Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

[Antonin Skoch]

Dear David,

did you use

-uselongbasewmedits

in your recon-all -long run?

If this flag is not used, the wm edits are transfered to long from cross, not 
from the base.

Regards,

Antonin Skoch



Andrew, thanks for your response. I am still not seeing the white matter edit 
performance that I am expecting, or that I have seen from using the cross 
stream on 5.3 in the past with a different dataset.I started with a new subject 
with two timepoints. I ran recon-all on both for 
the cross stream with no edits, and then ran the base. I edited the wm.mgz for 
the base, then ran “recon-all –autorecon2-wm –autorecon3 –base xx_base –tp 
xx_t1 –tp xx_t2”. I noticed the surfaces didn’t really change in the base, but 
I went ahead and ran the two long runs using “recon-all –all –long xx_tx 
xx_base” and although there are minor differences in the base and time point 
surfaces, the white matter edits I did on the base were largely ignored, and 
none of them were included in the time point long run wm.mgz files.

I am tempted to try these same analyses using Linux (I am running this on OSX 
10.11 currently), as I experienced a completely different response from the 
surface generation modules to my edits in the past when using Linux. I’m 
thinking this is a real long shot, but I cannot otherwise figure out why the 
software would be behaving so differently from my past experiences.

Any thoughts? Thanks!

Best,

David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885

IMPORTANT NOTICE:  This e-mail is meant only for the use of the intended 
recipient.  It may contain confidential information which is legally privileged 
or otherwise protected by law.  If you received this e-mail in error or from 
someone who was not authorized to send it to you, you are strictly prohibited 
from reviewing, using, disseminating, distributing or copying the e-mail.  
PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS 
MESSAGE FROM YOUR SYSTEM.  Thank you for your cooperation.

From: "Hoopes, Andrew" 
Date: Wednesday, March 15, 2017 at 12:47 PM
To: Freesurfer support list , David Semanek 

Cc: Bruce Fischl 
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 
Cross and Long Streams


Hi David



Try editing the base wm.mgz first instead of editing the long and cross wm 
files. Rerun autorecon2-wm and autorecon3 for the base dir, then completely 
rerun the longitudinals. The long surfaces are initialized from the base 
surfaces, so this could be why your wm fixes seem to have no effect.

You can find more info here:

https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits#CheatSheet

If editing the base doesn't solve the problem, you can send me the commands you 
ran in order and I can look into this further.

best,
Andrew


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of David Semanek 

Sent: Monday, March 13, 2017 11:55 AM
To: Bruce Fischl; Freesurfer support list
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 
Cross and Long Streams

Thanks, I have uploaded the cross and long stream processing from one subject 
which requires numerous white matter edits to correct defects in the white 
matter surfaces; the file is on the ftp server as dsemanek.zip.

Both of the cross subject folders, s02_t1 and s02_t2 have had edits done to 
both the brainmask as well as the wm files, and autorecon2-wm and autorecon-3 
have been run on them, as well as the long folder for the first time point, 
s02_t1.long.s02_base.

It was in working with the rerun results of s02_t1.long.s02_base that I noticed 
the white matter surfaces after being regenerated with the edited wm.mgz did 
not reflect any of the edits. The easiest way to see this is to load the wm.mgz 
with the white matter surfaces and scroll through the slices, there are 
numerous areas where the contours of the white matter surfaces do not follow 
the voxels of the wm.mgz volume, mostly near what should be identified as 
hyperintense gray matter. I’m fairly certain the white matter surfaces didn’t 
change at all after running autorecon2-wm with the wm.mgz edits.

Thanks for taking a look at our data.

Best,

David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885

IMPORTANT NOTICE:  This e-mail is meant only for the use of the intended 

[Freesurfer] Postdoc position at the Ohio State University

[Zeynep Saygin]

POSTDOCTORAL FELLOW, The Ohio State University, Dept. of Psychology –
Saygin Lab.  We seek an outstanding scientist with a recent Ph.D. in
cognitive neuroscience, developmental psychology, or related area, who has
experience with neuroimaging methods (MRI, fMRI, DWI, and/or functional
connectivity) and who is interested in any or all of the following:
understanding the functional and structural architecture of the brain, how
it develops in healthy individuals, and how it changes with disorders and
brain injury in both adults and children.  See http://web.mit.edu/zsaygin
for recent publications.  The fellow will be involved in conducting and
planning behavioral and neuroimaging research studies in neonates, infants,
children, and adults. Proficiency in programming is necessary.   This
position is fully funded.  Initial hire is for one year with additional
years contingent on fit and progress.



OSU is located in Columbus, Ohio and is home to a vibrant community of
cognitive neuroscientists, computational modelers, and vision scientists in
the Psychology Department and Center for Cognitive and Brain Sciences.
Fellows will have access to state-of-the-art MRI and EEG facilities located
inside the Psychology building.



Interested individuals should contact zsay...@mit.edu with a CV, names of 3
references, and a statement of research interests.

-- 
Zeynep M. Saygin, Ph.D.
MIT, Brain and Cognitive Sciences
MGH, Martinos Center
43 Vassar St. 46-4141
Cambridge, MA 02139
http://web.mit.edu/zsaygin
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Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

[David Semanek]

Andrew, thanks for your response. I am still not seeing the white matter edit 
performance that I am expecting, or that I have seen from using the cross 
stream on 5.3 in the past with a different dataset.

I started with a new subject with two timepoints. I ran recon-all on both for 
the cross stream with no edits, and then ran the base. I edited the wm.mgz for 
the base, then ran “recon-all –autorecon2-wm –autorecon3 –base xx_base –tp 
xx_t1 –tp xx_t2”. I noticed the surfaces didn’t really change in the base, but 
I went ahead and ran the two long runs using “recon-all –all –long xx_tx 
xx_base” and although there are minor differences in the base and time point 
surfaces, the white matter edits I did on the base were largely ignored, and 
none of them were included in the time point long run wm.mgz files.

I am tempted to try these same analyses using Linux (I am running this on OSX 
10.11 currently), as I experienced a completely different response from the 
surface generation modules to my edits in the past when using Linux. I’m 
thinking this is a real long shot, but I cannot otherwise figure out why the 
software would be behaving so differently from my past experiences.

Any thoughts? Thanks!

Best,

David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885

IMPORTANT NOTICE:  This e-mail is meant only for the use of the intended 
recipient.  It may contain confidential information which is legally privileged 
or otherwise protected by law.  If you received this e-mail in error or from 
someone who was not authorized to send it to you, you are strictly prohibited 
from reviewing, using, disseminating, distributing or copying the e-mail.  
PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS 
MESSAGE FROM YOUR SYSTEM.  Thank you for your cooperation.

From: "Hoopes, Andrew" 
Date: Wednesday, March 15, 2017 at 12:47 PM
To: Freesurfer support list , David Semanek 

Cc: Bruce Fischl 
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 
Cross and Long Streams


Hi David



Try editing the base wm.mgz first instead of editing the long and cross wm 
files. Rerun autorecon2-wm and autorecon3 for the base dir, then completely 
rerun the longitudinals. The long surfaces are initialized from the base 
surfaces, so this could be why your wm fixes seem to have no effect.

You can find more info here:

https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits#CheatSheet

If editing the base doesn't solve the problem, you can send me the commands you 
ran in order and I can look into this further.

best,
Andrew


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of David Semanek 

Sent: Monday, March 13, 2017 11:55 AM
To: Bruce Fischl; Freesurfer support list
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 
Cross and Long Streams

Thanks, I have uploaded the cross and long stream processing from one subject 
which requires numerous white matter edits to correct defects in the white 
matter surfaces; the file is on the ftp server as dsemanek.zip.

Both of the cross subject folders, s02_t1 and s02_t2 have had edits done to 
both the brainmask as well as the wm files, and autorecon2-wm and autorecon-3 
have been run on them, as well as the long folder for the first time point, 
s02_t1.long.s02_base.

It was in working with the rerun results of s02_t1.long.s02_base that I noticed 
the white matter surfaces after being regenerated with the edited wm.mgz did 
not reflect any of the edits. The easiest way to see this is to load the wm.mgz 
with the white matter surfaces and scroll through the slices, there are 
numerous areas where the contours of the white matter surfaces do not follow 
the voxels of the wm.mgz volume, mostly near what should be identified as 
hyperintense gray matter. I’m fairly certain the white matter surfaces didn’t 
change at all after running autorecon2-wm with the wm.mgz edits.

Thanks for taking a look at our data.

Best,

David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885

IMPORTANT NOTICE:  This e-mail is meant only for the use of the intended 
recipient.  It may contain confidential information which is legally privileged 
or otherwise protected by law.  If you received this e-mail in error or from 
someone who was not authorized to send 

Re: [Freesurfer] Error in Reconstruction of bert samples.

[zkaufman]

Thats odd. Does that file exist? What are the permissions of it?

  ls -l
/home/iplneurosurgery/Documents/freesurfer/subjects/bert/mri/brainmask.mgz




> IPL Neurosurgery has shared a OneDrive file with you. To view it,
> click the link below.
>
>
> 
> [https://r1.res.office365.com/owa/prem/images/dc-generic_20.png]
>
> recon-all 1.log
>
>
>
>
> Hi,
>
>
> We have encountered a error in skull stripping process in bert sample. We
> are a novice. We attached the log.
>
>
> Command : recon-all -s bert -all
>
>
> #@# Skull Stripping Sat Mar 18 14:58:05 IST 2017
> /home/iplneurosurgery/Documents/freesurfer/subjects/bert/mri
>
>  mri_watershed -rusage
> /home/iplneurosurgery/Documents/freesurfer/subjects/bert/touch/rusage.mri_watershed.dat
> -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas
> /home/iplneurosurgery/Documents/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca
> transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
>
>
> Keeping brain edits brainmask.auto.mgz brainmask.mgz
> Mode:  T1 normalized volume
> Mode:  Use the information of atlas (default parms, --help for
> details)
> mghRead(/home/iplneurosurgery/Documents/freesurfer/subjects/bert/mri/brainmask.mgz,
> -1): read error
>
> *
> The input file is T1.mgz
> The output file is brainmask.auto.mgz
> No such file or directory
> Linux localhost.localdomain 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18
> 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s bert exited with ERRORS at Sat Mar 18 14:58:06 IST 2017
>
> freesurfer version:
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>
>
> Platform: Cent OS 7
>
>
> uname -a : 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017
> x86_64 x86_64 x86_64 GNU/Linux
>
> Any Suggestion will be appreciated.
>
>
> Thanking you,
>
>
> IPL Neurosurgery.
>
>
>
> Sent from Outlook
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] freesurfer license tx

[zkaufman]

Usually it would be /usr/local/freesurfer

If thats what you did than you may need root access to the machine to be
able to do that. So basically create the license.txt file in your home
directory than copy it to the frresurfer folder:

  sudo cp license.txt /usr/local/freesurfer/

Bottom line is you need to put that license.txt file in the same location
that freesurfer was installed (Under the freesurfer folder).



>
>
> i received the license through the email and tried to make a new text file
> contains the emailed licensed details .. i am confused where exactly to
> save it
>
> i tried to save it in the user/local/freesurfer but it show a permission
> error
> "ou do not have the permissions necessary to save the file. Please check
> that you typed the location correctly and try again"
>
>
> i am using the newest freesurfer release and the Ubuntu 16.04 I'm
> completely new to Linux and
>
> thanx a lot
>
> fatima
>
> PhD student
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

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[Freesurfer] Postdoctoral Position - Multimodal neuroimaging in dementia

[Heidi Foo]

Postdoctoral research fellow positions are available in the Department of
Neurology Research at the National Neuroscience Institute, Singapore. Our
focus is to use neuroimaging techniques as a surrogate pathological marker
to understand the underlying neurobiological basis of dementia especially
in the preclinical stages. We are seeking highly motivated individuals who
have extensive research experience in neuroimaging analyses (e.g.
structural, diffusion, functional MRI) using FreeSurfer, Statistical
Parametric Mapping, and FMRIB Software Library; and demonstrate academic
excellence including publications in first-class journals and conferences.
The postdoctoral candidate should have a Ph.D. (or equivalent) in
Neuroscience, Computer Science, Applied Mathematics/Statistics, Electrical
Engineering, Biomedical Engineering, or related fields. Good command of
programming tools including Matlab, C++, Linux, and scripting are necessary
to carry out the research work in this group. The candidate will support
our efforts either in advancing neuroimaging analysis technologies or in
neuroscience applications.

The successful candidate will be part of a diverse group including
neuroscientists, radiologists, psychologists, physicists, biostatistician,
and computer scientists, and will build upon the group's extensive
foundation on neuroimaging analysis. If interested, please email resume to
Professor Nagaendran Kandiah (nagaendran.kand...@singhealth.com.sg)
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[Freesurfer] preproc-sess -per-run vs. -per-session

[Feilong Ma]

Hi FreeSurfer Experts,

I was reading the document of preproc-sess, and it seems -per-run is
recommended instead of -per-session.  Here is the part:

> -per-run
> Motion correct and register using the middle time point of each run.
> This is the option that you should use.
> -per-session
> Motion correct and register using the first time point of the first
> run.  This is mainly for compatability with version 4.
>

Is there a reason to preprocess each run separately?  I know some people
motion correct and register all EPI volumes to the same reference EPI
volume, which also works well.

Thanks,
Feilong
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[Freesurfer] freesurfer license tx

[Almarshad F.]

i received the license through the email and tried to make a new text file 
contains the emailed licensed details .. i am confused where exactly to save it

i tried to save it in the user/local/freesurfer but it show a permission error
"ou do not have the permissions necessary to save the file. Please check that 
you typed the location correctly and try again"


i am using the newest freesurfer release and the Ubuntu 16.04 I'm completely 
new to Linux and

thanx a lot

fatima

PhD student

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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Error in Reconstruction of bert samples.

[Allison Moreau]

Hi,


It looks like Freesurfer can't read bert's brainmask.mgz volume. Can you 
ls -l bert's mri directory and see if that file is there and you have 
proper permission to read it? mri_watershed is looking for that file 
because the command says to keep the edits from brainmask.mgz, but that 
file is normally generated after the watershed step that is failing and 
I don't see any previous instances of recon-all in the log file where 
brainmask.mgz was created.



Best,

Allison


On 03/20/2017 02:05 AM, IPL Neurosurgery wrote:
IPL Neurosurgery has shared a OneDrive file with you. To view it, 
click the link below.




recon-all 1.log 
[recon-all 1.log]

Hi,


We have encountered a error in skull stripping process in bert sample. 
We are a novice. We attached the log.



*Command :* recon-all -s bert -all


#@# Skull Stripping Sat Mar 18 14:58:05 IST 2017
/home/iplneurosurgery/Documents/freesurfer/subjects/bert/mri

 mri_watershed -rusage 
/home/iplneurosurgery/Documents/freesurfer/subjects/bert/touch/rusage.mri_watershed.dat 
-keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas 
/home/iplneurosurgery/Documents/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca 
transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz



Keeping brain edits brainmask.auto.mgz brainmask.mgz
Mode:  T1 normalized volume
Mode:  Use the information of atlas (default parms, --help for 
details)
mghRead(/home/iplneurosurgery/Documents/freesurfer/subjects/bert/mri/brainmask.mgz, 
-1): read error


*
The input file is T1.mgz
The output file is brainmask.auto.mgz
No such file or directory
Linux localhost.localdomain 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 
18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux


recon-all -s bert exited with ERRORS at Sat Mar 18 14:58:06 IST 2017

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



*Platform: *Cent OS 7


*uname -a* *: *3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 
UTC 2017 x86_64 x86_64 x86_64 GNU/Linux


Any Suggestion will be appreciated.


Thanking you,


IPL Neurosurgery.



Sent from Outlook 



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but does not contain patient information, please contact the sender and properly
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[Freesurfer] Multiple comparisons

[Laura Ferrero Montes]

   Dear FS team,
  I would like to correct for multiple comparisons after I run  
command-line GLM analysis on stats tables. I would like to make a  
second level analysis between a control group and an autism group. I  
would like to know if  there is a command-line in FreeSurfer or if   
there is any program or toolkit in Matlab that allows to do that.

Thank you,
Laura

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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] T1 error

[Manuel Delgado]

Hello Bruce:

My apologies for the incomplete way to raise the question. Anyway, we have
solved it. Thank you very much.

On Fri, Mar 17, 2017 at 3:30 PM, Bruce Fischl 
wrote:

> Hi Manuel
>
> how do you know it is binary? Have you tried changing the window levels in
> freeview when you view it? And in general when you report errors please
> include the full screen output of what you ran, and in cases like this, and
> image to illustrate the issue.
>
> cheers
> Bruce
>
>
> On Fri, 17 Mar 2017, Manuel Delgado wrote:
>
> After recon-all (recon-all  -all -s 479_001), which finished without
>> errors,
>> the T1.mgz appears as a binary mask. I am using Freesurfer v 6.0 and
>> Ubuntu
>> 16.04. Please let me know if you need further files.
>> Thank you,
>>
>>
>> Manuel
>>
>> On Thu, Mar 16, 2017 at 4:09 PM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu>
>> wrote:
>>   what is the error exactly? Please provide the recon-all.log file
>>   and a
>>   description of the problem
>>
>>
>>   On 03/16/2017 06:28 AM, Manuel Delgado wrote:
>>   > Dear list,
>>   > After recon-all the T1 seems to have an error. Has anybody had
>>   this
>>   > problem before? Please find attached the image. I guess I have
>>   to
>>   > recon-all again. I am using v 6.0 with Ubuntu 16.04.
>>   > Thank you.
>>   >
>>   > --
>>   > *Manuel Delgado Alvarado, MD*
>>   > Neurology Department
>>   > Neuroimaging Unit
>>   > Valdecilla Biomedical Research Institute, IDIVAL
>>   > Santander, SPAIN
>>   >
>>   >
>>   > ___
>>   > Freesurfer mailing list
>>   > Freesurfer@nmr.mgh.harvard.edu
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>>   Douglas N. Greve, Ph.D.
>>   MGH-NMR Center
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>>
>> --
>> Manuel Delgado Alvarado, MD
>> Neurology Department
>> Neuroimaging Unit
>> Valdecilla Biomedical Research Institute, IDIVAL
>> Santander, SPAIN
>>
>>
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-- 
*Manuel Delgado Alvarado, MD*
Neurology Department
Neuroimaging Unit
Valdecilla Biomedical Research Institute, IDIVAL
Santander, SPAIN
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[Freesurfer] Error in Reconstruction of bert samples.

[IPL Neurosurgery]

IPL Neurosurgery has shared a OneDrive file with you. To view it, click the 
link below.



[https://r1.res.office365.com/owa/prem/images/dc-generic_20.png]

recon-all 1.log




Hi,


We have encountered a error in skull stripping process in bert sample. We are a 
novice. We attached the log.


Command : recon-all -s bert -all


#@# Skull Stripping Sat Mar 18 14:58:05 IST 2017
/home/iplneurosurgery/Documents/freesurfer/subjects/bert/mri

 mri_watershed -rusage 
/home/iplneurosurgery/Documents/freesurfer/subjects/bert/touch/rusage.mri_watershed.dat
 -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas 
/home/iplneurosurgery/Documents/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca
 transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz


Keeping brain edits brainmask.auto.mgz brainmask.mgz
Mode:  T1 normalized volume
Mode:  Use the information of atlas (default parms, --help for details)
mghRead(/home/iplneurosurgery/Documents/freesurfer/subjects/bert/mri/brainmask.mgz,
 -1): read error

*
The input file is T1.mgz
The output file is brainmask.auto.mgz
No such file or directory
Linux localhost.localdomain 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 
13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s bert exited with ERRORS at Sat Mar 18 14:58:06 IST 2017

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


Platform: Cent OS 7


uname -a : 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 
x86_64 x86_64 GNU/Linux

Any Suggestion will be appreciated.


Thanking you,


IPL Neurosurgery.



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