downloaded the dataset to a folder called 
`/home/developer/guest_shared/mv ds000174-1.0.1 Cannabis/` and the spaces in 
the folder name are confusing recon-all.  Can you rename that directory and 
remove the spaces?  You should be able to do that in the file explorer, but 
this should also work:

```
mv '/home/developer/guest_shared/mv ds000174-1.0.1 Cannabis/' 
/home/developer/guest_shared/mv-ds000174-1.0.1-Cannabis/
```

You should then be able to run the recon-all command.  However, when running 
recon-all, you might want to rename the subject from 'sub101' to 'sub101-sesBL' 
(recon-all -s sub101-sesBL) so that you don't confuse it with the follow-up 
session (ses-FU) in the dataset.

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf 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 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 "recon-all -s sub101 exited with ERRORS." Can you help me 
solve this?

I am completely new to coding/Ubuntu so I am also confused about the 
SUBJECTS_DIR. Where can I find that folder? I do not see 
/usr/local/freesurfer/7.2.0/subjects anywhere in the VM.

Also, if there is a better way to export and present my code to you other than 
copy-pasting it as I have done below, please let me know so I can do that with 
future emails.


developer@developer-VirtualBox:~/guest_shared/mv ds000174-1.0.1 
Cannabis/sub-101/ses-BL/anat$ recon-all -s sub101 -i sub-101_ses-BL_T1w.nii.gz 
-all
Subject Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
Current Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
INFO: SUBJECTS_DIR is /usr/local/freesurfer/7.2.0/subjects
Actual FREESURFER_HOME /usr/local/freesurfer/7.2.0
Linux developer-VirtualBox 5.4.0-109-generic #123~18.04.1-Ubuntu SMP Fri Apr 8 
09:48:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
/usr/local/freesurfer/7.2.0/subjects/sub101

 mri_convert /home/developer/guest_shared/mv ds000174-1.0.1 
Cannabis/sub-101/ses-BL/anat/sub-101_ses-BL_T1w.nii.gz 
/usr/local/freesurfer/7.2.0/subjects/sub101/mri/orig/001.mgz

mri_convert /home/developer/guest_shared/mv ds000174-1.0.1 
Cannabis/sub-101/ses-BL/anat/sub-101_ses-BL_T1w.nii.gz 
/usr/local/freesurfer/7.2.0/subjects/sub101/mri/orig/001.mgz

mri_convert: extra arguments 
("Cannabis/sub-101/ses-BL/anat/sub-101_ses-BL_T1w.nii.gz" and following)

type mri_convert -u for usage

Command exited with non-zero status 1
@#@FSTIME  2022:05:05:15:24:40 mri_convert N 4 e 0.00 S 0.00 U 0.00 P 100% M 
6204 F 0 R 242 W 0 c 0 w 1 I 0 O 0 L 0.19 0.11 0.04
@#@FSLOADPOST 2022:05:05:15:24:40 mri_convert N 4 0.19 0.11 0.04
Linux developer-VirtualBox 5.4.0-109-generic #123~18.04.1-Ubuntu SMP Fri Apr 8 
09:48:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub101 exited with ERRORS at Thu May  5 15:24:40 EDT 2022

For more details, see the log file 
/usr/local/freesurfer/7.2.0/subjects/sub101/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Thank you!
Joanna

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] Recon-All Error: "Command exited with non-zero status"

[Joanna L Eckhardt]

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 "recon-all -s sub101 exited with ERRORS." Can you help me 
solve this?

I am completely new to coding/Ubuntu so I am also confused about the 
SUBJECTS_DIR. Where can I find that folder? I do not see 
/usr/local/freesurfer/7.2.0/subjects anywhere in the VM.

Also, if there is a better way to export and present my code to you other than 
copy-pasting it as I have done below, please let me know so I can do that with 
future emails.


developer@developer-VirtualBox:~/guest_shared/mv ds000174-1.0.1 
Cannabis/sub-101/ses-BL/anat$ recon-all -s sub101 -i sub-101_ses-BL_T1w.nii.gz 
-all
Subject Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
Current Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
INFO: SUBJECTS_DIR is /usr/local/freesurfer/7.2.0/subjects
Actual FREESURFER_HOME /usr/local/freesurfer/7.2.0
Linux developer-VirtualBox 5.4.0-109-generic #123~18.04.1-Ubuntu SMP Fri Apr 8 
09:48:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
/usr/local/freesurfer/7.2.0/subjects/sub101

 mri_convert /home/developer/guest_shared/mv ds000174-1.0.1 
Cannabis/sub-101/ses-BL/anat/sub-101_ses-BL_T1w.nii.gz 
/usr/local/freesurfer/7.2.0/subjects/sub101/mri/orig/001.mgz

mri_convert /home/developer/guest_shared/mv ds000174-1.0.1 
Cannabis/sub-101/ses-BL/anat/sub-101_ses-BL_T1w.nii.gz 
/usr/local/freesurfer/7.2.0/subjects/sub101/mri/orig/001.mgz

mri_convert: extra arguments 
("Cannabis/sub-101/ses-BL/anat/sub-101_ses-BL_T1w.nii.gz" and following)

type mri_convert -u for usage

Command exited with non-zero status 1
@#@FSTIME  2022:05:05:15:24:40 mri_convert N 4 e 0.00 S 0.00 U 0.00 P 100% M 
6204 F 0 R 242 W 0 c 0 w 1 I 0 O 0 L 0.19 0.11 0.04
@#@FSLOADPOST 2022:05:05:15:24:40 mri_convert N 4 0.19 0.11 0.04
Linux developer-VirtualBox 5.4.0-109-generic #123~18.04.1-Ubuntu SMP Fri Apr 8 
09:48:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub101 exited with ERRORS at Thu May  5 15:24:40 EDT 2022

For more details, see the log file 
/usr/local/freesurfer/7.2.0/subjects/sub101/scripts/recon-all.log
To report a problem, see 
http://secure-web.cisco.com/1nsoXu7DCJVVepnD_TI4lsupkcqto3lUNXVTynw-dkWgX0jgK5OMP6_Zvr1ZiIw5bdjvsH7QIZbXzwlVuvV8YaYPH31dXZld0PLKJQ6n6zVlT1vUWUcUvBjU9xD9Ofzw8OBKU4eRC_2DIyDBkLIBwF4vsHAAyJZ-hBJL7quyFxlQJ0salWFI5a5qUmD_AkXgyYHjsrbT5WlaGtqn-I72qhlbZm7rYYNqy2AO94040Acgj_3O1wejt1NmgePGUIMn08354kq_0lTEmwZFZX3GhybUyvRiTJq2YRAfWTZBVP9vbm7ve54riG7fhPUzP37cI/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting


Thank you!
Joanna

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] recon-all error

[cooperr1]

External Email - Use Caution

Dear Yujing,

 

I had the same problem with Dcm2niix, but I can open and extract them with 
dcm2nii. I’m not sure what that means!

 

Best,

Rebecca

 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Huang, Yujing
Sent: Thursday, 28 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.

 

Best,

 

Yujing

 

 

 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > On Behalf Of Rebecca 
Elizabeth Cooper
Sent: Tuesday, April 26, 2022 5:59 PM
To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu> >
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 mailto:yhuan...@mgh.harvard.edu> > wrote:

Hi Rebecca,

 

Thanks for sending the file. But it doesn’t seem that I have the permission to 
access it.

 

Yujing 

 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > On Behalf Of Rebecca 
Elizabeth Cooper
Sent: Monday, April 25, 2022 7:12 PM
To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu> >
Subject: Re: [Freesurfer] recon-all error

 

External Email - Use Caution

Dear Yujing,

 

Thank you kindly for your support. Please see attached.

 

Kind regards,

Rebecca

 
<https://secure-web.cisco.com/1SSpigVok3m_G93QOxuw_bIlBxpj6W-yzTn9nFuH8olwKGNPUJiiAldzsoTZik1dzFpQRsKqf-VmPcDZAyiVk0F1gsPqeKQg0XtVNnTXofiZxgvTMF3ojKm-HQlJRe8gZw_Jnet3fWjXh_3xgvuVcYGEkH55RRdGHjmXGPZv7HjynG7fo1dbyY1rR5zoa1bkmnzPT8PpSz1NeZ1tgD0wCzuNBe-x7_28iiDmIbYrRLsXZb6T6NshcPDlBwIz0vKfcvPNu1B_0O4zUF0obxlVvkOVnuEdinQv4K8h6hNfwsb6vgMexKTsRnehjx5rtNHa2x2qSlhW96T6Bp-JP60om3w/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1l-ZiyouIRcvEgR258PYb5B90P2b3EFDg%2Fview%3Fusp%3Ddrive_web>
  Downloads.zip

 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > On Behalf Of Huang, Yujing
Sent: Tuesday, 26 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 
debug?

 

Thanks.

 

Yujing

 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > On Behalf Of Huang, Yujing
Sent: Saturday, April 23, 2022 1:50 PM
To: 'Freesurfer support list' mailto:freesurfer@nmr.mgh.harvard.edu> >
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://secure-web.cisco.com/1Swb2oS6hDVyvEnob9HiqJ3vv48refI6wmxC3PAZbvpWnceOxMkeYxcebCPqkVaLSNgG6VxoxEz26TRJ4RxBV5jWaqFMRTq7XZhd2c0Aud7Bdss9XZxI137TQO0m2MTefk54kPhZ0opUewOFNdWPHqMvsXVewXnvr0KVTzmDNGSqfmIJ08UCbtC-gAhcyvbGqxK7FfDhAXJvsv7xPxYrFTxyoZmRG9wYZF0shHunkZOs5gUch8cDlYjiA6sS6YKaGt0hgNEsA6edCTApA_vm7_9wkT1Gis0d8FKje6z4qWWKqjtAwxjbaf-QhFvyzOVwlxWZqVgFJkIWZxVH4furhFQ/https%3A%2F%2Fgithub.com%2Frordenlab%2Fdcm2niix>
 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/12H2e8xCjrEi-wbb98756SfSMuEwEOb12bspDfWR5MA902FANozPWRbUXsyyL6gN9KEwHx6CuWYNCXonjEXr5aFAfX4Z006TCkWCN7_kN-Bjv4ICPa40hXz9vS2F6d2E_ioG7bqYAPbNvCaZSeJk0JFgxvlcdKvEAx-0cOry-Kpdvt353hndbN7tEkUP5i4Uz7INcDb-OIfQoShj0XmsIhvxzso9Mn_NE2Prbo9kL5JqJoATNSdkUJRceDyGRyu6yzSASHxlWOpixCofpkrEvy03AEtdN4sow1neidzbMCklPa4BDrej7-nKzW3GK_8-dXibJfTbfRkdMm1ayRQ13NQ/https%3A%2F%2Fgithub.com%2Frordenlab%2Fdcm2niix

 

I use the following command to do conversion: dcm2niix -o  -f 
"%s_%p" 

 

Please note that  needs to be specified as last parameter.  '-f <>' 
specifies output file name format - "%s_%p" will have series no + protocol as 
prefix. 

 

Hope these helps.

 

Best,

 

Yujing

 

 


  _  


From: freesurfer-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > on behalf of 
coope...@student.unimelb.edu.au <mailto:coope...@student.unime

Re: [Freesurfer] recon-all error

[Huang, Yujing]

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.

Best,

Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Rebecca 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 
mailto:yhuan...@mgh.harvard.edu>> wrote:
Hi Rebecca,

Thanks for sending the file. But it doesn’t seem that I have the permission to 
access it.

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Rebecca Elizabeth Cooper
Sent: Monday, April 25, 2022 7:12 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all error


External Email - Use Caution
Dear Yujing,

Thank you kindly for your support. Please see attached.

Kind regards,
Rebecca
[Image removed by sender.] 
Downloads.zip<https://secure-web.cisco.com/1SSpigVok3m_G93QOxuw_bIlBxpj6W-yzTn9nFuH8olwKGNPUJiiAldzsoTZik1dzFpQRsKqf-VmPcDZAyiVk0F1gsPqeKQg0XtVNnTXofiZxgvTMF3ojKm-HQlJRe8gZw_Jnet3fWjXh_3xgvuVcYGEkH55RRdGHjmXGPZv7HjynG7fo1dbyY1rR5zoa1bkmnzPT8PpSz1NeZ1tgD0wCzuNBe-x7_28iiDmIbYrRLsXZb6T6NshcPDlBwIz0vKfcvPNu1B_0O4zUF0obxlVvkOVnuEdinQv4K8h6hNfwsb6vgMexKTsRnehjx5rtNHa2x2qSlhW96T6Bp-JP60om3w/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1l-ZiyouIRcvEgR258PYb5B90P2b3EFDg%2Fview%3Fusp%3Ddrive_web>[Image
 removed by sender.]

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Huang, Yujing
Sent: Tuesday, 26 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 
debug?

Thanks.

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Huang, Yujing
Sent: Saturday, April 23, 2022 1:50 PM
To: 'Freesurfer support list' 
mailto:freesurfer@nmr.mgh.harvard.edu>>
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:
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://github.com/rordenlab/dcm2niix<https://secure-web.cisco.com/1Swb2oS6hDVyvEnob9HiqJ3vv48refI6wmxC3PAZbvpWnceOxMkeYxcebCPqkVaLSNgG6VxoxEz26TRJ4RxBV5jWaqFMRTq7XZhd2c0Aud7Bdss9XZxI137TQO0m2MTefk54kPhZ0opUewOFNdWPHqMvsXVewXnvr0KVTzmDNGSqfmIJ08UCbtC-gAhcyvbGqxK7FfDhAXJvsv7xPxYrFTxyoZmRG9wYZF0shHunkZOs5gUch8cDlYjiA6sS6YKaGt0hgNEsA6edCTApA_vm7_9wkT1Gis0d8FKje6z4qWWKqjtAwxjbaf-QhFvyzOVwlxWZqVgFJkIWZxVH4furhFQ/https%3A%2F%2Fgithub.com%2Frordenlab%2Fdcm2niix>

I use the following command to do conversion: dcm2niix -o  -f 
"%s_%p" 

Please note that  needs to be specified as last parameter.  '-f <>' 
specifies output file name format - "%s_%p" will have series no + protocol as 
prefix.

Hope these helps.

Best,

Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of 
coope...@student.unimelb.edu.au<mailto:coope...@student.unimelb.edu.au> 
mailto:coope...@student.unimelb.edu.au>>
Sent: Saturday, April 23, 2022 2:44 AM
To: 'Freesurfer support list' 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all error


External Email - Use Caution

Hi Yujing,



I guess not. This is the output:



cooperr@marge:/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms$ 
mri_probedicom --i 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256



ERROR: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256
 is not a dicom file or some other problem



Entering IsDICOM 
(/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256)



ERROR: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256
 is not a dicom file or some other problem



I also ra

Re: [Freesurfer] recon-all error

[Rebecca Elizabeth Cooper]

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 
wrote:

> Hi Rebecca,
>
>
>
> Thanks for sending the file. But it doesn’t seem that I have the
> permission 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 support list 
> *Subject:* Re: [Freesurfer] recon-all error
>
>
>
> *External Email - Use Caution*
>
> Dear Yujing,
>
>
>
> Thank you kindly for your support. Please see attached.
>
>
>
> Kind regards,
>
> Rebecca
>
> *[image: Image removed by sender.] Downloads.zip
> <https://secure-web.cisco.com/1SSpigVok3m_G93QOxuw_bIlBxpj6W-yzTn9nFuH8olwKGNPUJiiAldzsoTZik1dzFpQRsKqf-VmPcDZAyiVk0F1gsPqeKQg0XtVNnTXofiZxgvTMF3ojKm-HQlJRe8gZw_Jnet3fWjXh_3xgvuVcYGEkH55RRdGHjmXGPZv7HjynG7fo1dbyY1rR5zoa1bkmnzPT8PpSz1NeZ1tgD0wCzuNBe-x7_28iiDmIbYrRLsXZb6T6NshcPDlBwIz0vKfcvPNu1B_0O4zUF0obxlVvkOVnuEdinQv4K8h6hNfwsb6vgMexKTsRnehjx5rtNHa2x2qSlhW96T6Bp-JP60om3w/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1l-ZiyouIRcvEgR258PYb5B90P2b3EFDg%2Fview%3Fusp%3Ddrive_web>**[image:
> Image removed by sender.]*
>
>
>
> *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,
>
>
>
> 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 debug?
>
>
>
> Thanks.
>
>
>
> Yujing
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Huang, Yujing
> *Sent:* Saturday, April 23, 2022 1:50 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:
>
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/17Ga0Xp3SP-CwTjSyxKsZeuTrgi6PpoirdFYSw1C92Ho9dbRuQ2edmCex8QhiTy5y5Cs23DSgVQ3raixqX1CCAYc4jqqGEkMfifaT9qn5lZY0V5u49HuYtMSpfl3ALWhlVVEGRw-1lrEgUfxwjlLaCNKPi7mXrXnTamJDmd-gI6fHx5x9Hrs8kLDNyuPywIbEhb6ACqCM2iigyvCET3XPFsV6d7P519XoIKBFdwsR3RMW1qL-HOfyjuuVJcT9UDNwz4ZvD0QoKk3kXMIvmIbsRA5AGmVIyS9ONlsG5HyGRdXx5OtiA8CPUEIa2-TnspNu1ppPe8sf09ihQa19o9-hAg/https%3A%2F%2Fgithub.com%2Frordenlab%2Fdcm2niix
> <https://secure-web.cisco.com/1Swb2oS6hDVyvEnob9HiqJ3vv48refI6wmxC3PAZbvpWnceOxMkeYxcebCPqkVaLSNgG6VxoxEz26TRJ4RxBV5jWaqFMRTq7XZhd2c0Aud7Bdss9XZxI137TQO0m2MTefk54kPhZ0opUewOFNdWPHqMvsXVewXnvr0KVTzmDNGSqfmIJ08UCbtC-gAhcyvbGqxK7FfDhAXJvsv7xPxYrFTxyoZmRG9wYZF0shHunkZOs5gUch8cDlYjiA6sS6YKaGt0hgNEsA6edCTApA_vm7_9wkT1Gis0d8FKje6z4qWWKqjtAwxjbaf-QhFvyzOVwlxWZqVgFJkIWZxVH4furhFQ/https%3A%2F%2Fgithub.com%2Frordenlab%2Fdcm2niix>
>
>
>
> I use the following command to do conversion: dcm2niix -o  -f
> "%s_%p" 
>
>
>
> Please note that  needs to be specified as last parameter.  '-f
> <>' specifies output file name format - "%s_%p" will have series no +
> protocol as prefix.
>
>
>
> Hope these helps.
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
>
> --
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-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:
>
>
>
> cooperr@marge:/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms$
> mri_probedicom --i
> /data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256
>
>
>
> ERROR:
> /data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256
> is not a dicom file or some other problem
>
>
>
> Entering IsDICOM
> (/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/1

Re: [Freesurfer] recon-all error

[Huang, Yujing]

Hi Rebecca,

Thanks for sending the file. But it doesn’t seem that I have the permission to 
access it.

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Rebecca Elizabeth Cooper
Sent: Monday, April 25, 2022 7:12 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all error


External Email - Use Caution
Dear Yujing,

Thank you kindly for your support. Please see attached.

Kind regards,
Rebecca
[Image removed by sender.] 
Downloads.zip<https://secure-web.cisco.com/1SSpigVok3m_G93QOxuw_bIlBxpj6W-yzTn9nFuH8olwKGNPUJiiAldzsoTZik1dzFpQRsKqf-VmPcDZAyiVk0F1gsPqeKQg0XtVNnTXofiZxgvTMF3ojKm-HQlJRe8gZw_Jnet3fWjXh_3xgvuVcYGEkH55RRdGHjmXGPZv7HjynG7fo1dbyY1rR5zoa1bkmnzPT8PpSz1NeZ1tgD0wCzuNBe-x7_28iiDmIbYrRLsXZb6T6NshcPDlBwIz0vKfcvPNu1B_0O4zUF0obxlVvkOVnuEdinQv4K8h6hNfwsb6vgMexKTsRnehjx5rtNHa2x2qSlhW96T6Bp-JP60om3w/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1l-ZiyouIRcvEgR258PYb5B90P2b3EFDg%2Fview%3Fusp%3Ddrive_web>[Image
 removed by sender.]

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Huang, Yujing
Sent: Tuesday, 26 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 
debug?

Thanks.

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Huang, Yujing
Sent: Saturday, April 23, 2022 1:50 PM
To: 'Freesurfer support list' 
mailto:freesurfer@nmr.mgh.harvard.edu>>
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:
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://github.com/rordenlab/dcm2niix<https://secure-web.cisco.com/1Swb2oS6hDVyvEnob9HiqJ3vv48refI6wmxC3PAZbvpWnceOxMkeYxcebCPqkVaLSNgG6VxoxEz26TRJ4RxBV5jWaqFMRTq7XZhd2c0Aud7Bdss9XZxI137TQO0m2MTefk54kPhZ0opUewOFNdWPHqMvsXVewXnvr0KVTzmDNGSqfmIJ08UCbtC-gAhcyvbGqxK7FfDhAXJvsv7xPxYrFTxyoZmRG9wYZF0shHunkZOs5gUch8cDlYjiA6sS6YKaGt0hgNEsA6edCTApA_vm7_9wkT1Gis0d8FKje6z4qWWKqjtAwxjbaf-QhFvyzOVwlxWZqVgFJkIWZxVH4furhFQ/https%3A%2F%2Fgithub.com%2Frordenlab%2Fdcm2niix>

I use the following command to do conversion: dcm2niix -o  -f 
"%s_%p" 

Please note that  needs to be specified as last parameter.  '-f <>' 
specifies output file name format - "%s_%p" will have series no + protocol as 
prefix.

Hope these helps.

Best,

Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of 
coope...@student.unimelb.edu.au<mailto:coope...@student.unimelb.edu.au> 
mailto:coope...@student.unimelb.edu.au>>
Sent: Saturday, April 23, 2022 2:44 AM
To: 'Freesurfer support list' 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all error


External Email - Use Caution

Hi Yujing,



I guess not. This is the output:



cooperr@marge:/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms$ 
mri_probedicom --i 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256



ERROR: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256
 is not a dicom file or some other problem



Entering IsDICOM 
(/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256)



ERROR: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256
 is not a dicom file or some other problem



I also ran straight to the dicom files themselves, with the same response:



cooperr@marge:/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms$ 
mri_probedicom --i 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001



ERROR: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
 is not a dicom file or some other problem



Entering IsDICOM 
(/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001)

Opening 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
 as part10

DCM_FILEOPENFAILED

   20092 DCM failed to open file: 
/da

Re: [Freesurfer] recon-all error

[Rebecca Elizabeth Cooper]

External Email - Use Caution

Dear Yujing,



Thank you kindly for your support. Please see attached.



Kind regards,

Rebecca
 Downloads.zip
<https://secure-web.cisco.com/1SSpigVok3m_G93QOxuw_bIlBxpj6W-yzTn9nFuH8olwKGNPUJiiAldzsoTZik1dzFpQRsKqf-VmPcDZAyiVk0F1gsPqeKQg0XtVNnTXofiZxgvTMF3ojKm-HQlJRe8gZw_Jnet3fWjXh_3xgvuVcYGEkH55RRdGHjmXGPZv7HjynG7fo1dbyY1rR5zoa1bkmnzPT8PpSz1NeZ1tgD0wCzuNBe-x7_28iiDmIbYrRLsXZb6T6NshcPDlBwIz0vKfcvPNu1B_0O4zUF0obxlVvkOVnuEdinQv4K8h6hNfwsb6vgMexKTsRnehjx5rtNHa2x2qSlhW96T6Bp-JP60om3w/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1l-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,



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 debug?



Thanks.



Yujing



*From:* freesurfer-boun...@nmr.mgh.harvard.edu <
freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Huang, Yujing
*Sent:* Saturday, April 23, 2022 1:50 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://secure-web.cisco.com/1Swb2oS6hDVyvEnob9HiqJ3vv48refI6wmxC3PAZbvpWnceOxMkeYxcebCPqkVaLSNgG6VxoxEz26TRJ4RxBV5jWaqFMRTq7XZhd2c0Aud7Bdss9XZxI137TQO0m2MTefk54kPhZ0opUewOFNdWPHqMvsXVewXnvr0KVTzmDNGSqfmIJ08UCbtC-gAhcyvbGqxK7FfDhAXJvsv7xPxYrFTxyoZmRG9wYZF0shHunkZOs5gUch8cDlYjiA6sS6YKaGt0hgNEsA6edCTApA_vm7_9wkT1Gis0d8FKje6z4qWWKqjtAwxjbaf-QhFvyzOVwlxWZqVgFJkIWZxVH4furhFQ/https%3A%2F%2Fgithub.com%2Frordenlab%2Fdcm2niix



I use the following command to do conversion: dcm2niix -o  -f
"%s_%p" 



Please note that  needs to be specified as last parameter.  '-f
<>' specifies output file name format - "%s_%p" will have series no +
protocol as prefix.



Hope these helps.



Best,



Yujing




--

*From:* freesurfer-boun...@nmr.mgh.harvard.edu <
freesurfer-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:



cooperr@marge:/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms$
mri_probedicom --i
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256



ERROR:
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256
is not a dicom file or some other problem



Entering IsDICOM
(/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256)



ERROR:
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256
is not a dicom file or some other problem



I also ran straight to the dicom files themselves, with the same response:



cooperr@marge:/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms$
mri_probedicom --i
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001



ERROR:
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
is not a dicom file or some other problem



Entering IsDICOM
(/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001)

Opening
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
as part10

DCM_FILEOPENFAILED

   20092 DCM failed to open file:
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
in DCM_OpenFile

Opening as littleendian

DCM_FILEOPENFAILED

Opening as bigendian

DCM_FILEOPENFAILED

Opening as format conversion

DCM_ILLEGALOPTION

Leaving IsDICOM
(/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001)



ERROR:
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
is not a dicom file or some other problem



Thank you,



Rebecca





*From:* freesurfer-boun...@nmr.mgh.harvard.edu <
freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Huang, Yujing
*Sent:* Friday, 22 April 2022 11:11 PM
*To:* 'Freesurfer support list' 
*Subject:* Re: [Freesurfer] recon-all error



H

Re: [Freesurfer] recon-all error

[Huang, Yujing]

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 
debug?

Thanks.

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Huang, Yujing
Sent: Saturday, April 23, 2022 1:50 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://github.com/rordenlab/dcm2niix

I use the following command to do conversion: dcm2niix -o  -f 
"%s_%p" 

Please note that  needs to be specified as last parameter.  '-f <>' 
specifies output file name format - "%s_%p" will have series no + protocol as 
prefix.

Hope these helps.

Best,

Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of 
coope...@student.unimelb.edu.au<mailto:coope...@student.unimelb.edu.au> 
mailto:coope...@student.unimelb.edu.au>>
Sent: Saturday, April 23, 2022 2:44 AM
To: 'Freesurfer support list' 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all error


External Email - Use Caution

Hi Yujing,



I guess not. This is the output:



cooperr@marge:/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms$ 
mri_probedicom --i 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256



ERROR: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256
 is not a dicom file or some other problem



Entering IsDICOM 
(/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256)



ERROR: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256
 is not a dicom file or some other problem



I also ran straight to the dicom files themselves, with the same response:



cooperr@marge:/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms$ 
mri_probedicom --i 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001



ERROR: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
 is not a dicom file or some other problem



Entering IsDICOM 
(/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001)

Opening 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
 as part10

DCM_FILEOPENFAILED

   20092 DCM failed to open file: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
 in DCM_OpenFile

Opening as littleendian

DCM_FILEOPENFAILED

Opening as bigendian

DCM_FILEOPENFAILED

Opening as format conversion

DCM_ILLEGALOPTION

Leaving IsDICOM 
(/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001)



ERROR: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
 is not a dicom file or some other problem



Thank you,



Rebecca





From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Huang, Yujing
Sent: Friday, 22 April 2022 11:11 PM
To: 'Freesurfer support list' 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all error



Hi Rebecca,



I'm wondering if the dicom files are being recognized.



Can you run the following command with some dicom files in the directory?

mri_probedicom --i  --d filetype



(Replace  with full path to dicom file.)



Thanks.



Yujing



From: 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>>
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 directory 
(ID=1003156). The parent folder contains several folders all labelled with 
different subject IDs, and within each contains the dicom directories.
  3.  I attempted this and received the error:



/Applications/freesurfer_v6/bin/dcmunpack -src 

Re: [Freesurfer] recon-all error

[Huang, Yujing]

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://github.com/rordenlab/dcm2niix

I use the following command to do conversion: dcm2niix -o  -f 
"%s_%p" 

Please note that  needs to be specified as last parameter.  '-f <>' 
specifies output file name format - "%s_%p" will have series no + protocol as 
prefix.

Hope these helps.

Best,

Yujing



From: freesurfer-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:



cooperr@marge:/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms$ 
mri_probedicom --i 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256



ERROR: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256
 is not a dicom file or some other problem



Entering IsDICOM 
(/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256)



ERROR: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256
 is not a dicom file or some other problem



I also ran straight to the dicom files themselves, with the same response:



cooperr@marge:/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms$ 
mri_probedicom --i 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001



ERROR: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
 is not a dicom file or some other problem



Entering IsDICOM 
(/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001)

Opening 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
 as part10

DCM_FILEOPENFAILED

   20092 DCM failed to open file: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
 in DCM_OpenFile

Opening as littleendian

DCM_FILEOPENFAILED

Opening as bigendian

DCM_FILEOPENFAILED

Opening as format conversion

DCM_ILLEGALOPTION

Leaving IsDICOM 
(/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001)



ERROR: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
 is not a dicom file or some other problem



Thank you,



Rebecca





From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Huang, Yujing
Sent: Friday, 22 April 2022 11:11 PM
To: 'Freesurfer support list' 
Subject: Re: [Freesurfer] recon-all error



Hi Rebecca,



I’m wondering if the dicom files are being recognized.



Can you run the following command with some dicom files in the directory?

mri_probedicom --i  --d filetype



(Replace  with full path to dicom file.)



Thanks.



Yujing



From: 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>>
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 directory 
(ID=1003156). The parent folder contains several folders all labelled with 
different subject IDs, and within each contains the dicom directories.
  3.  I attempted this and received the error:



/Applications/freesurfer_v6/bin/dcmunpack -src 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/



-rwxr-xr-x  1 chesterk  admin  23759 Jun 14  2018 
/Applications/freesurfer_v6/bin/dcmunpack

---

---

Searching for matching files

Fri Apr 22 15:32:30 AEST 2022

Fri Apr 22 15:32:30 AEST 2022

Found 114 total files.

  Interrogating each and every one of them.

  Be patient.

If you have collected the data in the Martinos center, this

will run faster if you kill this job and re-run with -martinos

Except, with changes in the file naming (Oct 2012), this does

not work.

cat: /tmp/dcmdir-all.23294: No such file or directory

Found 0 unique series:

Patient: Undefined variable.



With than

Re: [Freesurfer] recon-all error

[cooperr1]

External Email - Use Caution

Hi Yujing,

 

I guess not. This is the output:

 

cooperr@marge:/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms$ 
mri_probedicom --i 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256

 

ERROR: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256
 is not a dicom file or some other problem

 

Entering IsDICOM 
(/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256)

 

ERROR: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256
 is not a dicom file or some other problem

 

I also ran straight to the dicom files themselves, with the same response:

 

cooperr@marge:/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms$ 
mri_probedicom --i 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001

 

ERROR: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
 is not a dicom file or some other problem

 

Entering IsDICOM 
(/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001)

Opening 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
 as part10

DCM_FILEOPENFAILED

   20092 DCM failed to open file: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
 in DCM_OpenFile

Opening as littleendian

DCM_FILEOPENFAILED

Opening as bigendian

DCM_FILEOPENFAILED

Opening as format conversion

DCM_ILLEGALOPTION

Leaving IsDICOM 
(/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001)

 

ERROR: 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001
 is not a dicom file or some other problem

 

Thank you,

 

Rebecca

 

 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Huang, Yujing
Sent: Friday, 22 April 2022 11:11 PM
To: 'Freesurfer support list' 
Subject: Re: [Freesurfer] recon-all error

 

Hi Rebecca,

 

I’m wondering if the dicom files are being recognized. 

 

Can you run the following command with some dicom files in the directory?

mri_probedicom --i  --d filetype

 

(Replace  with full path to dicom file.)

 

Thanks.

 

Yujing

 

From: 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> >
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 directory 
(ID=1003156). The parent folder contains several folders all labelled with 
different subject IDs, and within each contains the dicom directories.
3.  I attempted this and received the error:

 

/Applications/freesurfer_v6/bin/dcmunpack -src 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/

 

-rwxr-xr-x  1 chesterk  admin  23759 Jun 14  2018 
/Applications/freesurfer_v6/bin/dcmunpack

---

---

Searching for matching files

Fri Apr 22 15:32:30 AEST 2022

Fri Apr 22 15:32:30 AEST 2022

Found 114 total files.

  Interrogating each and every one of them.

  Be patient.

If you have collected the data in the Martinos center, this

will run faster if you kill this job and re-run with -martinos

Except, with changes in the file naming (Oct 2012), this does

not work.

cat: /tmp/dcmdir-all.23294: No such file or directory

Found 0 unique series:

Patient: Undefined variable.

 

With thanks,

Rebecca

 

 

From: Huang, Yujing mailto:yhuan...@mgh.harvard.edu> 
> 
Sent: Friday, 22 April 2022 4:19 AM
To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu> >
Cc: coope...@student.unimelb.edu.au <mailto:coope...@student.unimelb.edu.au> 
Subject: RE: [Freesurfer] recon-all error

 

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



 Forwarded Message ---- 


Subject: 

[Freesurfer] recon-all error


Date

Re: [Freesurfer] recon-all error

[Huang, Yujing]

Hi Rebecca,

I’m wondering if the dicom files are being recognized.

Can you run the following command with some dicom files in the directory?
mri_probedicom --i  --d filetype

(Replace  with full path to dicom file.)

Thanks.

Yujing

From: coope...@student.unimelb.edu.au 
Sent: Friday, April 22, 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 directory 
(ID=1003156). The parent folder contains several folders all labelled with 
different subject IDs, and within each contains the dicom directories.
  3.  I attempted this and received the error:

/Applications/freesurfer_v6/bin/dcmunpack -src 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/

-rwxr-xr-x  1 chesterk  admin  23759 Jun 14  2018 
/Applications/freesurfer_v6/bin/dcmunpack
---
---
Searching for matching files
Fri Apr 22 15:32:30 AEST 2022
Fri Apr 22 15:32:30 AEST 2022
Found 114 total files.
  Interrogating each and every one of them.
  Be patient.
If you have collected the data in the Martinos center, this
will run faster if you kill this job and re-run with -martinos
Except, with changes in the file naming (Oct 2012), this does
not work.
cat: /tmp/dcmdir-all.23294: No such file or directory
Found 0 unique series:
Patient: Undefined variable.

With thanks,
Rebecca



From: Huang, Yujing mailto:yhuan...@mgh.harvard.edu>>
Sent: Friday, 22 April 2022 4:19 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: coope...@student.unimelb.edu.au<mailto:coope...@student.unimelb.edu.au>
Subject: RE: [Freesurfer] recon-all error

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


 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.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>


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.
Command: recon-all -s 1003156_dicom -i 
2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001 -all
Error message:
/Applications/freesurfer_v6/bin/mri_convert: line 3:  8196 Segmentation fault: 
11  mri_convert.bin "$@"
The recon-all.log is also attached.

I’ve also explored using dcmunpack and obtain the following result:
Command: dcmunpack -src 2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256
Message:
cat: /tmp/dcmdir-all.89439: No such file or directory
Found 0 unique series:
Patient: Undefined variable.

Do you have any idea what might be the problem?

Freesurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Platform: Mac OS X 10.13.3
Recon-all.log: attached.

With warm regards,
Rebecca Cooper

The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at 
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Re: [Freesurfer] recon-all error

[cooperr1]

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 directory 
(ID=1003156). The parent folder contains several folders all labelled with 
different subject IDs, and within each contains the dicom directories.
3.  I attempted this and received the error:

 

/Applications/freesurfer_v6/bin/dcmunpack -src 
/data/netapp01/work/ENIGMA_CHR/longitudinal/PACE/dicoms/1003156/2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/

 

-rwxr-xr-x  1 chesterk  admin  23759 Jun 14  2018 
/Applications/freesurfer_v6/bin/dcmunpack

---

---

Searching for matching files

Fri Apr 22 15:32:30 AEST 2022

Fri Apr 22 15:32:30 AEST 2022

Found 114 total files.

  Interrogating each and every one of them.

  Be patient.

If you have collected the data in the Martinos center, this

will run faster if you kill this job and re-run with -martinos

Except, with changes in the file naming (Oct 2012), this does

not work.

cat: /tmp/dcmdir-all.23294: No such file or directory

Found 0 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 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



 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.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> 





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.

Command: recon-all -s 1003156_dicom -i 
2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001 -all

Error message:
/Applications/freesurfer_v6/bin/mri_convert: line 3:  8196 Segmentation fault: 
11  mri_convert.bin "$@"

The recon-all.log is also attached.

 

I’ve also explored using dcmunpack and obtain the following result:

Command: dcmunpack -src 2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256

Message: 
cat: /tmp/dcmdir-all.89439: No such file or directory

Found 0 unique series:

Patient: Undefined variable.

 

Do you have any idea what might be the problem?

 

Freesurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

Platform: Mac OS X 10.13.3

Recon-all.log: attached.

 

With warm regards,

Rebecca Cooper

 

The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at 
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Re: [Freesurfer] recon-all error

[Huang, Yujing]

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


 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.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>




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.
Command: recon-all -s 1003156_dicom -i 
2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001 -all
Error message:
/Applications/freesurfer_v6/bin/mri_convert: line 3:  8196 Segmentation fault: 
11  mri_convert.bin "$@"
The recon-all.log is also attached.

I’ve also explored using dcmunpack and obtain the following result:
Command: dcmunpack -src 2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256
Message:
cat: /tmp/dcmdir-all.89439: No such file or directory
Found 0 unique series:
Patient: Undefined variable.

Do you have any idea what might be the problem?

Freesurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Platform: Mac OS X 10.13.3
Recon-all.log: attached.

With warm regards,
Rebecca Cooper

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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
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continue to communicate over unencrypted e-mail. 

[Freesurfer] recon-all error

[cooperr1]

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.

Command: recon-all -s 1003156_dicom -i
2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001 -all

Error message:
/Applications/freesurfer_v6/bin/mri_convert: line 3:  8196 Segmentation
fault: 11  mri_convert.bin "$@"

The recon-all.log is also attached.

 

I've also explored using dcmunpack and obtain the following result:

Command: dcmunpack -src 2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256

Message: 
cat: /tmp/dcmdir-all.89439: No such file or directory

Found 0 unique series:

Patient: Undefined variable.

 

Do you have any idea what might be the problem?

 

Freesurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

Platform: Mac OS X 10.13.3

Recon-all.log: attached.

 

With warm regards,

Rebecca Cooper

 



recon-all.log
Description: Binary data
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Re: [Freesurfer] recon-all error in a specific data

[Douglas N. Greve]

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 use the -hires option to recon-all).


On 4/7/2022 12:17 PM, Lee, Jeungchan wrote:


Hi freesurfer team,

I collected an MPRAGE in Bay2 scanner (0.75 x 0.75 x 0.75 mm 
resolution), and the recon-all procedures with freesurfer version 
6.0.0 and 7.1.1 were both failed. I'm not sure if this is due to the 
participant's large CSF or motion or something else.


I have attached the log files (recon-all.log and talairach.log from 
both versions), which I noticed a warning/error in the recon-all.log :


(version6.0.0) *WARNING*: only one run found. This is OK, but motion 
correction cannot be performed on one run, so I'll copy the run to 
rawavg and continue.


(version6.0.0 and 7.1.1) *ERROR*: talairach_afd: Talairach Transform: 
transforms/talairach.xfm ***FAILED*** (p=0., pval=0. < 
threshold=0.0050)


mritotal -verbose -debug -clobber -modeldir 
/space/lyon/9/pubsw/Linux2/packages/mni/current/bin/../share/mni_autoreg 
-protocol icbm transforms/tmp.talairach.7133/src.mnc 
transforms/talairach.auto.xfm


Can't locate shellwords.pl in @INC (@INC contains: 
/autofs/cluster/pubsw/1/pubsw/Linux2/packages/mni/1.4/bin/../lib/mni_autoreg 
/usr/local/freesurfer/stable6_0_0/mni/share/perl5 
/usr/local/lib64/perl5 /usr/local/share/perl5 
/usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl 
/usr/lib64/perl5 /usr/share/perl5 .) at 
/space/lyon/9/pubsw/Linux2/packages/mni/current/bin/mritotal line 460.


*ERROR*: mritotal failed, see transforms/talairach.log

I have tested the recon-all with another Bay2 data (from different 
project in our group), and it worked perfectly (with version 6.0.0) 
with the same script. Thus, I did not think this is due to my script 
or FS version..


Thanks,

Jeungchan


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Re: [Freesurfer] recon-all error: mpr2mni305 failed

[Douglas N. Greve]

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, and cor)


On 1/24/2022 2:58 AM, Hickling, Alice wrote:


External Email - Use Caution

Hi FreeSurfer Developers,


I’m trying to run recon-all on a high resolution (0.65mm iso) MP2RAGE 
however I am receiving the following error.


talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm

talairach_avi log file is transforms/talairach_avi.log...

ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

These are the options that I am using.

recon-all -all -s Freesurfer -i denoised_MP2RAGE.nii -T2 
mean_denoised_MP2RAGE_T2W.nii -T2pial -multistrip -hires


Please let me know if you can help.

  * FreeSurfer version: 7.2.0
(freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b)
  * Platform: CentOS Linux release 7.9.2009 (Core), Rocks release 7.0
(Manzanita)
  * Uname -a: Linux compute-0-14.local 3.10.0-957.27.2.el7.x86_64 #1
SMP Mon Jul 29 17:46:05 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
  * Recon-all.log: see attached
  * Talairach_avi.log: see attached

Best wishes,

Alice


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Re: [Freesurfer] recon-all: error in creating rh.white.H

[Peled, Noam]

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 rh.white.H

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 formatted with a file system 
that does not support symbolic links (e.g., a shared network drive from a 
Windows file server), the files cannot be created, leading to that error. Could 
that be the case?

Best,

Tim

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy 
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

> On 01/14/2022 5:02 PM Peled, Noam  wrote:
> 
>  
> Dear group
> A colleague of mine was trying to run recon-all on one of her patients and 
> received an error message.
> After looking at the attached log, I'm not sure what is the source of the 
> problem.
> The T1 looks quite good.
> She is using freesurfer-linux-centos8_x86_64-7.2.0-20210720-aa8f76b
> 
> Thanks!
> Noam
> 
> From: Gumenyuk, Valentina 
> Sent: Friday, January 14, 2022 10:48 AM
> To: Peled, Noam 
> Subject: UNMC error
> 
> 
> External Email - Use Caution
> freesurfer-linux-centos8_x86_64-7.2.0-20210720-aa8f76b
> 
> 
> Thanks!
> -Valia
> 
> The information in this e-mail may be privileged and confidential, intended 
> only for the use of the addressee(s) above. Any unauthorized use or 
> disclosure of this information is prohibited. If you have received this 
> e-mail by mistake, please delete it and immediately contact the sender.
> ___
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Re: [Freesurfer] recon-all: error in creating rh.white.H

[Tim Schäfer]

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 formatted with a file system 
that does not support symbolic links (e.g., a shared network drive from a 
Windows file server), the files cannot be created, leading to that error. Could 
that be the case?

Best,

Tim

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

> On 01/14/2022 5:02 PM Peled, Noam  wrote:
> 
>  
> Dear group
> A colleague of mine was trying to run recon-all on one of her patients and 
> received an error message.
> After looking at the attached log, I'm not sure what is the source of the 
> problem.
> The T1 looks quite good.
> She is using freesurfer-linux-centos8_x86_64-7.2.0-20210720-aa8f76b
> 
> Thanks!
> Noam
> 
> From: Gumenyuk, Valentina 
> Sent: Friday, January 14, 2022 10:48 AM
> To: Peled, Noam 
> Subject: UNMC error
> 
> 
> External Email - Use Caution
> freesurfer-linux-centos8_x86_64-7.2.0-20210720-aa8f76b
> 
> 
> Thanks!
> -Valia
> 
> The information in this e-mail may be privileged and confidential, intended 
> only for the use of the addressee(s) above. Any unauthorized use or 
> disclosure of this information is prohibited. If you have received this 
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[Freesurfer] RE: Freesurfer recon-all error “mri_convert: extra argument”

[Fischl, Bruce]

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 Caution
wow, that did the trick! recon-all is off and running. Thank you for catching 
this!

Travis

On Sat, Dec 11, 2021 at 1:24 PM Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:
USE CAUTION - EXTERNAL EMAIL

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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto: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.harvard.edu<mailto:freesurfer@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 used dcm2niix 
to convert from dicom to nifti. I can open the nifti file and everything looks 
normal. nNfti header info displayed in screenshot below and computer specs are 
listed in the attached recon-all log file (shortened). Not sure what the 
“mri_convert: extra argument” problem is. If anyone knows what I’m doing wrong, 
I would love some assistance!

Thanks,

Travis

Original T1 (after conversion from dicom)
[cid:image001.png@01D7EEAD.8FB86BE0]



Fri Dec 10 20:43:44 MST 2021
cd /usr/local/freesurfer/7.2.0/subjects/KH
setenv SUBJECTS_DIR /usr/local/freesurfer/7.2.0/subjects
/usr/local/freesurfer/7.2.0/bin/recon-all -s KH -i KH_T1.nii.gz -all -parallel 
-openmp 6
subjid KH
setenv SUBJECTS_DIR /usr/local/freesurfer/7.2.0/subjects
FREESURFER_HOME /usr/local/freesurfer/7.2.0
Actual FREESURFER_HOME /usr/local/freesurfer/7.2.0
build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
Linux BarrowPrismProcess 5.11.0-41-generic #45~20.04.1-Ubuntu SMP Wed Nov 10 
10:20:10 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
total used free shared buff/cache available
Mem: 31Gi 4.8Gi 4.1Gi 24Mi 22Gi 25Gi
Swap: 2.0Gi 2.0Mi 2.0Gi

program versions used
7.2.0 (freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b)
7.2.0
###
GCADIR /usr/local/freesurfer/7.2.0/average
GCA RB_all_2020-01-02.gca
GCASkull RB_all_withskull_2020_01_02.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /usr/local/freesurfer/7.2.0/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
###
/usr/local/freesurfer/7.2.0/subjects/KH
mri_convert /home/prism/Desktop/Processed Data/KH_T1.nii.gz 
/usr/local/freesurfer/7.2.0/subjects/KH/mri/orig/001.mgz
mri_convert /home/prism/Desktop/Processed Data/KH_T1.nii.gz 
/usr/local/freesurfer/7.2.0/subjects/KH/mri/orig/001.mgz
mri_convert: extra argument 
("/usr/local/freesurfer/7.2.0/subjects/KH/mri/orig/001.mgz")
type mri_convert -u for usage
Command exited with non-zero status 1
@#@FSTIME 2021:12:10:20:43:45 mri_convert N 3 e 0.00 S 0.00 U 0.00 P 100% M 
6284 F 0 R 247 W 0 c 0 w 1 I 0 O 0 L 0.32 0.25 0.21
@#@FSLOADPOST 2021:12:10:20:43:45 mri_convert N 3 0.32 0.25 0.21
Linux BarrowPrismProcess 5.11.0-41-generic #45~20.04.1-Ubuntu SMP Wed Nov 10 
10:20:10 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s KH exited with ERRORS at Fri Dec 10 20:43:45 MST 2021
To report a problem, see MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<https://secure-web.cisco.com/13sjWFha0n8fNWCE_a8WYSqy6Q3zdJxwlnV0NWfQFJE-nkxDlxet83b_hv0ATmn6VZeIzeVM6nUyVqX01VAC__lAlAdoH3QZJO3rv7NiQ8hgA64E0r1K0yU9tb4HYHFqyw0CMrJpJL-OiRqr_tUZDnYihEnGGh8lbUVUwwSuDQhj2qw_gW0DYGuXCw416YXkuiPpI0bELc12z2Tbm4nfFdL4f85R6hxQXXlHlWszSCXsrGih5a4TibdXqFlkNab9dwW4MNG6Xn8qw4xcAMJwi_fcmvM1yd9bQn7R6_id-xWDnfYsoTWqJ8Y9J7aN-37Yjpt0te2g8XlD2lDVxYtDsGw/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2F%2Fsecure-web.cisco.com%2F13ddiImmrJeyHcBtuL-2JQaEFuG60p6qT6OFYGZt3WA_uSvqI7pQar9v4E1Y3tAI7z9vXTThqivei1ezuBmvlgvnGKYjRZ-KkOvLJ6ku27j6LyonW035JoSWocyBFf2Bzk0k1TbxKHSkpUZaBHe_lNEBBmm2rJCqiuzOPqUT6x_n8ab-Wu9kYttwviNEXxeCOh6FjKGlHcehaVE0zOhjpqFWqGGidfFIXkNCg7JTaDe-55xGYEKc3KnvBFSG7RMz2EYXGTdBhbp8hqSfVKMqpXYbm00es2MSnEbHv1LQ8AC1juSG_-cyNi7fv5qX-Mv6P%2Fhttp%2A3A%2A2F%2A2Fsurfer.nmr.mgh.harvard.edu%2A2Ffswiki%2A2FBugReporting__%3BJSUlJSU%21%21CqLityr3mSQ%21UMRDlRtS79_xpOjVg04BHVSMwFn4tdKfl1K1oytYdgkAthl9YWBsXwlNB9zDYs7gN3REfpGb5A%24>

--
William T. McCuddy, PhD
Clinical Neuropsychologist
Department of Clinical Neuropsych

[Freesurfer] RE: Freesurfer recon-all error “mri_convert: extra argument”

[Fischl, Bruce]

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.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 used dcm2niix 
to convert from dicom to nifti. I can open the nifti file and everything looks 
normal. nNfti header info displayed in screenshot below and computer specs are 
listed in the attached recon-all log file (shortened). Not sure what the 
“mri_convert: extra argument” problem is. If anyone knows what I’m doing wrong, 
I would love some assistance!

Thanks,

Travis

Original T1 (after conversion from dicom)
[cid:image001.png@01D7EEA3.3050F190]



Fri Dec 10 20:43:44 MST 2021
cd /usr/local/freesurfer/7.2.0/subjects/KH
setenv SUBJECTS_DIR /usr/local/freesurfer/7.2.0/subjects
/usr/local/freesurfer/7.2.0/bin/recon-all -s KH -i KH_T1.nii.gz -all -parallel 
-openmp 6
subjid KH
setenv SUBJECTS_DIR /usr/local/freesurfer/7.2.0/subjects
FREESURFER_HOME /usr/local/freesurfer/7.2.0
Actual FREESURFER_HOME /usr/local/freesurfer/7.2.0
build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
Linux BarrowPrismProcess 5.11.0-41-generic #45~20.04.1-Ubuntu SMP Wed Nov 10 
10:20:10 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
total used free shared buff/cache available
Mem: 31Gi 4.8Gi 4.1Gi 24Mi 22Gi 25Gi
Swap: 2.0Gi 2.0Mi 2.0Gi

program versions used
7.2.0 (freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b)
7.2.0
###
GCADIR /usr/local/freesurfer/7.2.0/average
GCA RB_all_2020-01-02.gca
GCASkull RB_all_withskull_2020_01_02.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /usr/local/freesurfer/7.2.0/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
###
/usr/local/freesurfer/7.2.0/subjects/KH
mri_convert /home/prism/Desktop/Processed Data/KH_T1.nii.gz 
/usr/local/freesurfer/7.2.0/subjects/KH/mri/orig/001.mgz
mri_convert /home/prism/Desktop/Processed Data/KH_T1.nii.gz 
/usr/local/freesurfer/7.2.0/subjects/KH/mri/orig/001.mgz
mri_convert: extra argument 
("/usr/local/freesurfer/7.2.0/subjects/KH/mri/orig/001.mgz")
type mri_convert -u for usage
Command exited with non-zero status 1
@#@FSTIME 2021:12:10:20:43:45 mri_convert N 3 e 0.00 S 0.00 U 0.00 P 100% M 
6284 F 0 R 247 W 0 c 0 w 1 I 0 O 0 L 0.32 0.25 0.21
@#@FSLOADPOST 2021:12:10:20:43:45 mri_convert N 3 0.32 0.25 0.21
Linux BarrowPrismProcess 5.11.0-41-generic #45~20.04.1-Ubuntu SMP Wed Nov 10 
10:20:10 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s KH exited with ERRORS at Fri Dec 10 20:43:45 MST 2021
To report a problem, see MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://secure-web.cisco.com/13ddiImmrJeyHcBtuL-2JQaEFuG60p6qT6OFYGZt3WA_uSvqI7pQar9v4E1Y3tAI7z9vXTThqivei1ezuBmvlgvnGKYjRZ-KkOvLJ6ku27j6LyonW035JoSWocyBFf2Bzk0k1TbxKHSkpUZaBHe_lNEBBmm2rJCqiuzOPqUT6x_n8ab-Wu9kYttwviNEXxeCOh6FjKGlHcehaVE0zOhjpqFWqGGidfFIXkNCg7JTaDe-55xGYEKc3KnvBFSG7RMz2EYXGTdBhbp8hqSfVKMqpXYbm00es2MSnEbHv1LQ8AC1juSG_-cyNi7fv5qX-Mv6P/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>

--
William T. McCuddy, PhD
Clinical Neuropsychologist
Department of Clinical Neuropsychology
Joint Appointment in Neuroradiology


Barrow Neurological Institute
Dignity Health I St. Joseph’s Hospital and Medical Center
222 W. Thomas Rd, Suite 315
Phoenix, AZ 85013
602.406.3671 (O)
602.406.6115 (F)

Caution: This email is both proprietary and confidential, and not intended for 
transmission to or receipt by any unauthorized persons. If you believe that it 
has been received by you in error, do not read any attachments. Instead, kindly 
reply to the sender stating that you have received the message in error. Then 
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Re: [Freesurfer] recon-all error with T1 dcm images

[Douglas N. Greve]

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_Accelerated_Sagittal_MPRAGE__br_raw_20190122095958285_147_S786989_I1118713.dcm

The attachments are the recon-all script and the output log. Can you 
help me with this? Thanks


Best,
Wei

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The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If 
the e-mail was sent to you in error but does not contain patient information, 
please contact the sender and properly dispose of the e-mail.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] recon-all error with T1 dcm images

[Wei Shao]

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 output log. Can you help
me with this? Thanks

Best,
Wei


recon-all.log
Description: Binary data
module load nixpkgs/16.09
module load freesurfer/7.1.0

source $EBROOTFREESURFER/FreeSurferEnv.sh

export SUBJECTS_DIR=/home/weishao/scratch/ADNI-MCI/subjects

recon-all -all -i /home/weishao/scratch/ADNI-MCI/ADNI/032_S_6652/Accelerated_Sagittal_MPRAGE/2019-06-07_09_08_48.0/I1174541/ADNI_032_S_6652_MR_Accelerated_Sagittal_MPRAGE__br_raw_20190610135118632_19_S831455_I1174541.dcm \
-s S6652 -openmp 32


echo "job is done"

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Re: [Freesurfer] [recon-all error] Excessive topologic defect encountered

[Douglas N. Greve]

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 hard failure of recon-all.

The error message is:

CORRECTING DEFECT 0 (vertices=94923, convex hull=13109, v0=0)

error: Cannot allocate memory

error: Excessive topologic defect encountered: could not allocate 
518210721 edges for retessellation


The first thing I did was to fix a giant missing part of the brain in 
the brainmask.mgz by adjusting the watershed parameters.


Unfortunately that only brought the defective edges down from 
723387666 to „only“ 518210721.


I tried locating the error with the help of lh.defect_labels. But 
adjusting the threshold to look for defect 0 (min:0/max:1) just shows 
almost the whole brain in red.


The most obvious problem seems to be that the lh.orig.nofix and 
rh.orig.nofix are not seperated in the center. Unfortunately I don’t 
know how to fix this.


What kind of actions would you recommend?

Many thanks,

Alec

Here is a link to the subject folder: 
https://drive.google.com/drive/folders/1npA2yyjFxk2UEVbByTcIlMizKWSGPjKr?usp=sharing



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The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If 
the e-mail was sent to you in error but does not contain patient information, 
please contact the sender and properly dispose of the e-mail.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] [recon-all error] Excessive topologic defect encountered

[Alec Süwolto]

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 allocate 518210721 edges for retessellation The first thing I did was to fix a giant missing part of the brain in the brainmask.mgz by adjusting the watershed parameters.Unfortunately that only brought the defective edges down from 723387666 to „only“ 518210721. I tried locating the error with the help of lh.defect_labels. But adjusting the threshold to look for defect 0 (min:0/max:1) just shows almost the whole brain in red.The most obvious problem seems to be that the lh.orig.nofix and rh.orig.nofix are not seperated in the center. Unfortunately I don’t know how to fix this. What kind of actions would you recommend?Many thanks,Alec  Here is a link to the subject folder: https://drive.google.com/drive/folders/1npA2yyjFxk2UEVbByTcIlMizKWSGPjKr?usp=sharing  ___
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Re: [Freesurfer] Recon-all error: Label BA1_exvivo does not exist in SUBJECTS_DIR fsaverage

[Szulia Agata]

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. Thank you for your help.

I have another problem I cannot seem to solve and would appreciate your help 
with though - can I run matlab runner through fs on mac? The installation goes 
on without problems (fs is 7.2.0. and matlab is v84) and matlab starts to 
process my recon-all’d files, however it never finishes with success. I’ve read 
that big sur does not work with versions of matlab as old as the one that fs 
installs, however I don’t know how to install the newer ones through fs. I need 
to know volumes of hippocampal segments for my research project and cannot work 
my way around the problem with matlab here.

Thank you very much for your help,
Agata Szulia

On 6 Sep 2021, at 20:13, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:

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 problem with running recon-all on some subjects. Mostly, it does exit 
without errors, however sometimes it exits with "ERROR: Label BA1_exvivo does 
not exist in SUBJECTS_DIR fsaverage! The fsaverage link probably points to an 
older freesurfer version”. I have only one version of fs installed - 7.2.0. 
Does anyone know why does it happen and how to proceed with recon-all in such 
cases?

I attach recon-all log files.

Thank you very much for your help,
Agata

Klauzula poufności. Ta wiadomość pocztowa i wszelkie załączone do niej pliki są 
poufne i podlegają ochronie prawnej. Jeśli nie jesteś jej prawidłowym 
adresatem, jakiekolwiek wykorzystanie w tym zapoznanie się z treścią 
przesłanych informacji, jej ujawnienie, reprodukcja, dystrybucja lub inne 
rozpowszechnienie, są ściśle zabronione. Jeśli otrzymał/a Pan/i niniejszy 
przekaz wskutek błędu, proszę o niezwłocznie powiadomienie nadawcy i usunięcie 
otrzymanych informacji. Kontakt: Uniwersytet Medyczny w Łodzi, 90–419 Łódź, Al. 
Kościuszki 4, Rektorat – Centrala, Tel. 42 272 59 66 umed.lodz.pl 
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Re: [Freesurfer] Recon-all error: Label BA1_exvivo does not exist in SUBJECTS_DIR fsaverage

[Douglas N. Greve]

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 problem with running recon-all on some subjects. Mostly, it does exit 
without errors, however sometimes it exits with "ERROR: Label BA1_exvivo does 
not exist in SUBJECTS_DIR fsaverage! The fsaverage link probably points to an older 
freesurfer version”. I have only one version of fs installed - 7.2.0. Does anyone 
know why does it happen and how to proceed with recon-all in such cases?

I attach recon-all log files.

Thank you very much for your help,
Agata

Klauzula poufności. Ta wiadomość pocztowa i wszelkie załączone do niej pliki są 
poufne i podlegają ochronie prawnej. Jeśli nie jesteś jej prawidłowym 
adresatem, jakiekolwiek wykorzystanie w tym zapoznanie się z treścią 
przesłanych informacji, jej ujawnienie, reprodukcja, dystrybucja lub inne 
rozpowszechnienie, są ściśle zabronione. Jeśli otrzymał/a Pan/i niniejszy 
przekaz wskutek błędu, proszę o niezwłocznie powiadomienie nadawcy i usunięcie 
otrzymanych informacji. Kontakt: Uniwersytet Medyczny w Łodzi, 90–419 Łódź, Al. 
Kościuszki 4, Rektorat – Centrala, Tel. 42 272 59 66 umed.lodz.pl 
Confidentiality Notice - This e-mail is confidential, may be legally 
privileged. If you are not the intended recipient, you may not use, disclosure, 
distribute, copy, print or rely on this e-mail. If you received this e-mail in 
error, please notify the sender and delete the material from any 
computer.Contact:Medical University of Lodz, 90–419 Lodz, POLAND, 4 Kosciuszki 
Avenue, Rector’s Office, phone 0048 42 272 59 66 umed.lodz.pl

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Re: [Freesurfer] Recon-all error :Segmentation fault (core dumped)

[liub]

External Email - Use Caution

Yeah,you are right!

The prolem has been solved after modifying the 'bc' path.




Thank you very much!

Have a good day :)!

-原始邮件-
发件人:"Douglas N. Greve" 
发送时间:2021-06-02 05:52:10 (星期三)
收件人: freesurfer@nmr.mgh.harvard.edu
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 you get when 
you run
which bc



On 6/1/2021 9:59 AM, liub wrote:


External Email - Use Caution

Thank you for your help !





I have run the command:

mri_nu_correct.mni --debug --i orig.mgz --o nu.mgz --uchar 
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 (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/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 Caution

Hello FreeSurfer Developers,




I'm attempting to recon-all my NIfTI-1 data ,while after a few minutes of 
running,there was an error:

mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.897826/nu0.mgz 
/dev/shm/tmp.mri_nu_correct.mni.897826/nu0.mgz mul

Segmentation fault (core dumped) 

Command exited with non-zero status 1

Also when I ran the command "recon-all -all -s bert" using the official data in 
*/freesurfer/subjects/bert ,it raised the same error. I googled this error,but 
there's still no answer.I've attached the recon-all.log. The recon-all.log is 
belong to bert and recon-all(1).log is belong to my data.

Here is my operating system info :

uname -a: Linux HEUBME.com 4.18.0-193.28.1.el8_2.x86_64 #1 SMP Thu Oct 22 
00:20:22 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

Platform: CentOS Linux release 8.3.2011

FreeSurfer version: freesurfer-Linux-centos8_x86_64-7.1.1




Thank you for your kind help.




Best regards.



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Re: [Freesurfer] Recon-all error :Segmentation fault (core dumped)

[Douglas N. Greve]

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 you get when you run

which bc


On 6/1/2021 9:59 AM, liub wrote:


External Email - Use Caution

Thank you for your help !


I have run the command:

mri_nu_correct.mni --debug --i orig.mgz --o nu.mgz --uchar 
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 (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/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 Caution

Hello FreeSurfer Developers,

I'm attempting to recon-all my NIfTI-1 data ,while after a few
minutes of running,there was an error:

mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.897826/nu0.mgz
/dev/shm/tmp.mri_nu_correct.mni.897826/nu0.mgz mul

Segmentation fault (core dumped)

Command exited with non-zero status 1

Also when I ran the command "recon-all -all -s bert" using the
official data in */freesurfer/subjects/bert ,it raised the same
error. I googled this error,but there's still no answer.I've
attached the recon-all.log. The recon-all.log is belong to bert
and recon-all(1).log is belong to my data.

Here is my operating system info :

uname -a: Linux HEUBME.com 4.18.0-193.28.1.el8_2.x86_64 #1 SMP
Thu Oct 22 00:20:22 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

Platform: CentOS Linux release 8.3.2011

FreeSurfer version: freesurfer-Linux-centos8_x86_64-7.1.1

Thank you for your kind help.

Best regards.


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The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If 
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please contact the sender and properly dispose of the e-mail.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Recon-all error :Segmentation fault (core dumped)

[Douglas N. Greve]

What happens when you run the following two commands?
echo 5/6 | bc -l

echo "5/6" | bc -l


On 6/1/2021 9:59 AM, liub wrote:


External Email - Use Caution

Thank you for your help !


I have run the command:

mri_nu_correct.mni --debug --i orig.mgz --o nu.mgz --uchar 
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 (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/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 Caution

Hello FreeSurfer Developers,

I'm attempting to recon-all my NIfTI-1 data ,while after a few
minutes of running,there was an error:

mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.897826/nu0.mgz
/dev/shm/tmp.mri_nu_correct.mni.897826/nu0.mgz mul

Segmentation fault (core dumped)

Command exited with non-zero status 1

Also when I ran the command "recon-all -all -s bert" using the
official data in */freesurfer/subjects/bert ,it raised the same
error. I googled this error,but there's still no answer.I've
attached the recon-all.log. The recon-all.log is belong to bert
and recon-all(1).log is belong to my data.

Here is my operating system info :

uname -a: Linux HEUBME.com 4.18.0-193.28.1.el8_2.x86_64 #1 SMP
Thu Oct 22 00:20:22 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

Platform: CentOS Linux release 8.3.2011

FreeSurfer version: freesurfer-Linux-centos8_x86_64-7.1.1

Thank you for your kind help.

Best regards.


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The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If 
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please contact the sender and properly dispose of the e-mail.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Recon-all error :Segmentation fault (core dumped)

[liub]

External Email - Use Caution

Thank you for your help !





I have run the command:

mri_nu_correct.mni --debug --i orig.mgz --o nu.mgz --uchar 
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 (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/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 Caution

Hello FreeSurfer Developers,




I'm attempting to recon-all my NIfTI-1 data ,while after a few minutes of 
running,there was an error:

mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.897826/nu0.mgz 
/dev/shm/tmp.mri_nu_correct.mni.897826/nu0.mgz mul

Segmentation fault (core dumped) 

Command exited with non-zero status 1

Also when I ran the command "recon-all -all -s bert" using the official data in 
*/freesurfer/subjects/bert ,it raised the same error. I googled this error,but 
there's still no answer.I've attached the recon-all.log. The recon-all.log is 
belong to bert and recon-all(1).log is belong to my data.

Here is my operating system info :

uname -a: Linux HEUBME.com 4.18.0-193.28.1.el8_2.x86_64 #1 SMP Thu Oct 22 
00:20:22 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

Platform: CentOS Linux release 8.3.2011

FreeSurfer version: freesurfer-Linux-centos8_x86_64-7.1.1




Thank you for your kind help.




Best regards.



___
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set echo = 1 ;
set debug = 1 ;
set debug = 1
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 9 != 0 )

set flag = $argv[1] ; shift ;
set flag = --i
shift

switch ( $flag )
switch ( --i )
if ( $#argv == 0 ) goto arg1err ;
if ( 8 == 0 ) goto arg1err
set InVol = $argv[1] ; shift ;
set InVol = orig.mgz
shift
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 7 != 0 )

set flag = $argv[1] ; shift ;
set flag = --o
shift

switch ( $flag )
switch ( --o )
if ( $#argv == 0 ) goto arg1err ;
if ( 6 == 0 ) goto arg1err
set OutVol = $argv[1] ; shift ;
set OutVol = nu.mgz
shift
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 5 != 0 )

set flag = $argv[1] ; shift ;
set flag = --uchar
shift

switch ( $flag )
switch ( --uchar )
if ( $#argv < 1 ) goto arg1err ;
if ( 4 < 1 ) goto arg1err
set talxfm = $argv[1] ; shift ;
set talxfm = transforms/talairach.xfm
shift
if ( ! -e $talxfm ) then
if ( ! -e transforms/talairach.xfm ) then
set DoUchar = 1 ;
set DoUchar = 1
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 3 != 0 )

set flag = $argv[1] ; shift ;
set flag = --n
shift

switch ( $flag )
switch ( --n )
if ( $#argv == 0 ) goto arg1err ;
if ( 2 == 0 ) goto arg1err
set nIters = $argv[1] ; shift ;
set nIters = 2
shift
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 1 != 0 )

set flag = $argv[1] ; shift ;
set flag = --ants-n4
shift

switch ( $flag )
switch ( --ants-n4 )
set DoAntsN4 = 1 ;
set DoAntsN4 = 1
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 0 != 0 )

goto parse_args_return ;
goto parse_args_return


goto check_params ;
goto check_params
if ( $#InVol == 0 ) then
if ( 1 == 0 ) then
if ( ! -e $InVol ) then
if ( ! -e orig.mgz ) then
if ( $#OutVol == 0 ) then
if ( 1 == 0 ) then
if ( $DoAntsN3 && $DoAntsN4 ) then
if ( 0 && 1 ) then
if ( $DoAntsN3 ) then
if ( 0 ) then
if ( $DoAntsN4 ) then
if ( 1 ) then
which AntsN4BiasFieldCorrectionFs > & /dev/null
which AntsN4BiasFieldCorrectionFs
if ( $status ) then
if ( 0 ) then
endif
endif



set cmd = ( which bc )
set cmd = ( which bc )
$cmd
which bc
/usr/local/ashs_Linux64_rev103_20140612/ext/Linux/bin/bc
if ( $status ) then
if ( 0 ) then

goto check_params_return ;
goto check_params_return

set OutDir = `dirname $OutVol` ;
set OutDir = `dirname $OutVol`
dirname nu.mgz
mkdir -p $OutDir ;
mkdir -p .

if ( $#LF == 0 ) set LF = $OutDir/mri_nu_correct.mni.log
if ( 0 == 0 ) set LF = ./mri_nu_correct.mni.log
set LF = ./mri_nu_correct.mni.log
if ( -e $LF ) mv $LF $LF.bak
if ( -e ./mri_nu_correct.mni.log ) mv ./mri_nu_correct.mni.log 
./mri_nu_correct.mni.log.bak
mv ./mri_nu_correct.mni.log ./mri_nu_correct.mni.log.bak

pwd | tee -a $LF
pwd
tee -a ./mri_nu_correct.mni.log
/home/liubing/FreeSurfer/data/test_recon/ANDI1/mri
which mri_nu_correct.mni | tee -a $LF
which mri_nu_correct.mni
tee -a ./mri_nu_correct.mni.log
/home/liubing/FreeSurfer/freesurfer/bin/mri_nu_correct.mni
echo $cmdargs | tee -a $LF
echo --debug --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 
--ants-n4
tee -a ./mri_nu_correct.mni.log
--debug --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2

Re: [Freesurfer] Recon-all error :Segmentation fault (core dumped)

[Douglas N. Greve]

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 Caution

Hello FreeSurfer Developers,

I'm attempting to recon-all my NIfTI-1 data ,while after a few minutes 
of running,there was an error:


mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.897826/nu0.mgz 
/dev/shm/tmp.mri_nu_correct.mni.897826/nu0.mgz mul


Segmentation fault (core dumped)

Command exited with non-zero status 1

Also when I ran the command "recon-all -all -s bert" using the 
official data in */freesurfer/subjects/bert ,it raised the same error. 
I googled this error,but there's still no answer.I've attached the 
recon-all.log. The recon-all.log is belong to bert and 
recon-all(1).log is belong to my data.


Here is my operating system info :

uname -a: Linux HEUBME.com 4.18.0-193.28.1.el8_2.x86_64 #1 SMP Thu Oct 
22 00:20:22 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux


Platform: CentOS Linux release 8.3.2011

FreeSurfer version: freesurfer-Linux-centos8_x86_64-7.1.1

Thank you for your kind help.

Best regards.


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Re: [Freesurfer] Recon-all error

[g . toniol]

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,
> 
> 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 recon-all 
> on a .nii file ("s44891-153636-1-00192-1.nii") on a MacOs Big Sur. To do 
> so, I run the command below, where "S001" is the subject name and 
> "/Users/giorgio/Documents/MATLAB/spm12/Group 
> 0/S001/scans/struct/s44891-153636-1-00192-1.nii " is the path to the .nii 
> image file:
> 
> ..$ recon-all -s S001 -i /Users/giorgio/Documents/MATLAB/spm12/Group 
> 0/S001/scans/struct/s44891-153636-1-00192-1.nii -all 
> 
> However, I get the following error:
> 
> "ERROR: You cannot give recon-all a folder as input. It must be an image 
> file.
> If you have multiple files, you need multiple -i flags.
> Darwin macbook-pro.home 20.4.0 Darwin Kernel Version 20.4.0: Thu Apr 22 
> 21:46:47 PDT 2021; root:xnu-7195.101.2~1/RELEASE_X86_64 x86_64 recon-all -s 
> S001 exited with ERRORS at Mon May 24 15:50:32 CEST 2021"
> 
> My input volume is a .nii, an image file, and I copied its pathway 
> automatically so I do not think there are mistakes in the pathway to the 
> image: do you see why is it considered as a folder? Can you help me 
> troubleshoot?
> Thank you!
> Best,
> Giorgio
> 
> PS I have already tried to restart the program, to change directory on 
> terminal, to convert manually the files to .mgz, or to move the .nii file in 
> the freesurfer home (which gives the following error: ERROR: You are trying 
> to re-run an existing subject with (possibly) new input data (-i). If this is 
> truly new input data, you should delete the subject folder and re-run, or 
> specify a different subject name. If you are just continuing an analysis of 
> an existing subject, then omit all -i flags.)
> 
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[Freesurfer] Recon-all error

[g . toniol]

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 recon-all on a 
.nii file ("s44891-153636-1-00192-1.nii") on a MacOs Big Sur. To do so, I 
run the command below, where "S001" is the subject name and 
"/Users/giorgio/Documents/MATLAB/spm12/Group 
0/S001/scans/struct/s44891-153636-1-00192-1.nii " is the path to the .nii 
image file:

..$ recon-all -s S001 -i /Users/giorgio/Documents/MATLAB/spm12/Group 
0/S001/scans/struct/s44891-153636-1-00192-1.nii -all 

However, I get the following error:

"ERROR: You cannot give recon-all a folder as input. It must be an image file.
If you have multiple files, you need multiple -i flags.
Darwin macbook-pro.home 20.4.0 Darwin Kernel Version 20.4.0: Thu Apr 22 
21:46:47 PDT 2021; root:xnu-7195.101.2~1/RELEASE_X86_64 x86_64 recon-all -s 
S001 exited with ERRORS at Mon May 24 15:50:32 CEST 2021"

My input volume is a .nii, an image file, and I copied its pathway 
automatically so I do not think there are mistakes in the pathway to the image: 
do you see why is it considered as a folder? Can you help me troubleshoot?
Thank you!
Best,
Giorgio

PS I have already tried to restart the program, to change directory on 
terminal, to convert manually the files to .mgz, or to move the .nii file in 
the freesurfer home (which gives the following error: ERROR: You are trying to 
re-run an existing subject with (possibly) new input data (-i). If this is 
truly new input data, you should delete the subject folder and re-run, or 
specify a different subject name. If you are just continuing an analysis of an 
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Re: [Freesurfer] recon-all error: No such file or directory

[Douglas N. Greve]

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-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):
  File "/usr/local/freesurfer/python/scripts/rca-config", line 137, in 


    file.write(arg + '\n')
UnicodeEncodeError: 'ascii' codec can't encode character '\udcc1' in 
position 14: ordinal not in range(128)

ERROR: could not configure recon-all parameters

On Thu, Feb 18, 2021 at 9:20 PM Eduardo Bergonzoni Junqueira 
mailto:dubergonz...@usp.br>> wrote:


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*MailScanner has detected a 
possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall  
.

(base) eduardo@eduardo-X555UB:~/Área de Trabalho/Grant_Tractography$ export 
FREESURFER_HOME=/usr/local/freesurfer
(base) eduardo@eduardo-X555UB:~/Área de Trabalho/Grant_Tractography$ . 
$FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME       /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /usr/local/freesurfer/subjects
MNI_DIR           /usr/local/freesurfer/mni
FSL_DIR           /home/eduardo/fsl

I'm getting the following error when I run the command:

(base) eduardo@eduardo-X555UB:~/Área de
Trabalho/Grant_Tractography$ recon-all -s Grant_sub -i t1.nii.gz -all

   ERROR:

/home/eduardo/\301rea de Trabalho/Grant_Tractography: No such file or 
directory.

This error is strange for me. I don't know why it is showing
"\301rea de Trabalho/" if the correct name of the directory is
"Área de Trabalho". The t1.nii.gz is in the path directory I'm using in the 
terminal.

Please, can anybody help how to fix this bug? I've looked for similar bug 
reports. Probably it is something simple, but I couln't found how to solve the 
problem.

1) FreeSurfer version:
freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 2)
Platform: Ubuntu 20.04.1 3) uname -a: Linux eduardo-X555UB
5.8.0-43-generic #49~20.04.1-Ubuntu SMP Fri Feb 5 09:57:56 UTC
2021 x86_64 x86_64 x86_64 GNU/Linux

Best regards


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Re: [Freesurfer] recon-all error: No such file or directory

[Eduardo Bergonzoni Junqueira]

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):
  File "/usr/local/freesurfer/python/scripts/rca-config", line 137, in

file.write(arg + '\n')
UnicodeEncodeError: 'ascii' codec can't encode character '\udcc1' in
position 14: ordinal not in range(128)
ERROR: could not configure recon-all parameters

On Thu, Feb 18, 2021 at 9:20 PM Eduardo Bergonzoni Junqueira <
dubergonz...@usp.br> wrote:

> 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 
> https://secure-web.cisco.com/1LBFicwqnDaueJTJnse4_mduoj4rvakBKEqip8Dc7cnNhQxdHNr6cnY9hYnO3ObSTXt7iYRQbzd7mcgkqlJjee7GRozXHxSm0X-skycoRDwa4SLEwQ4044yZZt3pw8kSNkAMzCdMZgS38iFYuUYzBha4DICiqc5tomfmUfmqGpV8ifrCHkHJTx-_c_L8-mk_A0uivnGquvWTC4ZMk2UWZE46RRaNTL5hz0_1-3yOKJzbmKPZcFBs_5jMoexz7_V3B/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLinuxInstall.
>
> (base) eduardo@eduardo-X555UB:~/Área de Trabalho/Grant_Tractography$ export 
> FREESURFER_HOME=/usr/local/freesurfer
> (base) eduardo@eduardo-X555UB:~/Área de Trabalho/Grant_Tractography$ . 
> $FREESURFER_HOME/SetUpFreeSurfer.sh
>  freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /usr/local/freesurfer
> FSFAST_HOME   /usr/local/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /usr/local/freesurfer/subjects
> MNI_DIR   /usr/local/freesurfer/mni
> FSL_DIR   /home/eduardo/fsl
>
> I'm getting the following error when I run the command:
>
> (base) eduardo@eduardo-X555UB:~/Área de Trabalho/Grant_Tractography$
> recon-all -s Grant_sub -i t1.nii.gz -all
>
>   ERROR:
>
> /home/eduardo/\301rea de Trabalho/Grant_Tractography: No such file or 
> directory.
>
> This error is strange for me. I don't know why it is showing "\301rea de 
> Trabalho/" if the correct name of the directory is "Área de Trabalho". The 
> t1.nii.gz is in the path directory I'm using in the terminal.
>
> Please, can anybody help how to fix this bug? I've looked for similar bug 
> reports. Probably it is something simple, but I couln't found how to solve 
> the problem.
>
>
> 1) FreeSurfer version: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
> 2) Platform: Ubuntu 20.04.1
> 3) uname -a: Linux eduardo-X555UB 5.8.0-43-generic #49~20.04.1-Ubuntu SMP Fri 
> Feb 5 09:57:56 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
>
> Best regards
>
>
>
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[Freesurfer] recon-all error: No such file or directory

[Eduardo Bergonzoni Junqueira]

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
https://secure-web.cisco.com/1LNJqjy9_CcjRF6N2vjvepp4rKUty6HrwT4CmaUGa6hhi_5TL3eisFsAZfOBMirFKlq9ITST8d0xdNRnx9ok8ecgRZeN7XO2rVjd-lc8cOx8mrimVobKaVdBklCO9SdrxExhkyO5lBlLGG21bXMYmdyPFKRRdqzoOFbVciFJ9MZcwsMt_h-Bq4aYjqSilAhLjbD45TUGbPRdWdIk2zLve35oiWKvS9WcT5qtpvwaYdxCeYJzYqagPCujF7nVfRw6ZiG7M2j1OzoX8dj4v2-hOSg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLinuxInstall.

(base) eduardo@eduardo-X555UB:~/Área de Trabalho/Grant_Tractography$
export FREESURFER_HOME=/usr/local/freesurfer
(base) eduardo@eduardo-X555UB:~/Área de Trabalho/Grant_Tractography$ .
$FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
FSL_DIR   /home/eduardo/fsl

I'm getting the following error when I run the command:

(base) eduardo@eduardo-X555UB:~/Área de Trabalho/Grant_Tractography$
recon-all -s Grant_sub -i t1.nii.gz -all

  ERROR:

/home/eduardo/\301rea de Trabalho/Grant_Tractography: No such file or directory.

This error is strange for me. I don't know why it is showing "\301rea
de Trabalho/" if the correct name of the directory is "Área de
Trabalho". The t1.nii.gz is in the path directory I'm using in the
terminal.

Please, can anybody help how to fix this bug? I've looked for similar
bug reports. Probably it is something simple, but I couln't found how
to solve the problem.


1) FreeSurfer version: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
2) Platform: Ubuntu 20.04.1
3) uname -a: Linux eduardo-X555UB 5.8.0-43-generic #49~20.04.1-Ubuntu
SMP Fri Feb 5 09:57:56 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

Best regards
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Re: [Freesurfer] Recon-all Error

[Garcia Pallares, Erendira Xenia]

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 input dicom file (I50)
• The file after the “-s” flag represents the output directory (Subj001) after 
you have run recon-all

If you have more than one dicom file that you’d like to run through the recon 
pipeline you can add -i flags for each additional dicom.

You can find additional information 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 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 from norm.mgz...
error: 
mghRead(/home/developer/Desktop/BIBE_2020/Simulated_MRI/HC/rf0/t1_icbm_normal_1mm_pn1_rf0/mri/norm.mgz,
 -1): could not open file
error: mri_normalize: could not open source file norm.mgz”
Thanks!
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[Freesurfer] Recon-all Error

[Dimitri Brigide De Almeida Mantovani]

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 from norm.mgz...
error: 
mghRead(/home/developer/Desktop/BIBE_2020/Simulated_MRI/HC/rf0/t1_icbm_normal_1mm_pn1_rf0/mri/norm.mgz,
 -1): could not open file
error: mri_normalize: could not open source file norm.mgz"
Thanks!
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Re: [Freesurfer] Recon-all error: MatrixMultiply: m1 is null!

[Greve, Douglas N.,Ph.D.]

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 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 --label_left_white 2 
--label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 
--save_ribbon --parallel BT_055_base \n
SUBJECTS_DIR is /Applications/freesurfer/7.1.1/subjects/BT_long
loading input data...
Running hemis in parallel
Processing left hemi
Processing right hemi
computing distance to right white surface
computing distance to left white surface
error: MatrixMultiply: m1 is null!
Darwin PHTH-CDM-NBOASORT 18.5.0 Darwin Kernel Version 18.5.0: Mon Mar 11 
20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64 x86_64

recon-all -s BT_055_base exited with ERRORS at Mon Dec 14 15:43:27 PST 2020


Here are details of the computer and FS version I am using:


  *   OS: macOS Mojave (10.14.4)
  *   FS: 7.1.1

It seems to happen at random, whenever I run recon-all on the same subject 
again, the error doesn’t occur. This is true for cross-sectional, base, and 
long processing steps in my machine. I have seen an email relating to this 
issue before, but I wasn’t able to access the attachment file which would fix 
the problem.

I was wondering if you guys would be able to help?


Thank you
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




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Re: [Freesurfer] Recon-all error: MatrixMultiply: m1 is null! {Disarmed}

[Boa Sorte Silva, Narlon]

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 Dec 16, 2020, at 7:18 PM, Hoopes, Andrew 
mailto:ahoo...@mgh.harvard.edu>> wrote:

[CAUTION: Non-UBC Email]
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)
- Rerunning these failing recons without the parallel flag enabled
- Patching your version of recon-all by commenting out or removing the 
following (line 4217) from $FREESURFER_HOME/bin/recon-all:
if($OMP_NUM_THREADS > 1) set cmd = ($cmd --parallel)

Hope that helps,
Andrew

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Boa Sorte Silva, Narlon" 
mailto:narlon.si...@ubc.ca>>
Reply-To: FS Help 
mailto:freesurfer@nmr.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 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 --label_left_white 2 
--label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 
--save_ribbon --parallel BT_055_base \n
SUBJECTS_DIR is /Applications/freesurfer/7.1.1/subjects/BT_long
loading input data...
Running hemis in parallel
Processing left hemi
Processing right hemi
computing distance to right white surface
computing distance to left white surface
error: MatrixMultiply: m1 is null!
Darwin PHTH-CDM-NBOASORT 18.5.0 Darwin Kernel Version 18.5.0: Mon Mar 11 
20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64 x86_64

recon-all -s BT_055_base exited with ERRORS at Mon Dec 14 15:43:27 PST 2020


Here are details of the computer and FS version I am using:


  *   OS: macOS Mojave (10.14.4)
  *   FS: 7.1.1


It seems to happen at random, whenever I run recon-all on the same subject 
again, the error doesn’t occur. This is true for cross-sectional, base, and 
long processing steps in my machine. I have seen an email relating to this 
issue before, but I wasn’t able to access the attachment file which would fix 
the problem.

I was wondering if you guys would be able to help?


Thank you
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

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Re: [Freesurfer] Recon-all error: MatrixMultiply: m1 is null!

[Hoopes, Andrew]

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)
- Rerunning these failing recons without the parallel flag enabled
- Patching your version of recon-all by commenting out or removing the 
following (line 4217) from $FREESURFER_HOME/bin/recon-all:
if($OMP_NUM_THREADS > 1) set cmd = ($cmd --parallel)

Hope that helps,
Andrew

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 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 --label_left_white 2 
--label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 
--save_ribbon --parallel BT_055_base \n
SUBJECTS_DIR is /Applications/freesurfer/7.1.1/subjects/BT_long
loading input data...
Running hemis in parallel
Processing left hemi
Processing right hemi
computing distance to right white surface
computing distance to left white surface
error: MatrixMultiply: m1 is null!
Darwin PHTH-CDM-NBOASORT 18.5.0 Darwin Kernel Version 18.5.0: Mon Mar 11 
20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64 x86_64

recon-all -s BT_055_base exited with ERRORS at Mon Dec 14 15:43:27 PST 2020


Here are details of the computer and FS version I am using:


  *   OS: macOS Mojave (10.14.4)
  *   FS: 7.1.1

It seems to happen at random, whenever I run recon-all on the same subject 
again, the error doesn’t occur. This is true for cross-sectional, base, and 
long processing steps in my machine. I have seen an email relating to this 
issue before, but I wasn’t able to access the attachment file which would fix 
the problem.

I was wondering if you guys would be able to help?


Thank you
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

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[Freesurfer] Recon-all error: MatrixMultiply: m1 is null!

[Boa Sorte Silva, Narlon]

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 --label_left_white 2 
--label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 
--save_ribbon --parallel BT_055_base \n
SUBJECTS_DIR is /Applications/freesurfer/7.1.1/subjects/BT_long
loading input data...
Running hemis in parallel
Processing left hemi
Processing right hemi
computing distance to right white surface
computing distance to left white surface
error: MatrixMultiply: m1 is null!
Darwin PHTH-CDM-NBOASORT 18.5.0 Darwin Kernel Version 18.5.0: Mon Mar 11 
20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64 x86_64

recon-all -s BT_055_base exited with ERRORS at Mon Dec 14 15:43:27 PST 2020


Here are details of the computer and FS version I am using:


  *   OS: macOS Mojave (10.14.4)
  *   FS: 7.1.1

It seems to happen at random, whenever I run recon-all on the same subject 
again, the error doesn’t occur. This is true for cross-sectional, base, and 
long processing steps in my machine. I have seen an email relating to this 
issue before, but I wasn’t able to access the attachment file which would fix 
the problem.

I was wondering if you guys would be able to help?


Thank you
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

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Re: [Freesurfer] recon-all error {Disarmed}

[Greve, Douglas N.,Ph.D.]

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,

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 : MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer
I'm getting an error while performing step 4 of 'Running Freesurfer' heading.
Command that is giving error : recon-all -all -subjid 
Here my  is subject_0295

Error on the terminal : recon-all -s subject_0295 exited with ERRORS at Tue Dec 
 8 18:25:40 IST 2020

The freesurfer/subjects/subject_0295/scripts/recon-all.log file didn't mention 
any specific error.

I've searched the list and no similar errors have been reported. Does anyone 
have any thoughts on how to trouble-shoot this one? Also, I have attached the 
recon-all.log in case it's of any use.

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
2) Platform: Ubuntu 16.04.7 LTS
3) recon-all.log: see attached


--
Regards,
Ms. Devanshi Jain



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[Freesurfer] recon-all error {Disarmed}

[Devanshi jain]

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 :
https://secure-web.cisco.com/13_r_7kEeP_WS7SHxH0ECZXOxZuTEltmsSnlVNl81ZLfHEwNDB_11o3EFmEh8jBnC1DRib-gmQgxCzrNA2y7JAD-w_LU7bDv24QbcO5MeKe-gTkgaWnqJg26eUtDBwGTLk0S36S5lkRrXmCRiZB0Vo5JcvmWKq_fXgBxxGfdTbGXfKQG6TpTcO-fj934vAZik-fcyNAA495Ukja-dZgVLE2Acueds8sqLHs1zmUM1G3CIh9Bi3Y9Z1xozoa5FC1GnJHhYJKCLOw4GoZkdKRTaFQ/https%3A%2F%2Fneuroimage.usc.edu%2Fbrainstorm%2FTutorials%2FLabelFreeSurfer
I'm getting an error while performing step 4 of 'Running Freesurfer'
heading.
Command that is giving error : recon-all -all -subjid 
Here my  is subject_0295

Error on the terminal : recon-all -s subject_0295 exited with ERRORS at Tue
Dec  8 18:25:40 IST 2020

The freesurfer/subjects/subject_0295/scripts/recon-all.log file didn't
mention any specific error.

I've searched the list and no similar errors have been reported. Does
anyone have any thoughts on how to trouble-shoot this one? Also, I have
attached the recon-all.log in case it's of any use.

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
2) Platform: Ubuntu 16.04.7 LTS
3) recon-all.log: see attached


-- 
Regards,
Ms. Devanshi Jain
Tue Dec  8 17:55:11 IST 2020
/media/ayushi/TI10716000E/freesurfer/subjects/subject_0295
/media/ayushi/TI10716000E/freesurfer/bin/recon-all
-i mri_0295.nii -subjid subject_0295
subjid subject_0295
setenv SUBJECTS_DIR /media/ayushi/TI10716000E/freesurfer/subjects
FREESURFER_HOME /media/ayushi/TI10716000E/freesurfer
Actual FREESURFER_HOME /media/ayushi/TI10716000E/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux ayushi-Satellite-S55-C 4.15.0-126-generic #129~16.04.1-Ubuntu SMP Tue Nov 24 11:22:40 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  31172 
maxlocks unlimited
maxsignal31172 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem:8085540 1588064 5009496  212356 1487980 5975464
Swap:   8306684   0 8306684


program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2020/12/08-12:25:11-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $  User: ayushi  Machine: ayushi-Satellite-S55-C  Platform: Linux  PlatformVersion: 4.15.0-126-generic  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version 
stable5
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2020/12/08-12:25:11-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $  User: ayushi  Machine: ayushi-Satellite-S55-C  Platform: Linux  PlatformVersion: 4.15.0-126-generic  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2020/12/08-12:25:12-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  User: ayushi  Machine: ayushi-Satellite-S55-C  Platform: Linux  PlatformVersion: 4.15.0-126-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2020/12/08-12:25:12-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $  User: ayushi  Machine: ayushi-Satellite-S55-C  Platform: Linux  PlatformVersion: 4.15.0-126-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2020/12/08-12:25:12-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $  User: ayushi  Machine: ayushi-Satellite-S55-C  Platform: Linux  PlatformVersion: 4.15.0-126-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2020/12/08-12:25:13-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_gcut.cpp,v 1.14 

Re: [Freesurfer] Recon-all error

[Fischl, Bruce]

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 - 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 ERRORS."

I looked in the recon-all.error file and the only thing in that is "CMD 
mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix." 
Would this be the step where the error is happening?

I have checked the T1 thoroughly and it is good quality. What is the best way 
to debug why this is happening with our scans?
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[Freesurfer] Recon-all error

[Courtney Haswell]

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 ERRORS."

I looked in the recon-all.error file and the only thing in that is "CMD
mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix
../surf/rh.qsphere.nofix." Would this be the step where the error is
happening?

I have checked the T1 thoroughly and it is good quality. What is the best
way to debug why this is happening with our scans?
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Re: [Freesurfer] recon-all error

[Douglas N. Greve]

This is  not something we do. I have seen it done before, so do a search 
online and/or talk to the authros


On 9/6/2020 11:43 PM, Jie Zhao wrote:

 External Email - Use Caution

Hi, Bruce and all

The paper attached quoted "A semiautomated process was implemented to convert 
FreeSurfer generated
macaque surfaces into Caret file formats and to register the individual hemispheres 
to the F99 atlas."
Is the freesurfer have the function to generate macaque surface and how make it 
?

Best,
Jie


-原始邮件-
发件人: "Fischl, Bruce" 
发送时间: 2020-09-04 22:27:48 (星期五)
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 4, 2020 4:21 AM
To: Freesurfer support list 
Subject: 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 - Use Caution

Hi, Bruce

I reorineted the views in freesurfer , But the result was wrong again . Please 
check the figure attached, Is there any problem.

BTW, I got the Dicom file, it is .IMA format. How can I use it?

Thanks!
Jie



-Original Messages-
From: "Fischl, Bruce"  Sent Time:
2020-08-30
10:14:46 (Sunday)
To: "Freesurfer support list" 
Cc:
Subject: Re: [Freesurfer] recon-all error

Hi Jie

The orientations are incorrect. What freeview thinks is anterior/posterior (labeled with 
"A" and "P") is actually inferior/superior. Do you have the dicoms from this 
dataset? If not, how was it converted? You need to orient it properly so it shows correctly in 
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 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 list" 
Cc:
Subject: Re: [Freesurfer] recon-all error

Why do you want to change it? Can you post a snapshot from freeview so we can 
make sure we are on the same page?

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
 On Behalf Of Jie Zhao
Sent: Saturday, August 29, 2020 12:25 PM
To: Freesurfer support list 
Subject: Re: [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. 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 freeview, my
orientation on freeview is RAS. Could you tell me

freeview -v /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii

and make sure that the orientation it displays in is correct (that is, that 
what freeview thinks is anterior/superior/left are indeed those directions). 
Usually when we see this type of failure it is because the direction cosines in 
the input volume are incorrect (typically because the volume was at some point 
converted to analyze format). Not always, but usually.

Cheers
Bruce


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
 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 advice, Thanks

Kind Regards,
Jie



-Original Messages-----
From: "Hoopes, Andrew"  Sent Time:
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, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Jie Zhao" 
 wrote:

   

Re: [Freesurfer] recon-all error

[Fischl, Bruce]

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 4, 2020 4:21 AM
To: Freesurfer support list 
Subject: 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 - Use Caution
> 
> Hi, Bruce
> 
> I reorineted the views in freesurfer , But the result was wrong again . 
> Please check the figure attached, Is there any problem.
> 
> BTW, I got the Dicom file, it is .IMA format. How can I use it?
> 
> Thanks!
> Jie
> 
> 
> > -Original Messages-
> > From: "Fischl, Bruce"  Sent Time: 
> > 2020-08-30
> > 10:14:46 (Sunday)
> > To: "Freesurfer support list" 
> > Cc: 
> > Subject: Re: [Freesurfer] recon-all error
> > 
> > Hi Jie
> > 
> > The orientations are incorrect. What freeview thinks is anterior/posterior 
> > (labeled with "A" and "P") is actually inferior/superior. Do you have the 
> > dicoms from this dataset? If not, how was it converted? You need to orient 
> > it properly so it shows correctly in 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 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 list" 
> > > Cc: 
> > > Subject: Re: [Freesurfer] recon-all error
> > > 
> > > Why do you want to change it? Can you post a snapshot from freeview so we 
> > > can make sure we are on the same page?
> > > 
> > > -Original Message-
> > > From: freesurfer-boun...@nmr.mgh.harvard.edu
> > >  On Behalf Of Jie Zhao
> > > Sent: Saturday, August 29, 2020 12:25 PM
> > > To: Freesurfer support list 
> > > Subject: Re: [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. 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 freeview, my 
> > > > orientation on freeview is RAS. Could you tell me
> > > > 
> > > > freeview -v /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii
> > > > 
> > > > and make sure that the orientation it displays in is correct (that is, 
> > > > that what freeview thinks is anterior/superior/left are indeed those 
> > > > directions). Usually when we see this type of failure it is because the 
> > > > direction cosines in the input volume are incorrect (typically because 
> > > > the volume was at some point converted to analyze format). Not always, 
> > > > but usually.
> > > > 
> > > > Cheers
> > > > Bruce
> > > &g

Re: [Freesurfer] recon-all error

[Jie Zhao]

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 - Use Caution
> 
> Hi, Bruce
> 
> I reorineted the views in freesurfer , But the result was wrong again . 
> Please check the figure attached, Is there any problem.
> 
> BTW, I got the Dicom file, it is .IMA format. How can I use it?
> 
> Thanks!
> Jie
> 
> 
> > -Original Messages-
> > From: "Fischl, Bruce"  Sent Time: 2020-08-30 
> > 10:14:46 (Sunday)
> > To: "Freesurfer support list" 
> > Cc: 
> > Subject: Re: [Freesurfer] recon-all error
> > 
> > Hi Jie
> > 
> > The orientations are incorrect. What freeview thinks is anterior/posterior 
> > (labeled with "A" and "P") is actually inferior/superior. Do you have the 
> > dicoms from this dataset? If not, how was it converted? You need to orient 
> > it properly so it shows correctly in 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 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 list" 
> > > Cc: 
> > > Subject: Re: [Freesurfer] recon-all error
> > > 
> > > Why do you want to change it? Can you post a snapshot from freeview so we 
> > > can make sure we are on the same page?
> > > 
> > > -Original Message-
> > > From: freesurfer-boun...@nmr.mgh.harvard.edu
> > >  On Behalf Of Jie Zhao
> > > Sent: Saturday, August 29, 2020 12:25 PM
> > > To: Freesurfer support list 
> > > Subject: Re: [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. 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 freeview, my 
> > > > orientation on freeview is RAS. Could you tell me
> > > > 
> > > > freeview -v /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii
> > > > 
> > > > and make sure that the orientation it displays in is correct (that is, 
> > > > that what freeview thinks is anterior/superior/left are indeed those 
> > > > directions). Usually when we see this type of failure it is because the 
> > > > direction cosines in the input volume are incorrect (typically because 
> > > > the volume was at some point converted to analyze format). Not always, 
> > > > but usually.
> > > > 
> > > > Cheers
> > > > Bruce
> > > > 
> > > > 
> > > > -Original Message-
> > > > From: freesurfer-boun...@nmr.mgh.harvard.edu
> > > >  On Behalf Of Jie Zhao
> > > > Sent: Thursday, August 27, 2020 11:21 AM
> > > > To: Freesurfer support list 
> > &

Re: [Freesurfer] recon-all error

[Fischl, Bruce]

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 - Use Caution

Hi, Bruce

I reorineted the views in freesurfer , But the result was wrong again . Please 
check the figure attached, Is there any problem.

BTW, I got the Dicom file, it is .IMA format. How can I use it?

Thanks!
Jie


> -Original Messages-
> From: "Fischl, Bruce"  Sent Time: 2020-08-30 
> 10:14:46 (Sunday)
> To: "Freesurfer support list" 
> Cc: 
> Subject: Re: [Freesurfer] recon-all error
> 
> Hi Jie
> 
> The orientations are incorrect. What freeview thinks is anterior/posterior 
> (labeled with "A" and "P") is actually inferior/superior. Do you have the 
> dicoms from this dataset? If not, how was it converted? You need to orient it 
> properly so it shows correctly in 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 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 list" 
> > Cc: 
> > Subject: Re: [Freesurfer] recon-all error
> > 
> > Why do you want to change it? Can you post a snapshot from freeview so we 
> > can make sure we are on the same page?
> > 
> > -Original Message-
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
> >  On Behalf Of Jie Zhao
> > Sent: Saturday, August 29, 2020 12:25 PM
> > To: Freesurfer support list 
> > Subject: Re: [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. 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 freeview, my 
> > > orientation on freeview is RAS. Could you tell me
> > > 
> > > freeview -v /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii
> > > 
> > > and make sure that the orientation it displays in is correct (that is, 
> > > that what freeview thinks is anterior/superior/left are indeed those 
> > > directions). Usually when we see this type of failure it is because the 
> > > direction cosines in the input volume are incorrect (typically because 
> > > the volume was at some point converted to analyze format). Not always, 
> > > but usually.
> > > 
> > > Cheers
> > > Bruce
> > > 
> > > 
> > > -Original Message-
> > > From: freesurfer-boun...@nmr.mgh.harvard.edu
> > >  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 advice, Thanks
> > > 
> > > Kind Regards,
> > > Jie
> > > 
> > > 
> > > > -Original Messages-
> > > > From: "Hoopes, Andrew"  Sent Time: 
> > > > 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 

Re: [Freesurfer] recon-all error

[Douglas Greve]

Try running it with --no-surfs


On 8/29/20 12:34 PM, Jie Zhao wrote:


External Email - Use Caution

Hi, Douglas


I first heared the tkregisterfv, tryed the tkregisterfv --fstal --s 
mprage


the output error was this:

ERROR: cannot find /usr/local/freesurfer/subjects/mprage/surf/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 might not
work on all systems. You can try using tkregisterfv instead,
available here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/tkregisterfv

On 8/29/2020 11:26 AM, Jie Zhao wrote:

 External Email - Use Caution

Hi All

I tryed the tkregister2 to change the postion for Talairach 
Registration,but some error occured in the tkregister, so some button were not  
functioning well.

I can not find useful info. on the internet, could you tell me how to 
correct 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

This is the automatic failure detection raising a warning flag. Did you
notice that the output suggested that you take some action?

On 8/27/2020 11:39 AM, Fischl, Bruce wrote:

Hi Jie

I would start by looking at your input volume in freeview:

freeview -v /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii

and make sure that the orientation it displays in is correct (that is, that 
what freeview thinks is anterior/superior/left are indeed those directions). 
Usually when we see this type of failure it is because the direction cosines in 
the input volume are incorrect (typically because the volume was at some point 
converted to analyze format). Not always, but usually.

Cheers
Bruce


-Original Message-
From:freesurfer-boun...@nmr.mgh.harvard.edu  
  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 advice, Thanks

Kind Regards,
Jie



-Original Messages-
From: "Hoopes, Andrew"  Sent Time: 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,"freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Jie 
Zhao"wrote:

  External Email - Use Caution
  
  Hi Andrew
  
  Thanks fro your response.

  I have soruced the Freesurfer.
  Attached is the recon-all log.
  
  Best,

  Jie
  
  
  > -Original Messages-

  > From: "Hoopes, Andrew"  > Sent Time: 
2020-08-24 22:22:28 (Monday)
  > To: "Freesurfer 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 something else going wrong here based on those p values. Have 
you sourced freesurfer in your environment? Adding the freesurfer bin dir to your 
PATH will provide access to binaries, but there are a few other PATH variables and 
settings that get configured by running `source 
$FREESURFER_HOME/SetUpFreeSurfer.sh`.
  >
  > best
  > Andrew
  >
  > On 8/24/20, 10:12 AM,"freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Jie Zhao"wrote:
  >
  > External Email - Use Caution
  >
  > Hi, Tim
  >
  > Thanks for your quick response.
  > I set the PATH environment varible to include Freesurfer binary 
directory.
  >
  > I have the new problem when using recon-all , the error is like 
this:
  > ERROR: talairach_afd: Talairach Transform: 
transforms/talairach.xfm ***FAILED*** (p=0., pval=0. < threshold=0.0050
  >
  > How can solve this error?
  >
  > Regards,
  > Jie
  >
  > 

Re: [Freesurfer] recon-all error (incorrect orientation)

[Douglas Greve]

You can use the Transform volume tool in FreeView, though it will be a 
pain if you have to do a bunch. Getting the original dicoms is a much 
better place to start.


On 9/1/20 9:13 AM, Ellen Ji wrote:

External Email - Use Caution
Dear Bruce (and Jie),

I believe I am encountering the same problem as Jie - see the attached 
screenshot from freeview. I was given niftis for a cohort of subjects 
and some of them are sideways. Thus, this resulted in Talairach 
failure when performing recon-all and cannot simply be readjusted 
using tkregister2 as far as I know.


What is the easiest way to fix the orientation?

Many thanks for your help,

Ellen

On 8/30/2020 4:14 AM, Fischl, Bruce wrote:

Hi Jie

The orientations are incorrect. What freeview thinks is 
anterior/posterior (labeled with "A" and "P") is actually 
inferior/superior. Do you have the dicoms from this dataset? If not, 
how was it converted? You need to orient it properly so it shows 
correctly in 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 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 list" 
Cc:
Subject: Re: [Freesurfer] recon-all error

Why do you want to change it? Can you post a snapshot from freeview 
so we can make sure we are on the same page?


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
 On Behalf Of Jie Zhao
Sent: Saturday, August 29, 2020 12:25 PM
To: Freesurfer support list 
Subject: Re: [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. 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 freeview, my
orientation on freeview is RAS. Could you tell me

freeview -v /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii

and make sure that the orientation it displays in is correct (that 
is, that what freeview thinks is anterior/superior/left are indeed 
those directions). Usually when we see this type of failure it is 
because the direction cosines in the input volume are incorrect 
(typically because the volume was at some point converted to 
analyze format). Not always, but usually.


Cheers
Bruce


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
 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 advice, Thanks

Kind Regards,
Jie



-Original Messages-
From: "Hoopes, Andrew"  Sent Time:
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, "freesurfer-boun...@nmr.mgh.harvard.edu on 
behalf of Jie Zhao" behalf of zjuzhao...@zju.edu.cn> wrote:


 External Email - Use Caution
  Hi Andrew
  Thanks fro your response.
 I have soruced the Freesurfer.
 Attached is the recon-all log.
  Best,
 Jie
   > -Original Messages-
 > From: "Hoopes, Andrew" 
 > Sent Time: 2020-08-24 22:22:28 (Monday)
 > To: "Freesurfer 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 something else 
going wrong here based on those p values. Have you sourced 
freesurfer in your environment? Adding the freesurfer bin dir to 
your PATH will provide access to binaries, but there are a few 
other PATH variables and settings that get configured by running 
`source $FREESURFER_HOME/SetUpFreeSurfer.sh`.

 >
 > best
 > Andrew
 >
 > On 8/24/20, 10:12 AM, 
"freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Jie Zhao" 
zjuzhao...@zju.edu.cn> wrote:

 >
 > External Emai

Re: [Freesurfer] recon-all error

[Fischl, Bruce]

Hi Jie

The orientations are incorrect. What freeview thinks is anterior/posterior 
(labeled with "A" and "P") is actually inferior/superior. Do you have the 
dicoms from this dataset? If not, how was it converted? You need to orient it 
properly so it shows correctly in 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 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 list" 
> Cc: 
> Subject: Re: [Freesurfer] recon-all error
> 
> Why do you want to change it? Can you post a snapshot from freeview so we can 
> make sure we are on the same page?
> 
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  On Behalf Of Jie Zhao
> Sent: Saturday, August 29, 2020 12:25 PM
> To: Freesurfer support list 
> Subject: Re: [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. 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 freeview, my 
> > orientation on freeview is RAS. Could you tell me
> > 
> > freeview -v /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii
> > 
> > and make sure that the orientation it displays in is correct (that is, that 
> > what freeview thinks is anterior/superior/left are indeed those 
> > directions). Usually when we see this type of failure it is because the 
> > direction cosines in the input volume are incorrect (typically because the 
> > volume was at some point converted to analyze format). Not always, but 
> > usually.
> > 
> > Cheers
> > Bruce
> > 
> > 
> > -Original Message-
> > From: freesurfer-boun...@nmr.mgh.harvard.edu 
> >  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 advice, Thanks
> > 
> > Kind Regards,
> > Jie
> > 
> > 
> > > -Original Messages-
> > > From: "Hoopes, Andrew"  Sent Time: 
> > > 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, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf 
> > > of Jie Zhao"  > > zjuzhao...@zju.edu.cn> wrote:
> > > 
> > > External Email - Use Caution
> > > 
> > > Hi Andrew
> > > 
> > > Thanks fro your response.
> > > I have soruced the Freesurfer. 
> > > Attached is the recon-all log.  
> > > 
> > > Best,
> > > Jie
> > > 
> > > 
> > > > -Original Messages-
> > > > From: "Hoopes, Andrew" 
> > > > Sent Time: 2020-08-24 22:22:28 (Monday)
> > > > To: "Freesurfer 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 something else going wrong here based on 
> > > th

Re: [Freesurfer] recon-all error

[Fischl, Bruce]

Why do you want to change it? Can you post a snapshot from freeview so we can 
make sure we are on the same page?

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Jie Zhao
Sent: Saturday, August 29, 2020 12:25 PM
To: Freesurfer support list 
Subject: Re: [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. 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 freeview, my orientation on 
> freeview is RAS. Could you tell me 
> 
> freeview -v /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii
> 
> and make sure that the orientation it displays in is correct (that is, that 
> what freeview thinks is anterior/superior/left are indeed those directions). 
> Usually when we see this type of failure it is because the direction cosines 
> in the input volume are incorrect (typically because the volume was at some 
> point converted to analyze format). Not always, but usually.
> 
> Cheers
> Bruce
> 
> 
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  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 advice, Thanks
> 
> Kind Regards,
> Jie
> 
> 
> > -Original Messages-----
> > From: "Hoopes, Andrew"  Sent Time: 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, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
> > Jie Zhao"  > zjuzhao...@zju.edu.cn> wrote:
> > 
> > External Email - Use Caution
> > 
> > Hi Andrew
> > 
> > Thanks fro your response.
> > I have soruced the Freesurfer. 
> >     Attached is the recon-all log.  
> > 
> > Best,
> > Jie
> > 
> > 
> > > -Original Messages-
> > > From: "Hoopes, Andrew" 
> > > Sent Time: 2020-08-24 22:22:28 (Monday)
> > > To: "Freesurfer 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 something else going wrong here based on 
> > those p values. Have you sourced freesurfer in your environment? Adding the 
> > freesurfer bin dir to your PATH will provide access to binaries, but there 
> > are a few other PATH variables and settings that get configured by running 
> > `source $FREESURFER_HOME/SetUpFreeSurfer.sh`.
> > > 
> > > best
> > > Andrew
> > > 
> > > On 8/24/20, 10:12 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on 
> > behalf of Jie Zhao"  > zjuzhao...@zju.edu.cn> wrote:
> > > 
> > > External Email - Use Caution
> > > 
> > > Hi, Tim
> > > 
> > > Thanks for your quick response.
> > > I set the PATH environment varible to include Freesurfer binary 
> > directory.
> > > 
> > > I have the new problem when using recon-all , the error is like 
> > this:
> > > ERROR: talairach_afd: Talairach Transform: 
> > transforms/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&q

Re: [Freesurfer] recon-all error

[Jie Zhao]

External Email - Use Caution

Hi, Douglas




I first heared the tkregisterfv, tryed the tkregisterfv --fstal --s mprage

the output error was this:

ERROR: cannot find /usr/local/freesurfer/subjects/mprage/surf/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 might not work on all 
systems. You can try using tkregisterfv instead, available here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/tkregisterfv


On 8/29/2020 11:26 AM, Jie Zhao wrote:

External Email - Use Caution

Hi All

I tryed the tkregister2 to change the postion for Talairach Registration,but 
some error occured in the tkregister, so some button were not  functioning well.

I can not find useful info. on the internet, could you tell me how to correct 
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

This is the automatic failure detection raising a warning flag. Did you 
notice that the output suggested that you take some action?

On 8/27/2020 11:39 AM, Fischl, Bruce wrote:

Hi Jie

I would start by looking at your input volume in freeview:

freeview -v /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii

and make sure that the orientation it displays in is correct (that is, that 
what freeview thinks is anterior/superior/left are indeed those directions). 
Usually when we see this type of failure it is because the direction cosines in 
the input volume are incorrect (typically because the volume was at some point 
converted to analyze format). Not always, but usually.

Cheers
Bruce


-Original Message-
From: 
freesurfer-boun...@nmr.mgh.harvard.edu 
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 advice, Thanks

Kind Regards,
Jie



-Original Messages-
From: "Hoopes, Andrew"  Sent Time: 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, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Jie 
Zhao" wrote:

 External Email - Use Caution
 
 Hi Andrew
 
 Thanks fro your response.
 I have soruced the Freesurfer.
 Attached is the recon-all log.
 
 Best,
 Jie
 
 
 > -Original Messages-
 > From: "Hoopes, Andrew"  > Sent Time: 2020-08-24 
22:22:28 (Monday)
 > To: "Freesurfer 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 something else going wrong here based on those p values. Have 
you sourced freesurfer in your environment? Adding the freesurfer bin dir to 
your PATH will provide access to binaries, but there are a few other PATH 
variables and settings that get configured by running `source 
$FREESURFER_HOME/SetUpFreeSurfer.sh`.
 >
 > best
 > Andrew
 >
 > On 8/24/20, 10:12 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf 
of Jie Zhao" wrote:
 >
 > External Email - Use Caution
 >
 > Hi, Tim
 >
 > Thanks for your quick response.
 > I set the PATH environment varible to include Freesurfer binary 
directory.
 >
 > I have the new problem when using recon-all , the error is like this:
 > ERROR: talairach_afd: Talairach Transform: transforms/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 s

Re: [Freesurfer] recon-all error

[Jie Zhao]

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. 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 freeview, my orientation on 
> freeview is RAS. Could you tell me 
> 
> freeview -v /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii
> 
> and make sure that the orientation it displays in is correct (that is, that 
> what freeview thinks is anterior/superior/left are indeed those directions). 
> Usually when we see this type of failure it is because the direction cosines 
> in the input volume are incorrect (typically because the volume was at some 
> point converted to analyze format). Not always, but usually.
> 
> Cheers
> Bruce
> 
> 
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  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 advice, Thanks
> 
> Kind Regards,
> Jie
> 
> 
> > -Original Messages-----
> > From: "Hoopes, Andrew"  Sent Time: 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, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
> > Jie Zhao"  > zjuzhao...@zju.edu.cn> wrote:
> > 
> > External Email - Use Caution
> > 
> > Hi Andrew
> > 
> > Thanks fro your response.
> > I have soruced the Freesurfer. 
> >     Attached is the recon-all log.  
> > 
> > Best,
> > Jie
> > 
> > 
> > > -Original Messages-
> > > From: "Hoopes, Andrew" 
> > > Sent Time: 2020-08-24 22:22:28 (Monday)
> > > To: "Freesurfer 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 something else going wrong here based on 
> > those p values. Have you sourced freesurfer in your environment? Adding the 
> > freesurfer bin dir to your PATH will provide access to binaries, but there 
> > are a few other PATH variables and settings that get configured by running 
> > `source $FREESURFER_HOME/SetUpFreeSurfer.sh`.
> > > 
> > > best
> > > Andrew
> > > 
> > > On 8/24/20, 10:12 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on 
> > behalf of Jie Zhao"  > zjuzhao...@zju.edu.cn> wrote:
> > > 
> > > External Email - Use Caution
> > > 
> > > Hi, Tim
> > > 
> > > Thanks for your quick response.
> > > I set the PATH environment varible to include Freesurfer binary 
> > directory.
> > > 
> > > I have the new problem when using recon-all , the error is like 
> > this:
> > > ERROR: talairach_afd: Talairach Transform: 
> > transforms/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 

Re: [Freesurfer] recon-all error

[Jie Zhao]

External Email - Use Caution

tkregister2 --s mprage --fstal , below is the error:





Determinant 26.9764

subject = mprage
Zoom Factor = 2, SQR() = 4
FOV = 256
Opening window mprage
Opening mprage, xnum = 256, xdim = 512
Setting scale
Tcl_Init failed: Can't find a usable init.tcl in the following directories:
/usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4



This probably means that Tcl wasn't installed properly.

Tk_Init failed: invalid command name "tcl_findLibrary"
tkregister2: interface: /usr/local/freesurfer/tktools/tkregister2.tcl
tkregister.tcl: startup done
tkregister.tcl: default macro interface (to change: macro,mini,micro)
tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}
% invalid command name "tk::ScreenChanged"
while executing
"tk::ScreenChanged :0.0"
(changing screen in event binding)



-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 tkregisterfv instead, available here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/tkregisterfv


On 8/29/2020 11:26 AM, Jie Zhao wrote:

External Email - Use Caution

Hi All

I tryed the tkregister2 to change the postion for Talairach Registration,but 
some error occured in the tkregister, so some button were not  functioning well.

I can not find useful info. on the internet, could you tell me how to correct 
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

This is the automatic failure detection raising a warning flag. Did you 
notice that the output suggested that you take some action?

On 8/27/2020 11:39 AM, Fischl, Bruce wrote:

Hi Jie

I would start by looking at your input volume in freeview:

freeview -v /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii

and make sure that the orientation it displays in is correct (that is, that 
what freeview thinks is anterior/superior/left are indeed those directions). 
Usually when we see this type of failure it is because the direction cosines in 
the input volume are incorrect (typically because the volume was at some point 
converted to analyze format). Not always, but usually.

Cheers
Bruce


-Original Message-
From: 
freesurfer-boun...@nmr.mgh.harvard.edu 
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 advice, Thanks

Kind Regards,
Jie



-Original Messages-
From: "Hoopes, Andrew"  Sent Time: 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, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Jie 
Zhao" wrote:

 External Email - Use Caution
 
 Hi Andrew
 
 Thanks fro your response.
 I have soruced the Freesurfer.
 Attached is the recon-all log.
 
 Best,
 Jie
 
 
 > -Original Messages-
 > From: "Hoopes, Andrew"  > Sent Time: 2020-08-24 
22:22:28 (Monday)
 > To: "Freesurfer 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 something else going wrong here based on those p values. Have 
you sourced freesurfer in your environment? Adding the freesurfer bin dir to 
your PATH will provide access to binaries, but there are a few other PATH 
variables and settings that get configured by running `source 
$FREESURFER_HOME/SetUpFreeSurfer.sh`.
 >
 > best
 > Andrew
 >
 > On 8/24/20, 10:12 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf 
of Jie Zhao" wrote:
 >
 > External Email - Use Caution
 >
 > Hi, Tim
 >
 > Thanks for your quick response.
 > I set the PATH environment varible to include Freesurfer binary 
directory.
 >
 > I have the new problem when using recon-all , the error is like this:
 > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm 
***FAILED*** (p=0.000

Re: [Freesurfer] recon-all error

[Douglas N. Greve]

What is the error? tkregister2 is an old program, and it might not work 
on all systems. You can try using tkregisterfv instead, available here

https://gate.nmr.mgh.harvard.edu/safelinks/greve/tkregisterfv

On 8/29/2020 11:26 AM, Jie Zhao wrote:

 External Email - Use Caution

Hi All

I tryed the tkregister2 to change the postion for Talairach Registration,but 
some error occured in the tkregister, so some button were not  functioning well.

I can not find useful info. on the internet, could you tell me how to correct 
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

This is the automatic failure detection raising a warning flag. Did you
notice that the output suggested that you take some action?

On 8/27/2020 11:39 AM, Fischl, Bruce wrote:

Hi Jie

I would start by looking at your input volume in freeview:

freeview -v /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii

and make sure that the orientation it displays in is correct (that is, that 
what freeview thinks is anterior/superior/left are indeed those directions). 
Usually when we see this type of failure it is because the direction cosines in 
the input volume are incorrect (typically because the volume was at some point 
converted to analyze format). Not always, but usually.

Cheers
Bruce


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 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 advice, Thanks

Kind Regards,
Jie



-Original Messages-
From: "Hoopes, Andrew"  Sent Time: 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, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Jie Zhao" 
 wrote:

  External Email - Use Caution
  
  Hi Andrew
  
  Thanks fro your response.

  I have soruced the Freesurfer.
  Attached is the recon-all log.
  
  Best,

  Jie
  
  
  > -Original Messages-

  > From: "Hoopes, Andrew" 
  > Sent Time: 2020-08-24 22:22:28 (Monday)
  > To: "Freesurfer 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 something else going wrong here based on those p values. Have you 
sourced freesurfer in your environment? Adding the freesurfer bin dir to your PATH 
will provide access to binaries, but there are a few other PATH variables and 
settings that get configured by running `source 
$FREESURFER_HOME/SetUpFreeSurfer.sh`.
  >
  > best
  > Andrew
  >
  > On 8/24/20, 10:12 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Jie 
Zhao"  wrote:
  >
  > External Email - Use Caution
  >
  > Hi, Tim
  >
  > Thanks for your quick response.
  > I set the PATH environment varible to include Freesurfer binary 
directory.
  >
  > I have the new problem when using recon-all , the error is like 
this:
  > ERROR: talairach_afd: Talairach Transform: transforms/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
  > > >
  > > > D

Re: [Freesurfer] recon-all error

[Jie Zhao]

External Email - Use Caution

Hi All

I tryed the tkregister2 to change the postion for Talairach Registration,but 
some error occured in the tkregister, so some button were not  functioning well.

I can not find useful info. on the internet, could you tell me how to correct 
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
> 
> This is the automatic failure detection raising a warning flag. Did you 
> notice that the output suggested that you take some action?
> 
> On 8/27/2020 11:39 AM, Fischl, Bruce wrote:
> > Hi Jie
> >
> > I would start by looking at your input volume in freeview:
> >
> > freeview -v /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii
> >
> > and make sure that the orientation it displays in is correct (that is, that 
> > what freeview thinks is anterior/superior/left are indeed those 
> > directions). Usually when we see this type of failure it is because the 
> > direction cosines in the input volume are incorrect (typically because the 
> > volume was at some point converted to analyze format). Not always, but 
> > usually.
> >
> > Cheers
> > Bruce
> >
> >
> > -Original Message-
> > From: freesurfer-boun...@nmr.mgh.harvard.edu 
> >  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 advice, Thanks
> >
> > Kind Regards,
> > Jie
> >
> >
> >> -Original Messages-
> >> From: "Hoopes, Andrew"  Sent Time: 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, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
> >> Jie Zhao"  >> zjuzhao...@zju.edu.cn> wrote:
> >>
> >>  External Email - Use Caution
> >>  
> >>      Hi Andrew
> >>  
> >>  Thanks fro your response.
> >>  I have soruced the Freesurfer.
> >>  Attached is the recon-all log.
> >>  
> >>  Best,
> >>  Jie
> >>  
> >>  
> >>  > -Original Messages-
> >>  > From: "Hoopes, Andrew" 
> >>  > Sent Time: 2020-08-24 22:22:28 (Monday)
> >>  > To: "Freesurfer 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 something else going wrong here based on 
> >> those p values. Have you sourced freesurfer in your environment? Adding 
> >> the freesurfer bin dir to your PATH will provide access to binaries, but 
> >> there are a few other PATH variables and settings that get configured by 
> >> running `source $FREESURFER_HOME/SetUpFreeSurfer.sh`.
> >>  >
> >>  > best
> >>  > Andrew
> >>  >
> >>  > On 8/24/20, 10:12 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on 
> >> behalf of Jie Zhao"  >> zjuzhao...@zju.edu.cn> wrote:
> >>  >
> >>  >     External Email - Use Caution
> >>  >
> >>  > Hi, Tim
> >>  >
> >>  > Thanks for your quick response.
> >>  > I set the PATH environment varible to include Freesurfer binary 
> >> directory.
> >>  >
> >>  > I have the new problem when using recon-all , the error is like 
> >> this:
> >>  > ERROR: talairach_afd: Talairach Transform: 
> >> transforms/talairach.xfm ***FA

Re: [Freesurfer] recon-all error

[Douglas N. Greve]

This is the automatic failure detection raising a warning flag. Did you 
notice that the output suggested that you take some action?

On 8/27/2020 11:39 AM, Fischl, Bruce wrote:
> Hi Jie
>
> I would start by looking at your input volume in freeview:
>
> freeview -v /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii
>
> and make sure that the orientation it displays in is correct (that is, that 
> what freeview thinks is anterior/superior/left are indeed those directions). 
> Usually when we see this type of failure it is because the direction cosines 
> in the input volume are incorrect (typically because the volume was at some 
> point converted to analyze format). Not always, but usually.
>
> Cheers
> Bruce
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  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 advice, Thanks
>
> Kind Regards,
> Jie
>
>
>> -Original Messages-
>> From: "Hoopes, Andrew"  Sent Time: 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, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
>> Jie Zhao" > zjuzhao...@zju.edu.cn> wrote:
>>
>>  External Email - Use Caution
>>  
>>  Hi Andrew
>>  
>>  Thanks fro your response.
>>  I have soruced the Freesurfer.
>>  Attached is the recon-all log.
>>      
>>  Best,
>>  Jie
>>  
>>  
>>  > -Original Messages-
>>  > From: "Hoopes, Andrew" 
>>  > Sent Time: 2020-08-24 22:22:28 (Monday)
>>  > To: "Freesurfer 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 something else going wrong here based on 
>> those p values. Have you sourced freesurfer in your environment? Adding the 
>> freesurfer bin dir to your PATH will provide access to binaries, but there 
>> are a few other PATH variables and settings that get configured by running 
>> `source $FREESURFER_HOME/SetUpFreeSurfer.sh`.
>>  >
>>  > best
>>  > Andrew
>>  >
>>  > On 8/24/20, 10:12 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on 
>> behalf of Jie Zhao" > zjuzhao...@zju.edu.cn> wrote:
>>  >
>>  > External Email - Use Caution
>>  >
>>  > Hi, Tim
>>  >
>>  > Thanks for your quick response.
>>  > I set the PATH environment varible to include Freesurfer binary 
>> directory.
>>  >
>>  > I have the new problem when using recon-all , the error is like 
>> this:
>>  > ERROR: talairach_afd: Talairach Transform: 
>> transforms/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:
>>  > > >
>>

Re: [Freesurfer] recon-all error

[Fischl, Bruce]

Hi Jie

I would start by looking at your input volume in freeview:

freeview -v /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii

and make sure that the orientation it displays in is correct (that is, that 
what freeview thinks is anterior/superior/left are indeed those directions). 
Usually when we see this type of failure it is because the direction cosines in 
the input volume are incorrect (typically because the volume was at some point 
converted to analyze format). Not always, but usually.

Cheers
Bruce


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 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 advice, Thanks

Kind Regards,
Jie


> -Original Messages-
> From: "Hoopes, Andrew"  Sent Time: 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, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
> Jie Zhao"  zjuzhao...@zju.edu.cn> wrote:
> 
> External Email - Use Caution
> 
> Hi Andrew
> 
> Thanks fro your response.
> I have soruced the Freesurfer. 
> Attached is the recon-all log.  
> 
> Best,
> Jie
> 
> 
> > -Original Messages-
> > From: "Hoopes, Andrew" 
>     > Sent Time: 2020-08-24 22:22:28 (Monday)
> > To: "Freesurfer 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 something else going wrong here based on those p values. 
> Have you sourced freesurfer in your environment? Adding the freesurfer bin 
> dir to your PATH will provide access to binaries, but there are a few other 
> PATH variables and settings that get configured by running `source 
> $FREESURFER_HOME/SetUpFreeSurfer.sh`.
> > 
> > best
> > Andrew
> > 
> > On 8/24/20, 10:12 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf 
> of Jie Zhao"  zjuzhao...@zju.edu.cn> wrote:
> > 
> > External Email - Use Caution
> > 
> > Hi, Tim
> > 
> > Thanks for your quick response.
> > I set the PATH environment varible to include Freesurfer binary 
> directory.
> > 
> > I have the new problem when using recon-all , the error is like 
> this:
> > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm 
> ***FAILED*** (p=0., pval=0. < threshold=0.0050
>     > 
> > How can solve this error? 
> > 
> > Regards,
> > Jie
> > 
> > > -原始邮件-
> > > 发件人: "Tim Schäfer" 
> > > 发送时间: 2020-08-23 16:24:28 (星期日)
> > > 收件人: "Freesurfer support list" 
> > > 抄送: 
> > > 主题: Re: [Freesurfer] recon-all error
> > > 
> > > External Email - Use Caution
> > > 
> > > What happems if you type 'mri_ca_label' in your shell?
> > > 
> > > Did you setup your PATH environment variable to include the 
> Freesurfer binary directory?
> > > 
> > > Tim
> > > 
> > > > On August 23, 2020 at 9:34 AM Jie Zhao  
> wrote:
> > > > 
> > > > 
> > > > External Email - Use Caution
> > > > 
> > > > Dear freesurfer developer: 
> > > > 
> > > > I am using Freesurfer 7.1.1 and encounter an error like this 
> when using recon-all :
> > > > 
> > > > zhao@zhao-VirtualBox:~$ export 
> SUBJECTS_DIR=/usr/local/freesurfer/subjects
> > > > zhao@zhao-VirtualBox:~$ recon-all -s test4 -i sample-002.nii.gz 
> -autorecon1
> > > > Subject Stamp: 
> freesurfer-linux-centos6_x86_64-7.

Re: [Freesurfer] recon-all error

[Jie Zhao]

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 advice, Thanks

Kind Regards,
Jie


> -Original Messages-
> From: "Hoopes, Andrew" 
> Sent Time: 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, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
> Jie Zhao"  zjuzhao...@zju.edu.cn> wrote:
> 
> External Email - Use Caution
> 
> Hi Andrew
> 
> Thanks fro your response.
> I have soruced the Freesurfer. 
> Attached is the recon-all log.  
> 
> Best,
> Jie
> 
> 
> > -Original Messages-
> > From: "Hoopes, Andrew" 
>     > Sent Time: 2020-08-24 22:22:28 (Monday)
> > To: "Freesurfer 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 something else going wrong here based on those p values. 
> Have you sourced freesurfer in your environment? Adding the freesurfer bin 
> dir to your PATH will provide access to binaries, but there are a few other 
> PATH variables and settings that get configured by running `source 
> $FREESURFER_HOME/SetUpFreeSurfer.sh`.
> > 
> > best
> > Andrew
> > 
> > On 8/24/20, 10:12 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf 
> of Jie Zhao"  zjuzhao...@zju.edu.cn> wrote:
> > 
> > External Email - Use Caution
> > 
> > Hi, Tim
> > 
> > Thanks for your quick response.
> > I set the PATH environment varible to include Freesurfer binary 
> directory.
> > 
> > I have the new problem when using recon-all , the error is like 
> this:
> > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm 
> ***FAILED*** (p=0., pval=0. < threshold=0.0050
>     > 
> > How can solve this error? 
> > 
> > Regards,
> > Jie
> > 
> > > -原始邮件-
> > > 发件人: "Tim Schäfer" 
> > > 发送时间: 2020-08-23 16:24:28 (星期日)
> > > 收件人: "Freesurfer support list" 
> > > 抄送: 
> > > 主题: Re: [Freesurfer] recon-all error
> > > 
> > > External Email - Use Caution
> > > 
> > > What happems if you type 'mri_ca_label' in your shell?
> > > 
> > > Did you setup your PATH environment variable to include the 
> Freesurfer binary directory?
> > > 
> > > Tim
> > > 
> > > > On August 23, 2020 at 9:34 AM Jie Zhao  
> wrote:
> > > > 
> > > > 
> > > > External Email - Use Caution
> > > > 
> > > > Dear freesurfer developer: 
> > > > 
> > > > I am using Freesurfer 7.1.1 and encounter an error like this 
> when using recon-all :
> > > > 
> > > > zhao@zhao-VirtualBox:~$ export 
> SUBJECTS_DIR=/usr/local/freesurfer/subjects
> > > > zhao@zhao-VirtualBox:~$ recon-all -s test4 -i sample-002.nii.gz 
> -autorecon1
> > > > Subject Stamp: 
> freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
> > > > Current Stamp: 
> freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
> > > > INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
> > > > Actual FREESURFER_HOME /usr/local/freesurfer
> > > > Linux zhao-VirtualBox 4.15.0-20-generic #21-Ubuntu SMP Tue Apr 
> 24 06:16:15 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
> > > > Segmentation fault
> > > > ERROR: Executable 'mri_ca_label -all-info failed! Is it missing 
> from the distribution?'
> > > > 
> > > > What can I do to fix this?  Thanks
> > > > 
> > > > 
>

Re: [Freesurfer] recon-all error

[Hoopes, Andrew]

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, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Jie 
Zhao"  wrote:

External Email - Use Caution

Hi Andrew

Thanks fro your response.
I have soruced the Freesurfer. 
Attached is the recon-all log.  

Best,
Jie


> -Original Messages-
> From: "Hoopes, Andrew" 
> Sent Time: 2020-08-24 22:22:28 (Monday)
> To: "Freesurfer 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 something else going wrong here based on those p values. Have 
you sourced freesurfer in your environment? Adding the freesurfer bin dir to 
your PATH will provide access to binaries, but there are a few other PATH 
variables and settings that get configured by running `source 
$FREESURFER_HOME/SetUpFreeSurfer.sh`.
> 
> best
> Andrew
> 
> On 8/24/20, 10:12 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf 
of Jie Zhao"  wrote:
> 
> External Email - Use Caution
> 
> Hi, Tim
> 
> Thanks for your quick response.
> I set the PATH environment varible to include Freesurfer binary 
directory.
> 
> I have the new problem when using recon-all , the error is like this:
> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm 
***FAILED*** (p=0., pval=0. < threshold=0.0050
> 
> How can solve this error? 
> 
> Regards,
> Jie
> 
> > -原始邮件-
> > 发件人: "Tim Schäfer" 
> > 发送时间: 2020-08-23 16:24:28 (星期日)
> > 收件人: "Freesurfer support list" 
> > 抄送: 
> > 主题: Re: [Freesurfer] recon-all error
> > 
> > External Email - Use Caution
> > 
> > What happems if you type 'mri_ca_label' in your shell?
> > 
> > Did you setup your PATH environment variable to include the 
Freesurfer binary directory?
> > 
> > Tim
> > 
> > > On August 23, 2020 at 9:34 AM Jie Zhao  
wrote:
> > > 
> > > 
> > > External Email - Use Caution
> > > 
> > > Dear freesurfer developer: 
> > > 
> > > I am using Freesurfer 7.1.1 and encounter an error like this when 
using recon-all :
> > > 
> > > zhao@zhao-VirtualBox:~$ export 
SUBJECTS_DIR=/usr/local/freesurfer/subjects
> > > zhao@zhao-VirtualBox:~$ recon-all -s test4 -i sample-002.nii.gz 
-autorecon1
> > > Subject Stamp: 
freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
> > > Current Stamp: 
freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
> > > INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
> > > Actual FREESURFER_HOME /usr/local/freesurfer
> > > Linux zhao-VirtualBox 4.15.0-20-generic #21-Ubuntu SMP Tue Apr 24 
06:16:15 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
> > > Segmentation fault
> > > ERROR: Executable 'mri_ca_label -all-info failed! Is it missing 
from the distribution?'
> > > 
> > > What can I do to fix this?  Thanks
> > > 
> > > 
> > > 
> > > 
> > > Best regards
> > > 
> > > Jie Zhao
> > > 
> > > 
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> > -- 
> > Tim Schäfer
> > 
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] recon-all error

[Jie Zhao]

External Email - Use Caution

Hi Andrew

Thanks fro your response.
I have soruced the Freesurfer. 
Attached is the recon-all log.  

Best,
Jie


> -Original Messages-
> From: "Hoopes, Andrew" 
> Sent Time: 2020-08-24 22:22:28 (Monday)
> To: "Freesurfer 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 something else going wrong here based on those p values. 
> Have you sourced freesurfer in your environment? Adding the freesurfer bin 
> dir to your PATH will provide access to binaries, but there are a few other 
> PATH variables and settings that get configured by running `source 
> $FREESURFER_HOME/SetUpFreeSurfer.sh`.
> 
> best
> Andrew
> 
> On 8/24/20, 10:12 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
> Jie Zhao"  zjuzhao...@zju.edu.cn> wrote:
> 
> External Email - Use Caution
> 
> Hi, Tim
> 
> Thanks for your quick response.
> I set the PATH environment varible to include Freesurfer binary directory.
> 
> I have the new problem when using recon-all , the error is like this:
> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm 
> ***FAILED*** (p=0., pval=0. < threshold=0.0050
> 
> How can solve this error? 
> 
> Regards,
> Jie
> 
> > -原始邮件-----
>     > 发件人: "Tim Schäfer" 
> > 发送时间: 2020-08-23 16:24:28 (星期日)
> > 收件人: "Freesurfer support list" 
> > 抄送: 
> > 主题: Re: [Freesurfer] recon-all error
> > 
> > External Email - Use Caution
> > 
> > What happems if you type 'mri_ca_label' in your shell?
> > 
> > Did you setup your PATH environment variable to include the Freesurfer 
> binary directory?
> > 
> > Tim
> > 
> > > On August 23, 2020 at 9:34 AM Jie Zhao  wrote:
> > > 
> > > 
> > > External Email - Use Caution
> > > 
> > > Dear freesurfer developer: 
> > > 
> > > I am using Freesurfer 7.1.1 and encounter an error like this when 
> using recon-all :
> > > 
> > > zhao@zhao-VirtualBox:~$ export 
> SUBJECTS_DIR=/usr/local/freesurfer/subjects
> > > zhao@zhao-VirtualBox:~$ recon-all -s test4 -i sample-002.nii.gz 
> -autorecon1
> > > Subject Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
> > > Current Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
> > > INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
> > > Actual FREESURFER_HOME /usr/local/freesurfer
> > > Linux zhao-VirtualBox 4.15.0-20-generic #21-Ubuntu SMP Tue Apr 24 
> 06:16:15 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
> > > Segmentation fault
> > > ERROR: Executable 'mri_ca_label -all-info failed! Is it missing from 
> the distribution?'
> > > 
> > > What can I do to fix this?  Thanks
> > > 
> > > 
> > > 
> > > 
> > > Best regards
> > > 
> > > Jie Zhao
> > > 
> > > 
> > > ___
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> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> > -- 
> > Tim Schäfer
> > 
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recon-all log.odt
Description: application/vnd.oasis.opendocument.text
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Re: [Freesurfer] recon-all error

[Hoopes, Andrew]

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 something else going wrong here based on those p values. Have you 
sourced freesurfer in your environment? Adding the freesurfer bin dir to your 
PATH will provide access to binaries, but there are a few other PATH variables 
and settings that get configured by running `source 
$FREESURFER_HOME/SetUpFreeSurfer.sh`.

best
Andrew

On 8/24/20, 10:12 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Jie 
Zhao"  wrote:

External Email - Use Caution

Hi, Tim

Thanks for your quick response.
I set the PATH environment varible to include Freesurfer binary directory.

I have the new problem when using recon-all , the error is like this:
ERROR: talairach_afd: Talairach Transform: transforms/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
> > 
> > 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 sample-002.nii.gz 
-autorecon1
> > Subject Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
> > Current Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
> > INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
> > Actual FREESURFER_HOME /usr/local/freesurfer
> > Linux zhao-VirtualBox 4.15.0-20-generic #21-Ubuntu SMP Tue Apr 24 
06:16:15 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
> > Segmentation fault
> > ERROR: Executable 'mri_ca_label -all-info failed! Is it missing from 
the distribution?'
> > 
> > What can I do to fix this?  Thanks
> > 
> > 
> > 
> > 
> > Best regards
> > 
> > Jie Zhao
> > 
> > 
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> -- 
> Tim Schäfer
> 
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] recon-all error

[Douglas N. Greve]

The talairach automatic failure detection indicates that the talairach 
might have failed. Check your input image and the talairach transform. 
See this page

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview

On 8/24/2020 10:09 AM, Jie Zhao wrote:
>  External Email - Use Caution
>
> Hi, Tim
>
> Thanks for your quick response.
> I set the PATH environment varible to include Freesurfer binary directory.
>
> I have the new problem when using recon-all , the error is like this:
> ERROR: talairach_afd: Talairach Transform: transforms/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
>>>
>>> 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 sample-002.nii.gz -autorecon1
>>> Subject Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
>>> Current Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
>>> INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
>>> Actual FREESURFER_HOME /usr/local/freesurfer
>>> Linux zhao-VirtualBox 4.15.0-20-generic #21-Ubuntu SMP Tue Apr 24 06:16:15 
>>> UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
>>> Segmentation fault
>>> ERROR: Executable 'mri_ca_label -all-info failed! Is it missing from the 
>>> distribution?'
>>>
>>> What can I do to fix this?  Thanks
>>>
>>>
>>>
>>>
>>> Best regards
>>>
>>> Jie Zhao
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> -- 
>> Tim Schäfer
>>
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] recon-all error

[Jie Zhao]

External Email - Use Caution

Hi, Tim

Thanks for your quick response.
I set the PATH environment varible to include Freesurfer binary directory.

I have the new problem when using recon-all , the error is like this:
ERROR: talairach_afd: Talairach Transform: transforms/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
> > 
> > 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 sample-002.nii.gz -autorecon1
> > Subject Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
> > Current Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
> > INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
> > Actual FREESURFER_HOME /usr/local/freesurfer
> > Linux zhao-VirtualBox 4.15.0-20-generic #21-Ubuntu SMP Tue Apr 24 06:16:15 
> > UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
> > Segmentation fault
> > ERROR: Executable 'mri_ca_label -all-info failed! Is it missing from the 
> > distribution?'
> > 
> > What can I do to fix this?  Thanks
> > 
> > 
> > 
> > 
> > Best regards
> > 
> > Jie Zhao
> > 
> > 
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> -- 
> Tim Schäfer
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] recon-all error

[Tim Schäfer]

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
> 
> 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 sample-002.nii.gz -autorecon1
> Subject Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
> Current Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
> INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
> Actual FREESURFER_HOME /usr/local/freesurfer
> Linux zhao-VirtualBox 4.15.0-20-generic #21-Ubuntu SMP Tue Apr 24 06:16:15 
> UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
> Segmentation fault
> ERROR: Executable 'mri_ca_label -all-info failed! Is it missing from the 
> distribution?'
> 
> What can I do to fix this?  Thanks
> 
> 
> 
> 
> Best regards
> 
> Jie Zhao
> 
> 
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Tim Schäfer

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[Freesurfer] recon-all error

[Jie Zhao]

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 sample-002.nii.gz -autorecon1
Subject Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
Current Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
Linux zhao-VirtualBox 4.15.0-20-generic #21-Ubuntu SMP Tue Apr 24 06:16:15 UTC 
2018 x86_64 x86_64 x86_64 GNU/Linux
Segmentation fault
ERROR: Executable 'mri_ca_label -all-info failed! Is it missing from the 
distribution?'

What can I do to fix this?  Thanks




Best regards

Jie Zhao


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Re: [Freesurfer] recon-all error

[Zollei, Lilla,Ph.D.]

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...@nmr.mgh.harvard.edu 
 on behalf of Wilpert, Nina- Maria 

Sent: Tuesday, August 4, 2020 10:51 AM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Schülke-Gerstenfeld, Markus 
Subject: [Freesurfer] mri: recon-all error


External Email - Use Caution

Hello FreeSurfer Developers,



We are attempting to run the command recon-all on pediatric MRI images (1-13 
yrs), as described on your website:

cmd=”recon-all -i $Dir/*.nii.gz -s sub02_test  -all”



The command worked well for some of our subjects. For others, however, hard 
failures occurred and recon-all did not finish or we received the following 
error (please find the recon-all.log attached):

“recon-all -s sub02_reconall exited with ERRORS at….”



Would you have any recommendations on how to trouble-shoot these issues? We 
have attached the recon-all.log documents in case it's of any use.



1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

2) Platform: Linux

4) recon-all.log: see attached.



We would very much appreciate your help!



Kind regards,

Nina Wilpert







Nina-Maria Wilpert | medical student
T +49 (0) 30 450559858 | M +49 (0) 15783851445
E nina-maria.wilp...@charite.de

Department of Neuropediatrics

Charité, Universitätsmedizin Berlin

Institute of Anatomy

University of Leipzig

Genetics and Development of the Cerebral Cortex

Hôpital Necker-Enfants malades & IMAGINE, Paris




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Re: [Freesurfer] Recon-all error when refining pial surfaces with T2 FLAIR

[Douglas N. Greve]

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" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.



On 8/1/2020 12:08 AM, Pankush Kumar wrote:


External Email - Use Caution

Hello,

I am a student using freesurfer 7.1.0 having some trouble with 
recon-all on some subjects. I am trying to calculate pial surfaces by 
adding FLAIR images to my T1 (already processed on recon-all 
beforehand), but encounter the following error:


Starting loop over 121584 vertices
   vno = 0, t = 1.21632
   vno = 2, t = 3.38757
   vno = 4, t = 8.77043
   vno = 6, t = 11.8685
   vno = 8, t = 14.6273
error: Numerical result out of range
error: MRIhistogramLabelRegion: constant image

Log is attached. Other subjects get stuck on the vno = 8 step and 
run for days without progress. No artifacts in any of the images, but 
some have obvious structural variation such as enlarged and misshapen 
ventricles.


Thank you, any help would be greatly appreciated!

Sincerely,
Pankush Kumar

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Re: [Freesurfer] Recon-all error output

[Douglas N. Greve]

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 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 re-run recon-all on the same subject, same result 
was got again. May I know the cause of this error?


I upload the output result, log history and the T1.nii to the 
following share link, please feel free the check them:




https://www.dropbox.com/sh/lhbzct444n8ek8z/AADbtfyYEBNWZ4yYXPw7ejmwa?dl=0

Thank you.


Regards


Frank

---

*FRANK  C Y CHAU*


Research assistant

Division of Neurology

Department of Medicine


Tel: +852 6340 2553

Fax: 2872 5828


E-mail : cyfr...@hku.hk 



Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam 
Road, Hong Kong



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[Freesurfer] Recon-all error output

[Frank Chau]

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 re-run recon-all 
on the same subject, same result was got again. May I know the cause of this 
error?

I upload the output result, log history and the T1.nii to the following share 
link, please feel free the check them:



https://www.dropbox.com/sh/lhbzct444n8ek8z/AADbtfyYEBNWZ4yYXPw7ejmwa?dl=0

Thank you.


Regards


Frank

---

FRANK  C Y CHAU


Research assistant

Division of Neurology

Department of Medicine


Tel: +852 6340 2553

Fax: 2872 5828


E-mail : cyfr...@hku.hk



Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, 
Hong Kong
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Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1)

[Douglas N. Greve]

You can use ANTS N3 by adding -ants-n3 to the command line. In theory, 
you can use a mask, but I vaguely remember that there was a bug when 
someone tried it in our code



On 5/28/2020 12:37 PM, Schranzer René wrote:


External Email - Use Caution

Hi Douglas,

Thanks for your help!

Two more questions:

Is it possible to use the individual brain mask of my skull stripped 
data as a "mask image" for the step of the NU Intensity correction in 
recon-all with an additional flag to carry out 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-all error in CA Normalize 
(FreeSurfer V 7.1)


You can use it with all subjects then

On 5/28/2020 3:28 AM, Schranzer René wrote:

*External Email - Use Caution *

All subjects.

Best,

René

*Von:*freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>

<mailto: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
<mailto:freesurfer@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 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.mgz and continued processing with -autorecon2
and -autorecon3. In some subjects (at some timepoints), the
recon-all -autorecon2 -autorecon3 excited with errors, as
mentioned below. Now I have used the following command
"recon-all -hires -skullstrip -no-wsgcaatlas -s ${sbjID} -i
${sbj} -all" with the skull-stripped data and it worked fine
without errors. I also compared the T1.mgz from both
approaches and they looked identical.

My question, can I use this approach with the "-no-wsgcaatlas"
for all subjects or is there something to consider here?

Best, René




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Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1)

[Schranzer René]

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Hi Douglas,

Thanks for your help!
Two more questions:
Is it possible to use the individual brain mask of my skull stripped data as a 
"mask image" for the step of the NU Intensity correction in recon-all with an 
additional flag to carry out 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-all error in CA Normalize (FreeSurfer V 7.1)

You can use it with all subjects then
On 5/28/2020 3:28 AM, Schranzer René wrote:

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All subjects.

Best,
René

Von: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto: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<mailto:freesurfer@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:

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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. Therefore, I stopped after -autorecon1 and copied 
the T1.mgz to brainmask.mgz and brainmask.auto.mgz and continued processing 
with -autorecon2 and -autorecon3. In some subjects (at some timepoints), the 
recon-all -autorecon2 -autorecon3 excited with errors, as mentioned below. Now 
I have used the following command "recon-all -hires -skullstrip -no-wsgcaatlas 
-s ${sbjID} -i ${sbj} -all" with the skull-stripped data and it worked fine 
without errors. I also compared the T1.mgz from both approaches and they looked 
identical.
My question, can I use this approach with the "-no-wsgcaatlas" for all subjects 
or is there something to consider here?

Best, René




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Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1)

[Douglas N. Greve]

You can use it with all subjects then

On 5/28/2020 3:28 AM, Schranzer René wrote:


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 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 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.mgz and continued processing with -autorecon2 and
-autorecon3. In some subjects (at some timepoints), the recon-all
-autorecon2 -autorecon3 excited with errors, as mentioned below.
Now I have used the following command "recon-all -hires
-skullstrip -no-wsgcaatlas -s ${sbjID} -i ${sbj} -all" with the
skull-stripped data and it worked fine without errors. I also
compared the T1.mgz from both approaches and they looked identical.

My question, can I use this approach with the "-no-wsgcaatlas" for
all subjects or is there something to consider here?

Best, René



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Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1)

[Schranzer René]

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 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 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.mgz and continued processing 
with -autorecon2 and -autorecon3. In some subjects (at some timepoints), the 
recon-all -autorecon2 -autorecon3 excited with errors, as mentioned below. Now 
I have used the following command "recon-all -hires -skullstrip -no-wsgcaatlas 
-s ${sbjID} -i ${sbj} -all" with the skull-stripped data and it worked fine 
without errors. I also compared the T1.mgz from both approaches and they looked 
identical.
My question, can I use this approach with the "-no-wsgcaatlas" for all subjects 
or is there something to consider here?

Best, René



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Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1)

[Douglas N. Greve]

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. Therefore, I stopped after 
-autorecon1 and copied the T1.mgz to brainmask.mgz and 
brainmask.auto.mgz and continued processing with -autorecon2 and 
-autorecon3. In some subjects (at some timepoints), the recon-all 
-autorecon2 -autorecon3 excited with errors, as mentioned below. Now I 
have used the following command "recon-all -hires -skullstrip 
-no-wsgcaatlas -s ${sbjID} -i ${sbj} -all" with the skull-stripped 
data and it worked fine without errors. I also compared the T1.mgz 
from both approaches and they looked identical.


My question, can I use this approach with the "-no-wsgcaatlas" for all 
subjects or is there something to consider here?


Best, René


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Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1)

[Schranzer René]

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.mgz and continued processing 
with -autorecon2 and -autorecon3. In some subjects (at some timepoints), the 
recon-all -autorecon2 -autorecon3 excited with errors, as mentioned below. Now 
I have used the following command "recon-all -hires -skullstrip -no-wsgcaatlas 
-s ${sbjID} -i ${sbj} -all" with the skull-stripped data and it worked fine 
without errors. I also compared the T1.mgz from both approaches and they looked 
identical.
My question, can I use this approach with the "-no-wsgcaatlas" for all subjects 
or is there something to consider here?

Best, René
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