Re: [Freesurfer] mrisComputeCorrelationTerm: delta is not finite at vno 0

[Juhyoung Ryu]

I checked version of recon-all script using 'recon-all -version’ command
and 'freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c’ is printed.

Juhyoung

> On Feb 9, 2017, at 1:02 PM, Bruce Fischl  wrote:
> 
> What does
> 
> which recon-all
> 
> return?
> 
>> On Feb 8, 2017, at 10:54 PM, Juhyoung Ryu  wrote:
>> 
>> Yes, I set FREESURFER_HOME variable as '/Applications/freesurfer’, which I 
>> installed freesurfer v6.
>> I attached recon-all.log file below.
>> I can see 'build-stamp.txt: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c’ 
>> in log file.
>> 
>> Is there anything to check more?
>> 
>> Thank you,
>> Juhyoung
>> 
>> 
>> 
>> 
>>> On Feb 9, 2017, at 12:38 PM, Bruce Fischl  
>>> wrote:
>>> 
>>> sounds like you are using the old (5.2) recon-all. Are you sure it is 6 in 
>>> your path?
>>> 
>>> And can you email the list so others can answer?
>>> 
>>> thanks
>>> Bruce
>>> 
>>> 
 On Thu, 9 Feb 2017, Juhyoung Ryu wrote:
 
 Hi Bruce,
 I installed FREESURFER with version 6.0 for your recommendation and I got 
 an
 error:
 mri_em_register: could not open GCA
 /Applications/freesurfer/average/RB_all_2008-03-26.gca.
 That file not exist in ‘average' folder, and there is one similar
 file: RB_all_2016-05-10.vc700.gca
 Do you think I should drop that file manually from FREESURFER v5.2?
 Thank you in advance,Juhyoung
 
Begin forwarded message:
 From: Juhyoung Ryu 
 Subject: Re: [Freesurfer] mrisComputeCorrelationTerm: delta is not
 finite at vno 0
 Date: February 8, 2017 at 11:01:23 AM GMT+9
 To: Z K 
 Cc: Bruce Fischl 
 Hi Zeke and Bruce,
 Thank you very much for your help.
 I’ll try it now and share the results.
 Thanks!
 Juhyoung.
 
On Feb 8, 2017, at 8:13 AM, Z K
 wrote:
 Hello Juhyoung,
 I noticed from the recon-all.log files that you are using
 freesurfer v5.2. It was revealed that this version had issues
 regarding systematic white surface contraction and placement of
 the pial surface extending too far:
 https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-May/029581.html
 I would recommend processing these subjects with version 6.0
 https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
 -Zeke
 On 02/06/2017 01:43 AM, Juhyoung Ryu wrote:
 
Hi FS developers,
 
I received errors in one of steps in recon-all.
I analyzed 111 individual subjects' T1 data using
same method, but there
are errors in _only 14 subjects._
 
Below is screenshot image in the end of
recon-all.log file. I attached
log files from two exemplar subjects below, also.
 
I’d appreciate if you might help me.
Juhyoung.
 
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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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Re: [Freesurfer] mrisComputeCorrelationTerm: delta is not finite at vno 0

[Bruce Fischl]

What does

which recon-all

return?

> On Feb 8, 2017, at 10:54 PM, Juhyoung Ryu  wrote:
> 
> Yes, I set FREESURFER_HOME variable as '/Applications/freesurfer’, which I 
> installed freesurfer v6.
> I attached recon-all.log file below.
> I can see 'build-stamp.txt: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c’ 
> in log file.
> 
> Is there anything to check more?
> 
> Thank you,
> Juhyoung
> 
> 
> 
> 
>> On Feb 9, 2017, at 12:38 PM, Bruce Fischl  wrote:
>> 
>> sounds like you are using the old (5.2) recon-all. Are you sure it is 6 in 
>> your path?
>> 
>> And can you email the list so others can answer?
>> 
>> thanks
>> Bruce
>> 
>> 
>>> On Thu, 9 Feb 2017, Juhyoung Ryu wrote:
>>> 
>>> Hi Bruce,
>>> I installed FREESURFER with version 6.0 for your recommendation and I got an
>>> error:
>>> mri_em_register: could not open GCA
>>> /Applications/freesurfer/average/RB_all_2008-03-26.gca.
>>> That file not exist in ‘average' folder, and there is one similar
>>> file: RB_all_2016-05-10.vc700.gca
>>> Do you think I should drop that file manually from FREESURFER v5.2?
>>> Thank you in advance,Juhyoung
>>> 
>>> Begin forwarded message:
>>> From: Juhyoung Ryu 
>>> Subject: Re: [Freesurfer] mrisComputeCorrelationTerm: delta is not
>>> finite at vno 0
>>> Date: February 8, 2017 at 11:01:23 AM GMT+9
>>> To: Z K 
>>> Cc: Bruce Fischl 
>>> Hi Zeke and Bruce,
>>> Thank you very much for your help.
>>> I’ll try it now and share the results.
>>> Thanks!
>>> Juhyoung.
>>> 
>>> On Feb 8, 2017, at 8:13 AM, Z K
>>>  wrote:
>>> Hello Juhyoung,
>>> I noticed from the recon-all.log files that you are using
>>> freesurfer v5.2. It was revealed that this version had issues
>>> regarding systematic white surface contraction and placement of
>>> the pial surface extending too far:
>>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-May/029581.html
>>> I would recommend processing these subjects with version 6.0
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
>>> -Zeke
>>> On 02/06/2017 01:43 AM, Juhyoung Ryu wrote:
>>> 
>>> Hi FS developers,
>>> 
>>> I received errors in one of steps in recon-all.
>>> I analyzed 111 individual subjects' T1 data using
>>> same method, but there
>>> are errors in _only 14 subjects._
>>> 
>>> Below is screenshot image in the end of
>>> recon-all.log file. I attached
>>> log files from two exemplar subjects below, also.
>>> 
>>> I’d appreciate if you might help me.
>>> Juhyoung.
>>> 
>>> ___
>>> 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.
> 


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Re: [Freesurfer] mrisComputeCorrelationTerm: delta is not finite at vno 0

[Juhyoung Ryu]

Yes, I set FREESURFER_HOME variable as '/Applications/freesurfer’, which I 
installed freesurfer v6.
I attached recon-all.log file below.
I can see 'build-stamp.txt: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c’ in 
log file.

Is there anything to check more?

Thank you,
Juhyoung



recon-all.log
Description: Binary data


> On Feb 9, 2017, at 12:38 PM, Bruce Fischl  wrote:
> 
> sounds like you are using the old (5.2) recon-all. Are you sure it is 6 in 
> your path?
> 
> And can you email the list so others can answer?
> 
> thanks
> Bruce
> 
> 
> On Thu, 9 Feb 2017, Juhyoung Ryu wrote:
> 
>> Hi Bruce,
>> I installed FREESURFER with version 6.0 for your recommendation and I got an
>> error:
>> mri_em_register: could not open GCA
>> /Applications/freesurfer/average/RB_all_2008-03-26.gca.
>> That file not exist in ‘average' folder, and there is one similar
>> file: RB_all_2016-05-10.vc700.gca
>>  Do you think I should drop that file manually from FREESURFER v5.2?
>> Thank you in advance,Juhyoung
>> 
>>  Begin forwarded message:
>> From: Juhyoung Ryu 
>> Subject: Re: [Freesurfer] mrisComputeCorrelationTerm: delta is not
>> finite at vno 0
>> Date: February 8, 2017 at 11:01:23 AM GMT+9
>> To: Z K 
>> Cc: Bruce Fischl 
>> Hi Zeke and Bruce,
>> Thank you very much for your help.
>> I’ll try it now and share the results.
>> Thanks!
>> Juhyoung.
>> 
>>  On Feb 8, 2017, at 8:13 AM, Z K
>>   wrote:
>> Hello Juhyoung,
>> I noticed from the recon-all.log files that you are using
>> freesurfer v5.2. It was revealed that this version had issues
>> regarding systematic white surface contraction and placement of
>> the pial surface extending too far:
>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-May/029581.html
>> I would recommend processing these subjects with version 6.0
>>  https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
>> -Zeke
>> On 02/06/2017 01:43 AM, Juhyoung Ryu wrote:
>> 
>>  Hi FS developers,
>> 
>>  I received errors in one of steps in recon-all.
>>  I analyzed 111 individual subjects' T1 data using
>>  same method, but there
>>  are errors in _only 14 subjects._
>> 
>>  Below is screenshot image in the end of
>>  recon-all.log file. I attached
>>  log files from two exemplar subjects below, also.
>> 
>>  I’d appreciate if you might help me.
>>  Juhyoung.
>> 
>>  ___
>>  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.

___
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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] recon-all -autorecon2-cp -autorecon-wm -autorecon-pial issue

[Bruce Fischl]

Hi Qian

if you look at the recon-all help you will see:

USAGE: recon-all

 Required Arguments:
   -subjid 
   -

 Fully-Automated Directive:
  -all   : performs all stages of cortical reconstruction
  -autorecon-all : same as -all

 Manual-Intervention Workflow Directives:
  -autorecon1: process stages 1-5 (see below)
  -autorecon2: process stages 6-23
   after autorecon2, check white surfaces:
 a. if wm edit was required, then run -autorecon2-wm
 b. if control points added, then run -autorecon2-cp
 c. proceed to run -autorecon3
  -autorecon2-cp : process stages 12-23 (uses -f w/ mri_normalize, -keep 
w/ mri_seg)

  -autorecon2-wm : process stages 15-23
  -autorecon2-inflate1 : 6-18
  -autorecon2-perhemi : tess, sm1, inf1, q, fix, sm2, inf2, finalsurf, 
ribbon

  -autorecon3: process stages 24-34
 if edits made to correct pial, then run 
-autorecon-pial

  -hemi ?h   : just do lh or rh (default is to do both)


the pial surface regeneration is now part of autorecon3

cheers
Bruce


On 
Thu, 9 
Feb 2017, 冉倩 
wrote:




Hi Bruce,
I am a little confused about it. I found 'Manual-Intervention Workflow
Directives' on recon-all free surfer wiki web. 
[IMAGE]
It said if edits made to correct pial, run-autorecon2-pial. 
If I only edit pial, I run >recon-all -autrecon-pial -s  -sd
 to fix this issue, I also should rerunning autorecon3? or
which command I should use to continue to next step? Thanks a lot.
Best Regards,
Qian Ran



At 2017-02-09 08:55:34, "Bruce Fischl"  wrote:
>Hi Qian
>
>if you just want to regenerate the pial, then yes, edit the 
>brain.finalsurfs.mgz and run:

>
>recon-all -autrecon-pial -s  -sd 
>
>note that it is NOT autorecon2-pial, but just autorecon-pial (leave out the

>'2')
>
>cheeers
>Bruce
>
>
>On Thu, 9 Feb 2017, 冉倩 wrote:
>
>> Hi Bruce,
>> If I use brain.finalsurfs, then I run recon-all -autorecon2-pial -subjid
>> sub01 or recon-all -autorecon2-pial -autorecon3 -subjid sub01? autorecon3
>> still need rerunning? Thanks!
>> Best Regards,
>> Qian Ran
>> 
>> 
>> 
>> 
>> At 2017-02-08 12:19:35, "Bruce Fischl"  wrote

:
>> brain.finalsurfs is fine if you are just rerunning the pial. Edit
>> brainmask if you are starting earlier so all the downstream volumes
>> including brain.finalsurfs will have the dura removed
>> Cheers
>> Bruce
>> 
>> On Feb 7, 2017, at 10:45 PM, 冉倩  wrote:
>> 
>> 
>> 
>>

>>   brain.finalsurfs.mgz? not brainmask.mgz? 
>> or brain.finalsurfs.mgz for pial surface edit and brainmask for
>> wm surface edit?
>> 
>> 
>> At 2017-02-08 11:41:40, "Douglas Greve"

>>  wrote:
>>
>>   You should edit the brain.finalsurfs.mgz to remove
>>   the non-brain then run with -autorecon-pial
>> 
>>

>>   On 2/7/17 10:37 PM, 冉倩 wrote:
>> 
>>

>>   Hi Prof.Douglas Greve,
>> 
>> Yes, probematic surface normally existed near

>> supeiror dura ( aroun superior frontal lobe or
>> parietal lobe or central gry area). Just now I am
>> confused about the next steps.  If I manually erase
>> ( whether I can modfiy control point just like
>> modify wm) the dura on the brainmask.mgz to correct
>> pial surface. Then I shoud re-run command: recon-all
>> -autorecon2 -autorecon-3 sub01? or just recon-all
>> -autorecon2-pial -autorecon3 sub01? Thanks!
>> 
>> Best Regards,

>> Qian Ran
>> 
>> At 2017-02-08 11:21:57, "Douglas Greve"

>>  wrote:
>>
>>   I think Bruce is referring only to the
>>   first image. For the second image, it
>>   looks like most of the problematic
>>   surface is going through the amygdala or
>>   hippocampus in which case it does not
>>   need to be fixed.
>> 
>>

>>   On 2/7/17 9:57 PM, Bruce Fischl wrote:
>>   oh yes, it's grabbing a bit of
>>   dura. If you have a 1mm-ish T2 or
>>   FLAIR you can use it to
>>   automatically correct this type of
>>   problem. Or you can erase the dura
>>   in those regions on the
>>   brainmask.mgz and recreate the
>>   pial surface
>>
>>   cheers
>>   Bruce
>> 
>> 
>>

>>   On Wed, 8 Feb 2017, 冉倩 wrote:
>>
>> Hi Bruce,
>> Thanks for your reply.
>>
>> [IMAGE]
>> For this, I think pial
>> surface  (the location
>> where I circle)
>>  already
>> located outside of
>> brain. 
>> [IMAGE]
>> For this, pail surface
>> (near hippcamps I
>> think) located inside
>> of cortical I
>> think. 
>>
>> I mean if I manually
>> modify surface, how do
>> it? Thanks very much!
>> Best Regards,
>> Qian Ran
>>
>> At 2017-02-08
>> 09:54:30, "Bruce
>> Fischl"

Re: [Freesurfer] recon-all -autorecon2-cp -autorecon-wm -autorecon-pial issue

[冉倩]

Hi Bruce,
I am a little confused about it. I found 'Manual-Intervention Workflow 
Directives' on recon-all free surfer wiki web. 
It said if edits made to correct pial, run-autorecon2-pial. 
If I only edit pial, I run >recon-all -autrecon-pial -s  -sd 
 to fix this issue, I also should rerunning autorecon3? or which 
command I should use to continue to next step? Thanks a lot.
Best Regards,
Qian Ran






At 2017-02-09 08:55:34, "Bruce Fischl"  wrote:
>Hi Qian
>
>if you just want to regenerate the pial, then yes, edit the 
>brain.finalsurfs.mgz and run:
>
>recon-all -autrecon-pial -s  -sd 
>
>note that it is NOT autorecon2-pial, but just autorecon-pial (leave out the 
>'2')
>
>cheeers
>Bruce
>
>
>On Thu, 9 Feb 2017, 冉倩 wrote:
>
>> Hi Bruce,
>> If I use brain.finalsurfs, then I run recon-all -autorecon2-pial -subjid
>> sub01 or recon-all -autorecon2-pial -autorecon3 -subjid sub01? autorecon3
>> still need rerunning? Thanks!
>> Best Regards,
>> Qian Ran
>> 
>> 
>> 
>> 
>> At 2017-02-08 12:19:35, "Bruce Fischl"  wrote:
>> brain.finalsurfs is fine if you are just rerunning the pial. Edit
>> brainmask if you are starting earlier so all the downstream volumes
>> including brain.finalsurfs will have the dura removed
>> Cheers
>> Bruce
>> 
>> On Feb 7, 2017, at 10:45 PM, 冉倩  wrote:
>> 
>> 
>> 
>>
>>   brain.finalsurfs.mgz? not brainmask.mgz? 
>> or brain.finalsurfs.mgz for pial surface edit and brainmask for
>> wm surface edit?
>> 
>> 
>> At 2017-02-08 11:41:40, "Douglas Greve"
>>  wrote:
>>
>>   You should edit the brain.finalsurfs.mgz to remove
>>   the non-brain then run with -autorecon-pial
>> 
>>
>>   On 2/7/17 10:37 PM, 冉倩 wrote:
>> 
>>
>>   Hi Prof.Douglas Greve,
>> 
>> Yes, probematic surface normally existed near
>> supeiror dura ( aroun superior frontal lobe or
>> parietal lobe or central gry area). Just now I am
>> confused about the next steps.  If I manually erase
>> ( whether I can modfiy control point just like
>> modify wm) the dura on the brainmask.mgz to correct
>> pial surface. Then I shoud re-run command: recon-all
>> -autorecon2 -autorecon-3 sub01? or just recon-all
>> -autorecon2-pial -autorecon3 sub01? Thanks!
>> 
>> Best Regards,
>> Qian Ran
>> 
>> At 2017-02-08 11:21:57, "Douglas Greve"
>>  wrote:
>>
>>   I think Bruce is referring only to the
>>   first image. For the second image, it
>>   looks like most of the problematic
>>   surface is going through the amygdala or
>>   hippocampus in which case it does not
>>   need to be fixed.
>> 
>>
>>   On 2/7/17 9:57 PM, Bruce Fischl wrote:
>>   oh yes, it's grabbing a bit of
>>   dura. If you have a 1mm-ish T2 or
>>   FLAIR you can use it to
>>   automatically correct this type of
>>   problem. Or you can erase the dura
>>   in those regions on the
>>   brainmask.mgz and recreate the
>>   pial surface
>>
>>   cheers
>>   Bruce
>> 
>> 
>>
>>   On Wed, 8 Feb 2017, 冉倩 wrote:
>>
>> Hi Bruce,
>> Thanks for your reply.
>>
>> [IMAGE]
>> For this, I think pial
>> surface  (the location
>> where I circle)
>>  already
>> located outside of
>> brain. 
>> [IMAGE]
>> For this, pail surface
>> (near hippcamps I
>> think) located inside
>> of cortical I
>> think. 
>>
>> I mean if I manually
>> modify surface, how do
>> it? Thanks very much!
>> Best Regards,
>> Qian Ran
>>
>> At 2017-02-08
>> 09:54:30, "Bruce
>> Fischl"
>> 
>> wrote:
>> >Hi Qian
>> >
>> >I'm not sure I
>> understand what you
>> think is wrong in the
>> images you >included.
>> The first two
>> locations look quite
>> accurate to me, and
>> I'm not >positive but
>> I think the third
>> image the locations
>> you circle are
>> amygdala,
>>
>> >so not neocortical at
>> all
>> >
>> >cheers
>> >Bruce
>> >
>> >
>> >
>> >
>> >
>> >On Wed, 8 Feb 2017,
>> 冉倩 wrote:
>> >
>> >> >> >> Dear
>> Prof.Douglas Greve,
>> >>  Thanks for your
>> reply. I add parts of
>> problem screenshot of
>> white/pial
>> >> surface. 
>> >> >>   When I did
>> freesurfer for
>> structure analysis, I
>> was confused by some
>> 

Re: [Freesurfer] recon-all -autorecon2-cp -autorecon-wm -autorecon-pial issue

[Bruce Fischl]

Hi Qian

if you just want to regenerate the pial, then yes, edit the 
brain.finalsurfs.mgz and run:


recon-all -autrecon-pial -s  -sd 

note that it is NOT autorecon2-pial, but just autorecon-pial (leave out the 
'2')


cheeers
Bruce


On Thu, 9 Feb 2017, 冉倩 wrote:


Hi Bruce,
If I use brain.finalsurfs, then I run recon-all -autorecon2-pial -subjid
sub01 or recon-all -autorecon2-pial -autorecon3 -subjid sub01? autorecon3
still need rerunning? Thanks!
Best Regards,
Qian Ran




At 2017-02-08 12:19:35, "Bruce Fischl"  wrote:
brain.finalsurfs is fine if you are just rerunning the pial. Edit
brainmask if you are starting earlier so all the downstream volumes
including brain.finalsurfs will have the dura removed
Cheers
Bruce

On Feb 7, 2017, at 10:45 PM, 冉倩  wrote:




  brain.finalsurfs.mgz? not brainmask.mgz? 
or brain.finalsurfs.mgz for pial surface edit and brainmask for
wm surface edit?


At 2017-02-08 11:41:40, "Douglas Greve"
 wrote:

  You should edit the brain.finalsurfs.mgz to remove
  the non-brain then run with -autorecon-pial


  On 2/7/17 10:37 PM, 冉倩 wrote:


  Hi Prof.Douglas Greve,

Yes, probematic surface normally existed near
supeiror dura ( aroun superior frontal lobe or
parietal lobe or central gry area). Just now I am
confused about the next steps.  If I manually erase
( whether I can modfiy control point just like
modify wm) the dura on the brainmask.mgz to correct
pial surface. Then I shoud re-run command: recon-all
-autorecon2 -autorecon-3 sub01? or just recon-all
-autorecon2-pial -autorecon3 sub01? Thanks!

Best Regards,
Qian Ran

At 2017-02-08 11:21:57, "Douglas Greve"
 wrote:

  I think Bruce is referring only to the
  first image. For the second image, it
  looks like most of the problematic
  surface is going through the amygdala or
  hippocampus in which case it does not
  need to be fixed.


  On 2/7/17 9:57 PM, Bruce Fischl wrote:
  oh yes, it's grabbing a bit of
  dura. If you have a 1mm-ish T2 or
  FLAIR you can use it to
  automatically correct this type of
  problem. Or you can erase the dura
  in those regions on the
  brainmask.mgz and recreate the
  pial surface

  cheers
  Bruce



  On Wed, 8 Feb 2017, 冉倩 wrote:

Hi Bruce,
Thanks for your reply.

[IMAGE]
For this, I think pial
surface  (the location
where I circle)
 already
located outside of
brain. 
[IMAGE]
For this, pail surface
(near hippcamps I
think) located inside
of cortical I
think. 

I mean if I manually
modify surface, how do
it? Thanks very much!
Best Regards,
Qian Ran

At 2017-02-08
09:54:30, "Bruce
Fischl"

wrote:
>Hi Qian
>
>I'm not sure I
understand what you
think is wrong in the
images you >included.
The first two
locations look quite
accurate to me, and
I'm not >positive but
I think the third
image the locations
you circle are
amygdala,

>so not neocortical at
all
>
>cheers
>Bruce
>
>
>
>
>
>On Wed, 8 Feb 2017,
冉倩 wrote:
>
>> >> >> Dear
Prof.Douglas Greve,
>>  Thanks for your
reply. I add parts of
problem screenshot of
white/pial
>> surface. 
>> >>   When I did
freesurfer for
structure analysis, I
was confused by some
st
eps
>> and results. The
analysis stream was:
>> >> 1st: check data
orientation
>> >> 2nd : convert
nii.gz  to mgz
>> >> 3rd: recon-all
–all –subjid sub01
>> >> After these
steps finished , I
checked skullstrip,
segmentation quality.
The
>> problems as
following:
>> >> 1st: skullstrip
result not very well,
almost need manually
operation.
>> >>  After
manually operation, I
run:
>> >>  recon-all
–autorecon2
–autorecon3 –subjid
sub01
>> >> 2nd: parts of
white surface and pial
surface not very
exactly. I only did
>> adding control
  

Re: [Freesurfer] recon-all -autorecon2-cp -autorecon-wm -autorecon-pial issue

[冉倩]

Hi Bruce,
If I use brain.finalsurfs, then I run recon-all -autorecon2-pial -subjid sub01 
or recon-all -autorecon2-pial -autorecon3 -subjid sub01? autorecon3 still need 
rerunning? Thanks!
Best Regards,
Qian Ran





At 2017-02-08 12:19:35, "Bruce Fischl"  wrote:

brain.finalsurfs is fine if you are just rerunning the pial. Edit brainmask if 
you are starting earlier so all the downstream volumes including 
brain.finalsurfs will have the dura removed
Cheers
Bruce

On Feb 7, 2017, at 10:45 PM, 冉倩  wrote:






brain.finalsurfs.mgz? not brainmask.mgz? 
or brain.finalsurfs.mgz for pial surface edit and brainmask for wm surface edit?



At 2017-02-08 11:41:40, "Douglas Greve"  wrote:


You should edit the brain.finalsurfs.mgz to remove the non-brain then run with 
-autorecon-pial




On 2/7/17 10:37 PM, 冉倩 wrote:




Hi Prof.Douglas Greve,


Yes, probematic surface normally existed near supeiror dura ( aroun superior 
frontal lobe or parietal lobe or central gry area). Just now I am confused 
about the next steps.  If I manually erase ( whether I can modfiy control point 
just like modify wm) the dura on the brainmask.mgz to correct pial surface. 
Then I shoud re-run command: recon-all -autorecon2 -autorecon-3 sub01? or just 
recon-all -autorecon2-pial -autorecon3 sub01? Thanks!


Best Regards,
Qian Ran

At 2017-02-08 11:21:57, "Douglas Greve"  wrote:


I think Bruce is referring only to the first image. For the second image, it 
looks like most of the problematic surface is going through the amygdala or 
hippocampus in which case it does not need to be fixed.




On 2/7/17 9:57 PM, Bruce Fischl wrote:

oh yes, it's grabbing a bit of dura. If you have a 1mm-ish T2 or FLAIR you can 
use it to automatically correct this type of problem. Or you can erase the dura 
in those regions on the brainmask.mgz and recreate the pial surface

cheers
Bruce



On Wed, 8 Feb 2017, 冉倩 wrote:

Hi Bruce,
Thanks for your reply.

[IMAGE]
For this, I think pial surface  (the location where I circle)  already
located outside of brain. 
[IMAGE]
For this, pail surface (near hippcamps I think) located inside of cortical I
think. 

I mean if I manually modify surface, how do it? Thanks very much!
Best Regards,
Qian Ran

At 2017-02-08 09:54:30, "Bruce Fischl"  wrote:
>Hi Qian
>
>I'm not sure I understand what you think is wrong in the images you >included. 
>The first two locations look quite accurate to me, and I'm not >positive but I 
>think the third image the locations you circle are amygdala,

>so not neocortical at all
>
>cheers
>Bruce
>
>
>
>
>
>On Wed, 8 Feb 2017, 冉倩 wrote:
>
>> >> >> Dear Prof.Douglas Greve,
>>  Thanks for your reply. I add parts of problem screenshot of white/pial
>> surface. 
>> >>   When I did freesurfer for structure analysis, I was confused by some st
eps
>> and results. The analysis stream was:
>> >> 1st: check data orientation
>> >> 2nd : convert nii.gz  to mgz
>> >> 3rd: recon-all –all –subjid sub01
>> >> After these steps finished , I checked skullstrip, segmentation quality. 
>> >> The
>> problems as following:
>> >> 1st: skullstrip result not very well, almost need manually operation.
>> >>  After manually operation, I run:
>> >>  recon-all –autorecon2 –autorecon3 –subjid sub01
>> >> 2nd: parts of white surface and pial surface not very exactly. I only did
>> adding control points to modify white surface, then I run:
>> >>Recon-all –autorecon2-cp –autorecon3 –subjid sub01 brainmask.mgz
>> >> Several parts of pial surface exit errors. I added these as screenshot:
>> >> >> >> >> [IMAGE]
>> >> [IMAGE]
>> [IMAGE]
>> [IMAGE]
>> >> [IMAGE]
>> >> So when I met such issues, I should add control points for pial surface  
>> >> as
>> white surface did (or how I correct or edit pial; still use tkmedit tool?
) ?
>> Then I run: 
>> >> recon-all –autorecon2-pial  –autorecon3 sub01 ?
>> >> If white surface and pial surface all needed manually operated, whether I
>> could do like this: I add control points (-cp), edit wm (-wm), correct pi
al
>> (-pial ) at the same time, then I run:
>> >> recon-all –autorecon2-cp –autorecon2-wm –autorecon2-pail –autorecon3 sub0
1
>> or recon-all -autorecon2-cp brainmask.mgz -autorecon2-wm -autorecon2-pial
>> -autorecon3 sub01?
>> >> or any other suggestions?
>> >> Thanks very much!
>> Best Regards,
>> Qian Ran
>> >> At 2017-02-08 07:18:51, "Douglas Greve"  wrote
:
>>
>>   Hi Qian, things will be a lot easier if you imbed your comments
>>   and images in the email. From the text, I can't tell what you
>>   want exactly. The first question had to do with skull stripping.
>>   It looks like you had to make a manual edit. This is expected
>>   sometimes.  If it is more than that, what is the problem. In the
>>   second question, you had some problem with the quality of the
>>   white/pial 

[Freesurfer] ColorLut hippocampus subfields

[Arnaud Boré]

Dear Freesurfer developpers,

Is there a Freesurfer ColorLut that includes the new subfields of the
hippocampus ?
In the current colorlut there is no left/right for these subfields:
parasubiculum, GC-DG, HATA, molecular layer and tail. In addition, I think
it would be easier if the correct left/right labels would be used for the
segmentation.

Thank you in advance.
Arnaud Boré
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Re: [Freesurfer] dcm2niix

[Antonin Skoch]

Dear Graham,

you could also try mrconvert of mrtrix3. This tool is very useful and has very 
good support.

http://mrtrix.readthedocs.io/en/latest/reference/commands/mrconvert.html

community.mrtrix.org

Regards,

Antonin

Unfortunately I'm not allowed to share these files without direct IRB approval 
(even if they are anonymized). I just tried on some Siemens TrioTim data with 
the same results.Graham

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, February 08, 2017 2:47 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] dcm2niix

Can you upload the dicoms so I can test it out? filedrop address below


On 02/08/2017 02:13 PM, Warner, Graham Cary wrote:
> The set I'm look at now was collected on a GE Signa HDxt.
>
> Graham
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki,
> Anastasia [ayend...@mgh.harvard.edu]
> *Sent:* Wednesday, February 08, 2017 2:09 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] dcm2niix
>
> What scanner(s) was it acquired on?
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Warner, Graham
> Cary [gwar...@mgh.harvard.edu]
> *Sent:* Wednesday, February 08, 2017 2:07 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] dcm2niix
>
> I'm using a large dataset from mi2b2 which contains data from multiple
> vendors/models collected at different hospitals in the partners
> network between 2003 and 2016. The data I tried running mri_convert on
> was acquired in 2011.
>
> Graham
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki,
> Anastasia [ayend...@mgh.harvard.edu]
> *Sent:* Wednesday, February 08, 2017 1:55 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] dcm2niix
>
> Old versions of mri_convert (before 6.0) used to output a default
> Siemens gradient table - this was not read from the header of the
> dicom file itself. The 6.0 version reads the table from the header, as
> long as it is a relatively modern dicom file that has the table in a
> standard position in the header. When/where was your data acquired?
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Warner, Graham
> Cary [gwar...@mgh.harvard.edu]
> *Sent:* Wednesday, February 08, 2017 1:21 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] dcm2niix
>
> I just tried it on a few and while it was able to generate the nii
> files it failed to generate the bval/bvec files I'm looking for. Is it
> not typical behavior for mri_convert to generate bval/bvec files for
> DTI runs or is this an error?
>
> Graham
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki,
> Anastasia [ayend...@mgh.harvard.edu]
> *Sent:* Wednesday, February 08, 2017 10:15 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] dcm2niix
>
> Hi Graham – Have you tried mri_convert? The 6.0 version should be able
> to extract diffusion gradient tables and b-value tables from most
> standard recent dicoms.
>
> a.y
>
> From:  > on behalf of "Warner,
> Graham Cary" >
> Reply-To: Freesurfer support list  >
> Date: Wednesday, February 8, 2017 at 10:01 AM
> To: "freesurfer@nmr.mgh.harvard.edu
> "
> >
> Subject: [Freesurfer] dcm2niix
>
> Hi all,
>
> Can we get dcm2niix added to the system instance of fsl? It can't find
> it in 5.0.7 or 5.0.9 (please let me know if it is somewhere else and
> I'm just not seeing it). I'm having problems generating .bval and
> .bvec files from certain DTI datasets using dcm2nii and the NITRC guys
> told me I should be using dcm2niix.
>
> Thanks,
> Graham___
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners 

Re: [Freesurfer] dcm2niix

[Warner, Graham Cary]

Unfortunately I'm not allowed to share these files without direct IRB approval 
(even if they are anonymized). I just tried on some Siemens TrioTim data with 
the same results.

Graham

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, February 08, 2017 2:47 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] dcm2niix

Can you upload the dicoms so I can test it out? filedrop address below


On 02/08/2017 02:13 PM, Warner, Graham Cary wrote:
> The set I'm look at now was collected on a GE Signa HDxt.
>
> Graham
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki,
> Anastasia [ayend...@mgh.harvard.edu]
> *Sent:* Wednesday, February 08, 2017 2:09 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] dcm2niix
>
> What scanner(s) was it acquired on?
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Warner, Graham
> Cary [gwar...@mgh.harvard.edu]
> *Sent:* Wednesday, February 08, 2017 2:07 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] dcm2niix
>
> I'm using a large dataset from mi2b2 which contains data from multiple
> vendors/models collected at different hospitals in the partners
> network between 2003 and 2016. The data I tried running mri_convert on
> was acquired in 2011.
>
> Graham
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki,
> Anastasia [ayend...@mgh.harvard.edu]
> *Sent:* Wednesday, February 08, 2017 1:55 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] dcm2niix
>
> Old versions of mri_convert (before 6.0) used to output a default
> Siemens gradient table - this was not read from the header of the
> dicom file itself. The 6.0 version reads the table from the header, as
> long as it is a relatively modern dicom file that has the table in a
> standard position in the header. When/where was your data acquired?
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Warner, Graham
> Cary [gwar...@mgh.harvard.edu]
> *Sent:* Wednesday, February 08, 2017 1:21 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] dcm2niix
>
> I just tried it on a few and while it was able to generate the nii
> files it failed to generate the bval/bvec files I'm looking for. Is it
> not typical behavior for mri_convert to generate bval/bvec files for
> DTI runs or is this an error?
>
> Graham
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki,
> Anastasia [ayend...@mgh.harvard.edu]
> *Sent:* Wednesday, February 08, 2017 10:15 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] dcm2niix
>
> Hi Graham – Have you tried mri_convert? The 6.0 version should be able
> to extract diffusion gradient tables and b-value tables from most
> standard recent dicoms.
>
> a.y
>
> From:  > on behalf of "Warner,
> Graham Cary" >
> Reply-To: Freesurfer support list  >
> Date: Wednesday, February 8, 2017 at 10:01 AM
> To: "freesurfer@nmr.mgh.harvard.edu
> "
> >
> Subject: [Freesurfer] dcm2niix
>
> Hi all,
>
> Can we get dcm2niix added to the system instance of fsl? It can't find
> it in 5.0.7 or 5.0.9 (please let me know if it is somewhere else and
> I'm just not seeing it). I'm having problems generating .bval and
> .bvec files from certain DTI datasets using dcm2nii and the NITRC guys
> told me I should be using dcm2niix.
>
> Thanks,
> Graham
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing list

Re: [Freesurfer] dcm2niix

[Douglas N Greve]

Can you upload the dicoms so I can test it out? filedrop address below


On 02/08/2017 02:13 PM, Warner, Graham Cary wrote:
> The set I'm look at now was collected on a GE Signa HDxt.
>
> Graham
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, 
> Anastasia [ayend...@mgh.harvard.edu]
> *Sent:* Wednesday, February 08, 2017 2:09 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] dcm2niix
>
> What scanner(s) was it acquired on?
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Warner, Graham 
> Cary [gwar...@mgh.harvard.edu]
> *Sent:* Wednesday, February 08, 2017 2:07 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] dcm2niix
>
> I'm using a large dataset from mi2b2 which contains data from multiple 
> vendors/models collected at different hospitals in the partners 
> network between 2003 and 2016. The data I tried running mri_convert on 
> was acquired in 2011.
>
> Graham
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, 
> Anastasia [ayend...@mgh.harvard.edu]
> *Sent:* Wednesday, February 08, 2017 1:55 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] dcm2niix
>
> Old versions of mri_convert (before 6.0) used to output a default 
> Siemens gradient table - this was not read from the header of the 
> dicom file itself. The 6.0 version reads the table from the header, as 
> long as it is a relatively modern dicom file that has the table in a 
> standard position in the header. When/where was your data acquired?
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Warner, Graham 
> Cary [gwar...@mgh.harvard.edu]
> *Sent:* Wednesday, February 08, 2017 1:21 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] dcm2niix
>
> I just tried it on a few and while it was able to generate the nii 
> files it failed to generate the bval/bvec files I'm looking for. Is it 
> not typical behavior for mri_convert to generate bval/bvec files for 
> DTI runs or is this an error?
>
> Graham
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, 
> Anastasia [ayend...@mgh.harvard.edu]
> *Sent:* Wednesday, February 08, 2017 10:15 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] dcm2niix
>
> Hi Graham – Have you tried mri_convert? The 6.0 version should be able 
> to extract diffusion gradient tables and b-value tables from most 
> standard recent dicoms.
>
> a.y
>
> From:  > on behalf of "Warner, 
> Graham Cary" >
> Reply-To: Freesurfer support list  >
> Date: Wednesday, February 8, 2017 at 10:01 AM
> To: "freesurfer@nmr.mgh.harvard.edu 
> " 
> >
> Subject: [Freesurfer] dcm2niix
>
> Hi all,
>
> Can we get dcm2niix added to the system instance of fsl? It can't find 
> it in 5.0.7 or 5.0.9 (please let me know if it is somewhere else and 
> I'm just not seeing it). I'm having problems generating .bval and 
> .bvec files from certain DTI datasets using dcm2nii and the NITRC guys 
> told me I should be using dcm2niix.
>
> Thanks,
> Graham
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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 

Re: [Freesurfer] FNIRT all NaN's

[Funk, Quentin]

Sent this to the wrong list. Apologies.



Quentin Funk, PhD
Houston Methodist Research Institute
713-363-9003

From: Funk, Quentin
Sent: Wednesday, February 8, 2017 11:17 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: FNIRT all NaN's


Freesurfer experts,


I have a few fractional anisotropy images linearly registered to an FA atlas. 
I'd like to run FNIRT on them with reference the FA Atlas, but when I do, the 
output is entirely NaNs.


I ran the program in verbose mode--and everything is NaN's. e.g.:




SSD = -nann = 0Disp reg = nanInt reg = -nanTotal Cost = nan
Jacobian range is nan -- nan
***Going to next resolution level***
Setting subsampling
Setting reg mode
Setting lambda
New Lambda: 30
SSD = -nann = 0Disp reg = nanInt reg = -nanTotal Cost = nan
SSD = -nann = 0Disp reg = nanInt reg = -nanTotal Cost = nan
SSD = -nann = 0Disp reg = nanInt reg = -nanTotal Cost = nan
SSD = -nann = 0Disp reg = nanInt reg = -nanTotal Cost = nan


Is this simply because there are NaN's in the input image? Will replacing them 
with 0 fix the issue, or will it lead to strange behaviour in FNIRT?


Any help is appreciated.


Quentin Funk, PhD
Houston Methodist Research Institute
713-363-9003

Houston Methodist. Leading Medicine. U.S. News & World Report has recognized 
Houston Methodist as one of the nation’s top 20 hospitals, placing it for the 
second time on the magazine’s prestigious Honor Roll. It is also designated as 
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houstonmethodist.org. Follow us at  twitter.com/MethodistHosp and 
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recipient(s). Any review, use, distribution or disclosure by others is strictly 
prohibited. If you are not the intended recipient (or authorized to receive for 
the recipient), please contact the sender and delete all copies of the message. 
Thank you.
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The information in this e-mail is intended only for the person to whom it is
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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] dcm2niix

[Warner, Graham Cary]

The set I'm look at now was collected on a GE Signa HDxt.

Graham

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia 
[ayend...@mgh.harvard.edu]
Sent: Wednesday, February 08, 2017 2:09 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] dcm2niix

What scanner(s) was it acquired on?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Warner, Graham Cary 
[gwar...@mgh.harvard.edu]
Sent: Wednesday, February 08, 2017 2:07 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] dcm2niix

I'm using a large dataset from mi2b2 which contains data from multiple 
vendors/models collected at different hospitals in the partners network between 
2003 and 2016. The data I tried running mri_convert on was acquired in 2011.

Graham

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia 
[ayend...@mgh.harvard.edu]
Sent: Wednesday, February 08, 2017 1:55 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] dcm2niix

Old versions of mri_convert (before 6.0) used to output a default Siemens 
gradient table - this was not read from the header of the dicom file itself. 
The 6.0 version reads the table from the header, as long as it is a relatively 
modern dicom file that has the table in a standard position in the header. 
When/where was your data acquired?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Warner, Graham Cary 
[gwar...@mgh.harvard.edu]
Sent: Wednesday, February 08, 2017 1:21 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] dcm2niix

I just tried it on a few and while it was able to generate the nii files it 
failed to generate the bval/bvec files I'm looking for. Is it not typical 
behavior for mri_convert to generate bval/bvec files for DTI runs or is this an 
error?

Graham

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia 
[ayend...@mgh.harvard.edu]
Sent: Wednesday, February 08, 2017 10:15 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] dcm2niix

Hi Graham – Have you tried mri_convert? The 6.0 version should be able to 
extract diffusion gradient tables and b-value tables from most standard recent 
dicoms.

a.y

From: 
>
 on behalf of "Warner, Graham Cary" 
>
Reply-To: Freesurfer support list 
>
Date: Wednesday, February 8, 2017 at 10:01 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
>
Subject: [Freesurfer] dcm2niix

Hi all,

Can we get dcm2niix added to the system instance of fsl? It can't find it in 
5.0.7 or 5.0.9 (please let me know if it is somewhere else and I'm just not 
seeing it). I'm having problems generating .bval and .bvec files from certain 
DTI datasets using dcm2nii and the NITRC guys told me I should be using 
dcm2niix.

Thanks,
Graham
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Re: [Freesurfer] dcm2niix

[Warner, Graham Cary]

I'm using a large dataset from mi2b2 which contains data from multiple 
vendors/models collected at different hospitals in the partners network between 
2003 and 2016. The data I tried running mri_convert on was acquired in 2011.

Graham

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia 
[ayend...@mgh.harvard.edu]
Sent: Wednesday, February 08, 2017 1:55 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] dcm2niix

Old versions of mri_convert (before 6.0) used to output a default Siemens 
gradient table - this was not read from the header of the dicom file itself. 
The 6.0 version reads the table from the header, as long as it is a relatively 
modern dicom file that has the table in a standard position in the header. 
When/where was your data acquired?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Warner, Graham Cary 
[gwar...@mgh.harvard.edu]
Sent: Wednesday, February 08, 2017 1:21 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] dcm2niix

I just tried it on a few and while it was able to generate the nii files it 
failed to generate the bval/bvec files I'm looking for. Is it not typical 
behavior for mri_convert to generate bval/bvec files for DTI runs or is this an 
error?

Graham

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia 
[ayend...@mgh.harvard.edu]
Sent: Wednesday, February 08, 2017 10:15 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] dcm2niix

Hi Graham – Have you tried mri_convert? The 6.0 version should be able to 
extract diffusion gradient tables and b-value tables from most standard recent 
dicoms.

a.y

From: 
>
 on behalf of "Warner, Graham Cary" 
>
Reply-To: Freesurfer support list 
>
Date: Wednesday, February 8, 2017 at 10:01 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
>
Subject: [Freesurfer] dcm2niix

Hi all,

Can we get dcm2niix added to the system instance of fsl? It can't find it in 
5.0.7 or 5.0.9 (please let me know if it is somewhere else and I'm just not 
seeing it). I'm having problems generating .bval and .bvec files from certain 
DTI datasets using dcm2nii and the NITRC guys told me I should be using 
dcm2niix.

Thanks,
Graham
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The information in this e-mail is intended only for the person to whom it is
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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] dcm2niix

[Yendiki, Anastasia]

What scanner(s) was it acquired on?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Warner, Graham Cary 
[gwar...@mgh.harvard.edu]
Sent: Wednesday, February 08, 2017 2:07 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] dcm2niix

I'm using a large dataset from mi2b2 which contains data from multiple 
vendors/models collected at different hospitals in the partners network between 
2003 and 2016. The data I tried running mri_convert on was acquired in 2011.

Graham

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia 
[ayend...@mgh.harvard.edu]
Sent: Wednesday, February 08, 2017 1:55 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] dcm2niix

Old versions of mri_convert (before 6.0) used to output a default Siemens 
gradient table - this was not read from the header of the dicom file itself. 
The 6.0 version reads the table from the header, as long as it is a relatively 
modern dicom file that has the table in a standard position in the header. 
When/where was your data acquired?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Warner, Graham Cary 
[gwar...@mgh.harvard.edu]
Sent: Wednesday, February 08, 2017 1:21 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] dcm2niix

I just tried it on a few and while it was able to generate the nii files it 
failed to generate the bval/bvec files I'm looking for. Is it not typical 
behavior for mri_convert to generate bval/bvec files for DTI runs or is this an 
error?

Graham

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia 
[ayend...@mgh.harvard.edu]
Sent: Wednesday, February 08, 2017 10:15 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] dcm2niix

Hi Graham – Have you tried mri_convert? The 6.0 version should be able to 
extract diffusion gradient tables and b-value tables from most standard recent 
dicoms.

a.y

From: 
>
 on behalf of "Warner, Graham Cary" 
>
Reply-To: Freesurfer support list 
>
Date: Wednesday, February 8, 2017 at 10:01 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
>
Subject: [Freesurfer] dcm2niix

Hi all,

Can we get dcm2niix added to the system instance of fsl? It can't find it in 
5.0.7 or 5.0.9 (please let me know if it is somewhere else and I'm just not 
seeing it). I'm having problems generating .bval and .bvec files from certain 
DTI datasets using dcm2nii and the NITRC guys told me I should be using 
dcm2niix.

Thanks,
Graham
___
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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.

[Freesurfer] LGI using Yeo Atlas

[Martin Juneja]

Hi,

I used following command to extract LGI values from a set of subjects:

recon-all -s  -localGI

Output stats is saved in lh.aparc_lgi.stats file. By default, its
calculating LGI values of 35 areas using *Desikan-Killiany Atlas *but I am
interested in calculating LGI values using Yeo atlas of 7 networks. I was
wondering how can I change the default atlas to Yeo atlas to get LGI value
for each subject.

Thanks a lot.
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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] dcm2niix

[Yendiki, Anastasia]

Old versions of mri_convert (before 6.0) used to output a default Siemens 
gradient table - this was not read from the header of the dicom file itself. 
The 6.0 version reads the table from the header, as long as it is a relatively 
modern dicom file that has the table in a standard position in the header. 
When/where was your data acquired?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Warner, Graham Cary 
[gwar...@mgh.harvard.edu]
Sent: Wednesday, February 08, 2017 1:21 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] dcm2niix

I just tried it on a few and while it was able to generate the nii files it 
failed to generate the bval/bvec files I'm looking for. Is it not typical 
behavior for mri_convert to generate bval/bvec files for DTI runs or is this an 
error?

Graham

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia 
[ayend...@mgh.harvard.edu]
Sent: Wednesday, February 08, 2017 10:15 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] dcm2niix

Hi Graham – Have you tried mri_convert? The 6.0 version should be able to 
extract diffusion gradient tables and b-value tables from most standard recent 
dicoms.

a.y

From: 
>
 on behalf of "Warner, Graham Cary" 
>
Reply-To: Freesurfer support list 
>
Date: Wednesday, February 8, 2017 at 10:01 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
>
Subject: [Freesurfer] dcm2niix

Hi all,

Can we get dcm2niix added to the system instance of fsl? It can't find it in 
5.0.7 or 5.0.9 (please let me know if it is somewhere else and I'm just not 
seeing it). I'm having problems generating .bval and .bvec files from certain 
DTI datasets using dcm2nii and the NITRC guys told me I should be using 
dcm2niix.

Thanks,
Graham
___
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] dcm2niix

[Warner, Graham Cary]

I just tried it on a few and while it was able to generate the nii files it 
failed to generate the bval/bvec files I'm looking for. Is it not typical 
behavior for mri_convert to generate bval/bvec files for DTI runs or is this an 
error?

Graham

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia 
[ayend...@mgh.harvard.edu]
Sent: Wednesday, February 08, 2017 10:15 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] dcm2niix

Hi Graham – Have you tried mri_convert? The 6.0 version should be able to 
extract diffusion gradient tables and b-value tables from most standard recent 
dicoms.

a.y

From: 
>
 on behalf of "Warner, Graham Cary" 
>
Reply-To: Freesurfer support list 
>
Date: Wednesday, February 8, 2017 at 10:01 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
>
Subject: [Freesurfer] dcm2niix

Hi all,

Can we get dcm2niix added to the system instance of fsl? It can't find it in 
5.0.7 or 5.0.9 (please let me know if it is somewhere else and I'm just not 
seeing it). I'm having problems generating .bval and .bvec files from certain 
DTI datasets using dcm2nii and the NITRC guys told me I should be using 
dcm2niix.

Thanks,
Graham
___
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] FNIRT all NaN's

[Douglas N Greve]

Shouldn't you post this to the FSL list?


On 02/08/2017 12:17 PM, Funk, Quentin wrote:
>
> Freesurfer experts,
>
>
> I have a few fractional anisotropy images linearly registered to an FA 
> atlas. I'd like to run FNIRT on them with reference the FA Atlas, but 
> when I do, the output is entirely NaNs.
>
>
> I ran the program in verbose mode--and everything is NaN's. e.g.:
>
>
> SSD = -nann = 0Disp reg = nanInt reg = -nan  Total Cost = nan
> Jacobian range is nan -- nan
> ***Going to next resolution level***
> Setting subsampling
> Setting reg mode
> Setting lambda
> New Lambda: 30
> SSD = -nann = 0Disp reg = nanInt reg = -nanTotal Cost 
> = nan
> SSD = -nann = 0Disp reg = nanInt reg = -nanTotal Cost 
> = nan
> SSD = -nann = 0Disp reg = nanInt reg = -nanTotal Cost 
> = nan
> SSD = -nann = 0Disp reg = nanInt reg = -nanTotal Cost 
> = nan
>
>
> Is this simply because there are NaN's in the input image? Will 
> replacing them with 0 fix the issue, or will it lead to strange 
> behaviour in FNIRT?
>
>
> Any help is appreciated.
>
>
> Quentin Funk, PhD
> Houston Methodist Research Institute
> 713-363-9003 
>
> Houston Methodist. Leading Medicine.
>
> /U.S. News & World Report/ has recognized Houston Methodist as one of 
> the nation’s top 20 hospitals, placing it for the second time on the 
> magazine’s prestigious Honor Roll. It is also designated as a Magnet 
> hospital for excellence in nursing. Visit us at houstonmethodist.org 
> . Follow us at twitter.com/MethodistHosp 
>  and facebook.com/HoustonMethodist.
>
> ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston 
> Methodist and/or its relevant affiliates and may contain restricted 
> and privileged material for the sole use of the intended recipient(s). 
> Any review, use, distribution or disclosure by others is strictly 
> prohibited. If you are not the intended recipient (or authorized to 
> receive for the recipient), please contact the sender and delete all 
> copies of the message. Thank you.
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Usage of norm.mgz rather than brain.mgz

[Bruce Fischl]

Hi Andrew

the brain.mgz is very aggressively filtered explicitly for cortex and 
wipes away some subcortical boundaries (e.g. lateral thalamus).


cheers
Bruce
On Wed, 8 
Feb 2017, Andrew Davis wrote:



Hello FreeSurfer Developers,

I have been using FreeSurfer for segmenting T1-weighted images, and I have a 
question related to using the two outputs norm.mgz and brain.mgz.

It is my understanding that, by default, FreeSurfer uses the norm.mgz volume to 
do partial volume weighting when outputting segmentation volumes to aseg.stats 
based on aseg.mgz [^1]. Further, I understand that
brain.mgz is output from a second normalization step in the recon-all processing 
stream, having taken norm.mgz as an input [^2].  The wiki says "Intensity 
normalization works better when the skull has been removed.
Creates a new brain.mgz volume".

My question is: if brain.mgz is meant to be an improved version of norm.mgz, 
why not use brain.mgz for partial volume weighting?  What advantages does 
norm.mgz provide?

Thanks much,
Andrew Davis

[^1]: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
[^2]: https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all


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

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

[Pål Gunnar Larsson]

Hei

Dette er  en tekstfil i web diskusjonsforum. Det er mange som bruker 
Freesurfer. Teksten dreier seg om ny lisensfil i samband med en ny versjon. Det 
aktuelle mailen angår ikke meg. Jeg bruker gammel Freesurfer på jobben som ikke 
trenger ny lisensfil.

Hilsen

Pål

Dr. philos. Pål G. Larsson
Seksjonsleder Klinisk nevrofysiologi
Nevrokirurgisk avdeling
Oslo Universitetssykehus
Postboks 4950 Nydalen
0424 Oslo

Tlf.:  23074407
Mobil: 93429791

E-mail: p...@ous-hf.no

Denne meldingen innholder ikke sensitiv informasjon som bryter med Ous sine 
regler for taushetsplikt

Fra: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] På vegne av Taylor Hilton
Sendt: 8. februar 2017 15:45
Til: Freesurfer support list
Emne: Re: [Freesurfer] recon-all issue {Disarmed}

Apologies, that was an old log, attaching the relevant one here.



On Feb 7, 2017, at 6:02 PM, Douglas Greve 
> wrote:

According to the log file, the error is that you need a new license:
GNU libc version: 2.23
ERROR: Systems running GNU glibc version greater than 2.15
require a newly formatted license file (it's free). Please
download a new one from the following page:
MailScanner has detected a possible fraud attempt from 
"na01.safelinks.protection.outlook.com" claiming to be 
http://surfer.nmr.mgh.harvard.edu/registration.html


On 2/7/17 12:49 PM, Taylor Hilton wrote:
Yes I’ll attach it here.  I’m using a linux server(Ubuntu).




On Feb 7, 2017, at 12:32 PM, Douglas Greve 
> wrote:

Can you send the full recon-all.log? What platform are you running on?

On 2/7/17 11:19 AM, Taylor Hilton wrote:
Hi all,

Having trouble with an error running "recon-all -subjid ${i} -autorecon2” 
across all subjects.

Below is where it has the error in recon-all.log.  We also tried running the 
last command (“ln -s …”) manually and got the error “ln: failed to 
create symbolic link ‘lh.white.H’: Operation not supported.” whereas the 
rest of the commands ran normally.

#
#@# Curv .H and .K lh Tue Feb  7 07:29:43 EST 2017
/home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/surf

 mris_curvature -w lh.white.preaparc

total integrated curvature = 18.936*4pi (237.960) --> -18 handles
ICI = 230.2, FI = 1697.2, variation=29040.790
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...done.
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
Linux pfc 4.4.0-59-generic #80-Ubuntu SMP Fri Jan 6 17:47:47 UTC 2017 x86_64 
x86_64 x86_64 GNU/Linux

recon-all -s 10007 exited with ERRORS at Tue Feb  7 07:29:46 EST 2017

To report a problem, see MailScanner has detected a possible fraud attempt from 
"na01.safelinks.protection.outlook.com" claiming to be 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

————————————————————————————————————————————————


We also tried the solution laid out in this thread with no luck:
 MailScanner has detected a possible fraud attempt from 
"na01.safelinks.protection.outlook.com" claiming to be 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040473.html

Any help is very appreciated!

- B. Taylor Hilton
Lab Data Coordinator, University of Pittsburgh







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[Freesurfer] Usage of norm.mgz rather than brain.mgz

[Andrew Davis]

Hello FreeSurfer Developers,

I have been using FreeSurfer for segmenting T1-weighted images, and I have
a question related to using the two outputs norm.mgz and brain.mgz.

It is my understanding that, by default, FreeSurfer uses the norm.mgz
volume to do partial volume weighting when outputting segmentation volumes
to aseg.stats based on aseg.mgz [^1]. Further, I understand that brain.mgz
is output from a second normalization step in the recon-all processing
stream, having taken norm.mgz as an input [^2].  The wiki says "*Intensity
normalization works better when the skull has been removed. Creates a new
brain.mgz volume*".

My question is: if brain.mgz is meant to be an improved version of
norm.mgz, why not use brain.mgz for partial volume weighting?  What
advantages does norm.mgz provide?

Thanks much,
Andrew Davis

[^1]: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
[^2]: https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all

​​
​
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[Freesurfer] FNIRT all NaN's

[Funk, Quentin]

Freesurfer experts,


I have a few fractional anisotropy images linearly registered to an FA atlas. 
I'd like to run FNIRT on them with reference the FA Atlas, but when I do, the 
output is entirely NaNs.


I ran the program in verbose mode--and everything is NaN's. e.g.:




SSD = -nann = 0Disp reg = nanInt reg = -nanTotal Cost = nan
Jacobian range is nan -- nan
***Going to next resolution level***
Setting subsampling
Setting reg mode
Setting lambda
New Lambda: 30
SSD = -nann = 0Disp reg = nanInt reg = -nanTotal Cost = nan
SSD = -nann = 0Disp reg = nanInt reg = -nanTotal Cost = nan
SSD = -nann = 0Disp reg = nanInt reg = -nanTotal Cost = nan
SSD = -nann = 0Disp reg = nanInt reg = -nanTotal Cost = nan


Is this simply because there are NaN's in the input image? Will replacing them 
with 0 fix the issue, or will it lead to strange behaviour in FNIRT?


Any help is appreciated.


Quentin Funk, PhD
Houston Methodist Research Institute
713-363-9003

Houston Methodist. Leading Medicine. U.S. News & World Report has recognized 
Houston Methodist as one of the nation’s top 20 hospitals, placing it for the 
second time on the magazine’s prestigious Honor Roll. It is also designated as 
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houstonmethodist.org. Follow us at  twitter.com/MethodistHosp and 
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Re: [Freesurfer] extract area.pial stats

[Clara Kühn]

alright. Thank you so much!

- Ursprüngliche Mail -
Von: "Douglas N Greve" 
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 8. Februar 2017 17:45:38
Betreff: Re: [Freesurfer] extract area.pial stats

No. The program is from version 6 so it is expecting v6 naming conventions


On 02/08/2017 11:38 AM, Clara Kühn wrote:
> Thank you, I think it worked. I've attached the file again.
> There was one error message in the terminal output though:
>
> atlas_icv (eTIV) = 1287829 mm^3(det: 1.512705 )
> /nobackup/etsch2/kids/prepost-61kids//ZF1K.base/mri/aseg.presurf.mgz doesn't 
> exist, using old naming conventions
>
> Is that something to worry about?
>
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve" 
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Mittwoch, 8. Februar 2017 17:34:06
> Betreff: Re: [Freesurfer] extract area.pial stats
>
> It either has to be in your path or you need to supply the full path when 
> running it, like this
> $SUBJECTS_DIR/mris_anatomical_stats-doug
>
>
> On 02/08/2017 11:27 AM, Clara Kühn wrote:
>> I'm so sorry, I don't know anything about programming...
>> I downloaded it, copied it into my SUBJECTS_DIR as 
>> mris_anatomical_stats-doug and tried to run the whole thing again like this:
>>
>> mris_anatomical_stats-doug -mgz -cortex 
>> $SUBJECTS_DIR/ZF1K.base/label/lh.cortex.label -f 
>> $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc.pial.stats -b -a 
>> $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -c 
>> $SUBJECTS_DIR/ZF1K.base/label/aparc.annot.ctab ZF1K.base lh pial
>>
>> but then I got this error:
>>
>> bash: mris_anatomical_stats-doug: command not found
>>
>>
>>
>> - Ursprüngliche Mail -
>> Von: "Douglas N Greve" 
>> An: freesurfer@nmr.mgh.harvard.edu
>> Gesendet: Mittwoch, 8. Februar 2017 17:08:26
>> Betreff: Re: [Freesurfer] extract area.pial stats
>>
>> You don't need to open it. Just download it and put it in your path. You
>> may want to call it something slightly differnt so that you don't
>> confuse it with the v5.3 version
>>
>>
>> On 02/08/2017 10:53 AM, Clara Kühn wrote:
>>> thanks. What kind of format is it? How do I open it?
>>>
>>> Cheers
>>> Clara
>>>
>>> - Ursprüngliche Mail -
>>> Von: "Douglas N Greve" 
>>> An: freesurfer@nmr.mgh.harvard.edu
>>> Gesendet: Mittwoch, 8. Februar 2017 16:43:47
>>> Betreff: Re: [Freesurfer] extract area.pial stats
>>>
>>> Try this version (same as version 6)
>>>
>>> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_anatomical_stats
>>>
>>>
>>>
>>> On 02/08/2017 04:55 AM, Clara Kühn wrote:
 Hi Doug,

 thanks for your reply. I tried it out and attached the lh.aparc.pial.stats 
 file for you to take a look at. As far as I can tell it's still reporting 
 the white surface area. Or am I reading it wrong?

 Cheers Clara

 - Ursprüngliche Mail -
 Von: "Douglas Greve" 
 An: freesurfer@nmr.mgh.harvard.edu
 Gesendet: Mittwoch, 8. Februar 2017 00:15:22
 Betreff: Re: [Freesurfer] extract area.pial stats

 try

 cd $SUBJECTS_DIR/subject/surf

 mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
 ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c 
 ../label/aparc.annot.ctab subject lh pial


 On 2/7/17 4:48 AM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I'm trying to extract a total Pial Surface Area like it is extracted for 
> White Surface Area in the ?h.aparc.stats file. I have tried this command 
> but it doesn't seem to include Pial Surface Area:
>
> mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f 
> $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial
>
> How could I extract the total Pial Surface Area for each participant?
>
> Thank you for you help!
> Clara
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
 ___
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 The information in this e-mail is intended only for the person to whom it 
 is
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 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 
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Re: [Freesurfer] extract area.pial stats

[Douglas N Greve]

No. The program is from version 6 so it is expecting v6 naming conventions


On 02/08/2017 11:38 AM, Clara Kühn wrote:
> Thank you, I think it worked. I've attached the file again.
> There was one error message in the terminal output though:
>
> atlas_icv (eTIV) = 1287829 mm^3(det: 1.512705 )
> /nobackup/etsch2/kids/prepost-61kids//ZF1K.base/mri/aseg.presurf.mgz doesn't 
> exist, using old naming conventions
>
> Is that something to worry about?
>
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve" 
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Mittwoch, 8. Februar 2017 17:34:06
> Betreff: Re: [Freesurfer] extract area.pial stats
>
> It either has to be in your path or you need to supply the full path when 
> running it, like this
> $SUBJECTS_DIR/mris_anatomical_stats-doug
>
>
> On 02/08/2017 11:27 AM, Clara Kühn wrote:
>> I'm so sorry, I don't know anything about programming...
>> I downloaded it, copied it into my SUBJECTS_DIR as 
>> mris_anatomical_stats-doug and tried to run the whole thing again like this:
>>
>> mris_anatomical_stats-doug -mgz -cortex 
>> $SUBJECTS_DIR/ZF1K.base/label/lh.cortex.label -f 
>> $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc.pial.stats -b -a 
>> $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -c 
>> $SUBJECTS_DIR/ZF1K.base/label/aparc.annot.ctab ZF1K.base lh pial
>>
>> but then I got this error:
>>
>> bash: mris_anatomical_stats-doug: command not found
>>
>>
>>
>> - Ursprüngliche Mail -
>> Von: "Douglas N Greve" 
>> An: freesurfer@nmr.mgh.harvard.edu
>> Gesendet: Mittwoch, 8. Februar 2017 17:08:26
>> Betreff: Re: [Freesurfer] extract area.pial stats
>>
>> You don't need to open it. Just download it and put it in your path. You
>> may want to call it something slightly differnt so that you don't
>> confuse it with the v5.3 version
>>
>>
>> On 02/08/2017 10:53 AM, Clara Kühn wrote:
>>> thanks. What kind of format is it? How do I open it?
>>>
>>> Cheers
>>> Clara
>>>
>>> - Ursprüngliche Mail -
>>> Von: "Douglas N Greve" 
>>> An: freesurfer@nmr.mgh.harvard.edu
>>> Gesendet: Mittwoch, 8. Februar 2017 16:43:47
>>> Betreff: Re: [Freesurfer] extract area.pial stats
>>>
>>> Try this version (same as version 6)
>>>
>>> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_anatomical_stats
>>>
>>>
>>>
>>> On 02/08/2017 04:55 AM, Clara Kühn wrote:
 Hi Doug,

 thanks for your reply. I tried it out and attached the lh.aparc.pial.stats 
 file for you to take a look at. As far as I can tell it's still reporting 
 the white surface area. Or am I reading it wrong?

 Cheers Clara

 - Ursprüngliche Mail -
 Von: "Douglas Greve" 
 An: freesurfer@nmr.mgh.harvard.edu
 Gesendet: Mittwoch, 8. Februar 2017 00:15:22
 Betreff: Re: [Freesurfer] extract area.pial stats

 try

 cd $SUBJECTS_DIR/subject/surf

 mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
 ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c 
 ../label/aparc.annot.ctab subject lh pial


 On 2/7/17 4:48 AM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I'm trying to extract a total Pial Surface Area like it is extracted for 
> White Surface Area in the ?h.aparc.stats file. I have tried this command 
> but it doesn't seem to include Pial Surface Area:
>
> mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f 
> $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial
>
> How could I extract the total Pial Surface Area for each participant?
>
> Thank you for you help!
> Clara
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
 ___
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] extract area.pial stats

[Clara Kühn]

Thank you, I think it worked. I've attached the file again. 
There was one error message in the terminal output though:

atlas_icv (eTIV) = 1287829 mm^3(det: 1.512705 )
/nobackup/etsch2/kids/prepost-61kids//ZF1K.base/mri/aseg.presurf.mgz doesn't 
exist, using old naming conventions

Is that something to worry about?


- Ursprüngliche Mail -
Von: "Douglas N Greve" 
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 8. Februar 2017 17:34:06
Betreff: Re: [Freesurfer] extract area.pial stats

It either has to be in your path or you need to supply the full path when 
running it, like this
$SUBJECTS_DIR/mris_anatomical_stats-doug


On 02/08/2017 11:27 AM, Clara Kühn wrote:
> I'm so sorry, I don't know anything about programming...
> I downloaded it, copied it into my SUBJECTS_DIR as mris_anatomical_stats-doug 
> and tried to run the whole thing again like this:
>
> mris_anatomical_stats-doug -mgz -cortex 
> $SUBJECTS_DIR/ZF1K.base/label/lh.cortex.label -f 
> $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc.pial.stats -b -a 
> $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -c 
> $SUBJECTS_DIR/ZF1K.base/label/aparc.annot.ctab ZF1K.base lh pial
>
> but then I got this error:
>
> bash: mris_anatomical_stats-doug: command not found
>
>
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve" 
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Mittwoch, 8. Februar 2017 17:08:26
> Betreff: Re: [Freesurfer] extract area.pial stats
>
> You don't need to open it. Just download it and put it in your path. You
> may want to call it something slightly differnt so that you don't
> confuse it with the v5.3 version
>
>
> On 02/08/2017 10:53 AM, Clara Kühn wrote:
>> thanks. What kind of format is it? How do I open it?
>>
>> Cheers
>> Clara
>>
>> - Ursprüngliche Mail -
>> Von: "Douglas N Greve" 
>> An: freesurfer@nmr.mgh.harvard.edu
>> Gesendet: Mittwoch, 8. Februar 2017 16:43:47
>> Betreff: Re: [Freesurfer] extract area.pial stats
>>
>> Try this version (same as version 6)
>>
>> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_anatomical_stats
>>
>>
>>
>> On 02/08/2017 04:55 AM, Clara Kühn wrote:
>>> Hi Doug,
>>>
>>> thanks for your reply. I tried it out and attached the lh.aparc.pial.stats 
>>> file for you to take a look at. As far as I can tell it's still reporting 
>>> the white surface area. Or am I reading it wrong?
>>>
>>> Cheers Clara
>>>
>>> - Ursprüngliche Mail -
>>> Von: "Douglas Greve" 
>>> An: freesurfer@nmr.mgh.harvard.edu
>>> Gesendet: Mittwoch, 8. Februar 2017 00:15:22
>>> Betreff: Re: [Freesurfer] extract area.pial stats
>>>
>>> try
>>>
>>> cd $SUBJECTS_DIR/subject/surf
>>>
>>> mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
>>> ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c 
>>> ../label/aparc.annot.ctab subject lh pial
>>>
>>>
>>> On 2/7/17 4:48 AM, Clara Kühn wrote:
 Dear FreeSurfer experts,

 I'm trying to extract a total Pial Surface Area like it is extracted for 
 White Surface Area in the ?h.aparc.stats file. I have tried this command 
 but it doesn't seem to include Pial Surface Area:

 mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f 
 $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial

 How could I extract the total Pial Surface Area for each participant?

 Thank you for you help!
 Clara
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] extract area.pial stats

[Bruce Fischl]

try typing:

rehash

then run it again
On Wed, 8 Feb 2017, Clara Kühn wrote:


I'm so sorry, I don't know anything about programming...
I downloaded it, copied it into my SUBJECTS_DIR as mris_anatomical_stats-doug 
and tried to run the whole thing again like this:

mris_anatomical_stats-doug -mgz -cortex 
$SUBJECTS_DIR/ZF1K.base/label/lh.cortex.label -f 
$SUBJECTS_DIR/ZF1K.base/stats/lh.aparc.pial.stats -b -a 
$SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -c 
$SUBJECTS_DIR/ZF1K.base/label/aparc.annot.ctab ZF1K.base lh pial

but then I got this error:

bash: mris_anatomical_stats-doug: command not found



- Ursprüngliche Mail -
Von: "Douglas N Greve" 
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 8. Februar 2017 17:08:26
Betreff: Re: [Freesurfer] extract area.pial stats

You don't need to open it. Just download it and put it in your path. You
may want to call it something slightly differnt so that you don't
confuse it with the v5.3 version


On 02/08/2017 10:53 AM, Clara Kühn wrote:

thanks. What kind of format is it? How do I open it?

Cheers
Clara

- Ursprüngliche Mail -
Von: "Douglas N Greve" 
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 8. Februar 2017 16:43:47
Betreff: Re: [Freesurfer] extract area.pial stats

Try this version (same as version 6)

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



On 02/08/2017 04:55 AM, Clara Kühn wrote:

Hi Doug,

thanks for your reply. I tried it out and attached the lh.aparc.pial.stats file 
for you to take a look at. As far as I can tell it's still reporting the white 
surface area. Or am I reading it wrong?

Cheers Clara

- Ursprüngliche Mail -
Von: "Douglas Greve" 
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 8. Februar 2017 00:15:22
Betreff: Re: [Freesurfer] extract area.pial stats

try

cd $SUBJECTS_DIR/subject/surf

mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c 
../label/aparc.annot.ctab subject lh pial


On 2/7/17 4:48 AM, Clara Kühn wrote:

Dear FreeSurfer experts,

I'm trying to extract a total Pial Surface Area like it is extracted for White 
Surface Area in the ?h.aparc.stats file. I have tried this command but it 
doesn't seem to include Pial Surface Area:

mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f 
$SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial

How could I extract the total Pial Surface Area for each participant?

Thank you for you help!
Clara
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



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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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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] extract area.pial stats

[Douglas N Greve]

It either has to be in your path or you need to supply the full path when 
running it, like this
$SUBJECTS_DIR/mris_anatomical_stats-doug


On 02/08/2017 11:27 AM, Clara Kühn wrote:
> I'm so sorry, I don't know anything about programming...
> I downloaded it, copied it into my SUBJECTS_DIR as mris_anatomical_stats-doug 
> and tried to run the whole thing again like this:
>
> mris_anatomical_stats-doug -mgz -cortex 
> $SUBJECTS_DIR/ZF1K.base/label/lh.cortex.label -f 
> $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc.pial.stats -b -a 
> $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -c 
> $SUBJECTS_DIR/ZF1K.base/label/aparc.annot.ctab ZF1K.base lh pial
>
> but then I got this error:
>
> bash: mris_anatomical_stats-doug: command not found
>
>
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve" 
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Mittwoch, 8. Februar 2017 17:08:26
> Betreff: Re: [Freesurfer] extract area.pial stats
>
> You don't need to open it. Just download it and put it in your path. You
> may want to call it something slightly differnt so that you don't
> confuse it with the v5.3 version
>
>
> On 02/08/2017 10:53 AM, Clara Kühn wrote:
>> thanks. What kind of format is it? How do I open it?
>>
>> Cheers
>> Clara
>>
>> - Ursprüngliche Mail -
>> Von: "Douglas N Greve" 
>> An: freesurfer@nmr.mgh.harvard.edu
>> Gesendet: Mittwoch, 8. Februar 2017 16:43:47
>> Betreff: Re: [Freesurfer] extract area.pial stats
>>
>> Try this version (same as version 6)
>>
>> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_anatomical_stats
>>
>>
>>
>> On 02/08/2017 04:55 AM, Clara Kühn wrote:
>>> Hi Doug,
>>>
>>> thanks for your reply. I tried it out and attached the lh.aparc.pial.stats 
>>> file for you to take a look at. As far as I can tell it's still reporting 
>>> the white surface area. Or am I reading it wrong?
>>>
>>> Cheers Clara
>>>
>>> - Ursprüngliche Mail -
>>> Von: "Douglas Greve" 
>>> An: freesurfer@nmr.mgh.harvard.edu
>>> Gesendet: Mittwoch, 8. Februar 2017 00:15:22
>>> Betreff: Re: [Freesurfer] extract area.pial stats
>>>
>>> try
>>>
>>> cd $SUBJECTS_DIR/subject/surf
>>>
>>> mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
>>> ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c 
>>> ../label/aparc.annot.ctab subject lh pial
>>>
>>>
>>> On 2/7/17 4:48 AM, Clara Kühn wrote:
 Dear FreeSurfer experts,

 I'm trying to extract a total Pial Surface Area like it is extracted for 
 White Surface Area in the ?h.aparc.stats file. I have tried this command 
 but it doesn't seem to include Pial Surface Area:

 mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f 
 $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial

 How could I extract the total Pial Surface Area for each participant?

 Thank you for you help!
 Clara
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] extract area.pial stats

[Clara Kühn]

I'm so sorry, I don't know anything about programming... 
I downloaded it, copied it into my SUBJECTS_DIR as mris_anatomical_stats-doug 
and tried to run the whole thing again like this:

mris_anatomical_stats-doug -mgz -cortex 
$SUBJECTS_DIR/ZF1K.base/label/lh.cortex.label -f 
$SUBJECTS_DIR/ZF1K.base/stats/lh.aparc.pial.stats -b -a 
$SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -c 
$SUBJECTS_DIR/ZF1K.base/label/aparc.annot.ctab ZF1K.base lh pial

but then I got this error:

bash: mris_anatomical_stats-doug: command not found



- Ursprüngliche Mail -
Von: "Douglas N Greve" 
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 8. Februar 2017 17:08:26
Betreff: Re: [Freesurfer] extract area.pial stats

You don't need to open it. Just download it and put it in your path. You 
may want to call it something slightly differnt so that you don't 
confuse it with the v5.3 version


On 02/08/2017 10:53 AM, Clara Kühn wrote:
> thanks. What kind of format is it? How do I open it?
>
> Cheers
> Clara
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve" 
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Mittwoch, 8. Februar 2017 16:43:47
> Betreff: Re: [Freesurfer] extract area.pial stats
>
> Try this version (same as version 6)
>
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_anatomical_stats
>
>
>
> On 02/08/2017 04:55 AM, Clara Kühn wrote:
>> Hi Doug,
>>
>> thanks for your reply. I tried it out and attached the lh.aparc.pial.stats 
>> file for you to take a look at. As far as I can tell it's still reporting 
>> the white surface area. Or am I reading it wrong?
>>
>> Cheers Clara
>>
>> - Ursprüngliche Mail -
>> Von: "Douglas Greve" 
>> An: freesurfer@nmr.mgh.harvard.edu
>> Gesendet: Mittwoch, 8. Februar 2017 00:15:22
>> Betreff: Re: [Freesurfer] extract area.pial stats
>>
>> try
>>
>> cd $SUBJECTS_DIR/subject/surf
>>
>> mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
>> ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c 
>> ../label/aparc.annot.ctab subject lh pial
>>
>>
>> On 2/7/17 4:48 AM, Clara Kühn wrote:
>>> Dear FreeSurfer experts,
>>>
>>> I'm trying to extract a total Pial Surface Area like it is extracted for 
>>> White Surface Area in the ?h.aparc.stats file. I have tried this command 
>>> but it doesn't seem to include Pial Surface Area:
>>>
>>> mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f 
>>> $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial
>>>
>>> How could I extract the total Pial Surface Area for each participant?
>>>
>>> Thank you for you help!
>>> Clara
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> 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.
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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

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

Re: [Freesurfer] extract area.pial stats

[Douglas N Greve]

You don't need to open it. Just download it and put it in your path. You 
may want to call it something slightly differnt so that you don't 
confuse it with the v5.3 version


On 02/08/2017 10:53 AM, Clara Kühn wrote:
> thanks. What kind of format is it? How do I open it?
>
> Cheers
> Clara
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve" 
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Mittwoch, 8. Februar 2017 16:43:47
> Betreff: Re: [Freesurfer] extract area.pial stats
>
> Try this version (same as version 6)
>
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_anatomical_stats
>
>
>
> On 02/08/2017 04:55 AM, Clara Kühn wrote:
>> Hi Doug,
>>
>> thanks for your reply. I tried it out and attached the lh.aparc.pial.stats 
>> file for you to take a look at. As far as I can tell it's still reporting 
>> the white surface area. Or am I reading it wrong?
>>
>> Cheers Clara
>>
>> - Ursprüngliche Mail -
>> Von: "Douglas Greve" 
>> An: freesurfer@nmr.mgh.harvard.edu
>> Gesendet: Mittwoch, 8. Februar 2017 00:15:22
>> Betreff: Re: [Freesurfer] extract area.pial stats
>>
>> try
>>
>> cd $SUBJECTS_DIR/subject/surf
>>
>> mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
>> ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c 
>> ../label/aparc.annot.ctab subject lh pial
>>
>>
>> On 2/7/17 4:48 AM, Clara Kühn wrote:
>>> Dear FreeSurfer experts,
>>>
>>> I'm trying to extract a total Pial Surface Area like it is extracted for 
>>> White Surface Area in the ?h.aparc.stats file. I have tried this command 
>>> but it doesn't seem to include Pial Surface Area:
>>>
>>> mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f 
>>> $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial
>>>
>>> How could I extract the total Pial Surface Area for each participant?
>>>
>>> Thank you for you help!
>>> Clara
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> 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.
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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

[Z K]

This error suggests to me that you are mounting some external drive, or 
docker container, or some mix of file systems incompatible with symlinks?

Try moving the subject to a local directory


On 02/08/2017 10:41 AM, Taylor Hilton wrote:
> This is the output: ln: failed to create symbolic link 'lh.white.H':
> Operation not supported
>
>> On Feb 8, 2017, at 10:38 AM, Douglas N Greve
>> > wrote:
>>
>> can you run the commands below and tell me what happens?
>>
>> cd /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/surf
>> ln -s lh.white.preaparc.H lh.white.H
>>
>>
>> On 02/08/2017 09:44 AM, Taylor Hilton wrote:
>>> Apologies, that was an old log, attaching the relevant one here.
>>>
>>>
>>>
>>>
 On Feb 7, 2017, at 6:02 PM, Douglas Greve 
 > wrote:

 According to the log file, the error is that you need a new license:

 GNU libc version: 2.23
 ERROR: Systems running GNU glibc version greater than 2.15
 require a newly formatted license file (it's free). Please
 download a new one from the following page:
 *MailScanner has detected a possible fraud attempt from
 "na01.safelinks.protection.outlook.com
 " claiming to be*
 https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html=01%7C01%7CBTH22%40pitt.edu%7C446b463cf36a4889e95708d450389542%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1=CHwu5i2iSGCh56pKWyVyp3ygYwdOQ0WSEBes26448ro%3D=0



 On 2/7/17 12:49 PM, Taylor Hilton wrote:
> Yes I’ll attach it here.  I’m using a linux server(Ubuntu).
>
>
>
>
>> On Feb 7, 2017, at 12:32 PM, Douglas Greve
>> >  >
>> wrote:
>>
>> Can you send the full recon-all.log? What platform are you running on?
>>
>>
>> On 2/7/17 11:19 AM, Taylor Hilton wrote:
>>> Hi all,
>>>
>>> Having trouble with an error running "recon-all -subjid ${i}
>>> -autorecon2” across all subjects.
>>>
>>> Below is where it has the error in recon-all.log.  We also tried
>>> running the last command (“ln -s …”) manually and got the error
>>> “ln: failed to create symbolic link ‘lh.white.H’: Operation not
>>> supported.” whereas the rest of the commands ran normally.
>>>
>>> #
>>> #@# Curv .H and .K lh Tue Feb  7 07:29:43 EST 2017
>>> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/surf
>>>
>>> mris_curvature -w lh.white.preaparc
>>>
>>> total integrated curvature = 18.936*4pi (237.960) --> -18 handles
>>> ICI = 230.2, FI = 1697.2, variation=29040.790
>>> writing Gaussian curvature to ./lh.white.preaparc.K...done.
>>> writing mean curvature to ./lh.white.preaparc.H...done.
>>> rm -f lh.white.H
>>> ln -s lh.white.preaparc.H lh.white.H
>>> Linux pfc 4.4.0-59-generic #80-Ubuntu SMP Fri Jan 6 17:47:47 UTC
>>> 2017 x86_64 x86_64 x86_64 GNU/Linux
>>>
>>> recon-all -s 10007 exited with ERRORS at Tue Feb  7 07:29:46 EST 2017
>>>
>>> To report a problem, see *MailScanner has detected a possible
>>> fraud attempt from "na01.safelinks.protection.outlook.com
>>> "
>>> claiming to be*
>>> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting=01%7C01%7CBTH22%40pitt.edu%7C446b463cf36a4889e95708d450389542%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1=Qjbe1jS%2BeKSdSGHHfJQKx%2FFQWrSd5B1ckHOVz9dh%2FmU%3D=0
>>> 
>>>
>>> 
>>>
>>>
>>> We also tried the solution laid out in this thread with no luck:
>>> *MailScanner has detected a possible fraud attempt from
>>> "na01.safelinks.protection.outlook.com
>>> " claiming to be*
>>> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2F%2Ffreesurfer%2F2014-September%2F040473.html=01%7C01%7CBTH22%40pitt.edu%7C446b463cf36a4889e95708d450389542%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1=KAGwvmXgr4Zkz%2FWWQAdxAzIrjRurig4783AvKVU3lGs%3D=0
>>> 

Re: [Freesurfer] extract area.pial stats

[Clara Kühn]

thanks. What kind of format is it? How do I open it?

Cheers 
Clara

- Ursprüngliche Mail -
Von: "Douglas N Greve" 
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 8. Februar 2017 16:43:47
Betreff: Re: [Freesurfer] extract area.pial stats

Try this version (same as version 6)

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



On 02/08/2017 04:55 AM, Clara Kühn wrote:
> Hi Doug,
>
> thanks for your reply. I tried it out and attached the lh.aparc.pial.stats 
> file for you to take a look at. As far as I can tell it's still reporting the 
> white surface area. Or am I reading it wrong?
>
> Cheers Clara
>
> - Ursprüngliche Mail -
> Von: "Douglas Greve" 
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Mittwoch, 8. Februar 2017 00:15:22
> Betreff: Re: [Freesurfer] extract area.pial stats
>
> try
>
> cd $SUBJECTS_DIR/subject/surf
>
> mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
> ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c 
> ../label/aparc.annot.ctab subject lh pial
>
>
> On 2/7/17 4:48 AM, Clara Kühn wrote:
>> Dear FreeSurfer experts,
>>
>> I'm trying to extract a total Pial Surface Area like it is extracted for 
>> White Surface Area in the ?h.aparc.stats file. I have tried this command but 
>> it doesn't seem to include Pial Surface Area:
>>
>> mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f 
>> $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial
>>
>> How could I extract the total Pial Surface Area for each participant?
>>
>> Thank you for you help!
>> Clara
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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.
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

[Taylor Hilton]

This is the output: ln: failed to create symbolic link 'lh.white.H': Operation 
not supported

> On Feb 8, 2017, at 10:38 AM, Douglas N Greve  
> wrote:
> 
> can you run the commands below and tell me what happens?
> 
> cd /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/surf
> ln -s lh.white.preaparc.H lh.white.H
> 
> 
> On 02/08/2017 09:44 AM, Taylor Hilton wrote:
>> Apologies, that was an old log, attaching the relevant one here.
>> 
>> 
>> 
>> 
>>> On Feb 7, 2017, at 6:02 PM, Douglas Greve >>  
>>> >> 
>>> wrote:
>>> 
>>> According to the log file, the error is that you need a new license:
>>> 
>>> GNU libc version: 2.23
>>> ERROR: Systems running GNU glibc version greater than 2.15
>>> require a newly formatted license file (it's free). Please
>>> download a new one from the following page:
>>> *MailScanner has detected a possible fraud attempt from 
>>> "na01.safelinks.protection.outlook.com 
>>> " claiming to be* 
>>> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html=01%7C01%7CBTH22%40pitt.edu%7C446b463cf36a4889e95708d450389542%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1=CHwu5i2iSGCh56pKWyVyp3ygYwdOQ0WSEBes26448ro%3D=0
>>>  
>>> 
>>> 
>>> 
>>> 
>>> On 2/7/17 12:49 PM, Taylor Hilton wrote:
 Yes I’ll attach it here.  I’m using a linux server(Ubuntu).
 
 
 
 
> On Feb 7, 2017, at 12:32 PM, Douglas Greve 
>  
> >> 
> wrote:
> 
> Can you send the full recon-all.log? What platform are you running on?
> 
> 
> On 2/7/17 11:19 AM, Taylor Hilton wrote:
>> Hi all,
>> 
>> Having trouble with an error running "recon-all -subjid ${i} 
>> -autorecon2” across all subjects.
>> 
>> Below is where it has the error in recon-all.log.  We also tried 
>> running the last command (“ln -s …”) manually and got the error 
>> “ln: failed to create symbolic link ‘lh.white.H’: Operation not 
>> supported.” whereas the rest of the commands ran normally.
>> 
>> #
>> #@# Curv .H and .K lh Tue Feb  7 07:29:43 EST 2017
>> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/surf
>> 
>> mris_curvature -w lh.white.preaparc
>> 
>> total integrated curvature = 18.936*4pi (237.960) --> -18 handles
>> ICI = 230.2, FI = 1697.2, variation=29040.790
>> writing Gaussian curvature to ./lh.white.preaparc.K...done.
>> writing mean curvature to ./lh.white.preaparc.H...done.
>> rm -f lh.white.H
>> ln -s lh.white.preaparc.H lh.white.H
>> Linux pfc 4.4.0-59-generic #80-Ubuntu SMP Fri Jan 6 17:47:47 UTC 
>> 2017 x86_64 x86_64 x86_64 GNU/Linux
>> 
>> recon-all -s 10007 exited with ERRORS at Tue Feb  7 07:29:46 EST 2017
>> 
>> To report a problem, see *MailScanner has detected a possible 
>> fraud attempt from "na01.safelinks.protection.outlook.com 
>> " 
>> claiming to be* 
>> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting=01%7C01%7CBTH22%40pitt.edu%7C446b463cf36a4889e95708d450389542%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1=Qjbe1jS%2BeKSdSGHHfJQKx%2FFQWrSd5B1ckHOVz9dh%2FmU%3D=0
>>  
>> 
>>  
>> >  
>> >
>> 
>> 
>> 
>> 
>> We also tried the solution laid out in this thread with no luck:
>> *MailScanner has detected a possible fraud attempt from 
>> 

Re: [Freesurfer] extract area.pial stats

[Douglas N Greve]

Try this version (same as version 6)

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



On 02/08/2017 04:55 AM, Clara Kühn wrote:
> Hi Doug,
>
> thanks for your reply. I tried it out and attached the lh.aparc.pial.stats 
> file for you to take a look at. As far as I can tell it's still reporting the 
> white surface area. Or am I reading it wrong?
>
> Cheers Clara
>
> - Ursprüngliche Mail -
> Von: "Douglas Greve" 
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Mittwoch, 8. Februar 2017 00:15:22
> Betreff: Re: [Freesurfer] extract area.pial stats
>
> try
>
> cd $SUBJECTS_DIR/subject/surf
>
> mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
> ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c 
> ../label/aparc.annot.ctab subject lh pial
>
>
> On 2/7/17 4:48 AM, Clara Kühn wrote:
>> Dear FreeSurfer experts,
>>
>> I'm trying to extract a total Pial Surface Area like it is extracted for 
>> White Surface Area in the ?h.aparc.stats file. I have tried this command but 
>> it doesn't seem to include Pial Surface Area:
>>
>> mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f 
>> $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial
>>
>> How could I extract the total Pial Surface Area for each participant?
>>
>> Thank you for you help!
>> Clara
>> ___
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> http://www.partners.org/complianceline . If the e-mail was sent to you in 
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Recon-all - finished with errors

[Douglas N Greve]

that is bizarre. Can you upload

lh.area.mid to our file drop (see end of email)


On 02/08/2017 05:21 AM, Bunday, Karen wrote:
> Yes, that's it. It just back to the command line after that.
>
> What do you think the problem is?
>
> BW
> Karen
>
> Karen Bunday, PhD
> Research Associate
> Sobell Department of Motor Neuroscience and Movement Disorders
> Institute of Neurology, University College London
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
> Sent: 07 February 2017 23:08
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Recon-all - finished with errors
>
> Is that the entire terminal output?
>
>
> On 2/7/17 6:46 AM, Bunday, Karen wrote:
>> Hi
>>
>> Thank you for your email.
>>
>> I checked the disk space and there is over 300 GB left.
>>
>> I ran the code as you suggested, this is the output:
>>
>> "WARNING: # of slices=-92 in header - assuming 124...
>> Read_signal (/Applications/Freesurfer/subjects/subjKZ/surf/I.001):
>> could not open file
>>
>> No such file or directory
>>
>>mris_calc: could not establish read access to 'lh.area.mid'
>>
>> No such file or directory"
>>
>> It's odd as I did manage to run this subject before, but needed to re-run 
>> with a different .nii and now it will not complete.
>>
>> BW
>> Karen
>>
>> Karen Bunday, PhD
>> Research Associate
>> Sobell Department of Motor Neuroscience and Movement Disorders
>> Institute of Neurology, University College London
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N
>> Greve
>> Sent: 06 February 2017 18:05
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Recon-all - finished with errors
>>
>> That is a strange error. Can you run the following command to try to
>> replicate:
>>
>> cd  /Applications/freesurfer/subjects/subjKZ/surf
>>
>> mris_calc -o lh.area.mid lh.area.mid div 2
>>
>> also, make sure that you have not run out of space on that disk
>>
>>
>> On 02/06/2017 09:56 AM, Bunday, Karen wrote:
>>> Dear FS members
>>>
>>> I am having trouble with using the "recon-all" function on one
>>> particular subject. "recon-all" does not complete and finishes with
>>> errors, it seems it does not complete both hemispheres. I am no
>>> expert in FS so I don't really understand why this is happening and I
>>> am unable to understand the log (attached). Could someone help
>>> interpret the log so that I may be able to process this subject?
>>>
>>> Many thanks
>>>
>>> Karen
>>>
>>> Karen Bunday, PhD
>>>
>>> Research Associate
>>>
>>> Sobell Department of Motor Neuroscience and Movement Disorders
>>>
>>> Institute of Neurology, University College London
>>>
>>> 33 Queen Square
>>>
>>> London
>>>
>>> WC1N 3BG
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing:
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
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>> 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.
>>
>>
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
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>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

Re: [Freesurfer] selxavg3-sess: F-contrast but multiple dimension in sig

[Douglas N Greve]

if you used the identity matrix then it is the first one


On 02/08/2017 08:43 AM, Seung-Goo KIM wrote:
> Thank you very much, Doug,
>
> One more question: so the sig have all T-test results of contrasts 
> like [1 0 0 … 0], [0 1 0 ... 0], …, [0 0 0 … 1], right? or [1 -1/(N-1) 
> -1/(N-1), … -1/(N-1)] ?
>
> Best,
> -- 
> Seung-Goo KIM
>
>> On 2017-02-06, at 18:54, Douglas N Greve > > wrote:
>>
>> yes, fsig is the F test. The sig has the result of all the individual
>> t-tests
>>
>>
>> On 02/06/2017 08:41 AM, Seung-Goo KIM wrote:
>>> Dear surfers,
>>>
>>> I computed F-contrast using selxavg3-sess with an identity matrix as a
>>> contrast matrix. My question is about the result file “sig.*”. As far
>>> as I understand, the “sig.*” file contains signed-minnus-log-p-values
>>> (like, -log10(p)*Sign(t)) for a certain contrast.
>>>
>>> So I expected the dimension should be #vertices-by-1, but the sig.*
>>> file is in the dimension of #vertices-by-1-by-1-by-#regressors. I
>>> would appreciate post-hoc tests after F-test, but the dimension
>>> doesn’t look like one… or is it? like i-th regressor v.s. (N-i)
>>> regressors? If one can tell where I can find p-values for the F-test,
>>> and what are the values in the sig.* file.
>>>
>>> + wait. is "fsig.*” for the F-test? and “sig.*” for a set of
>>> one-vs.-the-others contrasts? I would still appreciate if one can
>>> confirm it.
>>>
>>> Best regards,
>>> --
>>> Seung-Goo KIM
>>>
>>> Research Group for Cortical Networks and Cognitive Functions,
>>> Max Planck Institute for Human Cognitive and Brain Sciences,
>>> Stephanstraße 1A, 04103 Leipzig, Germany.
>>> Phone: +49 341 9940 2618 | Fax: +49 341 9940 2624
>>> http://www.cbs.mpg.de/~skim 
>>> 
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu 
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu 
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 
>> 
>> FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
>> 
>> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> 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.
>
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] recon-all issue {Disarmed}

[Douglas N Greve]

can you run the commands below and tell me what happens?

cd /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/surf
ln -s lh.white.preaparc.H lh.white.H


On 02/08/2017 09:44 AM, Taylor Hilton wrote:
> Apologies, that was an old log, attaching the relevant one here.
>
>
>
>
>> On Feb 7, 2017, at 6:02 PM, Douglas Greve > > wrote:
>>
>> According to the log file, the error is that you need a new license:
>>
>> GNU libc version: 2.23
>> ERROR: Systems running GNU glibc version greater than 2.15
>> require a newly formatted license file (it's free). Please
>> download a new one from the following page:
>> *MailScanner has detected a possible fraud attempt from 
>> "na01.safelinks.protection.outlook.com" claiming to be* 
>> http://surfer.nmr.mgh.harvard.edu/registration.html
>>
>>
>>
>> On 2/7/17 12:49 PM, Taylor Hilton wrote:
>>> Yes I’ll attach it here.  I’m using a linux server(Ubuntu).
>>>
>>>
>>>
>>>
 On Feb 7, 2017, at 12:32 PM, Douglas Greve 
 > wrote:

 Can you send the full recon-all.log? What platform are you running on?


 On 2/7/17 11:19 AM, Taylor Hilton wrote:
> Hi all,
>
> Having trouble with an error running "recon-all -subjid ${i} 
> -autorecon2” across all subjects.
>
> Below is where it has the error in recon-all.log.  We also tried 
> running the last command (“ln -s …”) manually and got the error 
> “ln: failed to create symbolic link ‘lh.white.H’: Operation not 
> supported.” whereas the rest of the commands ran normally.
>
> #
> #@# Curv .H and .K lh Tue Feb  7 07:29:43 EST 2017
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/surf
>
>  mris_curvature -w lh.white.preaparc
>
> total integrated curvature = 18.936*4pi (237.960) --> -18 handles
> ICI = 230.2, FI = 1697.2, variation=29040.790
> writing Gaussian curvature to ./lh.white.preaparc.K...done.
> writing mean curvature to ./lh.white.preaparc.H...done.
> rm -f lh.white.H
> ln -s lh.white.preaparc.H lh.white.H
> Linux pfc 4.4.0-59-generic #80-Ubuntu SMP Fri Jan 6 17:47:47 UTC 
> 2017 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s 10007 exited with ERRORS at Tue Feb  7 07:29:46 EST 2017
>
> To report a problem, see *MailScanner has detected a possible 
> fraud attempt from "na01.safelinks.protection.outlook.com" 
> claiming to be* 
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 
> 
>
> 
>
>
> We also tried the solution laid out in this thread with no luck:
> *MailScanner has detected a possible fraud attempt from 
> "na01.safelinks.protection.outlook.com" claiming to be* 
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040473.html
>  
> 
>
> Any help is very appreciated!
>
> - B. Taylor Hilton
> Lab Data Coordinator, University of Pittsburgh
>
>
>
>
>
>
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Re: [Freesurfer] dcm2niix

[Yendiki, Anastasia]

Hi Graham – Have you tried mri_convert? The 6.0 version should be able to 
extract diffusion gradient tables and b-value tables from most standard recent 
dicoms.

a.y

From: 
>
 on behalf of "Warner, Graham Cary" 
>
Reply-To: Freesurfer support list 
>
Date: Wednesday, February 8, 2017 at 10:01 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
>
Subject: [Freesurfer] dcm2niix

Hi all,

Can we get dcm2niix added to the system instance of fsl? It can't find it in 
5.0.7 or 5.0.9 (please let me know if it is somewhere else and I'm just not 
seeing it). I'm having problems generating .bval and .bvec files from certain 
DTI datasets using dcm2nii and the NITRC guys told me I should be using 
dcm2niix.

Thanks,
Graham
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[Freesurfer] dcm2niix

[Warner, Graham Cary]

Hi all,

Can we get dcm2niix added to the system instance of fsl? It can't find it in 
5.0.7 or 5.0.9 (please let me know if it is somewhere else and I'm just not 
seeing it). I'm having problems generating .bval and .bvec files from certain 
DTI datasets using dcm2nii and the NITRC guys told me I should be using 
dcm2niix.

Thanks,
Graham
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Re: [Freesurfer] selxavg3-sess: F-contrast but multiple dimension in sig

[Seung-Goo KIM]

Thank you very much, Doug,

One more question: so the sig have all T-test results of contrasts like [1 0 0 
… 0], [0 1 0 ... 0], …, [0 0 0 … 1], right? or [1 -1/(N-1) -1/(N-1), … 
-1/(N-1)] ?

Best,
-- 
Seung-Goo KIM

> On 2017-02-06, at 18:54, Douglas N Greve  wrote:
> 
> yes, fsig is the F test. The sig has the result of all the individual 
> t-tests
> 
> 
> On 02/06/2017 08:41 AM, Seung-Goo KIM wrote:
>> Dear surfers,
>> 
>> I computed F-contrast using selxavg3-sess with an identity matrix as a 
>> contrast matrix. My question is about the result file “sig.*”. As far 
>> as I understand, the “sig.*” file contains signed-minnus-log-p-values 
>> (like, -log10(p)*Sign(t)) for a certain contrast.
>> 
>> So I expected the dimension should be #vertices-by-1, but the sig.* 
>> file is in the dimension of #vertices-by-1-by-1-by-#regressors. I 
>> would appreciate post-hoc tests after F-test, but the dimension 
>> doesn’t look like one… or is it? like i-th regressor v.s. (N-i) 
>> regressors? If one can tell where I can find p-values for the F-test, 
>> and what are the values in the sig.* file.
>> 
>> + wait. is "fsig.*” for the F-test? and “sig.*” for a set of 
>> one-vs.-the-others contrasts? I would still appreciate if one can 
>> confirm it.
>> 
>> Best regards,
>> -- 
>> Seung-Goo KIM
>> 
>> Research Group for Cortical Networks and Cognitive Functions,
>> Max Planck Institute for Human Cognitive and Brain Sciences,
>> Stephanstraße 1A, 04103 Leipzig, Germany.
>> Phone: +49 341 9940 2618 | Fax: +49 341 9940 2624
>> http://www.cbs.mpg.de/~skim  
>> >
>> 
>> 
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu 
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>> 
> 
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 
> 
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
> 
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 
> 
> 
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> 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.

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Re: [Freesurfer] Recon-all - finished with errors

[Bunday, Karen]

Yes, that's it. It just back to the command line after that.

What do you think the problem is?

BW
Karen

Karen Bunday, PhD
Research Associate
Sobell Department of Motor Neuroscience and Movement Disorders
Institute of Neurology, University College London

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: 07 February 2017 23:08
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all - finished with errors

Is that the entire terminal output?


On 2/7/17 6:46 AM, Bunday, Karen wrote:
> Hi
>
> Thank you for your email.
>
> I checked the disk space and there is over 300 GB left.
>
> I ran the code as you suggested, this is the output:
>
> "WARNING: # of slices=-92 in header - assuming 124...
> Read_signal (/Applications/Freesurfer/subjects/subjKZ/surf/I.001): 
> could not open file
>
> No such file or directory
>
>   mris_calc: could not establish read access to 'lh.area.mid'
>
> No such file or directory"
>
> It's odd as I did manage to run this subject before, but needed to re-run 
> with a different .nii and now it will not complete.
>
> BW
> Karen
>
> Karen Bunday, PhD
> Research Associate
> Sobell Department of Motor Neuroscience and Movement Disorders 
> Institute of Neurology, University College London
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N 
> Greve
> Sent: 06 February 2017 18:05
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Recon-all - finished with errors
>
> That is a strange error. Can you run the following command to try to
> replicate:
>
> cd  /Applications/freesurfer/subjects/subjKZ/surf
>
> mris_calc -o lh.area.mid lh.area.mid div 2
>
> also, make sure that you have not run out of space on that disk
>
>
> On 02/06/2017 09:56 AM, Bunday, Karen wrote:
>> Dear FS members
>>
>> I am having trouble with using the "recon-all" function on one 
>> particular subject. "recon-all" does not complete and finishes with 
>> errors, it seems it does not complete both hemispheres. I am no 
>> expert in FS so I don't really understand why this is happening and I 
>> am unable to understand the log (attached). Could someone help 
>> interpret the log so that I may be able to process this subject?
>>
>> Many thanks
>>
>> Karen
>>
>> Karen Bunday, PhD
>>
>> Research Associate
>>
>> Sobell Department of Motor Neuroscience and Movement Disorders
>>
>> Institute of Neurology, University College London
>>
>> 33 Queen Square
>>
>> London
>>
>> WC1N 3BG
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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Re: [Freesurfer] extract area.pial stats

[Clara Kühn]

Hi Doug,

thanks for your reply. I tried it out and attached the lh.aparc.pial.stats file 
for you to take a look at. As far as I can tell it's still reporting the white 
surface area. Or am I reading it wrong?

Cheers Clara

- Ursprüngliche Mail -
Von: "Douglas Greve" 
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 8. Februar 2017 00:15:22
Betreff: Re: [Freesurfer] extract area.pial stats

try

cd $SUBJECTS_DIR/subject/surf

mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c 
../label/aparc.annot.ctab subject lh pial


On 2/7/17 4:48 AM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I'm trying to extract a total Pial Surface Area like it is extracted for 
> White Surface Area in the ?h.aparc.stats file. I have tried this command but 
> it doesn't seem to include Pial Surface Area:
>
> mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f 
> $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial
>
> How could I extract the total Pial Surface Area for each participant?
>
> Thank you for you help!
> Clara
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lh.aparc.pial.stats
Description: Binary data
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[Freesurfer] PET ROI analysis

[Donatas Sederevicius]

?Hello FreeSurfer Developers,


I have done partial volume correction of PET data as described in PETSurfer 
stream. Now, I want to extract a mean intensity value of my ROI for each 
subject. This ROI is defined in the fsaverage space and saved as a label. What 
would be the best way to do it? Should I start from mri_label2label command to 
map the label to the individual anatomical space or there is another, maybe 
easier way to do it?


Thanks in advance.


-Donatas
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