Re: [Freesurfer] recon-all errors (cannot execute binary file +

[김민지]

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do not wish to continue communication over unencrypted e-mail,

-Original Message-From:  "김민지" minjik0...@kaist.ac.krTo: 
"Freesurfer support list" freesurfer@nmr.mgh.harvard.edu; Cc:Sent:  
2024-01-17 (수) 13:01:17 (UTC+09:00)Subject: Re: [Freesurfer] recon-all errors 
(cannot execute binary file 
+External Email - Use 
Caution

do not wish to continue communication over unencrypted e-mail



-Original Message-From:  "윤혜정" hyejung7...@amc.seoul.krTo: 
"Freesurfer support list" freesurfer@nmr.mgh.harvard.edu; Cc:Sent:  
2024-01-17 (수) 10:49:56 (UTC+09:00)Subject: [Freesurfer] recon-all errors 
(cannot execute binary file 
+External Email - Use 
Caution

Good day.

When I run recon-all for my nii files I get either one of the following error 
messages:

1. ERROR: could not configure recon-all parameters Killed

2.ERROR: could not configure recon-all parameters
/Applications/freesurfer/bin/fspython: line 20: 
/Applications/freesurfer/python/bin/python3: cannot execute binary file
/Applications/freesurfer/bin/fspython: line 20: 
/Applications/freesurfer/python/bin/python3: Undefined error: 0

Or

3. a Pop Up message "_struct.cpython-38-darwin.so" cannot be opened because the 
developer cannot be verified.
mac OS cannot verify that this app is free from malware.

I googled the third error message and tried "Allow anyways" from the privacy 
setting. Then the next message pops up, then the next and the next.

Could you please help me to understand the cause of the above 3 error 
messages?
I tried to redownload freesurfer as well as python but none worked.

Thank you in advance.

Best,
Alice mailto:hyejung7...@amc.seoul.kr

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Re: [Freesurfer] recon-all errors (cannot execute binary file +

[김민지]

External Email - Use Caution

do not wish to continue communication over unencrypted e-mail



-Original Message-From:  "윤혜정" hyejung7...@amc.seoul.krTo: 
"Freesurfer support list" freesurfer@nmr.mgh.harvard.edu; Cc:Sent:  
2024-01-17 (수) 10:49:56 (UTC+09:00)Subject: [Freesurfer] recon-all errors 
(cannot execute binary file 
+External Email - Use 
Caution

Good day.

When I run recon-all for my nii files I get either one of the following error 
messages:

1. ERROR: could not configure recon-all parameters Killed

2.ERROR: could not configure recon-all parameters
/Applications/freesurfer/bin/fspython: line 20: 
/Applications/freesurfer/python/bin/python3: cannot execute binary file
/Applications/freesurfer/bin/fspython: line 20: 
/Applications/freesurfer/python/bin/python3: Undefined error: 0

Or

3. a Pop Up message "_struct.cpython-38-darwin.so" cannot be opened because the 
developer cannot be verified.
mac OS cannot verify that this app is free from malware.

I googled the third error message and tried "Allow anyways" from the privacy 
setting. Then the next message pops up, then the next and the next.

Could you please help me to understand the cause of the above 3 error 
messages?
I tried to redownload freesurfer as well as python but none worked.

Thank you in advance.

Best,
Alice mailto:hyejung7...@amc.seoul.kr

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Re: [Freesurfer] recon-all errors (cannot execute binary file +

[fsbuild]

External Email - Use Caution

It looks like you did not use the .pkg file installer to install Freesurfer on 
the Mac, otherwise you would have a path like /Applications/freesurfer/7.4.1 to 
use as FREESURFER_HOME. The installer should ensure the privileges should 
be correct to run commands.  There are several 7.X freesurfer releases, 
but the latest release is 7.4.1 and you can download it via the link, e.g.,
https://secure-web.cisco.com/1bTTDiznaFEJgJPDoi2yskrFqRdt_lNsr8LZ0PFjdBlc19JuHE6WaWHssFDdzwRLVMRUHA3qj7h4ea64BhZk97t2IniNpnSEBUfevruwnZRT-WXrHBzlmbnxwfB-eUVqRKZYuKEwgZupdFOKnrwiz0xxPKw5DTxfL31t8mtljoZBWCtHjo8uXtSylGlGyZRzw2b6Kjz5JBf1zzrJTR_GSBoP7UPjKW3-cqENylh36UvAaYHpdFnPoZ4CrWPzQwkw7vmD7cmQcG6jBsy_w7nUkvkrhCZTYVfLg5BUluX8L0H85LGn_CikykHFVbAsE-L8Zih6Q9g6D25IvisceU2Rl_g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-macOS-darwin_x86_64-7.4.1.pkg
I would first remove what you have on your system from the terminal window with,
$ sudo rm -rf /Applications/freesurfer
Then in a Finder Window navigate to the Downloads folder (or to wherever you 
downloaded freesurfer-macOS-darwin_x86_64-7.4.1..pkg). You should be able 
to RIGHT CLICK on that file, select open with the default pkg installer, and 
then enter your password etc. to install it. Right clicking should bypass 
having to do some of the security exemptions in system preferences.
Once the install is complete, setup the Freesurfer environment in the terminal 
window,
$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh 
freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME/Applications/freesurfer/7.4.1
FSFAST_HOME  /Applications/freesurfer/7.4.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/7.4.1/subjects
MNI_DIR
/Applications/freesurfer/7.4.1/mni
You also need a license file, license.txt. Once you complete the license 
request form 
athttps://secure-web.cisco.com/1Svw39fuKLV2rL8mAOfpPDMZrLLodE_ScR0sKC5od9QRlt9jwKuDUSQ6WtLlT9V17W1wUaBdznmlv7nMRbyPA6LYSYXyCAnP8F-Tuz_VE6STeVAxkh40QhJ8_Hz3w6xgC49SELup9uGscJnea_a5_YfPe4v_s5sGckdUErRUBLgOMN41ow4CikTKbC-IfUIre0ikhv0rLYF0iFjK9EZGFCuzHN7-z5cvA1mPBIjRTyGJsmV-behjR7Zpaho6a5uOuq1I4CB61WxtecgERQIEuY6PCEpMSMO1vfX-v7GEXY61w_SZ_5yg0kRQoolU2kwNaTPReDO7q7kH9B3AAFtRMPQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html%26nbsp;you
 will receive a file “licesne..txt” via the email address used in the form. 
 Download/copy the license.txt file to your machine from the email.
If your home directory is for example /Users/hyejung then you will see the 
following in the terminal window,
$ cd$ pwd/Users/hyejung$ echo $HOME/Users/hyejung
… if you downloaded license.txt into your Download folder ...
$ cd Downloads$ ls license.txtlicense.txt$ cp -p -f license.txt 
$HOME/.$ cd $HOME$ ls license.txtlicense.txt
You could also use the Finder to navigate and drag/drop the license.txt into 
your home directory. Once it it there, set the environment variable 
FS_LICENSE so freesurfer commands will find the license when they run,
$ export FS_LICENSE=$HOME/license.txt
Then it should work to run freesurfer commands from the terminal window 
including freeview.
- R.

On Jan 16, 2024, at 20:47, 윤혜정 hyejung7...@amc.seoul.kr 
wrote:External Email - Use 
CautionGood day.When I run 
recon-all for my nii files I get either one of the following error 
messages:1.ERROR: could not configure recon-all parameters 
Killed2.ERROR: could not configure recon-all 
parameters/Applications/freesurfer/bin/fspython: line 20: 
/Applications/freesurfer/python/bin/python3: cannot execute binary 
file/Applications/freesurfer/bin/fspython: line 20: 
/Applications/freesurfer/python/bin/python3: Undefined error: 0Or3. a Pop 
Up message"_struct.cpython-38-darwin.so" cannot be opened because the 
developer cannot be verified.mac OS cannot verify that this app is free 
from malware.I googled the third error message and tried"Allow 
anyways"from the privacy setting.Then the next message pops up, 
then the next and the next.Could you please help me to understand the 
cause of the above 3 error messages?I tried to redownload freesurfer as 
well as python but none worked.Thank you in 
advance.Best,Alice___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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this message immediately.  Continuing to send or respond to e-mail after 
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continue to 

Re: [Freesurfer] recon-all errors after mri_pretess

[Douglas N. Greve]

The log might not be capturing all the standard error output. Run this 
and send the output.log

recon-all -debug -s neo289e -segmentation -fill |& tee output.log


On 3/11/2022 3:19 PM, Alexopoulos, Dimitrios wrote:


External Email - Use Caution

Yes it fails every time at the same spot.  The log is attached.

Jim

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Douglas N. Greve

*Sent:* Wednesday, March 09, 2022 12:24 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] recon-all errors after mri_pretess

** External Email - Caution **

Does this fail every time like this? It looks like it just abruptly 
stopped. Does anything print out to standard error?


On 3/4/2022 11:18 AM, Alexopoulos, Dimitrios wrote:

*External Email - Use Caution *

Hi, we’re running FS 7.2 ‘recon-all -all’ on a subject and are
getting errors on our cluster (CentOS 8)

The attached recon-all.log file is attached for details. The last
several lines of the file are below. Any comments as to why its
failing? Jim.

pass   1 (--):   0 found -   0 modified |    TOTAL:   0

pass   1 (-+):   0 found -   0 modified |    TOTAL:   0

Total Number of Modified Voxels = 631 (out of 421942: 0.149547)

binarizing input wm segmentation...

Ambiguous edge configurations...

mri_pretess done

@#@FSTIME  2022:03:03:12:51:58 mri_pretess N 4 e 3.84 S 0.01 U
3.70 P 96% M 56636 F 1 R 2214 W 0 c 330 w 325 I 8801 O 646 L 3.37
3.47 3.45

@#@FSLOADPOST 2022:03:03:12:52:02 mri_pretess N 4 3.37 3.47 3.45

#

#@# Fill Thu Mar  3 12:52:02 CST 2022



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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] recon-all errors after mri_pretess

[Douglas N. Greve]

Does this fail every time like this? It looks like it just abruptly 
stopped. Does anything print out to standard error?


On 3/4/2022 11:18 AM, Alexopoulos, Dimitrios wrote:


External Email - Use Caution

Hi, we’re running FS 7.2 ‘recon-all -all’ on a subject and are getting 
errors on our cluster (CentOS 8)


The attached recon-all.log file is attached for details. The last 
several lines of the file are below. Any comments as to why its 
failing? Jim.


pass   1 (--):   0 found -   0 modified |    TOTAL:   0

pass   1 (-+):   0 found -   0 modified |    TOTAL:   0

Total Number of Modified Voxels = 631 (out of 421942: 0.149547)

binarizing input wm segmentation...

Ambiguous edge configurations...

mri_pretess done

@#@FSTIME  2022:03:03:12:51:58 mri_pretess N 4 e 3.84 S 0.01 U 3.70 P 
96% M 56636 F 1 R 2214 W 0 c 330 w 325 I 8801 O 646 L 3.37 3.47 3.45


@#@FSLOADPOST 2022:03:03:12:52:02 mri_pretess N 4 3.37 3.47 3.45

#

#@# Fill Thu Mar  3 12:52:02 CST 2022



The materials in this message are private and may contain Protected 
Healthcare Information or other information of a sensitive nature. If 
you are not the intended recipient, be advised that any unauthorized 
use, disclosure, copying or the taking of any action in reliance on 
the contents of this information is strictly prohibited. If you have 
received this email in error, please immediately notify the sender via 
telephone or return mail.



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 .
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Re: [Freesurfer] recon-all errors

[Mark Wagshul]

External Email - Use Caution

Doug,

Following up on this. Where can I upload the data for you to take a look? 
Thanks,

Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wags...@einsteinmed.org<mailto:mark.wags...@einsteinmed.org>

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This email message and any accompanying attachments may contain privileged 
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the sender at the email address above, delete this email from your computer, 
and destroy any copies in any form immediately.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Tuesday, June 1, 2021 6:02 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all errors

OK, I'll have to take a look at the data. Someone will be in touch about 
getting it.

On 6/1/2021 11:02 AM, Mark Wagshul wrote:

External Email - Use Caution

External Email - Use Caution
It works fine in 6.0, was in 7.1. The registration looks fine (the FLAIR is 
brain extracted, while the orig.mgz is not, is this expected, or was that my 
error, I don't recall which FLAIR image I fed in).

Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wags...@einsteinmed.org<mailto:mark.wags...@einsteinmed.org>

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This email message and any accompanying attachments may contain privileged 
information intended only for the named recipient(s). If you are not the 
intended recipient(s), you are hereby notified that the dissemination, 
distribution, and or copying of this message is strictly prohibited. If you 
receive this message in error, or are not the named recipient(s), please notify 
the sender at the email address above, delete this email from your computer, 
and destroy any copies in any form immediately.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 On Behalf Of Douglas N. Greve
Sent: Thursday, May 27, 2021 6:13 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all errors

Can you check the registration of the FLAIR and T1?
cd subject/mri
 tkregisterfv --mov orig/FLAIRraw.mgz --reg transforms/FLAIRraw.lta --targ 
orig.mgz



On 5/20/2021 4:33 PM, Mark Wagshul wrote:

External Email - Use Caution

External Email - Use Caution
Hi. I'm trying to run recon-all, with T1 and FLAIR images and running into 
errors, which seem to be associated with the FLAIR refinement of the pial 
surface.

recon-all -s 2019-10049-045-SP -FLAIR 
2019-10049-045-SP/VISIT_1/RAW/105_3D_FLAIR_SAGBrain.nii.gz -FLAIRpial -all


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

2.   cat /proc/version:  Linux version 2.6.32-696.6.3.el6.694g.x86_64 
(root@-home-lgu-olaf-RHEL-6ES-9-x86_64.larkspur<mailto:root@-home-lgu-olaf-RHEL-6ES-9-x86_64.larkspur>)
 (gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC) ) #1 SMP Wed Jul 12 
02:19:57 UTC 2017

3.   uname -a: Linux loginnode2 2.6.32-696.6.3.el6.694g.x86_64 #1 SMP 
Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

4.   recon-all.log attached

Thanks!

Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wags...@einsteinmed.org<mailto:mark.wags...@einsteinmed.org>

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Re: [Freesurfer] recon-all errors

[Mark Wagshul]

External Email - Use Caution

Doug,

Thanks. The one thing I thought of - the FLAIR data were hi-res 3D FLAIR which 
have a pretty long T2 and not great grey/white contrast (it's an MS project, so 
mostly acquired for quantifying lesion load). Not sure if this would affect the 
calculations. I tried playing around with the T2_min/max_inside/outside 
parameter going into mris_place_surface, but that didn't seem to help.
One more thing. I don't see this in the recon-all.log file, but when I try to 
individually run mris_place_surface, it quits with a segmentation fault. Not 
sure if that helps, or why this error wouldn't show up in the log file.

Thanks for the help!

Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wags...@einsteinmed.org<mailto:mark.wags...@einsteinmed.org>

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This email message and any accompanying attachments may contain privileged 
information intended only for the named recipient(s). If you are not the 
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the sender at the email address above, delete this email from your computer, 
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From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Tuesday, June 1, 2021 6:02 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all errors

OK, I'll have to take a look at the data. Someone will be in touch about 
getting it.

On 6/1/2021 11:02 AM, Mark Wagshul wrote:

External Email - Use Caution

External Email - Use Caution
It works fine in 6.0, was in 7.1. The registration looks fine (the FLAIR is 
brain extracted, while the orig.mgz is not, is this expected, or was that my 
error, I don't recall which FLAIR image I fed in).

Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wags...@einsteinmed.org<mailto:mark.wags...@einsteinmed.org>

[einstein-logo-rgb]
This email message and any accompanying attachments may contain privileged 
information intended only for the named recipient(s). If you are not the 
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distribution, and or copying of this message is strictly prohibited. If you 
receive this message in error, or are not the named recipient(s), please notify 
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From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 On Behalf Of Douglas N. Greve
Sent: Thursday, May 27, 2021 6:13 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all errors

Can you check the registration of the FLAIR and T1?
cd subject/mri
 tkregisterfv --mov orig/FLAIRraw.mgz --reg transforms/FLAIRraw.lta --targ 
orig.mgz



On 5/20/2021 4:33 PM, Mark Wagshul wrote:

External Email - Use Caution

External Email - Use Caution
Hi. I'm trying to run recon-all, with T1 and FLAIR images and running into 
errors, which seem to be associated with the FLAIR refinement of the pial 
surface.

recon-all -s 2019-10049-045-SP -FLAIR 
2019-10049-045-SP/VISIT_1/RAW/105_3D_FLAIR_SAGBrain.nii.gz -FLAIRpial -all


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

2.   cat /proc/version:  Linux version 2.6.32-696.6.3.el6.694g.x86_64 
(root@-home-lgu-olaf-RHEL-6ES-9-x86_64.larkspur<mailto:root@-home-lgu-olaf-RHEL-6ES-9-x86_64.larkspur>)
 (gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC) ) #1 SMP Wed Jul 12 
02:19:57 UTC 2017

3.   uname -a: Linux loginnode2 2.6.32-696.6.3.el6.694g.x86_64 #1 SMP 
Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

4.   recon-all.log attached

Thanks!

Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wags...@einsteinmed.org<mailto:mark.wags...@einsteinmed.org>

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This email message and any accompanying attachments may contain privileged 
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Re: [Freesurfer] recon-all errors

[Douglas N. Greve]

OK, I'll have to take a look at the data. Someone will be in touch about 
getting it.



On 6/1/2021 11:02 AM, Mark Wagshul wrote:


External Email - Use Caution

External Email - Use Caution

It works fine in 6.0, was in 7.1. The registration looks fine (the 
FLAIR is brain extracted, while the orig.mgz is not, is this expected, 
or was that my error, I don’t recall which FLAIR image I fed in).


Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011

FAX: 718-430-3399

Email:_mark.wags...@einsteinmed.org <mailto:mark.wags...@einsteinmed.org>_

einstein-logo-rgb

This email message and any accompanying attachments may contain 
privileged information intended only for the named recipient(s). If 
you are not the intended recipient(s), you are hereby notified that 
the dissemination, distribution, and or copying of this message is 
strictly prohibited. If you receive this message in error, or are not 
the named recipient(s), please notify the sender at the email address 
above, delete this email from your computer, and destroy any copies in 
any form immediately.


*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Douglas N. Greve

*Sent:* Thursday, May 27, 2021 6:13 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] recon-all errors

Can you check the registration of the FLAIR and T1?
cd subject/mri
 tkregisterfv --mov orig/FLAIRraw.mgz --reg transforms/FLAIRraw.lta 
--targ orig.mgz



On 5/20/2021 4:33 PM, Mark Wagshul wrote:

*External Email - Use Caution *

*External Email - Use Caution *

Hi. I’m trying to run recon-all, with T1 and FLAIR images and
running into errors, which seem to be associated with the FLAIR
refinement of the pial surface.

recon-all -s 2019-10049-045-SP –FLAIR
2019-10049-045-SP/VISIT_1/RAW/105_3D_FLAIR_SAGBrain.nii.gz
-FLAIRpial -all

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

2.cat /proc/version:  Linux version
2.6.32-696.6.3.el6.694g.x86_64
(root@-home-lgu-olaf-RHEL-6ES-9-x86_64.larkspur
<mailto:root@-home-lgu-olaf-RHEL-6ES-9-x86_64.larkspur>) (gcc
version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC) ) #1 SMP Wed Jul
12 02:19:57 UTC 2017

3.uname –a: Linux loginnode2 2.6.32-696.6.3.el6.694g.x86_64 #1
SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

4.recon-all.log attached

Thanks!

Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011

FAX: 718-430-3399

Email:_mark.wags...@einsteinmed.org
<mailto:mark.wags...@einsteinmed.org>_

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Re: [Freesurfer] recon-all errors

[Mark Wagshul]

External Email - Use Caution

It works fine in 6.0, was in 7.1. The registration looks fine (the FLAIR is 
brain extracted, while the orig.mgz is not, is this expected, or was that my 
error, I don't recall which FLAIR image I fed in).

Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wags...@einsteinmed.org<mailto:mark.wags...@einsteinmed.org>

[einstein-logo-rgb]
This email message and any accompanying attachments may contain privileged 
information intended only for the named recipient(s). If you are not the 
intended recipient(s), you are hereby notified that the dissemination, 
distribution, and or copying of this message is strictly prohibited. If you 
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the sender at the email address above, delete this email from your computer, 
and destroy any copies in any form immediately.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Thursday, May 27, 2021 6:13 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all errors

Can you check the registration of the FLAIR and T1?
cd subject/mri
 tkregisterfv --mov orig/FLAIRraw.mgz --reg transforms/FLAIRraw.lta --targ 
orig.mgz


On 5/20/2021 4:33 PM, Mark Wagshul wrote:

External Email - Use Caution

External Email - Use Caution
Hi. I'm trying to run recon-all, with T1 and FLAIR images and running into 
errors, which seem to be associated with the FLAIR refinement of the pial 
surface.

recon-all -s 2019-10049-045-SP -FLAIR 
2019-10049-045-SP/VISIT_1/RAW/105_3D_FLAIR_SAGBrain.nii.gz -FLAIRpial -all


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

2.   cat /proc/version:  Linux version 2.6.32-696.6.3.el6.694g.x86_64 
(root@-home-lgu-olaf-RHEL-6ES-9-x86_64.larkspur<mailto:root@-home-lgu-olaf-RHEL-6ES-9-x86_64.larkspur>)
 (gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC) ) #1 SMP Wed Jul 12 
02:19:57 UTC 2017

3.   uname -a: Linux loginnode2 2.6.32-696.6.3.el6.694g.x86_64 #1 SMP 
Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

4.   recon-all.log attached

Thanks!

Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wags...@einsteinmed.org<mailto:mark.wags...@einsteinmed.org>

[einstein-logo-rgb]
This email message and any accompanying attachments may contain privileged 
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distribution, and or copying of this message is strictly prohibited. If you 
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Re: [Freesurfer] recon-all errors

[Mark Wagshul]

External Email - Use Caution

Thanks. I've never used this command before to register the FLAIR, but I'm 
getting the following error:

[mwagshul@loginnode2 mri]$ tkregisterfv --mov orig/FLAIRraw.mgz --reg 
transforms/FLAIRraw.lta --targ orig.mgz
cd 
/gs/gsfs0/users/mrrc-all/PROJECTS/HOLTZER/MSAGING/MS_PROCESSING/2019-10049-044/mri
freeview -transform-volume -viewport cor -v 
orig.mgz:visible=1:name=orig.mgz(targ) 
/gs/gsfs0/users/mrrc-all/PROJECTS/HOLTZER/MSAGING/MS_PROCESSING/2019-10049-044/mri/orig/FLAIRraw.mgz:name=FLAIRraw.mgz(mov):reg=/gs/gsfs0/users/mrrc-all/PROJECTS/HOLTZER/MSAGING/MS_PROCESSING/2019-10049-044/mri/transforms/FLAIRraw.lta
/public/apps/freesurfer/7.1.0/bin/fsvglrun: line 20: conditional binary 
operator expected
/public/apps/freesurfer/7.1.0/bin/fsvglrun: line 20: syntax error near 
`FS_ALLOW_VGLRUN'
/public/apps/freesurfer/7.1.0/bin/fsvglrun: line 20: `if [[ ! -v 
FS_ALLOW_VGLRUN ]]; then'
[mwagshul@loginnode2 mri]$

Thanks for any advice on the issue here.

Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wags...@einsteinmed.org<mailto:mark.wags...@einsteinmed.org>

[einstein-logo-rgb]
This email message and any accompanying attachments may contain privileged 
information intended only for the named recipient(s). If you are not the 
intended recipient(s), you are hereby notified that the dissemination, 
distribution, and or copying of this message is strictly prohibited. If you 
receive this message in error, or are not the named recipient(s), please notify 
the sender at the email address above, delete this email from your computer, 
and destroy any copies in any form immediately.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Thursday, May 27, 2021 6:13 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all errors

Can you check the registration of the FLAIR and T1?
cd subject/mri
 tkregisterfv --mov orig/FLAIRraw.mgz --reg transforms/FLAIRraw.lta --targ 
orig.mgz


On 5/20/2021 4:33 PM, Mark Wagshul wrote:

External Email - Use Caution

External Email - Use Caution
Hi. I'm trying to run recon-all, with T1 and FLAIR images and running into 
errors, which seem to be associated with the FLAIR refinement of the pial 
surface.

recon-all -s 2019-10049-045-SP -FLAIR 
2019-10049-045-SP/VISIT_1/RAW/105_3D_FLAIR_SAGBrain.nii.gz -FLAIRpial -all


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

2.   cat /proc/version:  Linux version 2.6.32-696.6.3.el6.694g.x86_64 
(root@-home-lgu-olaf-RHEL-6ES-9-x86_64.larkspur<mailto:root@-home-lgu-olaf-RHEL-6ES-9-x86_64.larkspur>)
 (gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC) ) #1 SMP Wed Jul 12 
02:19:57 UTC 2017

3.   uname -a: Linux loginnode2 2.6.32-696.6.3.el6.694g.x86_64 #1 SMP 
Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

4.   recon-all.log attached

Thanks!

Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wags...@einsteinmed.org<mailto:mark.wags...@einsteinmed.org>

[einstein-logo-rgb]
This email message and any accompanying attachments may contain privileged 
information intended only for the named recipient(s). If you are not the 
intended recipient(s), you are hereby notified that the dissemination, 
distribution, and or copying of this message is strictly prohibited. If you 
receive this message in error, or are not the named recipient(s), please notify 
the sender at the email address above, delete this email from your computer, 
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Re: [Freesurfer] recon-all errors

[Douglas N. Greve]

Can you check the registration of the FLAIR and T1?
cd subject/mri
 tkregisterfv --mov orig/FLAIRraw.mgz --reg transforms/FLAIRraw.lta 
--targ orig.mgz




On 5/20/2021 4:33 PM, Mark Wagshul wrote:


External Email - Use Caution

External Email - Use Caution

Hi. I’m trying to run recon-all, with T1 and FLAIR images and running 
into errors, which seem to be associated with the FLAIR refinement of 
the pial surface.


recon-all -s 2019-10049-045-SP –FLAIR 
2019-10049-045-SP/VISIT_1/RAW/105_3D_FLAIR_SAGBrain.nii.gz -FLAIRpial 
-all


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


2)cat /proc/version:  Linux version 2.6.32-696.6.3.el6.694g.x86_64 
(root@-home-lgu-olaf-RHEL-6ES-9-x86_64.larkspur) (gcc version 4.4.7 
20120313 (Red Hat 4.4.7-18) (GCC) ) #1 SMP Wed Jul 12 02:19:57 UTC 2017


3)uname –a: Linux loginnode2 2.6.32-696.6.3.el6.694g.x86_64 #1 SMP 
Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux


4)recon-all.log attached

Thanks!

Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011

FAX: 718-430-3399

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Re: [Freesurfer] recon-all errors - mri_segstats and mri_relabel_hypointensities

[Bruce Fischl]

glad to hear it
Bruce
On Fri, 31 Jan 2020, Laurel Quinlan wrote:



External Email - Use Caution

Hi Bruce,

Thank you for your help! I removed the IsRunning.lh+rh script as well and
reran the recon. Everything seems to have worked!

-Laurel


From: freesurfer-boun...@nmr.mgh.harvard.edu
 on behalf of Bruce Fischl

Sent: Tuesday, January 28, 2020 3:37 PM
To: Freesurfer support list 
Cc: Greve, Douglas N.,Ph.D. 
Subject: Re: [Freesurfer] recon-all errors - mri_segstats and
mri_relabel_hypointensities  
Hi Laurel

if a subject dir already exists recon-all will exit unless you specify
-force. Alternatively you can try using the -make all flag, which should
rerun only the steps that are needed (assuming the reboot didn't happen
e.g. in the middle of writing a file)

cheers
Bruce
On Tue, 28 Jan 2020, Laurel Quinlan
wrote:

>
> External Email - Use Caution
>
> Hi Doug,
>
> Thanks for looking over that file. It is the correct recon-all file for
one
> of the problem brains. I discovered that there was a system reboot of some
> sort when the recon-all was processing for these problem brains, so that
is
> likely what caused the process to stop. How can I restart the recon-all
> process for these brains? I have tried just rerunning the recon-all
command
> but the process exits within a few moments each time. I am wondering if
> there is something I need to delete that was partially processed during
the
> first attempt.
>
> Thanks,
>
> Laurel 
>
>___
_
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Greve, Douglas
> N.,Ph.D. 
> Sent: Friday, January 24, 2020 9:34 AM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: [Freesurfer] recon-all errors - mri_segstats and
> mri_relabel_hypointensities  
> It did not look like there was an explicit error in that log file, it just
> stops at mris_volmask. Is that the right recon-all? Also, please just send
> the text file so that we don't have to unzip it.
>
> On 1/22/2020 4:39 PM, Laurel Quinlan wrote:
>
>   External Email - Use Caution
>
> Hi FS Support,
>
> I have two brains for which recon-all exited with errors after I
> edited the wm.mgz volume. It seems that the problem occurs during the
> mri_segstats and mri_relabel_hypointensities steps (if I'm reading the
> output of the command "tail scripts/recon-all.log" correctly). I
> attached one of the recon-all.log files as a zipped txt file. Please
> let me know if you have troubleshooting suggestions.
>
> Thank you for your help!  
>
> Laurel Quinlan
> Research Specialist
> Center for Healthy Minds
> University of Wisconsin-Madison
>
>
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>
>
>

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Re: [Freesurfer] recon-all errors - mri_segstats and mri_relabel_hypointensities

[Laurel Quinlan]

External Email - Use Caution

Hi Bruce,

Thank you for your help! I removed the IsRunning.lh+rh script as well and reran 
the recon. Everything seems to have worked!

-Laurel

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Tuesday, January 28, 2020 3:37 PM
To: Freesurfer support list 
Cc: Greve, Douglas N.,Ph.D. 
Subject: Re: [Freesurfer] recon-all errors - mri_segstats and 
mri_relabel_hypointensities

Hi Laurel

if a subject dir already exists recon-all will exit unless you specify
-force. Alternatively you can try using the -make all flag, which should
rerun only the steps that are needed (assuming the reboot didn't happen
e.g. in the middle of writing a file)

cheers
Bruce
On Tue, 28 Jan 2020, Laurel Quinlan
wrote:

>
> External Email - Use Caution
>
> Hi Doug,
>
> Thanks for looking over that file. It is the correct recon-all file for one
> of the problem brains. I discovered that there was a system reboot of some
> sort when the recon-all was processing for these problem brains, so that is
> likely what caused the process to stop. How can I restart the recon-all
> process for these brains? I have tried just rerunning the recon-all command
> but the process exits within a few moments each time. I am wondering if
> there is something I need to delete that was partially processed during the
> first attempt.
>
> Thanks,
>
> Laurel
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Greve, Douglas
> N.,Ph.D. 
> Sent: Friday, January 24, 2020 9:34 AM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: [Freesurfer] recon-all errors - mri_segstats and
> mri_relabel_hypointensities
> It did not look like there was an explicit error in that log file, it just
> stops at mris_volmask. Is that the right recon-all? Also, please just send
> the text file so that we don't have to unzip it.
>
> On 1/22/2020 4:39 PM, Laurel Quinlan wrote:
>
>   External Email - Use Caution
>
> Hi FS Support,
>
> I have two brains for which recon-all exited with errors after I
> edited the wm.mgz volume. It seems that the problem occurs during the
> mri_segstats and mri_relabel_hypointensities steps (if I'm reading the
> output of the command "tail scripts/recon-all.log" correctly). I
> attached one of the recon-all.log files as a zipped txt file. Please
> let me know if you have troubleshooting suggestions.
>
> Thank you for your help!
>
> Laurel Quinlan
> Research Specialist
> Center for Healthy Minds
> University of Wisconsin-Madison
>
>
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>
>
>
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Re: [Freesurfer] recon-all errors - mri_segstats and mri_relabel_hypointensities

[Bruce Fischl]

Hi Laurel

if a subject dir already exists recon-all will exit unless you specify 
-force. Alternatively you can try using the -make all flag, which should 
rerun only the steps that are needed (assuming the reboot didn't happen 
e.g. in the middle of writing a file)


cheers
Bruce
On Tue, 28 Jan 2020, Laurel Quinlan 
wrote:




External Email - Use Caution

Hi Doug,

Thanks for looking over that file. It is the correct recon-all file for one
of the problem brains. I discovered that there was a system reboot of some
sort when the recon-all was processing for these problem brains, so that is
likely what caused the process to stop. How can I restart the recon-all
process for these brains? I have tried just rerunning the recon-all command
but the process exits within a few moments each time. I am wondering if
there is something I need to delete that was partially processed during the
first attempt.

Thanks,

Laurel 


From: freesurfer-boun...@nmr.mgh.harvard.edu
 on behalf of Greve, Douglas
N.,Ph.D. 
Sent: Friday, January 24, 2020 9:34 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] recon-all errors - mri_segstats and
mri_relabel_hypointensities  
It did not look like there was an explicit error in that log file, it just
stops at mris_volmask. Is that the right recon-all? Also, please just send
the text file so that we don't have to unzip it.

On 1/22/2020 4:39 PM, Laurel Quinlan wrote:

  External Email - Use Caution

Hi FS Support,

I have two brains for which recon-all exited with errors after I
edited the wm.mgz volume. It seems that the problem occurs during the
mri_segstats and mri_relabel_hypointensities steps (if I'm reading the
output of the command "tail scripts/recon-all.log" correctly). I
attached one of the recon-all.log files as a zipped txt file. Please
let me know if you have troubleshooting suggestions.

Thank you for your help!  

Laurel Quinlan
Research Specialist
Center for Healthy Minds
University of Wisconsin-Madison


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Re: [Freesurfer] recon-all errors - mri_segstats and mri_relabel_hypointensities

[Laurel Quinlan]

External Email - Use Caution

Hi Doug,

Thanks for looking over that file. It is the correct recon-all file for one of 
the problem brains. I discovered that there was a system reboot of some sort 
when the recon-all was processing for these problem brains, so that is likely 
what caused the process to stop. How can I restart the recon-all process for 
these brains? I have tried just rerunning the recon-all command but the process 
exits within a few moments each time. I am wondering if there is something I 
need to delete that was partially processed during the first attempt.

Thanks,

Laurel

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Greve, Douglas N.,Ph.D. 

Sent: Friday, January 24, 2020 9:34 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] recon-all errors - mri_segstats and 
mri_relabel_hypointensities

It did not look like there was an explicit error in that log file, it just 
stops at mris_volmask. Is that the right recon-all? Also, please just send the 
text file so that we don't have to unzip it.

On 1/22/2020 4:39 PM, Laurel Quinlan wrote:

External Email - Use Caution

Hi FS Support,

I have two brains for which recon-all exited with errors after I edited the 
wm.mgz volume. It seems that the problem occurs during the mri_segstats and 
mri_relabel_hypointensities steps (if I'm reading the output of the command 
"tail scripts/recon-all.log" correctly). I attached one of the recon-all.log 
files as a zipped txt file. Please let me know if you have troubleshooting 
suggestions.

Thank you for your help!

Laurel Quinlan
Research Specialist
Center for Healthy Minds
University of Wisconsin-Madison




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Re: [Freesurfer] recon-all errors - mri_segstats and mri_relabel_hypointensities

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

It did not look like there was an explicit error in that log file, it just 
stops at mris_volmask. Is that the right recon-all? Also, please just send the 
text file so that we don't have to unzip it.

On 1/22/2020 4:39 PM, Laurel Quinlan wrote:

External Email - Use Caution

Hi FS Support,

I have two brains for which recon-all exited with errors after I edited the 
wm.mgz volume. It seems that the problem occurs during the mri_segstats and 
mri_relabel_hypointensities steps (if I'm reading the output of the command 
"tail scripts/recon-all.log" correctly). I attached one of the recon-all.log 
files as a zipped txt file. Please let me know if you have troubleshooting 
suggestions.

Thank you for your help!

Laurel Quinlan
Research Specialist
Center for Healthy Minds
University of Wisconsin-Madison




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Re: [Freesurfer] recon -all errors

[Jasmin Alves]

Hi Bruce,

 Could you elaborate on what you mean I need to specify the input volume?

Thanks,
Jasmin

On Wed, Jan 27, 2016 at 5:48 AM, Bruce Fischl 
wrote:

> Hi Jasmin
>
> if this is the first time you have run this subject (that is, the subject
> dir doesn't exist within $SUBJECTS_DIR), you still need to specify the
> input volume with -i  T1_original_joya.nii
>
> cheers
> Bruce
>
>
> On Tue, 26 Jan 2016, Jasmin Alves wrote:
>
> Bruce,
>> Sorry to be a pain, but for some reason, I cannot still get recon-all to
>> work.
>>
>> Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ recon-all -sd
>> /Desktop/Brain_Child_subs -i T1_original_joya.nii -subject joya -all &
>>
>> [1] 14655
>>
>> Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ ERROR: SUBJECTS_DIR
>> /Desktop/Brain_Child_subs does not exist.
>>
>> Thanks,
>>
>> Jasmin
>>
>>
>> On Tue, Jan 26, 2016 at 6:19 AM, Bruce Fischl > >
>> wrote:
>>   Hi Jasmin
>>
>>   you need a '-' sign first. It should be:
>>
>>   recon-all -sd /Desktop/Brain_Child_subs -i T1_original_joya.nii
>>   -subject \
>>   joya -all &
>>
>>   cheers
>>   Bruce
>>
>>   On Mon, 25 Jan 2016, Jasmin Alves wrote:
>>
>> Hi Bruce,
>> Thanks for the reply, I attempted to direct
>> Subjects_dir to the folder with
>> my data but I received the following error.
>>
>> Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$
>> export
>> SUBJECTS_DIR=/Desktop/Brain_Child_subs
>>
>> Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$
>> recon-all -sd
>> /Desktop/Brain_Child_subs -i T1_original_joya.nii
>> -subject joya all &
>>
>> [1] 13867
>>
>> Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$
>> ERROR: Flag all
>> unrecognized.
>>
>> -sd /Desktop/Brain_Child_subs -i
>> T1_original_joya.nii -subject joya all
>>
>> Darwin Jasmins-MacBook-Pro.local 14.5.0 Darwin
>> Kernel Version 14.5.0: Tue
>> Sep  1 21:23:09 PDT 2015;
>> root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64
>>
>> recon-all -s joya exited with ERRORS at Mon Jan 25
>> 21:12:58 PST 2016
>>
>> Thanks so much,
>>
>> Jasmin
>>
>>
>> On Mon, Jan 25, 2016 at 6:33 AM, Bruce Fischl
>> 
>> wrote:
>>   Hi Jasmin
>>
>>   you  need to create a directory where you have
>> write permission
>>   and room for the subject reconstruction to be
>> written to, then
>>   set the SUBJECTS_DIR environment variable to
>> point to it. At the
>>   moment you are trying to use the subject
>> directory we
>>   distribute, which is in some system (and
>> read-only) location.
>>   You can do this on the command line of
>> recon-all via:
>>
>>   recon-all -sd  ...
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Sun, 24 Jan 2016, Jasmin Alves wrote:
>>
>>   Hello Freesurfer,
>>
>>   I am trying to learn freesurfer and ran into
>> the following
>>   issues below
>>   running the recon -all command.
>>
>>   FREESURFER_HOME: /Applications/freesurfer
>>
>>   Build stamp:
>> freesurfer-Darwin-lion-stable-pub-v5.3.0
>>
>>   Kernel info: Darwin 14.5.0 x86_64
>>
>> 1)
>>
>>   joya
>>
>>2)
>>
>>Jasmins-MacBook-Pro:subjects jasminalves$
>> recon-all -i
>>   T1_original_joya.nii
>>   -subject joya -all &
>>
>>
>>   3)
>>
>>   [1] 12300
>>
>>   Jasmins-MacBook-Pro:subjects jasminalves$
>> mkdir:
>>   /Applications/freesurfer/subjects/joya:
>> Permission denied
>>
>>   mkdir:
>> /Applications/freesurfer/subjects/joya/scripts:
>>   Permission denied
>>
>>   mkdir:
>> /Applications/freesurfer/subjects/joya/scripts:
>>   Permission denied
>>
>>   cp:
>>
>>
>> /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt:
>>   No such
>>   file or directory
>>
>>   cat:
>>
>>
>> /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt:
>>   No such
>>   file or directory
>>
>>   INFO: FreeSurfer build stamps do not match
>>
>>   Subject Stamp:
>>
>>   

Re: [Freesurfer] recon -all errors

[Bruce Fischl]

Hi Jasmin

oh, I take it back. It looks like the SUBJECTS_DIR you pointed it at didn't 
exist. Create it first with


mkdir /Desktop/Brain_Child_subs

then try rerunning.
Bruce


On Wed, 27 Jan 2016, Jasmin Alves wrote:


Hi Bruce,
 Could you elaborate on what you mean I need to specify the input volume? 

Thanks,
Jasmin

On Wed, Jan 27, 2016 at 5:48 AM, Bruce Fischl 
wrote:
  Hi Jasmin

  if this is the first time you have run this subject (that is,
  the subject dir doesn't exist within $SUBJECTS_DIR), you still
  need to specify the input volume with -i  T1_original_joya.nii

  cheers
  Bruce

  On Tue, 26 Jan 2016, Jasmin Alves wrote:

Bruce,
Sorry to be a pain, but for some reason, I cannot
still get recon-all to
work. 

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$
recon-all -sd
/Desktop/Brain_Child_subs -i T1_original_joya.nii
-subject joya -all &

[1] 14655

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$
ERROR: SUBJECTS_DIR
/Desktop/Brain_Child_subs does not exist.

Thanks,

Jasmin


On Tue, Jan 26, 2016 at 6:19 AM, Bruce Fischl

wrote:
      Hi Jasmin

      you need a '-' sign first. It should be:

      recon-all -sd /Desktop/Brain_Child_subs -i
T1_original_joya.nii
      -subject \
      joya -all &

      cheers
      Bruce

      On Mon, 25 Jan 2016, Jasmin Alves wrote:

            Hi Bruce, 
            Thanks for the reply, I attempted to
direct
            Subjects_dir to the folder with
            my data but I received the following
error. 

            Jasmins-MacBook-Pro:Brain_Child_subs
jasminalves$
            export
            SUBJECTS_DIR=/Desktop/Brain_Child_subs

            Jasmins-MacBook-Pro:Brain_Child_subs
jasminalves$
            recon-all -sd
            /Desktop/Brain_Child_subs -i
T1_original_joya.nii
            -subject joya all &

            [1] 13867

            Jasmins-MacBook-Pro:Brain_Child_subs
jasminalves$
            ERROR: Flag all
            unrecognized.

            -sd /Desktop/Brain_Child_subs -i
            T1_original_joya.nii -subject joya all

            Darwin Jasmins-MacBook-Pro.local 14.5.0
Darwin
            Kernel Version 14.5.0: Tue
            Sep  1 21:23:09 PDT 2015;
            root:xnu-2782.50.1~1/RELEASE_X86_64
x86_64

            recon-all -s joya exited with ERRORS at
Mon Jan 25
            21:12:58 PST 2016

            Thanks so much,

            Jasmin


            On Mon, Jan 25, 2016 at 6:33 AM, Bruce
Fischl
            
            wrote:
                  Hi Jasmin

                  you  need to create a directory
where you have
            write permission
                  and room for the subject
reconstruction to be
            written to, then
                  set the SUBJECTS_DIR environment
variable to
            point to it. At the
                  moment you are trying to use the
subject
            directory we
                  distribute, which is in some
system (and
            read-only) location.
                  You can do this on the command
line of
            recon-all via:

                  recon-all -sd 
...

                  cheers
                  Bruce


                  On Sun, 24 Jan 2016, Jasmin Alves
wrote:

                  Hello Freesurfer,

                  I am trying to learn freesurfer
and ran into
            the following
                  issues below
                  running the recon -all command. 

                  FREESURFER_HOME:
/Applications/freesurfer

                  Build stamp:
            freesurfer-Darwin-lion-stable-pub-v5.3.0

                  Kernel info: Darwin 14.5.0 x86_64

                    1) 

                  joya

   

Re: [Freesurfer] recon -all errors

[Jasmin Alves]

This directory already exists. I had already made it, which is why I am
confused that it cannot be found.

On Wed, Jan 27, 2016 at 10:43 AM, Bruce Fischl 
wrote:

> Hi Jasmin
>
> oh, I take it back. It looks like the SUBJECTS_DIR you pointed it at
> didn't exist. Create it first with
>
> mkdir /Desktop/Brain_Child_subs
>
> then try rerunning.
> Bruce
>
>
>
> On Wed, 27 Jan 2016, Jasmin Alves wrote:
>
> Hi Bruce,
>>  Could you elaborate on what you mean I need to specify the input volume?
>>
>> Thanks,
>> Jasmin
>>
>> On Wed, Jan 27, 2016 at 5:48 AM, Bruce Fischl > >
>> wrote:
>>   Hi Jasmin
>>
>>   if this is the first time you have run this subject (that is,
>>   the subject dir doesn't exist within $SUBJECTS_DIR), you still
>>   need to specify the input volume with -i  T1_original_joya.nii
>>
>>   cheers
>>   Bruce
>>
>>   On Tue, 26 Jan 2016, Jasmin Alves wrote:
>>
>> Bruce,
>> Sorry to be a pain, but for some reason, I cannot
>> still get recon-all to
>> work.
>>
>> Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$
>> recon-all -sd
>> /Desktop/Brain_Child_subs -i T1_original_joya.nii
>> -subject joya -all &
>>
>> [1] 14655
>>
>> Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$
>> ERROR: SUBJECTS_DIR
>> /Desktop/Brain_Child_subs does not exist.
>>
>> Thanks,
>>
>> Jasmin
>>
>>
>> On Tue, Jan 26, 2016 at 6:19 AM, Bruce Fischl
>> 
>> wrote:
>>   Hi Jasmin
>>
>>   you need a '-' sign first. It should be:
>>
>>   recon-all -sd /Desktop/Brain_Child_subs -i
>> T1_original_joya.nii
>>   -subject \
>>   joya -all &
>>
>>   cheers
>>   Bruce
>>
>>   On Mon, 25 Jan 2016, Jasmin Alves wrote:
>>
>> Hi Bruce,
>> Thanks for the reply, I attempted to
>> direct
>> Subjects_dir to the folder with
>> my data but I received the following
>> error.
>>
>> Jasmins-MacBook-Pro:Brain_Child_subs
>> jasminalves$
>> export
>> SUBJECTS_DIR=/Desktop/Brain_Child_subs
>>
>> Jasmins-MacBook-Pro:Brain_Child_subs
>> jasminalves$
>> recon-all -sd
>> /Desktop/Brain_Child_subs -i
>> T1_original_joya.nii
>> -subject joya all &
>>
>> [1] 13867
>>
>> Jasmins-MacBook-Pro:Brain_Child_subs
>> jasminalves$
>> ERROR: Flag all
>> unrecognized.
>>
>> -sd /Desktop/Brain_Child_subs -i
>> T1_original_joya.nii -subject joya all
>>
>> Darwin Jasmins-MacBook-Pro.local 14.5.0
>> Darwin
>> Kernel Version 14.5.0: Tue
>> Sep  1 21:23:09 PDT 2015;
>> root:xnu-2782.50.1~1/RELEASE_X86_64
>> x86_64
>>
>> recon-all -s joya exited with ERRORS at
>> Mon Jan 25
>> 21:12:58 PST 2016
>>
>> Thanks so much,
>>
>> Jasmin
>>
>>
>> On Mon, Jan 25, 2016 at 6:33 AM, Bruce
>> Fischl
>> 
>> wrote:
>>   Hi Jasmin
>>
>>   you  need to create a directory
>> where you have
>> write permission
>>   and room for the subject
>> reconstruction to be
>> written to, then
>>   set the SUBJECTS_DIR environment
>> variable to
>> point to it. At the
>>   moment you are trying to use the
>> subject
>> directory we
>>   distribute, which is in some
>> system (and
>> read-only) location.
>>   You can do this on the command
>> line of
>> recon-all via:
>>
>>   recon-all -sd 
>> ...
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Sun, 24 Jan 2016, Jasmin Alves
>> wrote:
>>
>>   Hello 

Re: [Freesurfer] recon -all errors

[Bruce Fischl]

Hi Jasmin

if this is the first time you have run this subject (that is, the subject 
dir doesn't exist within $SUBJECTS_DIR), you still need to specify the 
input volume with -i  T1_original_joya.nii


cheers
Bruce

On Tue, 26 Jan 2016, Jasmin Alves wrote:


Bruce,
Sorry to be a pain, but for some reason, I cannot still get recon-all to
work. 

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ recon-all -sd
/Desktop/Brain_Child_subs -i T1_original_joya.nii -subject joya -all &

[1] 14655

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ ERROR: SUBJECTS_DIR
/Desktop/Brain_Child_subs does not exist.

Thanks,

Jasmin


On Tue, Jan 26, 2016 at 6:19 AM, Bruce Fischl 
wrote:
  Hi Jasmin

  you need a '-' sign first. It should be:

  recon-all -sd /Desktop/Brain_Child_subs -i T1_original_joya.nii
  -subject \
  joya -all &

  cheers
  Bruce

  On Mon, 25 Jan 2016, Jasmin Alves wrote:

Hi Bruce, 
Thanks for the reply, I attempted to direct
Subjects_dir to the folder with
my data but I received the following error. 

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$
export
SUBJECTS_DIR=/Desktop/Brain_Child_subs

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$
recon-all -sd
/Desktop/Brain_Child_subs -i T1_original_joya.nii
-subject joya all &

[1] 13867

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$
ERROR: Flag all
unrecognized.

-sd /Desktop/Brain_Child_subs -i
T1_original_joya.nii -subject joya all

Darwin Jasmins-MacBook-Pro.local 14.5.0 Darwin
Kernel Version 14.5.0: Tue
Sep  1 21:23:09 PDT 2015;
root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64

recon-all -s joya exited with ERRORS at Mon Jan 25
21:12:58 PST 2016

Thanks so much,

Jasmin


On Mon, Jan 25, 2016 at 6:33 AM, Bruce Fischl

wrote:
      Hi Jasmin

      you  need to create a directory where you have
write permission
      and room for the subject reconstruction to be
written to, then
      set the SUBJECTS_DIR environment variable to
point to it. At the
      moment you are trying to use the subject
directory we
      distribute, which is in some system (and
read-only) location.
      You can do this on the command line of
recon-all via:

      recon-all -sd  ...

      cheers
      Bruce


      On Sun, 24 Jan 2016, Jasmin Alves wrote:

      Hello Freesurfer,

      I am trying to learn freesurfer and ran into
the following
      issues below
      running the recon -all command. 

      FREESURFER_HOME: /Applications/freesurfer

      Build stamp:
freesurfer-Darwin-lion-stable-pub-v5.3.0

      Kernel info: Darwin 14.5.0 x86_64

        1) 

      joya

       2) 

       Jasmins-MacBook-Pro:subjects jasminalves$
recon-all -i
      T1_original_joya.nii
      -subject joya -all &


      3)

      [1] 12300 

      Jasmins-MacBook-Pro:subjects jasminalves$
mkdir:
      /Applications/freesurfer/subjects/joya:
Permission denied

      mkdir:
/Applications/freesurfer/subjects/joya/scripts:
      Permission denied

      mkdir:
/Applications/freesurfer/subjects/joya/scripts:
      Permission denied

      cp:
     
/Applications/freesurfer/subjects/joya/scripts/build-stamp.txt:
      No such
      file or directory

      cat:
     
/Applications/freesurfer/subjects/joya/scripts/build-stamp.txt:
      No such
      file or directory

      INFO: FreeSurfer build stamps do not match

      Subject Stamp: 

      Current Stamp:
freesurfer-Darwin-lion-stable-pub-v5.3.0

      INFO: SUBJECTS_DIR is
/Applications/freesurfer/subjects

      Actual FREESURFER_HOME
/Applications/freesurfer

      /Applications/freesurfer/subjects/joya: No
such file or
      directory.


      [1]+  Exit 1                  recon-all -i
      T1_original_joya.nii -subject
      joya -a

      Thank you,Jasmin

Jasmin 

Re: [Freesurfer] recon -all errors

[Jasmin Alves]

Bruce,

Sorry to be a pain, but for some reason, I cannot still get recon-all to
work.

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ recon-all -sd
/Desktop/Brain_Child_subs -i T1_original_joya.nii -subject joya -all &

[1] 14655

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ ERROR: SUBJECTS_DIR
/Desktop/Brain_Child_subs does not exist.

Thanks,

Jasmin

On Tue, Jan 26, 2016 at 6:19 AM, Bruce Fischl 
wrote:

> Hi Jasmin
>
> you need a '-' sign first. It should be:
>
> recon-all -sd /Desktop/Brain_Child_subs -i T1_original_joya.nii -subject \
> joya -all &
>
> cheers
> Bruce
>
>
> On Mon, 25 Jan 2016, Jasmin Alves wrote:
>
> Hi Bruce,
>> Thanks for the reply, I attempted to direct Subjects_dir to the folder
>> with
>> my data but I received the following error.
>>
>> Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ export
>> SUBJECTS_DIR=/Desktop/Brain_Child_subs
>>
>> Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ recon-all -sd
>> /Desktop/Brain_Child_subs -i T1_original_joya.nii -subject joya all &
>>
>> [1] 13867
>>
>> Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ ERROR: Flag all
>> unrecognized.
>>
>> -sd /Desktop/Brain_Child_subs -i T1_original_joya.nii -subject joya all
>>
>> Darwin Jasmins-MacBook-Pro.local 14.5.0 Darwin Kernel Version 14.5.0: Tue
>> Sep  1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64
>>
>> recon-all -s joya exited with ERRORS at Mon Jan 25 21:12:58 PST 2016
>>
>> Thanks so much,
>>
>> Jasmin
>>
>>
>> On Mon, Jan 25, 2016 at 6:33 AM, Bruce Fischl > >
>> wrote:
>>   Hi Jasmin
>>
>>   you  need to create a directory where you have write permission
>>   and room for the subject reconstruction to be written to, then
>>   set the SUBJECTS_DIR environment variable to point to it. At the
>>   moment you are trying to use the subject directory we
>>   distribute, which is in some system (and read-only) location.
>>   You can do this on the command line of recon-all via:
>>
>>   recon-all -sd  ...
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Sun, 24 Jan 2016, Jasmin Alves wrote:
>>
>>   Hello Freesurfer,
>>
>>   I am trying to learn freesurfer and ran into the following
>>   issues below
>>   running the recon -all command.
>>
>>   FREESURFER_HOME: /Applications/freesurfer
>>
>>   Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>>
>>   Kernel info: Darwin 14.5.0 x86_64
>>
>> 1)
>>
>>   joya
>>
>>2)
>>
>>Jasmins-MacBook-Pro:subjects jasminalves$ recon-all -i
>>   T1_original_joya.nii
>>   -subject joya -all &
>>
>>
>>   3)
>>
>>   [1] 12300
>>
>>   Jasmins-MacBook-Pro:subjects jasminalves$ mkdir:
>>   /Applications/freesurfer/subjects/joya: Permission denied
>>
>>   mkdir: /Applications/freesurfer/subjects/joya/scripts:
>>   Permission denied
>>
>>   mkdir: /Applications/freesurfer/subjects/joya/scripts:
>>   Permission denied
>>
>>   cp:
>>   /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt:
>>   No such
>>   file or directory
>>
>>   cat:
>>   /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt:
>>   No such
>>   file or directory
>>
>>   INFO: FreeSurfer build stamps do not match
>>
>>   Subject Stamp:
>>
>>   Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>>
>>   INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
>>
>>   Actual FREESURFER_HOME /Applications/freesurfer
>>
>>   /Applications/freesurfer/subjects/joya: No such file or
>>   directory.
>>
>>
>>   [1]+  Exit 1  recon-all -i
>>   T1_original_joya.nii -subject
>>   joya -a
>>
>>   Thank you,Jasmin
>>
>> Jasmin AlvesPredoctoral Student
>> Medical Biology Graduate Program
>> University of Southern California
>> jal...@usc.edu
>>
>>
>>
>> ___
>> 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 Partners Compliance
>> HelpLine at
>> http://www.partners.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.
>>
>>
>>
>>
>> --
>> Jasmin AlvesPredoctoral Student
>> Medical Biology Graduate Program
>> University of Southern California
>> jal...@usc.edu
>>
>>
>>
> ___
> 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 

Re: [Freesurfer] recon -all errors

[Bruce Fischl]

Hi Jasmin

you need a '-' sign first. It should be:

recon-all -sd /Desktop/Brain_Child_subs -i T1_original_joya.nii -subject \
joya -all &

cheers
Bruce

On Mon, 25 Jan 2016, Jasmin Alves 
wrote:



Hi Bruce, 
Thanks for the reply, I attempted to direct Subjects_dir to the folder with
my data but I received the following error. 

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ export
SUBJECTS_DIR=/Desktop/Brain_Child_subs

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ recon-all -sd
/Desktop/Brain_Child_subs -i T1_original_joya.nii -subject joya all &

[1] 13867

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ ERROR: Flag all
unrecognized.

-sd /Desktop/Brain_Child_subs -i T1_original_joya.nii -subject joya all

Darwin Jasmins-MacBook-Pro.local 14.5.0 Darwin Kernel Version 14.5.0: Tue
Sep  1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64

recon-all -s joya exited with ERRORS at Mon Jan 25 21:12:58 PST 2016

Thanks so much,

Jasmin


On Mon, Jan 25, 2016 at 6:33 AM, Bruce Fischl 
wrote:
  Hi Jasmin

  you  need to create a directory where you have write permission
  and room for the subject reconstruction to be written to, then
  set the SUBJECTS_DIR environment variable to point to it. At the
  moment you are trying to use the subject directory we
  distribute, which is in some system (and read-only) location.
  You can do this on the command line of recon-all via:

  recon-all -sd  ...

  cheers
  Bruce


  On Sun, 24 Jan 2016, Jasmin Alves wrote:

  Hello Freesurfer,

  I am trying to learn freesurfer and ran into the following
  issues below
  running the recon -all command. 

  FREESURFER_HOME: /Applications/freesurfer

  Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

  Kernel info: Darwin 14.5.0 x86_64

    1) 

  joya

   2) 

   Jasmins-MacBook-Pro:subjects jasminalves$ recon-all -i
  T1_original_joya.nii
  -subject joya -all &


  3)

  [1] 12300 

  Jasmins-MacBook-Pro:subjects jasminalves$ mkdir:
  /Applications/freesurfer/subjects/joya: Permission denied

  mkdir: /Applications/freesurfer/subjects/joya/scripts:
  Permission denied

  mkdir: /Applications/freesurfer/subjects/joya/scripts:
  Permission denied

  cp:
  /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt:
  No such
  file or directory

  cat:
  /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt:
  No such
  file or directory

  INFO: FreeSurfer build stamps do not match

  Subject Stamp: 

  Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

  INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects

  Actual FREESURFER_HOME /Applications/freesurfer

  /Applications/freesurfer/subjects/joya: No such file or
  directory.


  [1]+  Exit 1                  recon-all -i
  T1_original_joya.nii -subject
  joya -a

  Thank you,Jasmin

Jasmin AlvesPredoctoral Student 
Medical Biology Graduate Program 
University of Southern California
jal...@usc.edu 



___
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 Partners Compliance
HelpLine at
http://www.partners.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.




--
Jasmin AlvesPredoctoral Student 
Medical Biology Graduate Program 
University of Southern California
jal...@usc.edu 


___
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 Partners Compliance HelpLine at
http://www.partners.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.

Re: [Freesurfer] recon -all errors

[Jasmin Alves]

Hi Bruce,

Thanks for the reply, I attempted to direct Subjects_dir to the folder with
my data but I received the following error.

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ export
SUBJECTS_DIR=/Desktop/Brain_Child_subs

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ recon-all -sd
/Desktop/Brain_Child_subs -i T1_original_joya.nii -subject joya all &

[1] 13867

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ ERROR: Flag all
unrecognized.

-sd /Desktop/Brain_Child_subs -i T1_original_joya.nii -subject joya all

Darwin Jasmins-MacBook-Pro.local 14.5.0 Darwin Kernel Version 14.5.0: Tue
Sep  1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64

recon-all -s joya exited with ERRORS at Mon Jan 25 21:12:58 PST 2016

Thanks so much,

Jasmin

On Mon, Jan 25, 2016 at 6:33 AM, Bruce Fischl 
wrote:

> Hi Jasmin
>
> you  need to create a directory where you have write permission and room
> for the subject reconstruction to be written to, then set the SUBJECTS_DIR
> environment variable to point to it. At the moment you are trying to use
> the subject directory we distribute, which is in some system (and
> read-only) location. You can do this on the command line of recon-all via:
>
> recon-all -sd  ...
>
> cheers
> Bruce
>
>
>
> On Sun, 24 Jan 2016, Jasmin Alves wrote:
>
> Hello Freesurfer,
>>
>> I am trying to learn freesurfer and ran into the following issues below
>> running the recon -all command.
>>
>> FREESURFER_HOME: /Applications/freesurfer
>>
>> Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>>
>> Kernel info: Darwin 14.5.0 x86_64
>>
>>   1)
>>
>> joya
>>
>>  2)
>>
>>  Jasmins-MacBook-Pro:subjects jasminalves$ recon-all -i
>> T1_original_joya.nii
>> -subject joya -all &
>>
>>
>> 3)
>>
>> [1] 12300
>>
>> Jasmins-MacBook-Pro:subjects jasminalves$ mkdir:
>> /Applications/freesurfer/subjects/joya: Permission denied
>>
>> mkdir: /Applications/freesurfer/subjects/joya/scripts: Permission denied
>>
>> mkdir: /Applications/freesurfer/subjects/joya/scripts: Permission denied
>>
>> cp: /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt: No
>> such
>> file or directory
>>
>> cat: /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt: No
>> such
>> file or directory
>>
>> INFO: FreeSurfer build stamps do not match
>>
>> Subject Stamp:
>>
>> Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>>
>> INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
>>
>> Actual FREESURFER_HOME /Applications/freesurfer
>>
>> /Applications/freesurfer/subjects/joya: No such file or directory.
>>
>>
>> [1]+  Exit 1  recon-all -i T1_original_joya.nii -subject
>> joya -a
>>
>> Thank you,Jasmin
>>
>> Jasmin AlvesPredoctoral Student
>> Medical Biology Graduate Program
>> University of Southern California
>> jal...@usc.edu
>>
>>
>>
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-- 
Jasmin Alves
Predoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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Re: [Freesurfer] recon -all errors

[Bruce Fischl]

Hi Jasmin

you  need to create a directory where you have write permission and room 
for the subject reconstruction to be written to, then set the SUBJECTS_DIR 
environment variable to point to it. At the moment you are trying to use 
the subject directory we distribute, which is in some system (and 
read-only) location. You can do this on the command line of recon-all via:


recon-all -sd  ...

cheers
Bruce


On Sun, 24 Jan 2016, Jasmin Alves 
wrote:



Hello Freesurfer,

I am trying to learn freesurfer and ran into the following issues below
running the recon -all command. 

FREESURFER_HOME: /Applications/freesurfer

Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

Kernel info: Darwin 14.5.0 x86_64

  1) 

joya

 2) 

 Jasmins-MacBook-Pro:subjects jasminalves$ recon-all -i T1_original_joya.nii
-subject joya -all &


3)

[1] 12300 

Jasmins-MacBook-Pro:subjects jasminalves$ mkdir:
/Applications/freesurfer/subjects/joya: Permission denied

mkdir: /Applications/freesurfer/subjects/joya/scripts: Permission denied

mkdir: /Applications/freesurfer/subjects/joya/scripts: Permission denied

cp: /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt: No such
file or directory

cat: /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt: No such
file or directory

INFO: FreeSurfer build stamps do not match

Subject Stamp: 

Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects

Actual FREESURFER_HOME /Applications/freesurfer

/Applications/freesurfer/subjects/joya: No such file or directory.


[1]+  Exit 1                  recon-all -i T1_original_joya.nii -subject
joya -a

Thank you,Jasmin

Jasmin AlvesPredoctoral Student 
Medical Biology Graduate Program 
University of Southern California
jal...@usc.edu 


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Re: [Freesurfer] Recon-all errors

[Bruce Fischl]

if there are both use -autorecon2-wm -autorecon3. There is also the 
option of adding control points and running -autorecon2-cp -autorecon3


cheers
Bruce
On 
Thu, 1 Aug 2013, Stéphane Poulin wrote:



Dear Freesurfer experts,
Regarding recon-all troubleshooting, my understanding is that you can edit wm 
and complete the pipeline with recon-all –autorecon2-wm. Similarly you can 
complete the pipeline with recon-all –autorecon2-pial if there is a problem 
with the pial surface.
If there are both white matter and pial surface edits, is there an “efficient” 
way to correct for both and complete the pipeline.
Thanks,
Stephane




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Re: [Freesurfer] recon-all errors

[Bruce Fischl]

Hi Linda

napo4128: something is wrong with the 001.mgz. How did you create it? 
The direction cosines definitely shouldn't have a 0 determinant


napo0195: this is new error for me. The topology fixing couldn't find a 
correct solution. If you upload the subject we'll see if we can replicate 
and fix this problem


napo4252: I've never seen this before either - mris_make_surfaces 
segfaulting right away. Maybe you ran out of disk space and one of the 
volumes/surfaces it needs is corrupted? Try running it by itself:

setenv SUBJECTS_DIR /home/virtualuser/freesurfer/lindadata/subjects
mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs napo4252 lh

and see if it happens again. If so, I guess I would go through all the 
volumes and surfaces and make sure that they are visually reasonable in 
tksurfer/tkmedit/freeview. If that doesn't reveal something, then upload 
this one as well

cheers
Bruce

On Fri, 14 Jun 2013, Linda Zhang wrote:

 Dear all,

 I've been running recon-all (subj) -all for a group of subjects on
 Freesurfer v5.1.0 on Virtualbox.  Three of them exited with errors,
 each one having a different error.  I've attached the recon-all.logs.
 For napo0195, the problem may be with the wm.mgz as someone mentioned
 before, but I don't know what the issue might be for the other two
 subjects.  Thanks for your help!

 Cheers,
 Linda

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Re: [Freesurfer] recon-all errors: v5.0.0; dataset 4

[Bruce Fischl]

Hi Sudhin

have you looked at the defect to see what is causing it? It's very big, 
which is probably the root of the problem.


Bruce
On Fri, 31 May 2013, Sudhin A. 
Shah wrote:




On May 28, 2013, at 3:48 PM, Sudhin A. Shah wrote:

  CORRECTING DEFECT 1 (vertices=33, convex hull=57)
  After retessellation of defect 1, euler #=-41
  (88676,260208,171491) : difference with theory (-61) = -20 

  CORRECTING DEFECT 2 (vertices=30163, convex hull=6211)
  error in the retessellation 
  normal vector of length zero at vertex 88778 with 0 faces
  vertex 88778 has 0 face
  No such file or directory
  Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic
  #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux

  recon-all -s IN387G exited with ERRORS at Thu May 16 05:11:49
  EDT 2013

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