Re: [Freesurfer] Missing Control Points and QATools

[Bruce Fischl]

Hi Matt

I'm sorry to hear it. I've never heard of anything of ours deleting the 
control.dat unless you run recon-all with the appropriate -clean switch.


I don't know an easy way to recover them. Do you need them back? You could
do something like copy the subject, run the intensity normalization on the 
copy, then look for points that are exactly 110 in the old 
(control-point-normalized) brain.mgz and the new one without control 
points, that are also wm in the aseg.mgz. This won't be exactly the control 
points, but would let you rerun without losing too much if that is what you 
are worried about


cheers
Bruce



On Tue, 12 Jun 2018, Matthew Peverill wrote:



External Email - Use Caution

Hi all,Sorry for the bump but I wanted to take one more shot at this. We're 
making it back but we've
lost many, many hours of editing work. Has anyone else had experiences with 
QAtools, or other
FreeSurfer utilities, removing control point data, or discovered any way to 
recover control.dat from
other files? Thank you,
   -Matt

On Mon, May 21, 2018 at 11:35 AM Matthew Peverill  wrote:
  Hello,
  We are finishing up manual inspection and editing of our dataset. As part 
of this
  process, we used QATools to generate QA reports. While we were running 
our reports the
  tmp/control.dat file was deleted from many of our subject directories 
(the brains had
  already been recon'd, so the corrected surfaces were not affected). The 
timing certainly
  suggests these were related, but we have no way of knowing if something 
else unrelated
  to QAtools happened that caused these files to be deleted. So two 
questions:

1) Has anyone else had an experience with QAtools where the control.dat file 
was deleted, or
have any insight about why this could have happened?
2) Is the data in control.dat stored anywhere else? For example, can it be 
recovered
from mri/ctrl_pts.mgz? We are mostly fine, but a few brains will need to have 
control points
re-applied.

Something of a shot in the dark, but we would love any suggestions. Thanks,
   -Matt

Version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
uname -a: Linux vmpfc 3.16.0-4-amd64 #1 SMP Debian 3.16.39-1+deb8u2 
(2017-03-07) x86_64
GNU/Linux


--
Matthew Peverill
mrpever...@gmail.com (preferred)



--
Matthew Peverill
857-277-9083
mrpever...@gmail.com (preferred)

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Re: [Freesurfer] Missing Control Points and QATools

[Matthew Peverill]

External Email - Use Caution

Hi all,
Sorry for the bump but I wanted to take one more shot at this. We're making
it back but we've lost many, many hours of editing work. Has anyone else
had experiences with QAtools, or other FreeSurfer utilities, removing
control point data, or discovered any way to recover control.dat from other
files? Thank you,
   -Matt

On Mon, May 21, 2018 at 11:35 AM Matthew Peverill 
wrote:

> Hello,
> We are finishing up manual inspection and editing of our dataset. As part
> of this process, we used QATools to generate QA reports. While we were
> running our reports the tmp/control.dat file was deleted from many of our
> subject directories (the brains had already been recon'd, so the corrected
> surfaces were not affected). The timing certainly suggests these were
> related, but we have no way of knowing if something else unrelated to
> QAtools happened that caused these files to be deleted. So two questions:
>
> 1) Has anyone else had an experience with QAtools where the control.dat
> file was deleted, or have any insight about why this could have happened?
> 2) Is the data in control.dat stored anywhere else? For example, can it be
> recovered from mri/ctrl_pts.mgz? We are mostly fine, but a few brains will
> need to have control points re-applied.
>
> Something of a shot in the dark, but we would love any suggestions. Thanks,
>-Matt
>
> Version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> uname -a: Linux vmpfc 3.16.0-4-amd64 #1 SMP Debian 3.16.39-1+deb8u2
> (2017-03-07) x86_64 GNU/Linux
>
>
> --
> Matthew Peverill
> mrpever...@gmail.com (preferred)
>


-- 
Matthew Peverill
857-277-9083
mrpever...@gmail.com (preferred)
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Re: [Freesurfer] tractstats2table - all tracts for multiple subjects

[Alexopoulos, Dimitrios]

External Email - Use Caution

Thx Anastasia.

This the command I used and the error:

[hellerml@login01 processed_data]$ tractstats2table --load-pathstats-from-file 
/scratch/jimalex/freesurfer6_0_chd_auck_6yr/processed_data/test.list --overall 
--tablefile test.table
Parsing the .stats files
Building the table..
ERROR: all stats files need to have the same pathwayname. try verbose option
These are the pathwaynames found: ['fmajor', 'fminor', 'lh.atr', 'lh.cab', 
'lh.ccg', 'lh.cst', 'lh.ilf', 'lh.slfp', 'lh.slft', 'lh.unc', 'rh.atr', 
'rh.cab', 'rh.ccg', 'rh.cst', 'rh.ilf', 'rh.slfp', 'rh.slft', 'rh.unc']

For example, the test .list input file I used for a single subject is below:

$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/fmajor_PP_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/fminor_PP_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.atr_PP_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.cab_PP_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.ccg_PP_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.slfp_PP_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.slft_PP_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.atr_PP_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.cab_PP_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.ccg_PP_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.cst_AS_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.slfp_PP_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.slft_PP_avg33_mni_bbr/pathstats.overall.txt
$SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt



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Information. If you are not the intended recipient, be advised that any 
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From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Tuesday, June 12, 2018 4:30 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] tractstats2table - all tracts for multiple subjects


Hi Jim - You can use the --load-pathstats-from-file option, as in the tutorial, 
to pass a text file that contains the paths to all the stats files that you 
want to include in the table. These can be from multiple subjects and/or tracts.



http://freesurfer.net/fswiki/FsTutorial/TraculaStatistics



Best,

a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Alexopoulos, Dimitrios 
mailto:dimitriosalexopou...@wustl.edu>>
Sent: Tuesday, June 12, 2018 5:08:20 PM
To: Freesurfer support list
Subject: [Freesurfer] tractstats2table - all tracts for multiple subjects


External Email - Use Caution

Hi,



For a group analysis, it possible to use 'tractstats2table' to generate a 
single table that contains all the tracts for multiple subjects?



It's not intuitively obvious looking at the options with the 'tractstats2table' 
utility.



Jim





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Information. If you are not the intended recipient, be advised that any 
unauthorized use, disclosure, copying, distribution or the taking of any action 
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have received this email in error, please immediately notify the sender via 
telephone or return email."







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 
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immediately notify the sender via telephone or return mail.


The materials in this message are private and may contain Protected Healthcare 
Information or other information of 

Re: [Freesurfer] dwi.ecclog file

[Yendiki, Anastasia]

Hi Loic - The command that computes the motion measures is dmri_motion, and it 
can take either the eddy_correct or eddy format as input. The former format 
contains affine registration matrices with respect to the reference frame 
(which usually is the first b=0). The latter format contains the 
shift/rotation/etc. parameters of the registration rather than the matrix 
itself. You can run dmri_motion without arguments to see details.


Best,

a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Daumail, Loic Jean 

Sent: Tuesday, June 12, 2018 5:33:17 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] dwi.ecclog file

Hello,

I have several questions regarding the dwi.ecclog file data from Tracula, using 
the FreeSurfer version V6.0.0.

1) Does Tracula still use eddy_correct from FSL, or was it updated with the new 
eddy function from FSL?

2) Are the values for each slice of dwi.ecclog relative to the first slice or 
to the previous slice, or to another template? is it the same for both rotation 
and translation values?

3) What is the coordinate system for the rotation values? Is there a way to 
determine the total rotation from these 9 values?

Thanks,

Sincerely,

Loic Daumail
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[Freesurfer] dwi.ecclog file

[Daumail, Loic Jean]

Hello,

I have several questions regarding the dwi.ecclog file data from Tracula, using 
the FreeSurfer version V6.0.0.

1) Does Tracula still use eddy_correct from FSL, or was it updated with the new 
eddy function from FSL?

2) Are the values for each slice of dwi.ecclog relative to the first slice or 
to the previous slice, or to another template? is it the same for both rotation 
and translation values?

3) What is the coordinate system for the rotation values? Is there a way to 
determine the total rotation from these 9 values?

Thanks,

Sincerely,

Loic Daumail
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Re: [Freesurfer] tractstats2table - all tracts for multiple subjects

[Yendiki, Anastasia]

Hi Jim - You can use the --load-pathstats-from-file option, as in the tutorial, 
to pass a text file that contains the paths to all the stats files that you 
want to include in the table. These can be from multiple subjects and/or tracts.


http://freesurfer.net/fswiki/FsTutorial/TraculaStatistics


Best,

a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alexopoulos, Dimitrios 

Sent: Tuesday, June 12, 2018 5:08:20 PM
To: Freesurfer support list
Subject: [Freesurfer] tractstats2table - all tracts for multiple subjects


External Email - Use Caution

Hi,



For a group analysis, it possible to use ‘tractstats2table’ to generate a 
single table that contains all the tracts for multiple subjects?



It’s not intuitively obvious looking at the options with the ‘tractstats2table’ 
utility.



Jim





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Information. If you are not the intended recipient, be advised that any 
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telephone or return email.”







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[Freesurfer] tractstats2table - all tracts for multiple subjects

[Alexopoulos, Dimitrios]

External Email - Use Caution

Hi,


For a group analysis, it possible to use 'tractstats2table' to generate a 
single table that contains all the tracts for multiple subjects?



It's not intuitively obvious looking at the options with the 'tractstats2table' 
utility.



Jim


"The materials in this email are private and may contain Protected Health 
Information. If you are not the intended recipient, be advised that any 
unauthorized use, disclosure, copying, distribution 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 email."



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Re: [Freesurfer] crypt_gkey = (null)

[Dicamillo, Robert]

Hello Aaron,

The build timestamp from the output below shows mri_convert is from 8/2014.  
When I look at the build timestamp on our stable 5.3 version of mri_convert I 
see it is from 5/2013.  So the version that you listed is about 1 year newer 
than the 5.3 release I can see.  It is possible that someone downloaded a 
daily/dev build of freesurfer at that time.

You might want to consider running the latest 6.0 release of Freesurfer 
(released in January 2017), which should be fine on CentOS 7.  It can be 
downloaded from, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall

I also suggest that you start out in a default/clean shell,  set 
FREESURFER_HOME, and then source the setup script for linux,  You can see the 
instructions on that same web page under “Setup and Configuration”.  The setup 
steps should work for version 5 or 6.

- rob

On Jun 12, 2018, at 2:43 PM, Aaron Tanenbaum 
mailto:aaron.b.tanenb...@gmail.com>> wrote:


External Email - Use Caution

I checked my system is not encrypted. I had someone else run the command on the 
same machine. It worked for them. So I changed my BASH environment to a default 
environment. I still get the same error.

I tried this again but with a different FreeSurfer 5.3. turns out the one I was 
using has been altered version of FreeSurfer.  I do not know how it was 
altered. It worked. so it has to do with the altered FreeSurfer.
I ran the command mri_convert -version  on both FreeSurfer.

for the unaltered i get the out put
mri_convert -version
stable5
altered version i get
mri_convert -version
dev build (use --all-info flag for full version info)

with this output i type in mri_convert --all-info
mri_convert  ProgramArguments: --all-info  ProgramVersion: $Name:  $  
TimeStamp: 2018/06/12-18:32:17-GMT  BuildTimeStamp: Aug 22 2014 21:04:47  CVS: 
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $  User: tanenbauma  
Machine: rocky  Platform: Linux  PlatformVersion: 3.10.0-862.el7.x86_64  
CompilerName: GCC  CompilerVersion: 40400
Wondering is this version of mri_convert a developmental version?
Also both version are the CentOS 6 build.


On Tue, Jun 12, 2018 at 1:01 PM Dicamillo, Robert 
mailto:rdicami...@mgh.harvard.edu>> wrote:
Hello Aaron,

You could check to see if the CentOS 7 system is using disk encryption, e.g., 
if the
following command return 1, then it would mean encryption is in use (which can 
be
an issue with FreeSurfer).

$ cat /proc/sys/crypto/fips_enabled

If it returns zero, it could be an issue with a system library like glibc on 
CentOS 7.5
(that does not happen on older versions of  CentOS).

Either way, this is not your doing ;-)


On Jun 12, 2018, at 11:51 AM, Aaron Tanenbaum 
mailto:aaron.b.tanenb...@gmail.com>> wrote:


External Email - Use Caution

I am currently running CentOS 7.5 and attempting to run FreeSurfer 5.3. When i 
get to the part where MRI_convert is creating the the orig001.mgz its gives me 
a segmentation fault. if i run this on a centos 6 system it works fine. below 
is the output of the program.


/data/gizmo/data1/freesurfer5.3/bin/mri_convert 
/data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm
 /data/anlab/Aaron/JoEtzl_testing/FreeSurfer/Test1/mri/orig/001.mgz
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from 
/data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm...
crypt_gkey = (null)
Segmentation fault (core dumped)



Did I do anything wrong?
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Re: [Freesurfer] crypt_gkey = (null)

[Aaron Tanenbaum]

External Email - Use Caution

I checked my system is not encrypted. I had someone else run the command on
the same machine. It worked for them. So I changed my BASH environment to a
default environment. I still get the same error.

I tried this again but with a different FreeSurfer 5.3. turns out the one I
was using has been altered version of FreeSurfer.  I do not know how it was
altered. It worked. so it has to do with the altered FreeSurfer.
I ran the command mri_convert -version  on both FreeSurfer.

for the unaltered i get the out put

*mri_convert -version stable5*
altered version i get

*mri_convert -version dev build (use --all-info flag for full version info)*

with this output i type in mri_convert --all-info
*mri_convert  ProgramArguments: --all-info  ProgramVersion: $Name:  $
TimeStamp: 2018/06/12-18:32:17-GMT  BuildTimeStamp: Aug 22 2014 21:04:47
CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $  User:
tanenbauma  Machine: rocky  Platform: Linux  PlatformVersion:
3.10.0-862.el7.x86_64  CompilerName: GCC  CompilerVersion: 40400*
Wondering is this version of mri_convert a developmental version?
Also both version are the CentOS 6 build.


On Tue, Jun 12, 2018 at 1:01 PM Dicamillo, Robert <
rdicami...@mgh.harvard.edu> wrote:

> Hello Aaron,
>
> You could check to see if the CentOS 7 system is using disk encryption,
> e.g., if the
> following command return 1, then it would mean encryption is in use (which
> can be
> an issue with FreeSurfer).
>
> $ cat /proc/sys/crypto/fips_enabled
>
> If it returns zero, it could be an issue with a system library like glibc
> on CentOS 7.5
> (that does not happen on older versions of  CentOS).
>
> Either way, this is not your doing ;-)
>
>
> On Jun 12, 2018, at 11:51 AM, Aaron Tanenbaum 
> wrote:
>
> External Email - Use Caution
>
> I am currently running CentOS 7.5 and attempting to run FreeSurfer 5.3.
> When i get to the part where MRI_convert is creating the the orig001.mgz
> its gives me a segmentation fault. if i run this on a centos 6 system it
> works fine. below is the output of the program.
>
>
> /data/gizmo/data1/freesurfer5.3/bin/mri_convert
> /data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm
> /data/anlab/Aaron/JoEtzl_testing/FreeSurfer/Test1/mri/orig/001.mgz
> $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
> reading from
> /data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm...
> crypt_gkey = (null)
> Segmentation fault (core dumped)
>
>
>
> Did I do anything wrong?
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>
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>
>
> The information in this e-mail is intended only for the person to whom it
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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 Partners Compliance
> HelpLine at
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Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

[Nikita Nogovitsyn]

External Email - Use Caution

Thank you Eugenio, there were no error messages or any observations that may 
indicate the computing process experienced perturbations...

Nikita

On Jun 12, 2018, at 12:19, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:


External Email - Use Caution
Uuuummm it seems it died unexpectedly, but there’s no error at the end of the 
log… are you sure that’s the complete file?
If not: did you get any other message on the screen when you tried to run this?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nikita Nogovitsyn 
mailto:n.nogovit...@ucalgary.ca>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, 12 June 2018 at 17:52
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing 
workflow question, more LH than RH files


External Email - Use Caution
My apologies. Here is the long-hippocampal-subfields-T1.log 
https://drive.google.com/open?id=1VIeYRRBT1fNOeucsYSW2R1792g7u5JBD



On Jun 12, 2018, at 10:45, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

External Email - Use Caution

Thanks, Nikita.
Can you please send us the file long-hippocampal-subfields-T1.log, which you 
can find under the base subject, for one of the failing cases?
Cheers,
/E


--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nikita Nogovitsyn 
mailto:n.nogovit...@ucalgary.ca>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, 12 June 2018 at 17:36
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing 
workflow question, more LH than RH files

External Email - Use Caution
Hi Eugenio,

Thank you very much for your prompt reply.

I was trying to support the tread titled Re: [Freesurfer] freesurfer 6 
hippocampal longitudinal processing workflow question, more LH than RH files

We received results from the cross-sectional segmentations - this version 
worked just great! All the recon-all procedures were managed via Linux based 
computing cluster. (We never had any perturbations in the performance there; 
1000+ subjects were processed on the cross-sectional pipeline without problems).

Once we triggered the longitude version - we faced multiple challenges. We 
observer a strange thing: once the longitudal version reached some undefined 
number of subjects (30-50 jobs) it only produces the left hemisphere text file. 
The recon all log says there are no errors.

We were also not sure what would be the most appropriate way to employ the 
longitudal version given 3 time points of the observation.

Here are all log files from the long version: 
https://drive.google.com/open?id=1qT_auSyboq5tXTgepIAeqgkttiVXMPNq

Thank you very much for your input and help, Eugenio.

Sincerely,
Nikita



On Jun 12, 2018, at 10:05, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

External Email - Use Caution

Hi Nikita,
Could you please be a bit more specific about your problem? What issue are you 
exactly referring to?
Also, can you please send us the log file of the hippocampal subfields (rather 
than of recon-all)?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nikita Nogovitsyn 
mailto:n.nogovit...@ucalgary.ca>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, 12 June 2018 at 16:49
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing 
workflow question, more LH than RH files

External Email - Use Caution
HI

I would like to report to have the same issue. There were no errors in the log 
yet the majority of results missing right hemisphere.

Attaching here the log file, or you can also access it via googledrive here: 
https://drive.google.com/open?id=13PVEWL4d6VuOJcIztWPTe83yz4Oi61Rv

Thanks
Nikita
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The information in 

Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Uuuummm it seems it died unexpectedly, but there’s no error at the end of the 
log… are you sure that’s the complete file?
If not: did you get any other message on the screen when you tried to run this?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Nikita Nogovitsyn 

Reply-To: Freesurfer support list 
Date: Tuesday, 12 June 2018 at 17:52
To: Freesurfer support list 
Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing 
workflow question, more LH than RH files


External Email - Use Caution
My apologies. Here is the long-hippocampal-subfields-T1.log 
https://drive.google.com/open?id=1VIeYRRBT1fNOeucsYSW2R1792g7u5JBD



On Jun 12, 2018, at 10:45, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

External Email - Use Caution

Thanks, Nikita.
Can you please send us the file long-hippocampal-subfields-T1.log, which you 
can find under the base subject, for one of the failing cases?
Cheers,
/E


--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nikita Nogovitsyn 
mailto:n.nogovit...@ucalgary.ca>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, 12 June 2018 at 17:36
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing 
workflow question, more LH than RH files

External Email - Use Caution
Hi Eugenio,

Thank you very much for your prompt reply.

I was trying to support the tread titled Re: [Freesurfer] freesurfer 6 
hippocampal longitudinal processing workflow question, more LH than RH files

We received results from the cross-sectional segmentations - this version 
worked just great! All the recon-all procedures were managed via Linux based 
computing cluster. (We never had any perturbations in the performance there; 
1000+ subjects were processed on the cross-sectional pipeline without problems).

Once we triggered the longitude version - we faced multiple challenges. We 
observer a strange thing: once the longitudal version reached some undefined 
number of subjects (30-50 jobs) it only produces the left hemisphere text file. 
The recon all log says there are no errors.

We were also not sure what would be the most appropriate way to employ the 
longitudal version given 3 time points of the observation.

Here are all log files from the long version: 
https://drive.google.com/open?id=1qT_auSyboq5tXTgepIAeqgkttiVXMPNq

Thank you very much for your input and help, Eugenio.

Sincerely,
Nikita



On Jun 12, 2018, at 10:05, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

External Email - Use Caution

Hi Nikita,
Could you please be a bit more specific about your problem? What issue are you 
exactly referring to?
Also, can you please send us the log file of the hippocampal subfields (rather 
than of recon-all)?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nikita Nogovitsyn 
mailto:n.nogovit...@ucalgary.ca>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, 12 June 2018 at 16:49
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing 
workflow question, more LH than RH files

External Email - Use Caution
HI

I would like to report to have the same issue. There were no errors in the log 
yet the majority of results missing right hemisphere.

Attaching here the log file, or you can also access it via googledrive here: 
https://drive.google.com/open?id=13PVEWL4d6VuOJcIztWPTe83yz4Oi61Rv

Thanks
Nikita
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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 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] Extract the entorhinal cortex as a mask

[Bruce Fischl]

I think you can use 1006 (left) and 2006 (right)

cheers
Bruce
On Tue, 12 Jun 2018, Erik 
O'Hanlon wrote:

>External Email - Use Caution
>
> Hi Bruce,
>
>
> Thanks. So if I use the following command
>
> mri_extract_Label aparc+aseg.mgz 216 EC.mgz
>
> would that give me both L and right EC extracted? is there any way to get the 
> left and right separately?
>
>
> Thanks so much for the help
>
>
> cheers
>
>
> Erik
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Bruce Fischl 
> 
> Sent: 12 June 2018 14:56:41
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Extract the entorhinal cortex as a mask
>
> Hi Erik
>
> yes, you can apply mri_extract_label to the aparc+aseg.mgz to extract EC
> as a volume mask
>
> cheers
> Bruce
> On Tue, 12 Jun 2018, Erik O'Hanlon wrote:
>
>>External Email - Use Caution
>>
>> Hi FS experts ,
>>
>>
>> I'd like to make masks for the entorhinal cortex to use for tractography. 
>> Can you advise what FS tool should be used? I've used the mri_extract_label 
>> for my hippocampal masks but not sure what files to use to extract EC ? I'm 
>> sure it's straightforward
>>
>>
>> Thanks for any advice
>>
>>
>> Best regards
>>
>>
>> Erik
>>
>> Erik O'Hanlon
>> Postdoctoral researcher
>>
>> [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]
>>
>> RCSI Psychiatry
>> Royal College of Surgeons in Ireland
>> Beaumont Road, Beaumont D9 Ireland
>> T: 8093740
>> E: erikohan...@rcsi.ie W: www.rcsi.com
>>
>>
>> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 
>> 2018-2022
>>
>>
>> RCSI LEADING THE WORLD TO BETTER HEALTH
>>
>> [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]
>>
>>
> ___
> 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.
>
>
> Erik O'Hanlon
> Postdoctoral researcher
>
> [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]
>
> RCSI Psychiatry
> Royal College of Surgeons in Ireland
> Beaumont Road, Beaumont D9 Ireland
> T: 8093740
> E: erikohan...@rcsi.ie W: www.rcsi.com
>
>
> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 
> 2018-2022
>
>
> RCSI LEADING THE WORLD TO BETTER HEALTH
>
> [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]
>
>
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Re: [Freesurfer] crypt_gkey = (null)

[Dicamillo, Robert]

Hello Aaron,

You could check to see if the CentOS 7 system is using disk encryption, e.g., 
if the
following command return 1, then it would mean encryption is in use (which can 
be
an issue with FreeSurfer).

$ cat /proc/sys/crypto/fips_enabled

If it returns zero, it could be an issue with a system library like glibc on 
CentOS 7.5
(that does not happen on older versions of  CentOS).

Either way, this is not your doing ;-)


On Jun 12, 2018, at 11:51 AM, Aaron Tanenbaum 
mailto:aaron.b.tanenb...@gmail.com>> wrote:


External Email - Use Caution

I am currently running CentOS 7.5 and attempting to run FreeSurfer 5.3. When i 
get to the part where MRI_convert is creating the the orig001.mgz its gives me 
a segmentation fault. if i run this on a centos 6 system it works fine. below 
is the output of the program.


/data/gizmo/data1/freesurfer5.3/bin/mri_convert 
/data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm
 /data/anlab/Aaron/JoEtzl_testing/FreeSurfer/Test1/mri/orig/001.mgz
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from 
/data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm...
crypt_gkey = (null)
Segmentation fault (core dumped)



Did I do anything wrong?
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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 Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

[Nikita Nogovitsyn]

External Email - Use Caution

My apologies. Here is the long-hippocampal-subfields-T1.log 
https://drive.google.com/open?id=1VIeYRRBT1fNOeucsYSW2R1792g7u5JBD


On Jun 12, 2018, at 10:45, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:


External Email - Use Caution

Thanks, Nikita.
Can you please send us the file long-hippocampal-subfields-T1.log, which you 
can find under the base subject, for one of the failing cases?
Cheers,
/E


--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nikita Nogovitsyn 
mailto:n.nogovit...@ucalgary.ca>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, 12 June 2018 at 17:36
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing 
workflow question, more LH than RH files


External Email - Use Caution

Hi Eugenio,

Thank you very much for your prompt reply.

I was trying to support the tread titled Re: [Freesurfer] freesurfer 6 
hippocampal longitudinal processing workflow question, more LH than RH files

We received results from the cross-sectional segmentations - this version 
worked just great! All the recon-all procedures were managed via Linux based 
computing cluster. (We never had any perturbations in the performance there; 
1000+ subjects were processed on the cross-sectional pipeline without problems).

Once we triggered the longitude version - we faced multiple challenges. We 
observer a strange thing: once the longitudal version reached some undefined 
number of subjects (30-50 jobs) it only produces the left hemisphere text file. 
The recon all log says there are no errors.

We were also not sure what would be the most appropriate way to employ the 
longitudal version given 3 time points of the observation.

Here are all log files from the long version: 
https://drive.google.com/open?id=1qT_auSyboq5tXTgepIAeqgkttiVXMPNq

Thank you very much for your input and help, Eugenio.

Sincerely,
Nikita


On Jun 12, 2018, at 10:05, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

External Email - Use Caution

Hi Nikita,
Could you please be a bit more specific about your problem? What issue are you 
exactly referring to?
Also, can you please send us the log file of the hippocampal subfields (rather 
than of recon-all)?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nikita Nogovitsyn 
mailto:n.nogovit...@ucalgary.ca>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, 12 June 2018 at 16:49
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing 
workflow question, more LH than RH files

External Email - Use Caution
HI

I would like to report to have the same issue. There were no errors in the log 
yet the majority of results missing right hemisphere.

Attaching here the log file, or you can also access it via googledrive here: 
https://drive.google.com/open?id=13PVEWL4d6VuOJcIztWPTe83yz4Oi61Rv

Thanks
Nikita
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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 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.

___
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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 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
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Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Thanks, Nikita.
Can you please send us the file long-hippocampal-subfields-T1.log, which you 
can find under the base subject, for one of the failing cases?
Cheers,
/E


--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Nikita Nogovitsyn 

Reply-To: Freesurfer support list 
Date: Tuesday, 12 June 2018 at 17:36
To: Freesurfer support list 
Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing 
workflow question, more LH than RH files


External Email - Use Caution
Hi Eugenio,

Thank you very much for your prompt reply.

I was trying to support the tread titled Re: [Freesurfer] freesurfer 6 
hippocampal longitudinal processing workflow question, more LH than RH files

We received results from the cross-sectional segmentations - this version 
worked just great! All the recon-all procedures were managed via Linux based 
computing cluster. (We never had any perturbations in the performance there; 
1000+ subjects were processed on the cross-sectional pipeline without problems).

Once we triggered the longitude version - we faced multiple challenges. We 
observer a strange thing: once the longitudal version reached some undefined 
number of subjects (30-50 jobs) it only produces the left hemisphere text file. 
The recon all log says there are no errors.

We were also not sure what would be the most appropriate way to employ the 
longitudal version given 3 time points of the observation.

Here are all log files from the long version: 
https://drive.google.com/open?id=1qT_auSyboq5tXTgepIAeqgkttiVXMPNq

Thank you very much for your input and help, Eugenio.

Sincerely,
Nikita


On Jun 12, 2018, at 10:05, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

External Email - Use Caution

Hi Nikita,
Could you please be a bit more specific about your problem? What issue are you 
exactly referring to?
Also, can you please send us the log file of the hippocampal subfields (rather 
than of recon-all)?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nikita Nogovitsyn 
mailto:n.nogovit...@ucalgary.ca>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, 12 June 2018 at 16:49
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing 
workflow question, more LH than RH files

External Email - Use Caution
HI

I would like to report to have the same issue. There were no errors in the log 
yet the majority of results missing right hemisphere.

Attaching here the log file, or you can also access it via googledrive here: 
https://drive.google.com/open?id=13PVEWL4d6VuOJcIztWPTe83yz4Oi61Rv

Thanks
Nikita
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Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

[Nikita Nogovitsyn]

External Email - Use Caution

Hi Eugenio,

Thank you very much for your prompt reply.

I was trying to support the tread titled Re: [Freesurfer] freesurfer 6 
hippocampal longitudinal processing workflow question, more LH than RH files

We received results from the cross-sectional segmentations - this version 
worked just great! All the recon-all procedures were managed via Linux based 
computing cluster. (We never had any perturbations in the performance there; 
1000+ subjects were processed on the cross-sectional pipeline without problems).

Once we triggered the longitude version - we faced multiple challenges. We 
observer a strange thing: once the longitudal version reached some undefined 
number of subjects (30-50 jobs) it only produces the left hemisphere text file. 
The recon all log says there are no errors.

We were also not sure what would be the most appropriate way to employ the 
longitudal version given 3 time points of the observation.

Here are all log files from the long version: 
https://drive.google.com/open?id=1qT_auSyboq5tXTgepIAeqgkttiVXMPNq

Thank you very much for your input and help, Eugenio.

Sincerely,
Nikita

On Jun 12, 2018, at 10:05, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:


External Email - Use Caution

Hi Nikita,
Could you please be a bit more specific about your problem? What issue are you 
exactly referring to?
Also, can you please send us the log file of the hippocampal subfields (rather 
than of recon-all)?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nikita Nogovitsyn 
mailto:n.nogovit...@ucalgary.ca>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, 12 June 2018 at 16:49
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing 
workflow question, more LH than RH files


External Email - Use Caution

HI

I would like to report to have the same issue. There were no errors in the log 
yet the majority of results missing right hemisphere.

Attaching here the log file, or you can also access it via googledrive here: 
https://drive.google.com/open?id=13PVEWL4d6VuOJcIztWPTe83yz4Oi61Rv

Thanks
Nikita
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Re: [Freesurfer] Extract the entorhinal cortex as a mask

[Erik O'Hanlon]

External Email - Use Caution

Hi Bruce,


Thanks. So if I use the following command

mri_extract_Label aparc+aseg.mgz 216 EC.mgz

would that give me both L and right EC extracted? is there any way to get the 
left and right separately?


Thanks so much for the help


cheers


Erik


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

Sent: 12 June 2018 14:56:41
To: Freesurfer support list
Subject: Re: [Freesurfer] Extract the entorhinal cortex as a mask

Hi Erik

yes, you can apply mri_extract_label to the aparc+aseg.mgz to extract EC
as a volume mask

cheers
Bruce
On Tue, 12 Jun 2018, Erik O'Hanlon wrote:

>External Email - Use Caution
>
> Hi FS experts ,
>
>
> I'd like to make masks for the entorhinal cortex to use for tractography. Can 
> you advise what FS tool should be used? I've used the mri_extract_label for 
> my hippocampal masks but not sure what files to use to extract EC ? I'm sure 
> it's straightforward
>
>
> Thanks for any advice
>
>
> Best regards
>
>
> Erik
>
> Erik O'Hanlon
> Postdoctoral researcher
>
> [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]
>
> RCSI Psychiatry
> Royal College of Surgeons in Ireland
> Beaumont Road, Beaumont D9 Ireland
> T: 8093740
> E: erikohan...@rcsi.ie W: www.rcsi.com
>
>
> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 
> 2018-2022
>
>
> RCSI LEADING THE WORLD TO BETTER HEALTH
>
> [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]
>
>
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Erik O'Hanlon
Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont D9 Ireland
T: 8093740
E: erikohan...@rcsi.ie W: www.rcsi.com


Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 
2018-2022


RCSI LEADING THE WORLD TO BETTER HEALTH

[cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]

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Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Nikita,
Could you please be a bit more specific about your problem? What issue are you 
exactly referring to?
Also, can you please send us the log file of the hippocampal subfields (rather 
than of recon-all)?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Nikita Nogovitsyn 

Reply-To: Freesurfer support list 
Date: Tuesday, 12 June 2018 at 16:49
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing 
workflow question, more LH than RH files


External Email - Use Caution
HI

I would like to report to have the same issue. There were no errors in the log 
yet the majority of results missing right hemisphere.

Attaching here the log file, or you can also access it via googledrive here: 
https://drive.google.com/open?id=13PVEWL4d6VuOJcIztWPTe83yz4Oi61Rv

Thanks
Nikita
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[Freesurfer] crypt_gkey = (null)

[Aaron Tanenbaum]

External Email - Use Caution

I am currently running CentOS 7.5 and attempting to run FreeSurfer 5.3.
When i get to the part where MRI_convert is creating the the orig001.mgz
its gives me a segmentation fault. if i run this on a centos 6 system it
works fine. below is the output of the program.


/data/gizmo/data1/freesurfer5.3/bin/mri_convert
/data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm
/data/anlab/Aaron/JoEtzl_testing/FreeSurfer/Test1/mri/orig/001.mgz
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from
/data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm...
crypt_gkey = (null)
Segmentation fault (core dumped)



Did I do anything wrong?
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Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

[Nikita Nogovitsyn]

External Email - Use Caution

HI

I would like to report to have the same issue. There were no errors in the log 
yet the majority of results missing right hemisphere.

Attaching here the log file, or you can also access it via googledrive here: 
https://drive.google.com/open?id=13PVEWL4d6VuOJcIztWPTe83yz4Oi61Rv

Thanks
Nikita
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[Freesurfer] Difference between Freesurfer and Voxel Based Morphometry

[Miguel Ángel Rivas Fernández]

External Email - Use Caution

Hi Freesurfer developers,


I´m starting in structural MRI analysis with Freesurfer and i would like to
know what is the main difference between freesurfer and the voxel based
morphometry approach. It is more appropiate to use a method for some
specific analysis?


Thanks in advance.


Best,

-- 
*Miguel Ángel Rivas Fernández*
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Re: [Freesurfer] Extract the entorhinal cortex as a mask

[Bruce Fischl]

Hi Erik

yes, you can apply mri_extract_label to the aparc+aseg.mgz to extract EC 
as a volume mask

cheers
Bruce
On Tue, 12 Jun 2018, Erik O'Hanlon wrote:

>External Email - Use Caution
>
> Hi FS experts ,
>
>
> I'd like to make masks for the entorhinal cortex to use for tractography. Can 
> you advise what FS tool should be used? I've used the mri_extract_label for 
> my hippocampal masks but not sure what files to use to extract EC ? I'm sure 
> it's straightforward
>
>
> Thanks for any advice
>
>
> Best regards
>
>
> Erik
>
> Erik O'Hanlon
> Postdoctoral researcher
>
> [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]
>
> RCSI Psychiatry
> Royal College of Surgeons in Ireland
> Beaumont Road, Beaumont D9 Ireland
> T: 8093740
> E: erikohan...@rcsi.ie W: www.rcsi.com
>
>
> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 
> 2018-2022
>
>
> RCSI LEADING THE WORLD TO BETTER HEALTH
>
> [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]
>
>
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[Freesurfer] Extract the entorhinal cortex as a mask

[Erik O'Hanlon]

External Email - Use Caution

Hi FS experts ,


I'd like to make masks for the entorhinal cortex to use for tractography. Can 
you advise what FS tool should be used? I've used the mri_extract_label for my 
hippocampal masks but not sure what files to use to extract EC ? I'm sure it's 
straightforward


Thanks for any advice


Best regards


Erik

Erik O'Hanlon
Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont D9 Ireland
T: 8093740
E: erikohan...@rcsi.ie W: www.rcsi.com


Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 
2018-2022


RCSI LEADING THE WORLD TO BETTER HEALTH

[cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]

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