Re: [Freesurfer] Ubuntu VM Error - /dev/sda1 contains a file system with errors

[Joanna L Eckhardt]

External Email - Use Caution

Hi R,

The instructions in that link fixed the problem! Thank you very much for your 
help. I'll be backing up my files right away and will continue to do that.

All my best,
Joanna

--

Joanna Eckhardt

Neurosciences Graduate Program

University of California, San Diego


From: fsbuild 
Sent: Wednesday, June 15, 2022 11:05 AM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Joanna L Eckhardt 
Subject: Re: [Freesurfer] Ubuntu VM Error - /dev/sda1 contains a file system 
with errors

If you have not run fsck with the -y option from the intramfs prompt, you could 
try the instructions in this post - which shows the error (on a different 
version of Ubuntu),

https://secure-web.cisco.com/1KDUU-oMeVgFdNaUBOuI9Rv9qw3YfSDqibzlcD6n5_7LK-92GXDwOo6bYdMyNCRHgYKviP4rnA0KXLONbomjNz6OCh8C5OMo9bvKo7l4fi07ydLIdzPSbqOkjiAiH28B1B5Y-zNEY9jnbHGyHygj4wisjtlsrczpIvBUyiRt44ePSTvsznMYwvUK1fsVTJqyjJBXURSE6LqwfhgyeTdcb36VYwRNTKv1eGNjp6n-6dX-XMLzpwBx7jNjr8_SNy2Lbab1suR4424o6jWUZzflGnWeLK1JjGKtDGapnggAIUBQMIiZYk3aH2q7zeVhOl0xR6wNyiv8xxvdHF2byOqg4PA/https%3A%2F%2Fostechnix.com%2Fhow-to-fix-busybox-initramfs-error-on-ubuntu%2F

You could revert the VM image back to your most recent snapshot, i.e., select 
the most recent snapshot in the list prior to the “current state” and then hit 
the restore button at the top (see screenshot).

If the current state of the VM cannot be repaired and boot, then you can run, 
copy or retrieve the versions of the files from the most recent snapshot that 
boots, e.g., to otherwise backup or use in a new clone or fresh copy of the VM. 
  I think it is possible to have a persistent mapping of paths to the Windows 
side, but I would not bother with that until you have a VM running again.

- R.



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[Freesurfer] Freesurfer Password

[Sean Amormino]

External Email - Use Caution

Hello! I need the password to expand the archive for Freesurfer 7.2.0 release 
in Ubuntu 18.04.06. Thanks!
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Re: [Freesurfer] FSL Password

[Rachel Wagner]

External Email - Use Caution

Thank you very much for the help! Upon trying that, I get this:

developer@developer-VirtualBox:~$ cd ~/Downloads
developer@developer-VirtualBox:~/Downloads$ $ sudo  python3  fslinstaller.py
$: command not found
developer@developer-VirtualBox:~/Downloads$ sudo  python3  fslinstaller.py
[sudo] password for developer:

I am strangely again stopped from being able to type anything at all. Is there 
a way to install without having to use admin privileges?

Thanks again,
Rachel

From: fsbuild
Sent: June 15, 2022 9:08 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Rachel Wagner
Subject: Re: [Freesurfer] FSL Password

You don't often get email from fsbu...@contbay.com. Learn why this is 
important
Try,

$ sudo  python3  fslinstaller.py

… then enter password for developer.  The sudo command will use admin 
privileges which may allow install to occur.

- R.


On Jun 15, 2022, at 20:54, Rachel Wagner  wrote:

External Email - Use Caution

Hello,

I am downloading FSL into ubuntu freesurfer VM, and have gotten the following 
prompt:

developer@developer-VirtualBox:~/Downloads$  python3 fslinstaller.py
--- FSL Installer - Version 3.2.3 ---
[Warning] Some operations of the installer require administative rights,
for example installing into the default folder of /usr/local.
If your account is an 'Administrator' (you have 'sudo' rights)
then you will be prompted for your administrator password
when necessary.
When asked a question, the default answer is given in square brackets.
Hit the Enter key to accept this default answer.
Where would you like the FSL install to be (including the FSL folder name)? 
[/usr/local/fsl]:
Downloading...
Checking FSL package
[OK] File downloaded
Installing FSL software version 6.0.5.2...
We require your password to continue...
password:


When I try to type in the password, I am unable to type at all, for some reason 
I can’t write anything in the terminal. Is there any way for me to troubleshoot?

Thanks very much!
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Re: [Freesurfer] FSL Password

[fsbuild]

External Email - Use Caution

Try,
$ sudo  python3  fslinstaller.py
… then enter password for developer.  The sudo command will use admin 
privileges which may allow install to occur.
- R.

On Jun 15, 2022, at 20:54, Rachel Wagner  
wrote:External Email - Use 
CautionHello,  I am 
downloading FSL into ubuntu freesurfer VM, and have gotten the following 
prompt: developer@developer-VirtualBox:~/Downloads$  python3 
fslinstaller..py--- FSL Installer - Version 3.2.3 ---[Warning] Some operations 
of the installer require administative rights,    for example 
installing into the default folder of /usr/local.    If your 
account is an 'Administrator' (you have 'sudo' rights)    then 
you will be prompted for your administrator password    when 
necessary.When asked a question, the default answer is given in square 
brackets.Hit the Enter key to accept this default answer.Where would you like 
the FSL install to be (including the FSL folder name)? 
[/usr/local/fsl]:Downloading...Checking FSL 
package[OK] File 
downloadedInstalling FSL software version 6.0.5.2...We require your password to 
continue...password:  When I try to type in the password, I am unable 
to type at all, for some reason I can’t write anything in the terminal. Is 
there any way for me to troubleshoot? Thanks very 
much!___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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 .
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continue to communicate over unencrypted e-mail. 

[Freesurfer] FSL Password

[Rachel Wagner]

External Email - Use Caution

Hello,

I am downloading FSL into ubuntu freesurfer VM, and have gotten the following 
prompt:

developer@developer-VirtualBox:~/Downloads$  python3 fslinstaller.py
--- FSL Installer - Version 3.2.3 ---
[Warning] Some operations of the installer require administative rights,
for example installing into the default folder of /usr/local.
If your account is an 'Administrator' (you have 'sudo' rights)
then you will be prompted for your administrator password
when necessary.
When asked a question, the default answer is given in square brackets.
Hit the Enter key to accept this default answer.
Where would you like the FSL install to be (including the FSL folder name)? 
[/usr/local/fsl]:
Downloading...
Checking FSL package
[OK] File downloaded
Installing FSL software version 6.0.5.2...
We require your password to continue...
password:


When I try to type in the password, I am unable to type at all, for some reason 
I can’t write anything in the terminal. Is there any way for me to troubleshoot?

Thanks very much!
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[Freesurfer] Nii to Img file

[Rachel Wagner]

External Email - Use Caution

Hello,

Thank you for your assistance!

I am trying to convert an nii nifti file to an img file within free surfer. 
I’ve used the mri convert function and did create the img file, but I’m getting 
an error message in SPM when I try to co-register it to another img file.

Is there a particular way I should be converting an nii file?

My only other thought is that potentially I’m not exporting properly. I am 
using ubunu VM on a windows computer, and need to export the two img files from 
ubuntu to my windows files so I can upload them in matlab. Is there a preferred 
way to export files out of the ubuntu VM?

Thanks very much again,
Rachel

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 .
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Re: [Freesurfer] SPM to FreeSurfer

[fsbuild]

External Email - Use Caution

Hello Rachel,
SUBJECTS_DIR is preset in the terminal window to point to the example subjects 
already provided with the freesurfer distribution 
under /usr/local/freesurfer/7.2.0/subjects.  You will see subject 
names under that directory like “bert”.  That SUBEJCTS_DIR setting is 
printed out when you start a new terminal window.
But it is not intended you process your own subjects there.  You don’t 
have permission to copy data into that location unless you use the “sudo” 
command.
It’s preferable to set SUBJECTS_DIR to point to a subdirectory where you have 
permission to read and write your own subject data files such as 
/home/developer   If you put your data under there, then you can set 
SUBEJCTS_DIR to instead be,
$ export SUBJECTS_DIR=/home/developer/subjects… under which you would 
presumably have directories referenced by subject name.
To see the value of SUBEJCTS_DIR in the terminal window,$ echo $SUBJECTS_DIR
To see the value of all environment variables in the terminal window,$ env | 
sort
You can change what SUBJECTS_DIR is set to in the terminal window by editing 
the file /home/developer/.bashrc  I would put any export command to change 
SUBJECTS_DIR from the subejcts provided with freesurfer at the end of that file.
- R.
On Jun 15, 2022, at 17:04, Rachel Wagner  
wrote:External Email - Use 
CautionHello,  I am 
trying to take my SPM images and cortically project them with free surfer 
(SpmPainting - Free Surfer Wiki (harvard.edu). As it might be quite obvious, I 
have very little experience using these softwares. I am typing in the 
suggested code as follows: developer@developer-VirtualBox:~$ mri_convert 
$SUBJECTS_DIR/subjectname/mri/brain.mgz brain.imgmri_convert 
/usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz brain.imgreading 
from /usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz...error: 
mghRead(/usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz, -1): 
could not open filedeveloper@developer-VirtualBox:~$ 
^Cdeveloper@developer-VirtualBox:~$ Is there something I am doing 
incorrectly? Thank 
you!Rachel___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer​
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Re: [Freesurfer] SPM to FreeSurfer

[Rachel Wagner]

External Email - Use Caution

Apologies for repeat email – I’m getting the following error message, is there 
something I should add?

developer@developer-VirtualBox:~$ mri_convert i.mgz i.img
mri_convert i.mgz i.img
reading from i.mgz...
error: mghRead(/home/developer/i.mgz, -1): could not open file
developer@developer-VirtualBox:~$

From: Rachel Wagner
Sent: June 15, 2022 5:04 PM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: SPM to FreeSurfer

Hello,

I am trying to take my SPM images and cortically project them with free surfer 
(SpmPainting - Free Surfer Wiki 
(harvard.edu).
 As it might be quite obvious, I have very little experience using these 
softwares.

I am typing in the suggested code as follows:
developer@developer-VirtualBox:~$ mri_convert 
$SUBJECTS_DIR/subjectname/mri/brain.mgz brain.img
mri_convert /usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz 
brain.img
reading from /usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz...
error: mghRead(/usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz, 
-1): could not open file
developer@developer-VirtualBox:~$ ^C
developer@developer-VirtualBox:~$

Is there something I am doing incorrectly?

Thank you!
Rachel

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 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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[Freesurfer] SPM to FreeSurfer

[Rachel Wagner]

External Email - Use Caution

Hello,

I am trying to take my SPM images and cortically project them with free surfer 
(SpmPainting - Free Surfer Wiki 
(harvard.edu).
 As it might be quite obvious, I have very little experience using these 
softwares.

I am typing in the suggested code as follows:
developer@developer-VirtualBox:~$ mri_convert 
$SUBJECTS_DIR/subjectname/mri/brain.mgz brain.img
mri_convert /usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz 
brain.img
reading from /usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz...
error: mghRead(/usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz, 
-1): could not open file
developer@developer-VirtualBox:~$ ^C
developer@developer-VirtualBox:~$

Is there something I am doing incorrectly?

Thank you!
Rachel
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 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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Re: [Freesurfer] FreeSurfer Passcode - Apologies!

[fsbuild]

External Email - Use Caution

Hello Rachel,
You should have just received the info for the Freesurfer Ubuntu VM. 

Replies to these requests are now being sent directly to the email of the 
requestor and are no longer copied to the Freesurfer list so as not to generate 
extra  list. From: Rachel Wagner 
Date: Wednesday, June 15, 2022 at 1:33 
PMTo: Sennott, Liam Ricker 
Subject: FreeSurfer Passcode - 
Apologies!External Email - Use 
CautionHello,  I hope 
this finds you well. My apologies for emailing you personally, I am a bit 
desperate - I am attempting to subscribe to the mailing list offered by the 
developers of FreeSurfer, as I need to email for the passcode I require to 
access the software. I am having trouble subscribing (for some reason I’m not 
getting the subscription confirming email) and thus cannot contact the listed 
email. I am wondering if you might be able to offer an alternative way to 
get in touch for the passcode I need to expand the archive (I downloaded the 
ubuntu VM and WinRAR)? Thanks!Rachel Wagner ​
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Re: [Freesurfer] Ubuntu VM Error - /dev/sda1 contains a file system with errors

[fsbuild]

External Email - Use Caution

If you have not run fsck with the -y option from the intramfs prompt, you could 
try the instructions in this post - which shows the error (on a different 
version of Ubuntu), 
https://secure-web.cisco.com/1G_OxjZo0eZ-YJ0rw8-xiLxDsmlEKgBMgmEnSsywbnbejdoa9nkNFoDEbPF9_QLgMW0NVJ7x3N2_C7B-5BYvZ-Pv7xFpX75OHvRHl8ZnbzM7hNGSkgTxkceozJD92YEVIIFFWSQMpIfqeRq5NVCyEkAtdJG30uTmL6Ty5O1YZ96R25d0fTaeSkm42-_HlHuYdZ_q-2UoKcMBTNUyPVmSo9IjRcg4sfTWEOyQsPCT1Uy4-emIfpmdh89VdvmEye1Of-mddv-AzHz360zMjDT3Jh3tHYI38PZnI-MQuGKh6Cy8xY5zTv95qyCHcSUQlUgePv7iY2BYtkJ93oRQmEpAnDA/https%3A%2F%2Fostechnix.com%2Fhow-to-fix-busybox-initramfs-error-on-ubuntu%2F
You could revert the VM image back to your most recent snapshot, i.e., select 
the most recent snapshot in the list prior to the “current state” and then hit 
the restore button at the top (see screenshot).

If the current state of the VM cannot be repaired and boot, then you can run, 
copy or retrieve the versions of the files from the most recent snapshot that 
boots, e.g., to otherwise backup or use in a new clone or fresh copy of the VM. 
  I think it is possible to have a persistent mapping of paths to the 
Windows side, but I would not bother with that until you have a VM running 
again.
- R.




snapshot_restore.png
Description: Binary data
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[Freesurfer] Problem with longitudinal processing

[Wittayer, Matthias]

External Email - Use Caution

Dear community,

I tried to process MS- patient's MRIs (mostly same scanner, same settings) 
Longitudinally over a long period of time. I first processed all timeponits 
crosssectionally and then initialised  the base image by recon- all - base TP1 
TP2 TP3 etc. Now I am trying to run label based morphometry and it seems some 
areas are growing rather than shrinking. Which is highly unlikely. I tried to 
exclude timepoint of a relapse to rule out perifocal edema interfering with 
measures but the problem remains.
Did anybody have the same problem?
Is it a potential bug or just a garbage in garbage out problem (though I don't 
know what would be wrong with our scans)?
Does it make sense to make an intermediate template for two timeponits only? 
I.e. recon- all -base TP1 TP2; recon -all -base TP2 TP3 ... and use them for 
longitudinal runs?

Thanks for your opinions. Best
Matthias
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Re: [Freesurfer] Ubuntu VM Error - /dev/sda1 contains a file system with errors

[Joanna L Eckhardt]

External Email - Use Caution

Hi R,

(I tried to reply in the other email thread with fsbu...@contbay.com but it 
said delivery failure with that email so I am responding here).

Thank you very much for your response. I was able to get through the first 2 
recovery steps but on step 3, it failed, see screenshot below, with the error: 
"failure: file system check of the root filesystem failed...requires a manual 
fsck."
Would you be able to help me attempt doing the manual fsck?

A few follow up questions:

  *   I would be fine with making a new VM image, but would that delete all of 
my current files in the VM? I have some processed scans that are not backed up 
to my windows drive (from now on, I will make sure to back them up knowing this 
could happen).
  *   I'll make sure to use the "shutdown signal" button when exiting from now 
on, as I have always used "power off the machine." Also, I do share a 
location/path between Windows file system and VM, as this is how I get my 
processed scans from open science grid (which sends output to windows) onto the 
VM. If sharing a path between the two could be corrupting the VM, is there 
another way to get files between them? Also, I am unsure if this is worth 
mentioning, but the shared path disappears every time I reboot the VM, so I 
have been just remounting it when I need to fileshare.

Thank you for your time and assistance,
Joanna

[cid:ca38917a-754a-4822-a924-a46129590ed7]


--

Joanna Eckhardt

Neurosciences Graduate Program

University of California, San Diego


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

Sent: Tuesday, June 14, 2022 8:08 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Joanna L Eckhardt 
Subject: Re: [Freesurfer] Ubuntu VM Error - /dev/sda1 contains a file system 
with errors


External Email - Use Caution

If you boot into recovery mode, there is an fsck option available there you can 
try.   I will send some screenshots of booting into recovery mode to your email 
directly.

- R.

On Jun 14, 2022, at 21:06, Joanna L Eckhardt  wrote:

External Email - Use Caution

Dear FS Help Team,

I run FS on Ubuntu VM Virtualbox 6.1 on Windows. Out of nowhere, my Virtualbox 
is no longer opening and has errors. See screenshots below. First screen looks 
like this upon launching the Virtualbox and so I click Ubuntu and then it shows 
the error /dev/sda1 contains a file system with errors, check forced. I tried 
doing a website fix that I found online: fsck -f /dev/sda1 but it did not work. 
Do you have any insights on how to resolve this issue?

Thank you very much for your time and assistance!

All my best,
Joanna






Joanna Eckhardt
Neurosciences Graduate Program
University of California, San Diego
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Re: [Freesurfer] I cannot start my first subject.

[Huang, Yujing]

Hi Refaat,

This tutorial talks about unpacking dicom files and basic recon-all options. It 
should help you get started - 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Practice

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of refaat el-said
Sent: Tuesday, June 14, 2022 7:59 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] I cannot start my first subject.


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Good morning
I installed Oracle VM virtual box
i am able to work on the tutorial patient bert but when I copied dicom file of 
a patient I could not work with it.
Are there instructions on how to import dicom files to the virtual box machine 
and the first step to prepare them for analysis?
Refaat
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Re: [Freesurfer] using brain mask from older FreeSurfer version on a newer

[Bouchra Guelib]

External Email - Use Caution

Actually, I didn't try this idea and also I don't know what's the
difference between brain mask from previous versions.

Le mar. 14 juin 2022 à 22:39, Aaron Tanenbaum 
a écrit :

> External Email - Use Caution
>
> Great. glad I was of some help. I still need my questions answered.
>
> On Tue, Jun 14, 2022 at 4:33 PM Bouchra Guelib <
> bouchra.gue...@univ-constantine2.dz> wrote:
>
>> External Email - Use Caution
>>
>> The problem is solved, I just changed the freesurfer version , thnx for
>> your help
>>
>> Le mar. 14 juin 2022 à 22:27, Aaron Tanenbaum <
>> aaron.b.tanenb...@gmail.com> a écrit :
>>
>>> External Email - Use Caution
>>>
>>> Our lab is moving from FreeSurfer 5.3 to 7.2. We have thousands of scans
>>> to do.  I see that you can give freesurfer a brainmask. I was thinking of
>>> giving freesurfer a brainmask from the previous from 5.3 to 7.1. Is this a
>>> wise idea? Do you have any objections?
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[Freesurfer] MeanItensities- PET

[Bouchra Guelib]

External Email - Use Caution

Hi,
I wonder if someone can help me to do  something similar to that:
"  the mean intensity of each FreeSurfer region (ROI) for the 45
subcortical and the 68 cortical regions were assessed the mean intensity of
each FreeSurfer region (ROI) for the 45 subcortical and the 68 cortical
regions were assessed to obtain  SVU".
Also, I found an article that mentioned that " the estimated total
intracranial volume (eTIV) is calculated, which is used later for
normalization of the volumetric measures".
My questions are:
1) In "  gtm.stats.dat" not all subcortical regions are mentioned, why?
2) I applied "mri_getmpc" to obtain the mean intensity, however, I could
not figure out what I should do after this step to obtain the mean
intensity and compute SVU.
3) why do they use eTIV, should I use it, and if yes how!
best regards.


-- 
*GUELIB Bouchra: *Ph.D. student
*Lire *Laboratory
University: Constantine 2-Abdelhamid Mehri- *Algeria *
Alternative email: guelibbouc...@gmail.com
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