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

[Bruce Fischl]

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 

Re: [Freesurfer] FreeSurfer error: mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.30405/nu1.mnc

[Muhammad Khan]

I'm not sure if "mri_convert *junc.mnc* junk.mgh" was a typo, however, I
tried both (junc.mnc, and junk.mnc), and there were errors on both.
You're right, I got the same error (using junk.mnc). I'm going to downgrade
and see if that helps.


On Tue, Feb 7, 2017 at 7:43 PM, Douglas Greve 
wrote:

> It may be the version of minc you are using. On our system, we use version 
> 1.5, but it seems to work with 2.2. I don't have access to 2.3. Can you try 
> this
>
> mri_convert orig.mgz orig.nii
> nii2mnc orig.nii junk.mnc
> mri_convert junc.mnc junk.mgh
>
> I'm thinking that the last command will fail
>
>
> On 2/7/17 6:27 PM, Muhammad Khan wrote:
>
> Thanks for getting back to me.
> I ran that command from the $SUBJECTS_DIR/TEST01/mri folder and this is
> the output:
>
> *-rw-rw-r-- 1 root 1590 31M Feb  7 10:14
>> ./tmp.mri_nu_correct.mni.30405/nu1.mnc*
>
>
> I do have multiple disks mounted on the server, but they all have more
> than enough space. The directory of the freesurfer folder has over 1.5TB.
> Are any temporary folders created in a different location other than the
> freesurfer directory?
>
> Thanks!
>
>
>
> On Tue, Feb 7, 2017 at 4:21 PM, Douglas Greve 
> wrote:
>
>> not sure what is going wrong here. For some reason mri_convert does not
>> think that the mnc file is a minc file. Can you verify that you did not run
>> out of space on that disk? Can you send the result of
>>
>> ls -l ./tmp.mri_nu_correct.mni.30405/nu1.mnc
>>
>> On 2/7/17 2:59 PM, Muhammad Khan wrote:
>>
>>
>>
>>
>> Hi FreeSurfer Developers,
>>
>> I have been trying the 'recon-all -all -s TEST01' command, however I run
>> into the following error:
>>
>> mri_convert ./tmp.mri_nu_correct.mni.30405/nu1.mnc orig_nu.mgz --like
>>> orig.mgz --conform
>>> mri_convert.bin ./tmp.mri_nu_correct.mni.30405/nu1.mnc orig_nu.mgz
>>> --like orig.mgz --conform
>>> ncopen: filename "./tmp.mri_nu_correct.mni.30405/nu1.mnc": Not a netCDF
>>> file
>>> miopen: MINC package entry point
>>> Error opening ./tmp.mri_nu_correct.mni.30405/nu1.mnc
>>> *mincRead(): error reading volume from file
>>> ./tmp.mri_nu_correct.mni.30405/nu1.mnc*
>>> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
>>> reading from ./tmp.mri_nu_correct.mni.30405/nu1.mnc...
>>> Linux charcot 2.6.32-642.1.1.el6.x86_64 #1 SMP Tue May 31 21:57:07 UTC
>>> 2016 x86_64 x86_64 x86_64 GNU/Linux
>>> recon-all -s TEST01 exited with ERRORS at Tue Feb  7 10:14:31 PST 2017
>>> For more details, see the log file /mnt/data/freesurfer/subjects/
>>> TEST01/scripts/recon-all.log
>>> To report a problem, see http://surfer.nmr.mgh.harvard.
>>> edu/fswiki/BugReporting
>>
>>
>> I tried looking in the email-archives, although people had the same
>> error, I wan unable to find a fix for it. My linux server is running on
>> CentOS 6.8 and I am using the latest freesurfer release (v.6.0).
>>
>> These are the versions of some of the programs that are installed on the
>> server:
>>
>>> charcot:~# mnc2nii -version
>>> program: 2.3.01
>>> libminc: 2.3.01
>>> netcdf : 4.3.3 of Feb  8 2016 14:56:05 $
>>> HDF5   : 1.8.15
>>
>>
>>
>>
>> 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0
>> 2) Platform: CentOS release 6.8 (Final)
>> 3) uname -a: Linux charcot 2.6.32-642.1.1.el6.x86_64 #1 SMP Tue May 31 
>> 21:57:07 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
>> 4) recon-all.log: see attached
>>
>> I have also attached my recon-all log file. If there is anything else I
>> can provide, please let me know.
>> Thanks,
>> Muhammad
>>
>> ___
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>>
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>> du/mailman/listinfo/freesurfer The information in this e-mail is
>> intended only for the person to whom it is addressed. If you believe this
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>> information, please contact the Partners Compliance HelpLine at
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> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the 

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

[冉倩]

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 surfaces, but there was not much detail or a picture.
>> >> >>
>>   On 2/7/17 8:22 AM, 冉倩 wrote:
>>   Hello Freesurfer Developers,
>> I have had last September Freesurfer course. When I operated my
>> data following that stream I met some problem in reon-all -all
>> step. Because I need put some screenshout to exaplain that
>> problems, I add word document in attachment. Thanks very much!
>> Best Regards,
>> Qian Ran
>> >> >>  
>> >> >> >> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> 

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

[Douglas Greve]

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 surfaces, but there was not much detail or a
picture.
>> >> >>
>>   On 2/7/17 8:22 AM, 冉倩 wrote:
>>   Hello Freesurfer Developers,
>> I have had last September Freesurfer course. When I operated my
>> data following that stream I met some problem in reon-all -all
>> step. Because I need put some screenshout 

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

[冉倩]

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 surfaces, but there was not much detail or a picture.
>> >> >>
>>   On 2/7/17 8:22 AM, 冉倩 wrote:
>>   Hello Freesurfer Developers,
>> I have had last September Freesurfer course. When I operated my
>> data following that stream I met some problem in reon-all -all
>> step. Because I need put some screenshout to exaplain that
>> problems, I add word document in attachment. Thanks very much!
>> Best Regards,
>> Qian Ran
>> >> >>  
>> >> >> >> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >> >> >> >>  
>> >> >>


 






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

[Douglas Greve]

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 surfaces, but there was not much detail or a 
picture.

>> >> >>
>>   On 2/7/17 8:22 AM, 冉倩 wrote:
>>   Hello Freesurfer Developers,
>> I have had last September Freesurfer course. When I operated my
>> data following that stream I met some problem in reon-all -all
>> step. Because I need put some screenshout to exaplain that
>> problems, I add word document in attachment. Thanks very much!
>> Best Regards,
>> Qian Ran
>> >> >>
>> >> >> >> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >> >> >> >>
>> >> >>









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

[冉倩]

Hi Bruce, 
Thanks for your suggestions. 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?
Thnanks!
Best Regards,
Qian Ran





At 2017-02-08 10:57:23, "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 surfaces, but there was not much detail or a picture.
>> >> 
>> >> 
>> >>
>> >>   On 2/7/17 8:22 AM, 冉倩 wrote:
>> >>   Hello Freesurfer Developers,
>> >> I have had last September Freesurfer course. When I operated my
>> >> data following that stream I met some problem in reon-all -all
>> >> step. Because I need put some screenshout to exaplain that
>> >> problems, I add word document in attachment. Thanks very much!
>> >> Best Regards,
>> >> Qian Ran
>> >> 
>> >> 
>> >>  
>> >> 
>> >> 
>> >> 
>> >> ___
>> >> Freesurfer mailing list
>> >> Freesurfer@nmr.mgh.harvard.edu
>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >> 
>> >> 
>> >> 
>> >> 
>> >>  
>> >> 
>> >> 
>> >>
>> 
>> 
>>  
>> 
>> 
>>
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The information in 

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

[Bruce Fischl]

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 surfaces, but there was not much detail or a picture.
>> 
>> 
>>

>>   On 2/7/17 8:22 AM, 冉倩 wrote:
>>   Hello Freesurfer Developers,
>> I have had last September Freesurfer course. When I operated my
>> data following that stream I met some problem in reon-all -all
>> step. Because I need put some screenshout to exaplain that
>> problems, I add word document in attachment. Thanks very much!
>> Best Regards,
>> Qian Ran
>> 
>> 
>>  
>> 
>> 
>> 
>> ___

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



 


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Re: [Freesurfer] FreeSurfer error: mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.30405/nu1.mnc

[Douglas Greve]

It may be the version of minc you are using. On our system, we use version 1.5, 
but it seems to work with 2.2. I don't have access to 2.3. Can you try this

mri_convert orig.mgz orig.nii
nii2mnc orig.nii junk.mnc
mri_convert junc.mnc junk.mgh

I'm thinking that the last command will fail


On 2/7/17 6:27 PM, Muhammad Khan wrote:

Thanks for getting back to me.
I ran that command from the $SUBJECTS_DIR/TEST01/mri folder and this 
is the output:


*-rw-rw-r-- 1 root 1590 31M Feb  7 10:14
./tmp.mri_nu_correct.mni.30405/nu1.mnc*


I do have multiple disks mounted on the server, but they all have more 
than enough space. The directory of the freesurfer folder has over 
1.5TB. Are any temporary folders created in a different location other 
than the freesurfer directory?


Thanks!



On Tue, Feb 7, 2017 at 4:21 PM, Douglas Greve 
> wrote:


not sure what is going wrong here. For some reason mri_convert
does not think that the mnc file is a minc file. Can you verify
that you did not run out of space on that disk? Can you send the
result of

ls -l ./tmp.mri_nu_correct.mni.30405/nu1.mnc


On 2/7/17 2:59 PM, Muhammad Khan wrote:




Hi FreeSurfer Developers,

I have been trying the 'recon-all -all -s TEST01' command,
however I run into the following error:

mri_convert ./tmp.mri_nu_correct.mni.30405/nu1.mnc
orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.30405/nu1.mnc
orig_nu.mgz --like orig.mgz --conform
ncopen: filename "./tmp.mri_nu_correct.mni.30405/nu1.mnc":
Not a netCDF file
miopen: MINC package entry point
Error opening ./tmp.mri_nu_correct.mni.30405/nu1.mnc
*mincRead(): error reading volume from file
./tmp.mri_nu_correct.mni.30405/nu1.mnc*
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.30405/nu1.mnc...
Linux charcot 2.6.32-642.1.1.el6.x86_64 #1 SMP Tue May 31
21:57:07 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s TEST01 exited with ERRORS at Tue Feb  7 10:14:31
PST 2017
For more details, see the log file
/mnt/data/freesurfer/subjects/TEST01/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



I tried looking in the email-archives, although people had the
same error, I wan unable to find a fix for it. My linux server is
running on CentOS 6.8 and I am using the latest freesurfer
release (v.6.0).

These are the versions of some of the programs that are installed
on the server:

charcot:~# mnc2nii -version
program: 2.3.01
libminc: 2.3.01
netcdf : 4.3.3 of Feb  8 2016 14:56:05 $
HDF5   : 1.8.15


1) FreeSurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0 2) Platform:
CentOS release 6.8 (Final) 3) uname -a: Linux charcot
2.6.32-642.1.1.el6.x86_64 #1 SMP Tue May 31 21:57:07 UTC 2016
x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached
I have also attached my recon-all log file. If there is anything
else I can provide, please let me know.
Thanks,
Muhammad

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

[Bruce Fischl]

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 steps
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 pial
(-pial ) at the same time, then I run:

recon-all –autorecon2-cp –autorecon2-wm –autorecon2-pail –autorecon3 sub01
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 surfaces, but there was not much detail or a picture.



  On 2/7/17 8:22 AM, 冉倩 wrote:
  Hello Freesurfer Developers,
I have had last September Freesurfer course. When I operated my
data following that stream I met some problem in reon-all -all
step. Because I need put some screenshout to exaplain that
problems, I add word document in attachment. Thanks very much!
Best Regards,
Qian Ran


 



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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] FreeSurfer error: mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.30405/nu1.mnc

[Muhammad Khan]

Thanks for getting back to me.
I ran that command from the $SUBJECTS_DIR/TEST01/mri folder and this is the
output:

*-rw-rw-r-- 1 root 1590 31M Feb  7 10:14
> ./tmp.mri_nu_correct.mni.30405/nu1.mnc*


I do have multiple disks mounted on the server, but they all have more than
enough space. The directory of the freesurfer folder has over 1.5TB. Are
any temporary folders created in a different location other than the
freesurfer directory?

Thanks!



On Tue, Feb 7, 2017 at 4:21 PM, Douglas Greve 
wrote:

> not sure what is going wrong here. For some reason mri_convert does not
> think that the mnc file is a minc file. Can you verify that you did not run
> out of space on that disk? Can you send the result of
>
> ls -l ./tmp.mri_nu_correct.mni.30405/nu1.mnc
>
> On 2/7/17 2:59 PM, Muhammad Khan wrote:
>
>
>
>
> Hi FreeSurfer Developers,
>
> I have been trying the 'recon-all -all -s TEST01' command, however I run
> into the following error:
>
> mri_convert ./tmp.mri_nu_correct.mni.30405/nu1.mnc orig_nu.mgz --like
>> orig.mgz --conform
>> mri_convert.bin ./tmp.mri_nu_correct.mni.30405/nu1.mnc orig_nu.mgz
>> --like orig.mgz --conform
>> ncopen: filename "./tmp.mri_nu_correct.mni.30405/nu1.mnc": Not a netCDF
>> file
>> miopen: MINC package entry point
>> Error opening ./tmp.mri_nu_correct.mni.30405/nu1.mnc
>> *mincRead(): error reading volume from file
>> ./tmp.mri_nu_correct.mni.30405/nu1.mnc*
>> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
>> reading from ./tmp.mri_nu_correct.mni.30405/nu1.mnc...
>> Linux charcot 2.6.32-642.1.1.el6.x86_64 #1 SMP Tue May 31 21:57:07 UTC
>> 2016 x86_64 x86_64 x86_64 GNU/Linux
>> recon-all -s TEST01 exited with ERRORS at Tue Feb  7 10:14:31 PST 2017
>> For more details, see the log file /mnt/data/freesurfer/subjects/
>> TEST01/scripts/recon-all.log
>> To report a problem, see http://surfer.nmr.mgh.harvard.
>> edu/fswiki/BugReporting
>
>
> I tried looking in the email-archives, although people had the same error,
> I wan unable to find a fix for it. My linux server is running on CentOS 6.8
> and I am using the latest freesurfer release (v.6.0).
>
> These are the versions of some of the programs that are installed on the
> server:
>
>> charcot:~# mnc2nii -version
>> program: 2.3.01
>> libminc: 2.3.01
>> netcdf : 4.3.3 of Feb  8 2016 14:56:05 $
>> HDF5   : 1.8.15
>
>
>
>
> 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0
> 2) Platform: CentOS release 6.8 (Final)
> 3) uname -a: Linux charcot 2.6.32-642.1.1.el6.x86_64 #1 SMP Tue May 31 
> 21:57:07 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
> 4) recon-all.log: see attached
>
> I have also attached my recon-all log file. If there is anything else I
> can provide, please let me know.
>
> Thanks,
> Muhammad
>
>
>
>
>
>
>
>
>
>
>
>
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Re: [Freesurfer] FreeSurfer error: mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.30405/nu1.mnc

[Douglas Greve]

not sure what is going wrong here. For some reason mri_convert does not 
think that the mnc file is a minc file. Can you verify that you did not 
run out of space on that disk? Can you send the result of


ls -l ./tmp.mri_nu_correct.mni.30405/nu1.mnc


On 2/7/17 2:59 PM, Muhammad Khan wrote:




Hi FreeSurfer Developers,

I have been trying the 'recon-all -all -s TEST01' command, however I 
run into the following error:


mri_convert ./tmp.mri_nu_correct.mni.30405/nu1.mnc orig_nu.mgz
--like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.30405/nu1.mnc orig_nu.mgz
--like orig.mgz --conform
ncopen: filename "./tmp.mri_nu_correct.mni.30405/nu1.mnc": Not a
netCDF file
miopen: MINC package entry point
Error opening ./tmp.mri_nu_correct.mni.30405/nu1.mnc
*mincRead(): error reading volume from file
./tmp.mri_nu_correct.mni.30405/nu1.mnc*
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.30405/nu1.mnc...
Linux charcot 2.6.32-642.1.1.el6.x86_64 #1 SMP Tue May 31 21:57:07
UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s TEST01 exited with ERRORS at Tue Feb  7 10:14:31 PST 2017
For more details, see the log file
/mnt/data/freesurfer/subjects/TEST01/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



I tried looking in the email-archives, although people had the same 
error, I wan unable to find a fix for it. My linux server is running 
on CentOS 6.8 and I am using the latest freesurfer release (v.6.0).


These are the versions of some of the programs that are installed on 
the server:


charcot:~# mnc2nii -version
program: 2.3.01
libminc: 2.3.01
netcdf : 4.3.3 of Feb  8 2016 14:56:05 $
HDF5   : 1.8.15


1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0 
2) Platform: CentOS release 6.8 (Final) 3) uname -a: Linux charcot 
2.6.32-642.1.1.el6.x86_64 #1 SMP Tue May 31 21:57:07 UTC 2016 x86_64 
x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached
I have also attached my recon-all log file. If there is anything else 
I can provide, please let me know.


Thanks,
Muhammad












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

[Douglas Greve]

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 surfaces, but there was not much 
detail or a picture.




On 2/7/17 8:22 AM, 冉倩 wrote:

Hello Freesurfer Developers,
I have had last September Freesurfer course. When I operated my data 
following that stream I met some problem in reon-all -all step. 
Because I need put some screenshout to exaplain that problems, I add 
word document in attachment. Thanks very much!

Best Regards,
Qian Ran




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Re: [Freesurfer] extract area.pial stats

[Douglas Greve]

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

[Z K]

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

[Douglas Greve]

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

[Douglas Greve]

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:
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] QDEC table .dat

[Douglas Greve]

I don't know what you did, but that is still a binary file not a text file


On 2/7/17 4:27 PM, Leblanc Élizabel wrote:

Hi Freesurfer's expert,

I have some trouble with the dec.table.dat file, as many others as I can see. I 
am using a mac OS x, I took an excel file with my 4 variables and open it in a 
.txt format. then I tried to convert it to a .dat file. I think it worked well 
(I wrote mv qdec.table.txt qdec.table.dat in the command terminal). But when I 
try to load the table using QDEC it still give me this error message.


Loading data table /Applications/freesurfer/subjects/qdec.table.dat...

ERROR: QdecDataTable::Load could not find column named 'fsid' or 'ID' in 
/Applications/freesurfer/subjects/qdec.table.dat!

Error loading the data table.

I have attached to this email my qdec table.

Can you please give me advice on how to create a qdec table (as simple as 
possible because I am not pretty familiar with it to this point).

Thank you very much


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Re: [Freesurfer] -FLAIRpial in v6.0 positions pial surfaces much more externally in comparison to v5.3

[Antonin Skoch]

Dear Matt,

I do not use HCP pipeline scripts for this project.

This is standard 1x1x1 mm3 data so I thought standard freeSurfer pipeline could 
work well here. 
I also thought that standard recon-all version 6.0 with this data should work 
better than v5.3 which, I expect, solved some issues with v5.3 (some of them I 
was discussing in the forum previously):

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41880.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42312.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41375.html

But anyway, thank you for your feedback.

Antonin



Since I believe you said you are using my code, I would recommend to stick
with 5.3 at this time.Peace,

Matt.

From:   on behalf of Antonin Skoch

Reply-To:  Freesurfer support list 
Date:  Tuesday, February 7, 2017 at 2:59 PM
To:  
Subject:  Re: [Freesurfer] -FLAIRpial in v6.0 positions pial surfaces much
more externally in comparison to v5.3

Dear Bruce,

thank you for the feedback. I would definitely be interested in 6.1 beta.
What is the approximate timeline of release?
We are working on quite large project (involving -FLAIRpial) and I have to
decide whether to go to v6.0 or to stick with v5.3.
Do you think that so far the 5.3 version is better for T2/FLAIR? Why this is
the case?

Antonin

Hi Antonin

yes, V6 was not meant for T2/FLAIR and we didn't test it extensively. We
have been optimizing things in the past week for T2/FLAIR and I expect 6.1
will be better for them. We can give you a beta soon if you like.
cheers
Bruce
  On Tue, 7 
Feb 2017, Antonin Skoch wrote:

> Dear experts,
> 
> I have reprocessed my groups of subjects (originally processed by v5.3) by
> v6.0. I am using -FLAIRpial for pial surface refinement.
> 
> I have noticed that the pial surfaces in v6.0 after -FLAIRpial are positioned
> much more externally in comparison to -FLAIRpial in v5.3. The v6.0 version
> includes to pial sheet much more partial volume voxels in
> comparison to v5.3.
> 
> In contrast to v5.3, where the surfaces after -FLAIRpial were mostly
> internally with respect to pial surfaces determined by T1, in v6.0 there are
> many regions where the pial surfaces after -FLAIRpial are placed
> much externally with respect to pial surfaces determined by T1.
> 
> See the screenshot (red surfaces are pial surfaces after -FLAIRpial with
> v6.0, yellow are surfaces after -FLAIRpial with v.5.3).
> 
> I have used -nsigma_above 8 in mris_make_surfaces to prevent excluding some
> cortical regions with high signal intensity but this I used consistently in
> both versions so it should not be the reason of difference.
> 
> I have uploaded the subject processed both by 5.3 and 6.0 version to your
> server, files FLAIRpial_v5.3.tar.gz and FLAIRpial_v6.0.tar.gz.
> 
> Could you please look at my data and check whether the pial surfaces after
> -FLAIRpial in v6.0 look OK from your perspective?
> 
> Regards,
> 
> Antonin Skoch___
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Re: [Freesurfer] -FLAIRpial in v6.0 positions pial surfaces much more externally in comparison to v5.3

[Matt Glasser]

Since I believe you said you are using my code, I would recommend to stick
with 5.3 at this time.

Peace,

Matt.

From:   on behalf of Antonin Skoch

Reply-To:  Freesurfer support list 
Date:  Tuesday, February 7, 2017 at 2:59 PM
To:  
Subject:  Re: [Freesurfer] -FLAIRpial in v6.0 positions pial surfaces much
more externally in comparison to v5.3

Dear Bruce,

thank you for the feedback. I would definitely be interested in 6.1 beta.
What is the approximate timeline of release?
We are working on quite large project (involving -FLAIRpial) and I have to
decide whether to go to v6.0 or to stick with v5.3.
Do you think that so far the 5.3 version is better for T2/FLAIR? Why this is
the case?

Antonin

Hi Antonin

yes, V6 was not meant for T2/FLAIR and we didn't test it extensively. We
have been optimizing things in the past week for T2/FLAIR and I expect 6.1
will be better for them. We can give you a beta soon if you like.
cheers
Bruce
  On Tue, 7 
Feb 2017, Antonin Skoch wrote:

> Dear experts,
> 
> I have reprocessed my groups of subjects (originally processed by v5.3) by
> v6.0. I am using -FLAIRpial for pial surface refinement.
> 
> I have noticed that the pial surfaces in v6.0 after -FLAIRpial are positioned
> much more externally in comparison to -FLAIRpial in v5.3. The v6.0 version
> includes to pial sheet much more partial volume voxels in
> comparison to v5.3.
> 
> In contrast to v5.3, where the surfaces after -FLAIRpial were mostly
> internally with respect to pial surfaces determined by T1, in v6.0 there are
> many regions where the pial surfaces after -FLAIRpial are placed
> much externally with respect to pial surfaces determined by T1.
> 
> See the screenshot (red surfaces are pial surfaces after -FLAIRpial with
> v6.0, yellow are surfaces after -FLAIRpial with v.5.3).
> 
> I have used -nsigma_above 8 in mris_make_surfaces to prevent excluding some
> cortical regions with high signal intensity but this I used consistently in
> both versions so it should not be the reason of difference.
> 
> I have uploaded the subject processed both by 5.3 and 6.0 version to your
> server, files FLAIRpial_v5.3.tar.gz and FLAIRpial_v6.0.tar.gz.
> 
> Could you please look at my data and check whether the pial surfaces after
> -FLAIRpial in v6.0 look OK from your perspective?
> 
> Regards,
> 
> Antonin Skoch
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[Freesurfer] QDEC table .dat

[Leblanc Élizabel]

Hi Freesurfer's expert,

I have some trouble with the dec.table.dat file, as many others as I can see. I 
am using a mac OS x, I took an excel file with my 4 variables and open it in a 
.txt format. then I tried to convert it to a .dat file. I think it worked well 
(I wrote mv qdec.table.txt qdec.table.dat in the command terminal). But when I 
try to load the table using QDEC it still give me this error message.


Loading data table /Applications/freesurfer/subjects/qdec.table.dat...

ERROR: QdecDataTable::Load could not find column named 'fsid' or 'ID' in 
/Applications/freesurfer/subjects/qdec.table.dat!

Error loading the data table.

I have attached to this email my qdec table.

Can you please give me advice on how to create a qdec table (as simple as 
possible because I am not pretty familiar with it to this point).

Thank you very much


qdec.table.dat
Description: qdec.table.dat
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Re: [Freesurfer] -first_wm_peak with -hires in v6.0 (search for peak in second derivative)

[Bruce Fischl]

if I can find the time!
On Tue, 7 Feb 2017, Antonin Skoch wrote:



Dear Bruce,

Would you recommend to use -first_wm_peak with -hires option? My tests with
-first_wm_peak on v6.0 ( with search for peak in second derivative) indicate
that the white surface is placed too much internally with respect to actual
gm/wm interface. See the screenshots (with -first_wm_peak and without
-first_wm_peak).

I think that before update to second derivative (december 2016) the
placement of white surface with -first_wm_peak was more anatomically
relevant. Do you plan also to optimize this for v6.1?

Regards,

Antonin


  Dear experts,

  I am reposting here my mail to FreeSurfer experts (so far
  without response) concerning my results of testing of
  mris_make_surfaces in V6 freeSurfer version with modified HCP
  pipeline (tested on dev version from 3rd January, which is
  practically the same as now released 6.0.0 version, since no
  additional commits regarding mris_make_surfaces have been done).

  My inquiry was concerning the change of behavior of
  -first_wm_peak option of  mris_make_surfaces in 6.0.0 version.
  Apart from previous version the -first_wm_peak option now tries
  to search also for peak in second derivative.

  It seems to me that this modification of -first_wm_peak behavior
  leads now to the white surface placement too internally in gray
  matter which is not very anatomically relevant. See the
  screenshots where I compared the results:

  1. standard recon-all -hires version 6.0.0 adding -first_wm_peak
  to mris_make_surfaces (trying to search for peak in second
  derivative)
  2. FreeSurferHiResWhite.sh with 6.0.0 version  and
  -first_wm_peak (trying to search for peak in second derivative)
  3. FreeSurferHiResWhite.sh with V6 beta version (from december
  2016, before change) and -first_wm_peak (without trying to
  search for peak in second derivative)
  4. standard recon-all -hires version 6.0.0 default setting, i.e.
  without adding -first_wm_peak to mris_make_surfaces - quite
  similar but not identical results to the 3 - some regions are
  more internally, some more externally wrt to 3 - the difference
  can be also caused by better gm/wm contrast in brain.finalsurfs
  wrt T1w_hires_norm used in FreeSurferHiResWhite.sh.

  Could you please get time to look at the results and comment on
  which option you assess as most anatomically relevant?

  Regards,

  Antonin Skoch



  Subject: Re: posts about recent updates of freesurfer V6beta

Dear experts,

I also investigated further the second issue -
change of the behavior of -first_wm_peak of
mris_make_surfaces.

I am using modified HCP pipeline where the
mris_make_surfaces -first_wm_peak is used. I worked
to adapt this pipeline to work with V6beta version
of FreeSurfer with using -cm flag to impose
high-resolution reconstruction.

With the change of behavior of -first_wm_peak option
(to look for first peak in 2nd derivative) by commit
in 20th December 2016 the results with up-to-date
versions are no longer compatible with previous
versions (where first peak in 1st derivative was
used I suppose).

My testing using -first_wm_peak with the version
after 20th December 2016 shows that the white
surface is placed much more internally towards white
matter. I am not sure the placement of white surface
so internally is anatomically relevant.

See the screenshots of examples where

1. -first_wm_peak with version from 3rd January 2017
using brain.finalsurfs
2. -first_wm_peak with version  from 3rd January
2017 using normalized T1w image (i.e. image without
which did not underwent full previous steps of
recon-all - this is default implementation of
FreeSurferHiResWhite.sh in HCP pipeline).
3. -first_wm_peak with version from November 2016
using normalized T1w image


All versions use -orig -orig_white options with
white surface generated by recon-all -white (i.e.
mris_make_surfaces run without -first_wm_peak using
brain.finalsurfs). This white surface generated by
recon-all -white in 3rd January version is shown in
screenshot 4.

Here are my specific questions / suggestions:

Do you think the -first_wm_peak results with the 3rd
January 2017 version are anatomically relevant?
To assure backward compatibility, I would vote for
keeping option to look for first peak in 1st
derivative in mris_make_surfaces (aside from the new
 

Re: [Freesurfer] -FLAIRpial in v6.0 positions pial surfaces much more externally in comparison to v5.3

[Antonin Skoch]

Dear Bruce,

thank you for the feedback. I would definitely be interested in 6.1 beta. What 
is the approximate timeline of release? 
We are working on quite large project (involving -FLAIRpial) and I have to 
decide whether to go to v6.0 or to stick with v5.3.
Do you think that so far the 5.3 version is better for T2/FLAIR? Why this is 
the case?

Antonin

Hi Antonin

yes, V6 was not meant for T2/FLAIR and we didn't test it extensively. We 
have been optimizing things in the past week for T2/FLAIR and I expect 6.1 
will be better for them. We can give you a beta soon if you like.cheers
Bruce
  On Tue, 7 
Feb 2017, Antonin Skoch wrote:

> Dear experts,
> 
> I have reprocessed my groups of subjects (originally processed by v5.3) by 
> v6.0. I am using -FLAIRpial for pial surface refinement.
> 
> I have noticed that the pial surfaces in v6.0 after -FLAIRpial are positioned 
> much more externally in comparison to -FLAIRpial in v5.3. The v6.0 version 
> includes to pial sheet much more partial volume voxels in
> comparison to v5.3.
> 
> In contrast to v5.3, where the surfaces after -FLAIRpial were mostly 
> internally with respect to pial surfaces determined by T1, in v6.0 there are 
> many regions where the pial surfaces after -FLAIRpial are placed
> much externally with respect to pial surfaces determined by T1.
> 
> See the screenshot (red surfaces are pial surfaces after -FLAIRpial with 
> v6.0, yellow are surfaces after -FLAIRpial with v.5.3).
> 
> I have used -nsigma_above 8 in mris_make_surfaces to prevent excluding some 
> cortical regions with high signal intensity but this I used consistently in 
> both versions so it should not be the reason of difference.
> 
> I have uploaded the subject processed both by 5.3 and 6.0 version to your 
> server, files FLAIRpial_v5.3.tar.gz and FLAIRpial_v6.0.tar.gz.
> 
> Could you please look at my data and check whether the pial surfaces after 
> -FLAIRpial in v6.0 look OK from your perspective?
> 
> Regards,
> 
> Antonin Skoch___
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Re: [Freesurfer] mrisComputeCorrelationTerm: delta is not finite at vno 0

[Bruce Fischl]

Hi Juhyoung

this is a pretty odd bug, but I do have a patch for it. What 
hardware/software environment are you using?


cheers
Bruce
On Mon, 6 Feb 2017, 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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Re: [Freesurfer] (no subject)

[Z K]

Also, what is this "old FreeSurfer 6". Are you referring to a beta?

On 02/07/2017 03:24 PM, Iglesias Gonzalez, Eugenio wrote:
> Dear Stephen,
> I would definitely rerun, for the sake of reproducibility. The results
> are sensitive not only to changes in the subfield module (which I
> believe I didn’t modify in between your release and the final 6.0), but
> also to changes in the main FreeSurfer stream. So, your results are
> different than what you’d get by rerunning everything with the final 6.0
> version.
> Cheers,
> /Eugenio
>
> Juan Eugenio Iglesias
> ERC Senior Research Fellow
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
>
>
>> On 7 Feb 2017, at 20:18, Smagula, Stephen Fearns > > wrote:
>>
>> Dear Dr. Iglesias,
>>
>> Using the originally released version 6 (the one that was
>> "unreleased") I ran the recon -all -all and the subfield segmentations
>> on a sample. I noticed that the program was taken down then put back
>> online after some updates.
>>
>> Do you recommend we re-run these segmentations with the newly released
>> version? That is, if the segmentation ran with the "old FreeSurfer 6",
>> would you expect there to be any difference with the new release?
>>
>> Thank you,
>> Stephen Smagula
>> Post-doc
>> University of Pittsburgh
>>
>> ___
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>> 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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Re: [Freesurfer] (no subject)

[Iglesias Gonzalez, Eugenio]

Dear Stephen,
I would definitely rerun, for the sake of reproducibility. The results are 
sensitive not only to changes in the subfield module (which I believe I didn’t 
modify in between your release and the final 6.0), but also to changes in the 
main FreeSurfer stream. So, your results are different than what you’d get by 
rerunning everything with the final 6.0 version.
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 7 Feb 2017, at 20:18, Smagula, Stephen Fearns 
> wrote:


Dear Dr. Iglesias,

Using the originally released version 6 (the one that was "unreleased") I ran 
the recon -all -all and the subfield segmentations on a sample. I noticed that 
the program was taken down then put back online after some updates.

Do you recommend we re-run these segmentations with the newly released version? 
That is, if the segmentation ran with the "old FreeSurfer 6", would you expect 
there to be any difference with the new release?

Thank you,
Stephen Smagula
Post-doc
University of Pittsburgh


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Re: [Freesurfer] T2 and control points

[miracle ozzoude]

Thank you very much Antonin. It worked.
Best,
Paul

On Tue, Feb 7, 2017 at 2:36 PM, Antonin Skoch  wrote:

> Dear Paul,
>
> I don't know it it solves your problem, but if you are using bash shell, you 
> have to source SetUpFreeSurfer.sh, not SetUpFreeSurfer.csh.
>
> And, do you have FREESURFER_HOME variable properly set before running the 
> script?
> To check that, put
> echo $FREESURFER_HOME
>
> to the beginning of the script.
>
> Antonin
>
> Thanks Antonin and Bruce.
> Also, I wrote a recon-all script and when I tried to run it, it gave me an
> error (command not found). Please can anyone help me diagnosis what's wrong
> with my scripts. I did set my subject directory to the current folder
> (setenv SUBJECTS_DIR  /../folder/; cd /../folder) before
> running the script. Thanks. The scripts is below
>
> #!bin/bash
> # FreeSurfer Pipeline (stages 1-31)
> # Written By Paul
>
> set -e
>
> # Source FreeSurfer
> source $FREESURFER_HOME/SetUpFreeSurfer.csh
>
> # Start Scripts
> echo -e "\n START: FreeSurferEntirePipeline"
>
> # Input Variables
> SubjectID="$1"
> SubjectDIR="$2"
> T1wImage="$3" #T1 FreeSurfer Input
> T2wImage="$4" #T2 FreeSurfer Input
>
>
> recon-all -s $SubjectID -autorecon-all -i "$T1wImage"_T1.nii -T2
> "$T2wImage"_T2.nii -T2pial -parallel -hires
>
> echo -e "done"
> Best,
> Paul
>
> On Tue, Feb 7, 2017 at 4:40 AM, Antonin Skoch  wrote:
>
> > Dear Paul,
> >
> > maybe this is implicit, but to assure:
> >
> > you have also to include -autorecon3.
> >
> > Therefore the full command is:
> >
> > recon-all -s subject_id -autorecon2-cp -autorecon3 -T2pial
> >
> > Antonin
> >
> > Yes, I think so
> >
> > > On Feb 5, 2017, at 2:47 PM, miracoo...@gmail.com wrote:
> > >
> > > Hello,
> > >  I ran the entire recon pipeline with T2 option and then added control
> > > points. Do I need to run recon-all -autorecon2-cp with T2 flag to redo the
> > > pial surface or not? Thanks.
> > > Paul
> > >
> >
>
>
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>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
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> contains patient information, please contact the Partners Compliance
> HelpLine at
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> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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[Freesurfer] (no subject)

[Smagula, Stephen Fearns]

Dear Dr. Iglesias,

Using the originally released version 6 (the one that was "unreleased") I ran 
the recon -all -all and the subfield segmentations on a sample. I noticed that 
the program was taken down then put back online after some updates.

Do you recommend we re-run these segmentations with the newly released version? 
That is, if the segmentation ran with the "old FreeSurfer 6", would you expect 
there to be any difference with the new release?

Thank you,
Stephen Smagula
Post-doc
University of Pittsburgh

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Re: [Freesurfer] -FLAIRpial in v6.0 positions pial surfaces much more externally in comparison to v5.3

[Bruce Fischl]

Hi Antonin

yes, V6 was not meant for T2/FLAIR and we didn't test it extensively. We 
have been optimizing things in the past week for T2/FLAIR and I expect 6.1 
will be better for them. We can give you a beta soon if you like.

cheers
Bruce
  On Tue, 7 
Feb 2017, Antonin Skoch wrote:

> Dear experts,
> 
> I have reprocessed my groups of subjects (originally processed by v5.3) by 
> v6.0. I am using -FLAIRpial for pial surface refinement.
> 
> I have noticed that the pial surfaces in v6.0 after -FLAIRpial are positioned 
> much more externally in comparison to -FLAIRpial in v5.3. The v6.0 version 
> includes to pial sheet much more partial volume voxels in
> comparison to v5.3.
> 
> In contrast to v5.3, where the surfaces after -FLAIRpial were mostly 
> internally with respect to pial surfaces determined by T1, in v6.0 there are 
> many regions where the pial surfaces after -FLAIRpial are placed
> much externally with respect to pial surfaces determined by T1.
> 
> See the screenshot (red surfaces are pial surfaces after -FLAIRpial with 
> v6.0, yellow are surfaces after -FLAIRpial with v.5.3).
> 
> I have used -nsigma_above 8 in mris_make_surfaces to prevent excluding some 
> cortical regions with high signal intensity but this I used consistently in 
> both versions so it should not be the reason of difference.
> 
> I have uploaded the subject processed both by 5.3 and 6.0 version to your 
> server, files FLAIRpial_v5.3.tar.gz and FLAIRpial_v6.0.tar.gz.
> 
> Could you please look at my data and check whether the pial surfaces after 
> -FLAIRpial in v6.0 look OK from your perspective?
> 
> Regards,
> 
> Antonin Skoch
> 
>
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Re: [Freesurfer] T2 and control points

[Antonin Skoch]

Dear Paul,

I don't know it it solves your problem, but if you are using bash shell, you 
have to source SetUpFreeSurfer.sh, not SetUpFreeSurfer.csh.

And, do you have FREESURFER_HOME variable properly set before running the 
script?
To check that, put 
echo $FREESURFER_HOME

to the beginning of the script.

Antonin

Thanks Antonin and Bruce.
Also, I wrote a recon-all script and when I tried to run it, it gave me an
error (command not found). Please can anyone help me diagnosis what's wrong
with my scripts. I did set my subject directory to the current folder
(setenv SUBJECTS_DIR  /../folder/; cd /../folder) before
running the script. Thanks. The scripts is below#!bin/bash
# FreeSurfer Pipeline (stages 1-31)
# Written By Paul

set -e

# Source FreeSurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh

# Start Scripts
echo -e "\n START: FreeSurferEntirePipeline"

# Input Variables
SubjectID="$1"
SubjectDIR="$2"
T1wImage="$3" #T1 FreeSurfer Input
T2wImage="$4" #T2 FreeSurfer Input


recon-all -s $SubjectID -autorecon-all -i "$T1wImage"_T1.nii -T2
"$T2wImage"_T2.nii -T2pial -parallel -hires

echo -e "done"
Best,
Paul

On Tue, Feb 7, 2017 at 4:40 AM, Antonin Skoch  wrote:

> Dear Paul,
>
> maybe this is implicit, but to assure:
>
> you have also to include -autorecon3.
>
> Therefore the full command is:
>
> recon-all -s subject_id -autorecon2-cp -autorecon3 -T2pial
>
> Antonin
>
> Yes, I think so
>
> > On Feb 5, 2017, at 2:47 PM, miracoo...@gmail.com wrote:
> >
> > Hello,
> >  I ran the entire recon pipeline with T2 option and then added control
> > points. Do I need to run recon-all -autorecon2-cp with T2 flag to redo the
> > pial surface or not? Thanks.
> > Paul
> >
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Re: [Freesurfer] T2 and control points

[miracle ozzoude]

Thanks Antonin and Bruce.
Also, I wrote a recon-all script and when I tried to run it, it gave me an
error (command not found). Please can anyone help me diagnosis what's wrong
with my scripts. I did set my subject directory to the current folder
(setenv SUBJECTS_DIR  /../folder/; cd /../folder) before
running the script. Thanks. The scripts is below

#!bin/bash
# FreeSurfer Pipeline (stages 1-31)
# Written By Paul

set -e

# Source FreeSurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh

# Start Scripts
echo -e "\n START: FreeSurferEntirePipeline"

# Input Variables
SubjectID="$1"
SubjectDIR="$2"
T1wImage="$3" #T1 FreeSurfer Input
T2wImage="$4" #T2 FreeSurfer Input


recon-all -s $SubjectID -autorecon-all -i "$T1wImage"_T1.nii -T2
"$T2wImage"_T2.nii -T2pial -parallel -hires

echo -e "done"
Best,
Paul

On Tue, Feb 7, 2017 at 4:40 AM, Antonin Skoch  wrote:

> Dear Paul,
>
> maybe this is implicit, but to assure:
>
> you have also to include -autorecon3.
>
> Therefore the full command is:
>
> recon-all -s subject_id -autorecon2-cp -autorecon3 -T2pial
>
> Antonin
>
> Yes, I think so
>
> > On Feb 5, 2017, at 2:47 PM, miracoo...@gmail.com wrote:
> >
> > Hello,
> >  I ran the entire recon pipeline with T2 option and then added control
> > points. Do I need to run recon-all -autorecon2-cp with T2 flag to redo the
> > pial surface or not? Thanks.
> > Paul
> >
>
>
>
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Re: [Freesurfer] recon-all issue {Disarmed}

[Taylor Hilton]

Yes I’ll attach it here.  I’m using a linux server(Ubuntu).

recon-all.log
Description: Binary data
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] recon-all issue

[Douglas Greve]

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 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting





We also tried the solution laid out in this thread with no luck:
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] recon-all issue

[Taylor Hilton]

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 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 





We also tried the solution laid out in this thread with no luck:
 
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] Percentage of cortex showing significant differences

[Douglas Greve]

For fsaverage, the surface area is 74612.58mm2  for lh fsaverage and 
73510.21 for rh. These will be listed as "SearchSpace_mm2" in the 
cluster summary table (if you used mri_glmfit-sim or mri_surfcluster)



On 2/6/17 7:09 PM, Bronwyn Overs wrote:

Dear mailing list,

I have completed a matlab based lme analysis using cortical thickness, 
and now have a list of significant clusters for each coefficient. I 
now want to know what proportion of the cortex differs significantly 
for each coefficient. I can add up the total size of the significant 
clusters for each coefficient, but I don’t know what value to use in 
the denominator (the total size of the cortex). Would it be the total 
area of the fsaverage inflated surface that I used in my analysis?


Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265

neura.edu.au 

Follow @neuraustralia on twitter 
Follow NeuRA on facebook 
Subscribe to 
the NeuRA Magazine 





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

[Bunday, Karen]

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
>
>
>
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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/

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[Freesurfer] extract area.pial stats

[Clara Kühn]

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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Re: [Freesurfer] T2 and control points

[Antonin Skoch]

Dear Paul,

maybe this is implicit, but to assure:

you have also to include -autorecon3.

Therefore the full command is:

recon-all -s subject_id -autorecon2-cp -autorecon3 -T2pial

Antonin

Yes, I think so

> On Feb 5, 2017, at 2:47 PM, miracoo...@gmail.com wrote:
> 
> Hello, 
>  I ran the entire recon pipeline with T2 option and then added control 
> points. Do I need to run recon-all -autorecon2-cp with T2 flag to redo the 
> pial surface or not? Thanks.  
> Paul
> 
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