[Freesurfer] freeview error (libpng12.so.0) on Ubuntu

[Jeffrey Crawford]

Hello all!

I know there are issues with freeview use on Ubuntu, but I hit a wall in fixing 
them.

I am currently getting this error when typing "freeview" into the command 
prompt:

"freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open 
shared object file: No such file or directory"

My current version of Freesurfer is: 
freesurfer-Linux-centos6_x86_64-stable-v6-beta-20161028-4cfbf2a.tar.gz

>From the research I did online, first, I used these commands from this mail 
>archive
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg43219.html

then installed what was supposed to fix something similar from the wiki
https://surfer.nmr.mgh.harvard.edu/fswiki/Download by doing "sudo apt-get 
install libjpeg62"

Now I have been trying to install "libpng12.so.0" or some variation on that, 
but linux does not seem to be able to find it.

Any help?

-Jeff
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[Freesurfer] V6 FS eTICV versus CAT12 TICV with Small Heads

[Jeffrey Crawford]

Hello everyone!

I have some questions about FS eTICV.
I read on the Wiki that eTICV is not the best measure of ICV and saw the same 
from other articles. The alternative I decided on was measuring the TICV using 
CAT12 from SPM. I decided to do a scatterplot of the eTICV from FS V6 and TICV 
from CAT12 to see how they match each other on measurment. FS is the variable 
on the Y-axis and CAT12 is the variable on the X-axis. If we assume that CAT12 
is more accurate than FS, then it looks as though the FS begins to become more 
inaccurate as the head size gets smaller.

[cid:image001.png@01D2579B.8A615E30]

So here are my questions:

1.  Is my interpretation of this scatterplot correct?

2.  Does FS generally have more difficulty measuring smaller heads? If so, 
then why?

3.  Is it more advised for me to use the CAT12 TICV measure as a covariate 
in my future analysis? Or maybe some other program that I don't know about?



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Re: [Freesurfer] Importance of Symbolic Links?

[Jeffrey Crawford]

Thank you for the info. It definitely puts some ease on my situation. 

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Z K
Sent: Sunday, November 20, 2016 9:14 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Importance of Symbolic Links?

You can use the -H flag when copying 'cp -RH' and it will follow the symlink's 
target rather than copying the symlink itself.

But either way that symlink exists in the subjects/bert folder and the 
existence of those symlinks is inconsequential to the actual running of qdec or 
other programs, as long as you are analyzing a different subject.

On 11/19/2016 11:45 AM, Jeffrey Crawford wrote:
> by Freesurfer: lh.white.H , lh.white.K, rh.white.H, and rh.white.K.
>
>
>
> My question is whether these links are important to qdec or other 
> Freesurfer analysis programs, such that me copying files that don't 
> contain them will result in errors down the line?
>
>
>
> Also, I recognize that I could reformat my usb to UDF and be able to 
> copy symbolic links. I tried this, but I found out that my Freesurfer 
> is running on a very old version of Fedora that doesn't support UDF. 
> So, until I get around to reinstalling Linux on this older computer, I 
> am stuck with my limitations.
>
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[Freesurfer] Importance of Symbolic Links?

[Jeffrey Crawford]

Hello everyone!

I have been fiddling with Version 6 and I have been encountering some 
difficulty copying Freesurfer folders onto my usb, because my usb cannot write 
"symbolic links".
There are four of them produced by Freesurfer: lh.white.H , lh.white.K, 
rh.white.H, and rh.white.K.

My question is whether these links are important to qdec or other Freesurfer 
analysis programs, such that me copying files that don't contain them will 
result in errors down the line?

Also, I recognize that I could reformat my usb to UDF and be able to copy 
symbolic links. I tried this, but I found out that my Freesurfer is running on 
a very old version of Fedora that doesn't support UDF. So, until I get around 
to reinstalling Linux on this older computer, I am stuck with my limitations.
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Re: [Freesurfer] Version 6 Beta on Virtual Box problem

[Jeffrey Crawford]

So, I discovered that I could delete the files inside of the Freesurfer folder, 
even though I could not delete the Freesurfer folder itself. However, when I 
replaced the interior of the file with the version 6 folders, I got a bunch of 
errors when I tried to run my first recon-all:

"recon-all -s 2007 \ -i /media/drive/3T_BSNIP_subjects/2007.nii

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20161028-4cfbf2a
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20161028-4cfbf2a
INFO: SUBJECTS_DIR is /media/E_big_daddy_drive/3T_BSNIP_subjects
Actual FREESURFER_HOME /usr/local/freesurfer
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 
UTC 2012 i686 i686 i386 GNU/Linux
/usr/local/freesurfer/bin/mri_convert: line 3: 
/usr/local/freesurfer/bin/mri_convert.bin: cannot execute binary file
/usr/local/freesurfer/bin/flirt.fsl: Exec format error. Binary file not 
executable.
/usr/local/freesurfer/bin/mri_convert: line 3: 
/usr/local/freesurfer/bin/mri_convert.bin: cannot execute binary file
/usr/local/freesurfer/tktools/tkregister2_cmdl: Exec format error.
.
"

The script continued on saying " Exec format error. Binary file not executable" 
for the rest of the files in the V6 folders.

I am sure this error is unique to my attempt at putting V6 on this 5.3 virtual 
box, because I followed the exact same steps on the Linux we have and 
everything worked fine. 

So, unless anyone has some ways for me to patch up this odd attempt of mine, 
then I think I will just move on to a linux virtual box. I will take your 
previously recommended link first and see how that helps.  

Thank you so much for your reply. 


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of 
zkauf...@nmr.mgh.harvard.edu
Sent: Thursday, November 17, 2016 12:10 PM
To: Freesurfer support list 
Cc: Freesurfer support list 
Subject: Re: [Freesurfer] Version 6 Beta on Virtual Box problem

> Hello everyone!
>
> I am currently using Virtual Box to run Freesurfer and I was wondering 
> if my plan to put the version 6 beta on to my current virtual box was 
> a valid one.
>
> My plan was to delete the Freesurfer folder off of the 5.3 virtual box 
> and replace it with the Freesurfer version 6 folder. However, the 
> virtual box is not letting me delete the Freesurfer folder.
> So I have some questions:
>
> 1.   Does anyone have an idea of how I would go about deleting the
> original Freesurfer folder, so I could continue with this plan?

Are you just getting a permissions error when you attempt to delete the folder? 
I created that disk image with freesurfer installed on it, but I would still 
think that the freesurfer folder could be deleted. Recall that the root 
password for the disk image is 'freesurfer' (without the quotes).

> 2.   Is this plan a good one?

Its a workable plan. The Virtual Box version of freesurfer has its limitations, 
but if it works for you than this plan seems adequate for testing purposes.

>
> 3.   Should I try and download another linux virtual box somewhere and
> put the version 6 beta on that?

This would be my suggestion. Try just installing any of the Ubuntu disk images 
and installing freesurfer within that
(http://www.osboxes.org/ubuntu/)



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[Freesurfer] Version 6 Beta on Virtual Box problem

[Jeffrey Crawford]

Hello everyone!

I am currently using Virtual Box to run Freesurfer and I was wondering if my 
plan to put the version 6 beta on to my current virtual box was a valid one.

My plan was to delete the Freesurfer folder off of the 5.3 virtual box and 
replace it with the Freesurfer version 6 folder. However, the virtual box is 
not letting me delete the Freesurfer folder.
So I have some questions:

1.   Does anyone have an idea of how I would go about deleting the original 
Freesurfer folder, so I could continue with this plan?

2.   Is this plan a good one?

3.   Should I try and download another linux virtual box somewhere and put 
the version 6 beta on that?
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Re: [Freesurfer] [WARNING : A/V UNSCANNABLE]RE: Left Thalamus and Pallidum segmentation problem

[Jeffrey Crawford]

Alright, I followed the directions online and believe I have sent my file 
"JeffSegFileExample" to your "transfer/incoming" folder in the ftp server. 

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Tuesday, November 15, 2016 5:12 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [WARNING : A/V UNSCANNABLE]RE: Left Thalamus and 
Pallidum segmentation problem

Hi Jeffrey

the tarred and gzipped subject folder should be a lot bigger - way too big to 
email. YOu'll need to upload it to our ftp site

cheers
Bruce
On Tue, 15 Nov 2016,
Jeffrey Crawford wrote:

> Here is the tar zip of the subject folder. This is the first time I have ever 
> done this type of compression, so please let me know if anything seems awry.
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce 
> Fischl
> Sent: Tuesday, November 15, 2016 3:05 PM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] Left Thalamus and Pallidum segmentation 
> problem
>
> Hi Jeffrey
>
> if you upload the entire subject dir (gzip and tar) we will take a look 
> cheers Bruce On Tue, 15 Nov 2016, Jeffrey Crawford wrote:
>
>> Thank you for replying so promptly.
>> I changed it to the norm.mgz, but it didn't alter how the segementation 
>> aligned with the brain. The norm.mgz shows the pallidum in more detail, but 
>> also that it is not contained with the segementation.
>>
>> So, I suppose my original question is still the same.
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce 
>> Fischl
>> Sent: Tuesday, November 15, 2016 12:06 PM
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Subject: Re: [Freesurfer] Left Thalamus and Pallidum segmentation 
>> problem
>>
>> Hi Jeffrey
>>
>> you can't tell the boundaries overlaying on the brainmask.mgz as it will 
>> erode thalamus and pallidum. Look at the norm.mgz to check whether the 
>> borders are accurate Bruce On Tue, 15 Nov 2016, Jeffrey Crawford wrote:
>>
>>>
>>> Hello there!
>>>
>>>  
>>>
>>> I was wondering if I could get some help on an issue I am noticing 
>>> in the segmentation of the left thalamus and left Pallidum on my scans.
>>> I’ve included pictures of tkmedit so you can see what I mean. The 
>>> tkmedit uses this code:  tkmedit SZ2014 brainmask.mgz lh.white -aux 
>>> norm.mgz -aux-surface rh.white -segmentation aparc+aseg.mgz
>>>
>>>  
>>>
>>> All of my scans have been through the entire recon-all process and , 
>>> out of my sample of about 172 patients and controls, just about 29 
>>> of them show this odd segmentation on, almost always, the left 
>>> hemisphere. The left thalamus seems to be over estimating the size and the 
>>> pallidum is underestimating its size. I was wondering why this would be and 
>>> if the community thought it would be okay to go back and manually edit the 
>>> segementation to fit the subcorticals structures better?
>>>
>>>  
>>>
>>> Also, since I have never done such editing, is it advisable or even 
>>> possible to do so?
>>>
>>>
>>>
>>
>

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[Freesurfer] FSL View in the virtual box version?

[Jeffrey Crawford]

Hello there!

I currently use the virtualbox version of freesurfer on my windows and the 
CentOS 4 (32b) version on a linux computer. I noticed today that the Virtual 
box version does not seem to have fsl view.

I found this link to a blog where this person has a virtual box that contained 
fslview, but I think his methods and version are different from the typical 
installation procedures.

http://kylemathewson.com/cnl-virtualbox-setup/

I was just wondering if it is possible to use fslview on the virtual box 
version or not and how I might go about obtaining that capability?
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