Re: [Freesurfer] freeview Core Dumped Error after upgrade in ubuntu

[Rovai Antonin]

External Email - Use Caution

Hi there!

thanks for the answer and your searches.

Actually I solved my issue, basically the last upgrade created a
circular depency issue in my nvidia driver packages, causing issues
with graphical applications. I think this, in the end, is unrelated to
the kernel upgrade.

Thanks again for your time!

Best

Antonin


Hôpital Erasme - ULB
Cliniques universitaires de Bruxelles
Route de Lennik 808 - B - 1070 Bruxelles
S www.erasme.ulb.ac.be

Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer
On Mon, 2020-10-26 at 19:50 +0100, fsbuild wrote:
> Hello Antonin,
>
> I’ve found a few posts that seem to indicate you can upgrade as well
> as downgrade the kernel (and its dependent packages) by editing the
> /etc/apt/sources.list to point to the Ubuntu distribution you want
> (and then running update, upgrade, dist-upgrade commands).   Not sure
> what the previous Ubuntu distribution name was for you, but this
> post, https://sypalo.com/how-to-upgrade-ubuntu, lists the
> distributions as,
>
> 18.04 - bionic
> 18.10 - cosmic
> 19.04 - disco
> 19.10 - eoan
> 20.04 - focal
> 20.10 - groovy
>
> While that post gives the example of *upgrading*, this post gives the
> example of *downgrading*,
> https://linuxconfig.org/how-to-downgrade-ubuntu-linux-system-to-its-previous-version
> , but I think they are essentially doing the same thing, i.e. it’s a
> function of the distribution name listed in /etc/apt/sources.list.
>
> Note that even if you are downgrading the kernel, as far as the apt
> package manager is concerned you still have to run the various
> “upgrade” commands to change the distribution to a different one even
> if it is older.
>
> - R.
>
>
> > On Oct 26, 2020, at 11:00, Rovai Antonin <
> > antonin.ro...@erasme.ulb.ac.be> wrote:
> >
> >External Email - Use Caution
> >
> > Dear experts,
> >
> > I use to have a perfectly working freesurfer installation on my
> > Ubuntu
> > 18.04 LTS machine, until that doomsday where I installed updates as
> > recommended by ubuntu itself.
> >
> > Now, each time I run freeview, I get the following error:
> >
> > Aborted (core dumped)
> >
> > I reinstalled freesurfer from scratch, fixing nothing.
> >
> > I think Ubuntu did a kernel upgrade; now I have a uname -r output =
> > 5.4.0-52-generic
> > I think it used to be 49 instead of 52 before the upgrade, but I am
> > not
> > sure.
> >
> > Do you know of any patch fixing this, by any chance?
> >
> > Thanks for your lights
> >
> > Antonin Rovai
> >
> > Hôpital Erasme - ULB
> > Cliniques universitaires de Bruxelles
> > Route de Lennik 808 - B - 1070 Bruxelles
> > S www.erasme.ulb.ac.be
> >
> > Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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[Freesurfer] NIH funded postdoctoral position

[Ron Killiany]

External Email - Use Caution

Hi everyone,

We have been fortunate to obtain funding for a postdoctoral position.  A
brief description is enclosed.  Please feel free to pass this along to
anyone who might be interested.

--ron

-- 
Ronald J. Killiany, Ph.D.
Center for Biomedical Imaging
Departments of Anatomy & Neurobiology, Neurology, Radiology and
Environmental Health
Boston University School of Medicine and Boston University School of Public
Health
700 Albany Street, W701
Boston, Massachusetts  02118

*phone:  617-358-8276*
fax:  617-638-4922


Luebke-Killiany Labs- Bioimaging postdoc.docx
Description: MS-Word 2007 document
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Re: [Freesurfer] [External] Re: Troubleshooting: Question Regarding Copying Freesurfer Output to Secondary Location

[Park, James]

External Email - Use Caution

Hi Andrew,

Thank you so much for your prompt response.

Our IT department was unfortunately a bit unfamiliar with these types of files.

We were not using rsync to move our files but instead just copying the files 
over through a file explorer.

Could you please point me in the right direction as to where I could access 
more information on rsync or moving data to a different location?

That would be super helpful!

Thank you again for your help.


Sincerely,

James Park



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Hoopes, Andrew 

Sent: Monday, October 26, 2020 7:16 PM
To: Freesurfer support list 
Subject: [External] Re: [Freesurfer] Troubleshooting: Question Regarding 
Copying Freesurfer Output to Secondary Location


Hi James,



It sounds like your target filesystem does not support symlinks? The answer to 
your question depends on how you are actually copying data, and you should 
probably contact your IT about this, but if you’re using rsync to move recons, 
you can supply the --copy-links flag to transform symlinks into referent 
file/dir.



best,

Andrew



From:  on behalf of "Park, James" 

Reply-To: FS Help 
Date: Monday, October 26, 2020 at 3:03 PM
To: FS Help 
Subject: [Freesurfer] Troubleshooting: Question Regarding Copying Freesurfer 
Output to Secondary Location



External Email - Use Caution

Hello,



My name is James Park, and I had a question regarding some issues with 
Freesurfer.



We noticed that for the freesurfer recon-all output there were multiple aliases 
files such as surf/rh.white.K among others.

Unfortunately we have been unable to copy these types of files to secondary 
locations (i.e. a network server).



I have confirmed this is not an issue with the computer-network connection as I 
have been able to copy other alias file types to the network location.

I was wondering if there is any workaround for this issue?



This was run on a Mac with macOS Catalina Version 10.15.7 using FreeSurfer 
version freesurfer-darwin-macOS-7.1.1-20200811-8b40551.



Thank you for your help in advance.



Sincerely,

James Park



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Re: [Freesurfer] Exited with errors, segmentation fault

[Hoopes, Andrew]

Hi Julia,

The -tp flags for the base creation require a subject ID as input, but you 
supplied a nifty file. That’s why it can’t find any subject files. See 
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing.

Best,
Andrew

From:  on behalf of Julia Lam 

Reply-To: FS Help 
Date: Monday, October 26, 2020 at 7:29 PM
To: FS Help 
Subject: Re: [Freesurfer] Exited with errors, segmentation fault


External Email - Use Caution
Hi,
Thank you for your email. Sorry about that. Here they are.
Best regards,
Julia


> 27 okt. 2020 kl. 00:17 skrev Hoopes, Andrew :
>
> Hi Julia,
> I think you might have forgotten to attach the logs :)
> Andrew
>
> On 10/25/20, 11:55 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
> Julia Lam"  julia@mau.se> wrote:
>
>External Email - Use Caution
>
>Hi Andrew,
>Thank you for your reply. Updating freesurfer solved the problem. However, 
> when I ran step 2 in the longitudinal processing three subjects exited with 
> errors. I’ve attached the recon-all.log and recon-all.error. What can I do to 
> solve this problem?
>
>Thank you in advance.
>
>Kind regards,
>Julia Lam
>
>> 20 okt. 2020 kl. 00:17 skrev Hoopes, Andrew :
>>
>> Hi Julia,
>>
>> This is a small bug that's been fixed in the 7.1.1 patch release. I would 
>> recommend updating freesurfer versions (there will be no differences in 
>> recon-all results).
>>
>> Best,
>> Andrew
>>
>> On 10/13/20, 8:44 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
>> Julia Lam" > julia@mau.se> wrote:
>>
>>   External Email - Use Caution
>>
>>   Hi,
>>   In one of 56 volumes, recon-all exited with errors (segmentation fault). I 
>> tried to rerun but received the same result. How can this be solved?
>>
>>   I’ve attached the recon-all.log and recon-all.error.
>>
>>   I am looking forward to your reply.
>>
>>   Kind regards,
>>   Julia Lam
>>
>>
>>
>>
>>
>> ___
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>
>
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Re: [Freesurfer] [External] Re: Troubleshooting: Question Regarding Copying Freesurfer Output to Secondary Location

[Hoopes, Andrew]

Hi James,

Rsync is a very common unix command for syncing/copying across filesystems. 
There’s plenty of information about it online, and you can access the help text 
through `man rysnc`. This might be useful 
https://www.tecmint.com/rsync-local-remote-file-synchronization-commands/

Best
Andrew

From:  on behalf of "Park, James" 

Reply-To: FS Help 
Date: Tuesday, October 27, 2020 at 12:12 PM
To: FS Help 
Subject: Re: [Freesurfer] [External] Re: Troubleshooting: Question Regarding 
Copying Freesurfer Output to Secondary Location


External Email - Use Caution
Hi Andrew,

Thank you so much for your prompt response.

Our IT department was unfortunately a bit unfamiliar with these types of files.

We were not using rsync to move our files but instead just copying the files 
over through a file explorer.

Could you please point me in the right direction as to where I could access 
more information on rsync or moving data to a different location?

That would be super helpful!

Thank you again for your help.


Sincerely,

James Park




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Hoopes, Andrew 

Sent: Monday, October 26, 2020 7:16 PM
To: Freesurfer support list 
Subject: [External] Re: [Freesurfer] Troubleshooting: Question Regarding 
Copying Freesurfer Output to Secondary Location


Hi James,



It sounds like your target filesystem does not support symlinks? The answer to 
your question depends on how you are actually copying data, and you should 
probably contact your IT about this, but if you’re using rsync to move recons, 
you can supply the --copy-links flag to transform symlinks into referent 
file/dir.



best,

Andrew



From:  on behalf of "Park, James" 

Reply-To: FS Help 
Date: Monday, October 26, 2020 at 3:03 PM
To: FS Help 
Subject: [Freesurfer] Troubleshooting: Question Regarding Copying Freesurfer 
Output to Secondary Location



External Email - Use Caution

Hello,



My name is James Park, and I had a question regarding some issues with 
Freesurfer.



We noticed that for the freesurfer recon-all output there were multiple aliases 
files such as surf/rh.white.K among others.

Unfortunately we have been unable to copy these types of files to secondary 
locations (i.e. a network server).



I have confirmed this is not an issue with the computer-network connection as I 
have been able to copy other alias file types to the network location.

I was wondering if there is any workaround for this issue?



This was run on a Mac with macOS Catalina Version 10.15.7 using FreeSurfer 
version freesurfer-darwin-macOS-7.1.1-20200811-8b40551.



Thank you for your help in advance.



Sincerely,

James Park



This e-mail message (including any attachments) is for the sole use of
the intended recipient(s) and may contain confidential and privileged
information. If the reader of this message is not the intended
recipient, you are hereby notified that any dissemination, distribution
or copying of this message (including any attachments) is strictly
prohibited.

If you have received this message in error, please contact
the sender by reply e-mail message and destroy all copies of the
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Re: [Freesurfer] [EXTERNAL] Re: Tracula: Calculation of MD values from other eigenvectors

[Yendiki, Anastasia]

Hi Cat - I am not sure what precise means. If the effects on these measures are 
the same over the entire tract, averaging the measures over the tract would 
actually increase SNR and make the effects (and their relationship) cleaner. If 
there are opposing effects in two different parts of the tract, averaging over 
the tract would wipe out the effects (and their relationship).

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Chong, Catherine (Cat), 
Ph.D. 
Sent: Tuesday, October 27, 2020 12:09 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] [EXTERNAL] Re: Tracula: Calculation of MD values from 
other eigenvectors


External Email - Use Caution

Dear Dr. Yendiki,



Thank you very much for your reply. Is it correct to assume then that the 
FA/MD/RD/AD values that are averaged over all the voxels for a given tract do 
not necessarily have a ‘precise’ relationship to one another?

With warm Regards,

Cat





From:  on behalf of "Yendiki, 
Anastasia" 
Reply-To: Freesurfer support list 
Date: Monday, October 26, 2020 at 8:26 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [EXTERNAL] Re: [Freesurfer] Tracula: Calculation of MD values from 
other eigenvectors



Hi Cat - The FA/MD/RD/AD at a specific voxel comes from first fitting a tensor 
to the intensity values of all the DWIs at that voxel and then finding the 
eigenvalues of the tensor at that voxel. The tracts work like ROIs - the 
FA/MD/RD/AD values are averaged over all the voxels in a tract.



Best,

Anastasia.



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Chong, Catherine (Cat), 
Ph.D. 
Sent: Wednesday, October 21, 2020 1:17 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Tracula: Calculation of MD values from other eigenvectors



External Email - Use Caution

Dear Tracula Experts,



We are trying to address a question from a reviewer who is wondering why we 
included all of the average diffusion parameters in our model  ( i.e. FA, 
MD,FA, RD, and AD) for distinguishing two groups of patients . The reviewer 
comments that MD values are calculated from AD and RD henceforth, including of 
all of the three parameters ( AD, RD, and MD) might have biased our analysis. I 
understand the reviewer’s concern that MD is calculated from adding all three 
eigenvalues/3, but I am uncertain about the relationship between the 
eigenvalues and the calculation of ‘average’ parameters for a given fibertract.



I am looking forward to your guidance,

With kind Regards,

Catherine


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Re: [Freesurfer] Tracula error: run list is longer than subject list

[Yendiki, Anastasia]

Hi Oshadi - Yes.

For future reference, if you have any doubts about command line usage, you can 
1. run "trac-all", without any arguments, and/or 2. read the tutorial:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula

Anastasia.

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

Sent: Monday, October 26, 2020 8:20 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list


External Email - Use Caution

I am double checking so the command is trac-all -prep -c /path/to/configuration 
file- is that what you meant?

Thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, October 26, 2020 5:12 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

What goes after "-c" in the trac-all command should be the configuration file, 
not the nifti file.

From: Shanika Jayakody 
Sent: Monday, October 26, 2020 5:01 PM
To: Yendiki, Anastasia 
Subject: Fw: Tracula error: run list is longer than subject list


External Email - Use Caution


Hi Anastasia

Thanks for your reply.

That file was a Dicom but it was named as "IM_0017". Anyways I tried with the 
extension (renamed the file too as IM_007.dcm)
Just to see if there is a different outcome, I ran trac-all on another subject 
too but still I get the same error.
I have two things to double check with you
1) our pre-processed files are nii, not dcm-I have changed the configuration 
file, bvals and bvec files as instructed in FreeSurfer wiki (attached) and did 
trac-all- this way the first error I get is illigal variable name. I am not 
sure if nii files won't work or if there is something wrong with my 
configuration file.
2) I ran trac-all on the same subjects dicom files (changed the configuration 
file accordingly)

Either way I get the same error (log file attached). It would be really great 
if you can suggest something-looking forward to hear from you.

Many thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, October 26, 2020 11:05 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Hi Oshadi - The first error in your log file is this:

ERROR: cannot find /home/admin/freesrufer/subjects/30141/30141Diffusion/IM_0017

Does that file exist? Does the file name have an extension that you're omitting?

Best,
Anastasia.


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

Sent: Monday, October 26, 2020 10:06 AM
To: Freesurfer support list ; Yendiki, 
Anastasia 
Subject: [Freesurfer] Fw: Tracula error: run list is longer than subject list


External Email - Use Caution

Hi Anastasia
Thanks again for helping with troubleshooting the error- I was wondering if you 
have any suggestions for me to try.
I have also tried running TRACULA on freesurfer tutorial data but get the same 
error

Best regards,
Oshadi


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

Sent: Tuesday, October 20, 2020 9:56 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

CAUTION: This email comes from an external source; the attachments and/or links 
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Hi Anastasia

Thanks for your reply. It was subjlist (sorry that was a typo in my email)
I have attached the
1) log file
2) cognfiuration file
3) bvec and bval files I have used.


I hope that's what you need- I am very new to FreeSurfer please let me know if 
you want me to send any more files.
Thank you for your help
Best regards
Oshadi


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, October 19, 2020 8:33 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Make sure to use "subjlist", not "sublist". If that is not the issue, then 
please attach your log file and configuration file - it's hard to guess the 
issue without more information.

Best,
Anastasia.

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

Sent: Monday, October 19, 2020 2:43 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Tracula error: run list is longer than subject list


External Email - Use Caution

Hello,

I have been trying to run trac-all on a DWI of a participant, 

Re: [Freesurfer] [External] Re: Troubleshooting: Question Regarding Copying Freesurfer Output to Secondary Location

[Park, James]

External Email - Use Caution

Thank you!

This has been super helpful.

Sincerely,
James Park

From: freesurfer-boun...@nmr.mgh.harvard.edu 

Date: Tuesday, October 27, 2020 at 2:21 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] [External] Re: Troubleshooting: Question Regarding 
Copying Freesurfer Output to Secondary Location
Hi James,

Rsync is a very common unix command for syncing/copying across filesystems. 
There’s plenty of information about it online, and you can access the help text 
through `man rysnc`. This might be useful 
https://www.tecmint.com/rsync-local-remote-file-synchronization-commands/

Best
Andrew

From:  on behalf of "Park, James" 

Reply-To: FS Help 
Date: Tuesday, October 27, 2020 at 12:12 PM
To: FS Help 
Subject: Re: [Freesurfer] [External] Re: Troubleshooting: Question Regarding 
Copying Freesurfer Output to Secondary Location


External Email - Use Caution
Hi Andrew,

Thank you so much for your prompt response.

Our IT department was unfortunately a bit unfamiliar with these types of files.

We were not using rsync to move our files but instead just copying the files 
over through a file explorer.

Could you please point me in the right direction as to where I could access 
more information on rsync or moving data to a different location?

That would be super helpful!

Thank you again for your help.


Sincerely,

James Park




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Hoopes, Andrew 

Sent: Monday, October 26, 2020 7:16 PM
To: Freesurfer support list 
Subject: [External] Re: [Freesurfer] Troubleshooting: Question Regarding 
Copying Freesurfer Output to Secondary Location


Hi James,



It sounds like your target filesystem does not support symlinks? The answer to 
your question depends on how you are actually copying data, and you should 
probably contact your IT about this, but if you’re using rsync to move recons, 
you can supply the --copy-links flag to transform symlinks into referent 
file/dir.



best,

Andrew



From:  on behalf of "Park, James" 

Reply-To: FS Help 
Date: Monday, October 26, 2020 at 3:03 PM
To: FS Help 
Subject: [Freesurfer] Troubleshooting: Question Regarding Copying Freesurfer 
Output to Secondary Location



External Email - Use Caution

Hello,



My name is James Park, and I had a question regarding some issues with 
Freesurfer.



We noticed that for the freesurfer recon-all output there were multiple aliases 
files such as surf/rh.white.K among others.

Unfortunately we have been unable to copy these types of files to secondary 
locations (i.e. a network server).



I have confirmed this is not an issue with the computer-network connection as I 
have been able to copy other alias file types to the network location.

I was wondering if there is any workaround for this issue?



This was run on a Mac with macOS Catalina Version 10.15.7 using FreeSurfer 
version freesurfer-darwin-macOS-7.1.1-20200811-8b40551.



Thank you for your help in advance.



Sincerely,

James Park



This e-mail message (including any attachments) is for the sole use of
the intended recipient(s) and may contain confidential and privileged
information. If the reader of this message is not the intended
recipient, you are hereby notified that any dissemination, distribution
or copying of this message (including any attachments) is strictly
prohibited.

If you have received this message in error, please contact
the sender by reply e-mail message and destroy all copies of the
original message (including attachments).
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Re: [Freesurfer] Tracula error: run list is longer than subject list {Disarmed}

[Shanika Jayakody]

External Email - Use Caution

Hi Anastasia

Thanks so much- it worked! just now.
But I have this error with trac-preprocessing I get "Error: data and 
bvals/bvecs do not contain the same number of entries"
As far as I know all my files have 66 entries so I am not sure what causes this.
If you have any suggestion please let me know

Thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Tuesday, October 27, 2020 2:39 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Hi Oshadi - Yes.

For future reference, if you have any doubts about command line usage, you can 
1. run "trac-all", without any arguments, and/or 2. read the tutorial:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula

Anastasia.

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

Sent: Monday, October 26, 2020 8:20 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list


External Email - Use Caution

I am double checking so the command is trac-all -prep -c /path/to/configuration 
file- is that what you meant?

Thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, October 26, 2020 5:12 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

What goes after "-c" in the trac-all command should be the configuration file, 
not the nifti file.

From: Shanika Jayakody 
Sent: Monday, October 26, 2020 5:01 PM
To: Yendiki, Anastasia 
Subject: Fw: Tracula error: run list is longer than subject list


External Email - Use Caution


Hi Anastasia

Thanks for your reply.

That file was a Dicom but it was named as "IM_0017". Anyways I tried with the 
extension (renamed the file too as IM_007.dcm)
Just to see if there is a different outcome, I ran trac-all on another subject 
too but still I get the same error.
I have two things to double check with you
1) our pre-processed files are nii, not dcm-I have changed the configuration 
file, bvals and bvec files as instructed in FreeSurfer wiki (attached) and did 
trac-all- this way the first error I get is illigal variable name. I am not 
sure if nii files won't work or if there is something wrong with my 
configuration file.
2) I ran trac-all on the same subjects dicom files (changed the configuration 
file accordingly)

Either way I get the same error (log file attached). It would be really great 
if you can suggest something-looking forward to hear from you.

Many thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, October 26, 2020 11:05 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Hi Oshadi - The first error in your log file is this:

ERROR: cannot find /home/admin/freesrufer/subjects/30141/30141Diffusion/IM_0017

Does that file exist? Does the file name have an extension that you're omitting?

Best,
Anastasia.


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

Sent: Monday, October 26, 2020 10:06 AM
To: Freesurfer support list ; Yendiki, 
Anastasia 
Subject: [Freesurfer] Fw: Tracula error: run list is longer than subject list


External Email - Use Caution

Hi Anastasia
Thanks again for helping with troubleshooting the error- I was wondering if you 
have any suggestions for me to try.
I have also tried running TRACULA on freesurfer tutorial data but get the same 
error

Best regards,
Oshadi


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

Sent: Tuesday, October 20, 2020 9:56 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

CAUTION: This email comes from an external source; the attachments and/or links 
may compromise our secure environment. Do not open or click on suspicious 
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Hi Anastasia

Thanks for your reply. It was subjlist (sorry that was a typo in my email)
I have attached the
1) l

Re: [Freesurfer] Tracula error: run list is longer than subject list {Disarmed}

[Shanika Jayakody]

External Email - Use Caution

Also, I am not sure if these are helpful for you to give me a suggestion-but I 
have attached here our original bvals and bvecs text files and the text files I 
have formatted according to configuration file tutorial.
I have tried with them both but get the same error
Thank you very much,
Oshadi



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

Sent: Tuesday, October 27, 2020 2:44 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list 
{Disarmed}

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Hi Anastasia

Thanks so much- it worked! just now.
But I have this error with trac-preprocessing I get "Error: data and 
bvals/bvecs do not contain the same number of entries"
As far as I know all my files have 66 entries so I am not sure what causes this.
If you have any suggestion please let me know

Thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Tuesday, October 27, 2020 2:39 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Hi Oshadi - Yes.

For future reference, if you have any doubts about command line usage, you can 
1. run "trac-all", without any arguments, and/or 2. read the tutorial:

MailScanner has detected a possible fraud attempt from 
"nam04.safelinks.protection.outlook.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula

Anastasia.

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

Sent: Monday, October 26, 2020 8:20 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list


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I am double checking so the command is trac-all -prep -c /path/to/configuration 
file- is that what you meant?

Thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, October 26, 2020 5:12 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

What goes after "-c" in the trac-all command should be the configuration file, 
not the nifti file.

From: Shanika Jayakody 
Sent: Monday, October 26, 2020 5:01 PM
To: Yendiki, Anastasia 
Subject: Fw: Tracula error: run list is longer than subject list


External Email - Use Caution


Hi Anastasia

Thanks for your reply.

That file was a Dicom but it was named as "IM_0017". Anyways I tried with the 
extension (renamed the file too as IM_007.dcm)
Just to see if there is a different outcome, I ran trac-all on another subject 
too but still I get the same error.
I have two things to double check with you
1) our pre-processed files are nii, not dcm-I have changed the configuration 
file, bvals and bvec files as instructed in FreeSurfer wiki (attached) and did 
trac-all- this way the first error I get is illigal variable name. I am not 
sure if nii files won't work or if there is something wrong with my 
configuration file.
2) I ran trac-all on the same subjects dicom files (changed the configuration 
file accordingly)

Either way I get the same error (log file attached). It would be really great 
if you can suggest something-looking forward to hear from you.

Many thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, October 26, 2020 11:05 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Hi Oshadi - The first error in your log file is this:

ERROR: cannot find /home/admin/freesrufer/subjects/30141/30141Diffusion/IM_0017

Does that file exist? Does the file name have an extension that you're omitting?

Best,
Anastasia.


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

Sent: Monday, October 26, 2020 10:06 AM
To: Freesurfer support list ; Yendiki, 
Anastasia 
Subject: [Freesurfer] Fw: Tracula error: r

Re: [Freesurfer] [EXTERNAL] Re: Tracula: Calculation of MD values from other eigenvectors

[Chong, Catherine (Cat), Ph.D.]

External Email - Use Caution

Dear Dr. Yendiki,

Thank you very much for your reply. Is it correct to assume then that the 
FA/MD/RD/AD values that are averaged over all the voxels for a given tract do 
not necessarily have a ‘precise’ relationship to one another?
With warm Regards,
Cat


From:  on behalf of "Yendiki, 
Anastasia" 
Reply-To: Freesurfer support list 
Date: Monday, October 26, 2020 at 8:26 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [EXTERNAL] Re: [Freesurfer] Tracula: Calculation of MD values from 
other eigenvectors

Hi Cat - The FA/MD/RD/AD at a specific voxel comes from first fitting a tensor 
to the intensity values of all the DWIs at that voxel and then finding the 
eigenvalues of the tensor at that voxel. The tracts work like ROIs - the 
FA/MD/RD/AD values are averaged over all the voxels in a tract.

Best,
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Chong, Catherine (Cat), 
Ph.D. 
Sent: Wednesday, October 21, 2020 1:17 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Tracula: Calculation of MD values from other eigenvectors


External Email - Use Caution

Dear Tracula Experts,



We are trying to address a question from a reviewer who is wondering why we 
included all of the average diffusion parameters in our model  ( i.e. FA, 
MD,FA, RD, and AD) for distinguishing two groups of patients . The reviewer 
comments that MD values are calculated from AD and RD henceforth, including of 
all of the three parameters ( AD, RD, and MD) might have biased our analysis. I 
understand the reviewer’s concern that MD is calculated from adding all three 
eigenvalues/3, but I am uncertain about the relationship between the 
eigenvalues and the calculation of ‘average’ parameters for a given fibertract.



I am looking forward to your guidance,

With kind Regards,

Catherine


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Re: [Freesurfer] Statistic Difference Region on the Fsaverage Turned into No Statistic Difference after Mapping onto the Subjects

[Douglas N. Greve]

When you run your original analysis, you probably smoothed the map 
before doing the group analysis. This smoothing would not be in your ROI 
analysis, and the difference could be pretty big if the label is small. 
Also, the area map will have a jacobian correction that will not be in 
the raw data.


On 10/19/2020 11:29 PM, 李梦君 wrote:


External Email - Use Caution

Dear FreeSurfer Developers:

   I compared the thickness, area, volume in the mild traumatic brain 
injury patients with health control by FreeSurFer, and found 
a statistic difference region in the cortex area, I defined 
the statistic difference region as a label on the fsaverage and mapped 
this label to subjects by Qdec/mri_label2label. The label defined on 
the fsaverage was mapped onto all subjects successfully, and the label 
in subjects matched well with the inflated cortex of subjects 
in Freeview  Then the area value of the label in every single subjects 
was extracted, and I found that there is no statistic difference in 
the area value between the mild traumatic brain injury patients and 
health control. I have checked the segmentation of every subjects and 
it was a good job done by FreeSurFer.


FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Platform: macOS High Sierra.

Best wishes
Mengjun Li
Second Xiangya Hospital
Central South University

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Re: [Freesurfer] Display results with tksurfer

[Douglas N. Greve]

Not sure. Ruopeng (cc'ed) can comment on the control of the color bar

On 10/20/2020 5:05 AM, Marina Fernández wrote:


External Email - Use Caution

Thanks for the reply Doug,

We used the tksurfer command lines because they were run in matlab 
after performing some analysis to obtain the figures of the results. 
With the scripts, these figures are automatically saved for later 
review. We would like to know if what you propose with freeview is 
appropriate for this and if we can modify the scale of min-max 
significant t values with the freeview options (I copy the previous 
message below).


Thank you so much for your attention.

Best regards,
Marina

---

Douglas N. Greve 
 
Mon, 19 Oct 2020 07:50:56 -0700 



Not sure, we don't use tksurfer that much anymore. Have you tried 
freeview? You can run freeview with tksurferfv and the same tksurfer 
arguments (makes it easier)


On 10/13/2020 5:03 AM, Marina Fernández wrote:

 External Email - Use Caution

Dear Freesurfer experts,

I would like to modify the values of the colorbar scale to display
results in the inflated surface with tksurfer, in such a way that
displayed values in the colorbar range from the minimum t- value
detected to the maximum t value detected. I have tried to use the
-fminmax flag, but the colorbar scale shows values from 0 to the
maximum t value. Is it possible to limit values of the colorbar
scale to min-max significant t values?On the other hand, is it
possible to invert the colors of the colorbar scale (e.g., red for
higher t values and yellow for lower t values)?

Thank you in advance.

Best regards,
Marina

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Re: [Freesurfer] surface/volume editing

[Douglas N. Greve]

Sorry for the delay. I actually don't have any programmatic way to force 
this change. You can move the surface around in freeview. Under 
Tools->RepositionSurface. Change "Intensity" to "Coordinate", then 
Shift+Left click near the surface to select the point on the surface you 
want to move (ie, the vertex), then Shift+Ctrol+Left to click on the 
location you want it to move to, then hit Apply. When it is the way you 
like it, save the surface. Note that recon-all will not notice this 
change and so will over-write it if you re-run recon-all. The next 
version will have a way to incorporate this into recon-all.


On 10/20/2020 6:40 PM, Jake Jensen wrote:


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Hi again, Doug,

I am just checking to make sure that the thread didn't get lost in the 
pile of requests, and whether or not you have had a chance to look at 
the surfaces I sent.


Thanks

Jake Jensen

On Tue, Oct 6, 2020 at 10:08 AM Jake Jensen > wrote:


Hi Doug,

just following up to see if you had any suggestions for resolving
the problem of the ?h.wm surfaces not pulling back even after
running it through the pipeline. If you are in need of more
screenshots or details, let me know.

Thanks,

Jacob Jensen

On Wed, Sep 30, 2020 at 8:37 AM Jake Jensen
mailto:jacobjensen...@gmail.com>> wrote:

Here are some pictures of the pial (red), wm (yellow), and
orig.nofix (green) surfaces with the brainmask.mgz and wm.mgz
volumes



On Wed, Sep 30, 2020 at 8:15 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

Can you send pictures of the ?h.orig.nofix surface in
addition to the white and pial?

On 9/29/2020 12:24 PM, Jake Jensen wrote:


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Douglas,
I have attempted to edit the wm.mgz and subsequently run
-autorecon2. However the ?h.white surface remains extended.

I have attached some before and after editing pictures,
which shows how the wm surface does not recede even when
it is removed.

Thanks



On Mon, Sep 28, 2020 at 9:04 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>>
wrote:

It looks like the orig extends too far, so try
editing the wm.mgz

On 9/25/2020 11:51 AM, Jake Jensen wrote:


External Email - Use Caution

Attached are a few snapshots of the ?.orig surfaces
(pink), pial (red), and wm (yellow)

On Fri, Sep 25, 2020 at 7:46 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

Can you show it with the ?h.orig surfaces? Those
should closely follow the boundary of the wm.mgz
volume

On 9/23/2020 2:11 PM, Jake Jensen wrote:


External Email - Use Caution

Hello,

I am attempting to edit a subject, but upon
removing voxels where the WM and pial surfaces
should not be, the WM surface does not
receed (pictures are attached).

I have attempted this with -all and
-autorecon2, running it again from the original
001.mgz file, as well as attempting to run it
from the beginning with -clean. The end result
is consistently the same, as seen in the
attached images. Additionally, it is strange
that the WM surface crosses the pial.

I could not seem to find a solution to this in
the archives.


FreeSurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Platform: OSX mojave
-all -autorecon2

Recon all log attached

Thank you!

-Jacob



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Re: [Freesurfer] LGI output question

[Douglas N. Greve]

I'm not sure what you mean by the mean area for the different LGI 
values. Can you elaborate?


On 10/20/2020 6:46 PM, Lab of Autism and Developmental Neuroscience, Lab 
of Autism and Developmental Neuroscience wrote:


External Email - Use Caution

Dear Freesurfer experts,

I have performed LGI for one of my subject pools and I was wondering 
if I can compute the mean area for the different LGI values instead of 
the area in the output tables? How should I edit the code below to 
accomplish this? Thank you and stay safe!
mri_segstats --annot my_subject_id lh aparc --i 
$SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats


All the best,
Alex

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Re: [Freesurfer] Group Analysis: Comparing four groups

[Douglas N. Greve]

Yes, that is all correct. I only have a few comments. One is that 15mm 
is a lot of smoothing; this is not wrong, just more than the 5-10 that I 
usually use. Second, you might want to use permutation instead of MCZ; 
the threshold of 4 should make MCZ control the false positives 
adequately, but you might lose a lot of your activation.


On 10/21/2020 11:07 AM, Steve Petersen wrote:


External Email - Use Caution

Dear Freesurfer experts,

This is the first time I perform group analysis in Freesurfer. My aim 
is to compare the cortical thickness in four groups matched in age, 
sex and years of education using the Monte Carlo multiple comparisons 
correction. I tried to follow the Freesufer tutorials 
 
to perform this group analysis and I would be really grateful whether 
someone can verify that all steps are correct. For example, for the 
cortical thickness (smooth = 15 FWHM) of the left hemisphere, the four 
steps that I followed were:


STEP 1. Assemble the cached Data (mris_preproc) using the fsgd file

mris_preproc --fsgd STUDY_4groups.fsgd \
  --cache-in thickness.fwhm15.fsaverage \
  --target fsaverage \
  --hemi lh \
  --out lh_J4G_thickness.15.mgh \

STEP 2. Perform a GLM Analysis (mri_glmfit)

mri_glmfit \
--y lh_J4G_thickness.15.mgh \
--fsgd STUDY_4groups.fsgd \
--C *group.effect.mtx* \
--surf fsaverage lh \
--cortex \
--glmdir left_hemisphere_thickness_results\


STEP 3. Perform Monte Carlo simulation

mri_glmfit-sim \
  --glmdir left_hemisphere_thickness_results \
  --sim mc-z 1 4 mc-z.abs \
  --sim-sign abs --cwpvalthresh 0.05\
  --overwrite \


*QUESTIONS:*

1. Have I followed the steps to perform the analysis correctly or do 
you think I forgot some important flag?



2. Before test differences between two groups (eg. group1 > group 2 
with the vector 1 -1 0 0) I would like to test any group effect. For 
that purpose, I created the group.effect.mtx contrast file (see 
below), is correct?

1 -1 0 0
0 1 -1 0
0 0 1 -1


Any help would be appreciated.

Best regards,


Steve




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Re: [Freesurfer] Issues with transferring edits from v6.0dev into v7.1

[Douglas N. Greve]

Hi Mel, sorry just getting to this and now the subject.tar.gz does not 
exist. Can you reupload and/or send the recon-all.log file?
doug



On 10/6/2020 9:24 AM, Melanie Ganz wrote:
>  External Email - Use Caution
>
> Dear FS list,
>
> as soon as samseg was available in FS v6dev we used it to process some
> of our data. The plan was always to wait for v7 to use a stable version,
> but edits were made already on v6FSdev, while we waited last spring for
> v7 to come out.
>
> Now I have been having issues with transferring edits from v6dev into
> v7.1, which I thought should be a straight forward thing to do.
>
> The way I did it, is I ran v7.1 on the raw data, then I copied the files
> where edits where made, e.g. brainmask.mgz, wm.mgz as well as
> control.dat. Finally, at this point I reran recon-all -all ( since I
> actually couldn't get recon-all with the -make flag to work).
>
> But I see my rerun fails with the error message:
>
> Saving brainmask.auto.mgz
> Command terminated by signal 11
> @#@FSTIME  2020:10:06:14:45:45 mri_watershed N 10 e 20.81 S 1.93 U 22.55
> P 117% M 893740 F 0 R 330549 W 0 c 83 w 1353 I 22344 O 2312 L 3.35 3.67 2.94
> @#@FSLOADPOST 2020:10:06:14:46:06 mri_watershed N 10 3.10 3.59 2.93
> Linux krogh 4.12.14-lp151.28.59-default #1 SMP Wed Aug 5 10:58:34 UTC
> 2020 (337e42e) x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s g612_GD exited with ERRORS at Tue Oct  6 14:46:06 CEST 2020
>
> and I don't understand why. The earlier FSrun with v7.1 ran fine and I
> also tried copying to a separate directory to check file permissions and
> the same error appears again.
>
> I have uploaded the subject to the ftp server at
> surfer.nmr.mgh.harvard.edu and it's called subject.tar.gz.
>
> Kind regards,
>
> Melanie
>
>

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Re: [Freesurfer] Display results with tksurfer

[Wang, Ruopeng]

Hi Marina,

If you meant to set threshold for surface overlay from the command-line, you 
can do it like this:

freeview -f lh.inflated:overlay=overlay_file:overlay_threshold=min,max

For more overlay options, you can run ‘freeview -h’ and look under ‘-f, 
--surface’ section.

Best,
Ruopeng

On Oct 20, 2020, at 5:05 AM, Marina Fernández 
mailto:marina.fdez.alva...@gmail.com>> wrote:


External Email - Use Caution

Thanks for the reply Doug,

We used the tksurfer command lines because they were run in matlab after 
performing some analysis to obtain the figures of the results. With the 
scripts, these figures are automatically saved for later review. We would like 
to know if what you propose with freeview is appropriate for this and if we can 
modify the scale of min-max significant t values with the freeview options (I 
copy the previous message below).

Thank you so much for your attention.

Best regards,
Marina

---

Douglas N. 
Greve
 Mon, 19 Oct 2020 07:50:56 
-0700

Not sure, we don't use tksurfer that much anymore. Have you tried freeview? You 
can run freeview with tksurferfv and the same tksurfer arguments (makes it 
easier)


On 10/13/2020 5:03 AM, Marina Fernández wrote:


External Email - Use Caution

Dear Freesurfer experts,



I would like to modify the values of the colorbar scale to display results in 
the inflated surface with tksurfer, in such a way that displayed values in the 
colorbar range from the minimum t- value detected to the maximum t value 
detected. I have tried to use the -fminmax flag, but the colorbar scale shows 
values from 0 to the maximum t value. Is it possible to limit values of the 
colorbar scale to min-max significant t values?

On the other hand, is it possible to invert the colors of the colorbar scale 
(e.g., red for higher t values and yellow for lower t values)?

Thank you in advance.

Best regards,
Marina

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Re: [Freesurfer] lh.white edits

[Douglas N. Greve]

You can move the surface around in freeview. Under 
Tools->RepositionSurface. Change "Intensity" to "Coordinate", then 
Shift+Left click near the surface to select the point on the surface you 
want to move (ie, the vertex), then Shift+Ctrol+Left to click on the 
location you want it to move to, then hit Apply. When it is the way you 
like it, save the surface. Note that recon-all will not notice this 
change and so will over-write it if you re-run recon-all. The next 
version will have a way to incorporate this into recon-all.


On 10/21/2020 7:00 PM, Wei Koo wrote:


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Hello FreeSurfer Developers,

I am trying to make edits to the white matter segmentation. I have 
tried making edits to wm.mgz and repeating recon2-wm but I was 
wondering if there is a way to make direct edits to lh.white?


I've searched the lists and did not seem to find anything regarding 
editing the surface directly.



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Re: [Freesurfer] Issue with extracted thickness value from significant cluster or peak vertex

[Douglas N. Greve]

On 10/22/2020 3:58 AM, Julian Macoveanu wrote:
>  External Email - Use Caution
>
> Hi,
> I am using FS 7.1.0. After running the surface thickness GLM analysis
> I get one cluster after correction for multiple comparison showing a
> significant group difference. I want to make a plot illustrating this
> group difference. However, when using the mean values from:
>
> cache.th30.abs.y.ocn.dat, I don’t see the expected group difference in
> these values.
>
> Question 1)
> Are the subjects cluster mean values in y.ocn.dat adjusted for the
> covariates I used in the fsgd file? E.g. age, sex and TIV?
No
>
> Question 2)
> I inserted these mean cluster values from y.ocn.dat in SPSS and tried
> verify the statistics both with and without adjustment for covariates
> and did not get the expected significant group region which I expected
> in either case. Why is this?
Probably your SPSS model is different. About once a year someone writes 
to the list to report this effect, but I never hear back when I ask them 
to confirm that the model is exactly the same. One thing you can easily 
try is to do the analysis in matlab using our tools, eg,
y = load('y.ocn.dat');
X = load('Xg.dat');
C = load('contrast/C.dat');
[beta rvar] = fast_glmfit(y,X);
[F p] = fast_fratio(beta,X,rvar,C);
p will be a vector of p-values, one for each cluster
>
> Question 3)
> I moved on to extract the thickness values from peak vertex in my
> significant cluster. For this I used mris_convert which I just wanted
> to be confirmed that is correct:
>
> mris_convert -c lh.thickness.fwhm15.fsaverage.mgh
> $freesurferdir/fsaverage/surf/lh.orig  output.asc
>
> After extracting the thickness value for all subjects from the peak
> vertex as reported by the sig.cluster.summary , I still have the same
> issue as before, I find no group expected group difference.
>
> Interestingly, the significant cluster I found is part of the
> superior_frontal region in aparc2009. When I extract these values it
> almost shows significant group differences in the entire region, in
> line with the surface GLM findings.
>
> Thanks,
> Julian
>
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Re: [Freesurfer] How is Total cortical gray matter volume calculated?

[Douglas N. Greve]

Yes, based on the surfaces. We use Anderson Winkler's truncated pyramid 
method.

On 10/22/2020 5:55 AM, Ian Hardingham wrote:
>  External Email - Use Caution
>
> Hi Freesurfers,
>
> Is "total cortical gray matter volume" from aseg.stats calculated based
> on the recon-all Surfaces?  Or using a different method?
>
> I ask because I have been trying to calculate the grey matter volume
> based on the area between the surfaces, and I have been getting
> different results.
>
> Thanks,
>
> Ian
>
>
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Re: [Freesurfer] mri_nu_correct error: flar --uchar not recignized

[Douglas N. Greve]

You aren't using 7.1.1, you are using 5.1, or maybe some mixture of 
them, which would explain why the --uchar opt is not recognized


On 10/22/2020 6:28 AM, erbilnurhan wrote:


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Hello FreeSurfer Developers,

I'm trying to compute volumetric data from MPRAGE images by using 
recon-all as decribed 
athttps://surfer.nmr.mgh.harvard.edu/fswiki/recon-all


I've got the following message:

mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar 
transforms/talairach.xfm --n 2

ERROR: flag --uchar not recognized

Does anyone have any thoughts on how to trouble-shoot this problem? 
Also, I've attached the recon-all.log in case it's of any use.


FreeSurfer version: freesurfer-darwin-macOS-7.1.1 
(freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0)


macOS high Sierra 10.13.6, x86_64
XQuartz 2.7.11 (xorg-server 1.18.4)

recon-all.log: see attached

Sincerely,

Nurhan Erbil

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Re: [Freesurfer] There is no view-label option after loading the .annot file

[Douglas N. Greve]

On 10/22/2020 9:52 AM, 1248742467 wrote:


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Hello, Fs
my freesurfer version is 6,  I see others have the view button after 
load .annot file, But my version does not have this option.
Do I need to update the version? And I have installed fs6, can I 
install fs 7.1 on the same machine?

Yes
What's more, After loading the .annot file in freeview, can I reset 
its name, index, color through view-label?

I'll cc Ruopeng  who can hopefully answer.



Looking forward to your reply

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Re: [Freesurfer] mri_surf2vol method one

[Douglas N. Greve]

We have not used .w files in years. Try converting the .w file to .mgz 
using mri_surf2surf (or even better, don't save them as .w files)


On 10/22/2020 4:03 PM, Yixin Ma wrote:


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Hi Freesurfer experts,

I'm trying to write the normals of the GM/WM meshes to the entire ribbon.

We usually do it by:
1) Generate normal files from rh.white and lh.white

mris_convert rh.whiterh.white.gii

mris_convert -nrh.whiterh.white.normals.asc


2) Use matlab 'read_normals' function to read the normals and write 
individual directions xyz as a paint format file.


g = gifti([path 'Analysis/' exam '/' subject '/surf/rh.white.gii']);

norm = read_normals(g,[path 'Analysis/' exam '/' subject 
'/surf/rh.white.normals.asc']);


write_wfile([path 'Analysis/' exam '/' subject 
'/surf/rh_normx.w'],norm(:,1));


write_wfile([path 'Analysis/' exam '/' subject 
'/surf/rh_normy.w'],norm(:,2));


write_wfile([path 'Analysis/' exam '/' subject 
'/surf/rh_normz.w'],norm(:,3));



3) Use mri_surf2vol method two to paint the normals into the ribbon. 
But the problem is that method two gives me lots of holes in the ribbon.
I'm wondering if it's possible to use mri_surf2vol method one to paint 
the normals into the ribbon because method one does not leave holes in 
the ribbon. However, it seems like the overlay does not accept paint 
file format (rh_normx.w). The overlay in method one accepts 
rh.thickness as an input, as shown in the example on the website. I'm 
wondering how to convert the painting files to have the same format as 
rh.thickness?


Thank you in advance,

Yixin

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Re: [Freesurfer] recon2-wm: does not start from -filled

[Douglas N. Greve]

Can you send the recon-all.log file?

On 10/22/2020 8:15 PM, Wei Koo wrote:


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Hello FreeSurfer Developers,

I am trying to recompute the surfaces after wm edits using this 
command line : recon-all -autorecon2-wm -hires -s subject_id , but 
when I do run that command, it starts at mri_normalization and not 
mri_filled which then gives me wm.mgz without the manual edits I've made.


FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0 (also 
tried with freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0)


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Re: [Freesurfer] Best mesh generation from hippocampus aseg segmentation

[Douglas N. Greve]

You can use mri_binarize with --match to specify the hippo seg id and 
--surf to output a surface. You may want to smooth it a little bit with 
--surf-smooth


On 10/22/2020 10:31 PM, Gonzalo Rojas Costa wrote:


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Hi:

Which is the best library or software to create the hippocampus mesh 
from aseg segmentation?


Sincerely


Gonzalo Rojas Costa

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Re: [Freesurfer] Help with mergecontrasts-sess function

[Douglas N. Greve]

You would just run mkcontrast-sess, eg, if your four conditions are 
ordered condA, condAcontrol, condB, condBcont, then
mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 2 -c 3 
-a 4
If you want it reversed, then just reverse the a's and c's

On 10/23/2020 4:39 AM, Paula Maldonado wrote:
>  External Email - Use Caution
>
> Dear experts,
> I am running an fMRI experiment in which I have four conditions: two main 
> conditions (condition A and condition B) and two respective control 
> conditions (condition Acontrol and condition Bcontrol).
> I would like to create a map showing significantly greater activity for 
> condition A relative to condition B, after subtracting out the activity for 
> the respective control conditions. In other words, I would like to perform 
> the following contrast:
> (condition A - condition A control) - (condition B - condition B control)
> Then I would like to have a map that shows the reverse contrast 
> too:(condition B - condition B control) - (condition A - condition A control).
>
> How do I do that?To obtain the first map: (condition A - condition A control) 
> - (condition B - condition B control) I have tried with the 
> mergecontrasts-sess function with the -conjunction flag and the OR option as 
> detailed below:
> mergecontrasts-sess -mergedcontrast conjres -conjunction or -analysis 
> analysisname -map sig -space sph -isxavg fixed -contrast Contrast1 2 pos 0 
> -contrast Contrast 2 pos 0 -s sessionsfMRI/Sub01/bold -hemi lh
>
> where Contrast1= (condition A - condition A control) and Contrast2= 
> (condition B - condition B control)
> however the map I get is exactly the same as (condition A - condition A 
> control), as if subtracting out Contrast 2 had no impact on the map.
>
> Thanks,
>
> Paula
>
>
>
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Re: [Freesurfer] Coordinate of orig.mgz

[Douglas N. Greve]

Is that using freeview or tksurfer? In any event, "orig" there refers to 
the ?h.orig surface


On 10/24/2020 2:10 AM, Kim, Gwang-Won wrote:


Dear expert,

I obtained “sig.mgh” from resting fMRI data using Freesurfer. Then, I 
opened the file using tksurfer. I selected vertex 156439 out of 163842 
in the file  “sig.mgh”.


In the terminal, there were several coordinates as followings:

Selected vertex 156439 out of 163842

Current -36.76 -22.70 -10.66

orig    -59.96 -33.44 8.59

pial 0.00 0.00 0.00

I have a question for orig “-59.96 -33.44 8.59”. The coordinate 
(x=59.96 y=-33.44 z=8.59) is in the 
~/freesurfer/7.1.1/subjects/fsaverage/mri/orig.mgz, right?


Thanks,

Gwangwon


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Re: [Freesurfer] FreeSurfer Coordinate Systems

[Douglas N. Greve]

[tkrR tkrA tkrS 1] would be [10 20 30]

On 10/24/2020 2:54 AM, Kim, Gwang-Won wrote:


Dear sir,

I’m going to process as follows:

I have a point on the surface ("Vertex RAS" in tksurfer) and want 
tocompute the Scanner RAS in orig.mgz that corresponds to this 
point:ScannerRAS = Norig*inv(Torig)*[tkrR tkrA tkrS 1]


If vertex RAS is x=10 y=20 z=30, [tkrR tkrA tkrS 1] is [10 0 0 1;  0 
20 0 1; 0 0 30 1], right?


I don’t know how I use [tkrR tkrA tkrS 1].  Please let me know.

Thanks


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Re: [Freesurfer] Convert FSL .nii ROI into FreeSurfer Label

[Douglas N. Greve]

A surface label or a volume label?

On 10/25/2020 2:17 PM, Hua, Jessica wrote:


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Hi FreeSurfer Experts,

How can I convert a .nii ROI into a FreeSurfer label? I was able to 
convert the .nii into a .mgh file but could not figure out how to 
convert to a label file.


Thank you,

Jessica

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Re: [Freesurfer] Fwd: Freesurfer edits

[Douglas N. Greve]

It looks like the image darkens a lot at the top. Try putting control 
points in the WWM near the start of the gyrus. make sure they are truly 
in WM!


On 10/25/2020 9:03 PM, Alexopoulos, Dimitrios wrote:


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Any comments from FS users to best best tackle these manual edits?

Jim

Get Outlook for Android 


*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alexopoulos, 
Dimitrios 

*Sent:* Tuesday, October 20, 2020, 10:25 AM
*To:* Freesurfer support list
*Subject:* [Freesurfer] Freesurfer edits

** External Email - Caution **

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Hi freesurfer editing experts.

Below are snapshots of the brainmask, aseg and wm.mgz for a 2 year old 
run through FS 7.1.1


I’m hoping for feedback on the best way to make the relevant edits to 
the three blue-circled regions.


1.In the superior regions I think control points will help to pick up 
some WM to help fuill


2.In the left hemisphere medial prefrontal (gyrus rectus) regions, the 
WM is overestimated. I presume removing WM voxels from the wm.mgz is 
the best approach?


3.The left temporal pole region is missing GM/cortex and there really 
isn’t any WM that would help with controls points or adding WM voxels. 
How can I add GM to this area?




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Re: [Freesurfer] Please help me. Stuck with this for too long!!!

[Douglas N. Greve]

On 10/26/2020 3:58 PM, Basavaraju, Rakshathi wrote:


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Dear Freesurfer team,

I have been trying to extract local gyrification index in a dataset 
according to a label which I have created.


1) First of all, I extracted lGI as per DKT areas, which one is lGI 
value in the ?h.pial_lgi.stats file (derived on running a lGI recon?)


# ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd 
MeanCurv GausCurv FoldInd CurvInd
caudalanteriorcingulate                  1094    774   2285  3.234 
0.889     0.129     0.031       15     1.3


Is the lGI of caudal anterior cingulate 3.234 or 1.3?

It is 3.234


2) I could register a label which I have created to the surface of 
individual subjects using mrilabel2label which ran alright, and I 
could view the label on the surface of the individual subject intact 
on freeview. But after that I am unable to extract lGI value from the 
designated label only using mris_anatomicalstats.


I used the following command: mris_anatomical_stats -l 
label/outlabelbase-0001.label -f stats/occipital_lGI.stats 
FS6-LGI-05-Feb-2020_schiz018_G1_MPRAGE rh pial_lgi


This throws the error: #MRISread: file 
'/mnt/share/projects/provenzano/Human/CHR_Rakshathi/LGI/FS6-LGI-05-Feb-2020_schiz018_G1_MPRAGE/surf/rh.pial_lgi' 
has many more faces than vertices!

Probably trying to use a scalar data file as a surface!

Try using mri_segstsats, like
mri_segstats --slabel subject rh  label/outlabelbase-0001.label --id 1 
--o mean.dat


Then I converted rh_pial.lgi to rh_pial.lgi.asc: mris_convert -c 
rh.pial_lgi rh.white rh.pial_lgi.asc
and then ran: mris_anatomical_stats -l label/outlabelbase-0001.label 
-f stats/occipital_lGI.stats FS6-LGI-05-Feb-2020_schiz018_G1_MPRAGE rh 
pial_lgi.asc


then the error: Segmentation fault (core dumped)

Kindly help me, this analysis is way overdue, and it is seeming like 
an endless tunnel only of new errors






Dr. Rakshathi Basavaraju (MD Psychiatry)
Postdoctoral Research Scientist
Taub Institute for Research on Alzheimer's Disease and the Aging Brain
Columbia University Medical Centre
622 West, 168th Street, New York - 10032
E-Mail: rb3...@cumc.columbia.edu 
_https://indiaalliance.org/fellow/rakshathi-basavaraju_


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Re: [Freesurfer] question about PETSurfer

[Douglas N. Greve]

as you note, the gtmseg.mgz has higher resolution and several new ROIs. 
the higher res is for partial volume correction. The inclusion of pons 
to for the possibility of using it as a reference region, which often 
happens in AD studies of FDG. Vermis is for use in serotonin studies so 
it can be excluded from the rest of cerebellar cortex as vermis might 
have some receptors there making is inappropriate to use as a reference 
region.


On 10/26/2020 9:55 PM, 蒋袁芳 wrote:


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Hello Freesurfer Developers,

I have some questions about why the first step of PETSurfer needs to 
create gtmseg.mgz segmentation.


I noticed that the differences between gtmseg.mgz and aseg.mgz are the 
gtmseg.mgz has a higher resolution and also to separate the pons and 
the vermis from the brainstem and the cerebellar. I would like to know 
whether the reason to create the gtmseg.mgz segmentation is because 
the ROI is based on the Pons?


If so, I also have read some other articles that the ROI is based in 
other regions. Why does the Freesurfer choose Pons instead? Also, what 
is the purpose of separating the vermis from the cerebellar? Is the 
reason to create the gtmseg.mgz segmentation just for the system to 
run the PVC?


looking forward to your reply.

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Re: [Freesurfer] Tracula error: run list is longer than subject list {Disarmed}

[Yendiki, Anastasia]

The two formats that you sent are not equivalent.

In the version where the gradient vectors saved in columns, the first 2 columns 
are:
0 -0.793264
0 -0.394167
0 0.464074

In the version where the gradient vectors saved in rows, the first 2 rows are:
0  -0.793264  -0.453844
-0.2799370.976579   0.920768

Which one is the correct version?


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

Sent: Tuesday, October 27, 2020 4:06 PM
To: Freesurfer support list ; Yendiki, 
Anastasia 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list 
{Disarmed}


External Email - Use Caution

Also, I am not sure if these are helpful for you to give me a suggestion-but I 
have attached here our original bvals and bvecs text files and the text files I 
have formatted according to configuration file tutorial.
I have tried with them both but get the same error
Thank you very much,
Oshadi



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

Sent: Tuesday, October 27, 2020 2:44 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list 
{Disarmed}

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Hi Anastasia

Thanks so much- it worked! just now.
But I have this error with trac-preprocessing I get "Error: data and 
bvals/bvecs do not contain the same number of entries"
As far as I know all my files have 66 entries so I am not sure what causes this.
If you have any suggestion please let me know

Thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Tuesday, October 27, 2020 2:39 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

Hi Oshadi - Yes.

For future reference, if you have any doubts about command line usage, you can 
1. run "trac-all", without any arguments, and/or 2. read the tutorial:

MailScanner has detected a possible fraud attempt from 
"nam04.safelinks.protection.outlook.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula

Anastasia.

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

Sent: Monday, October 26, 2020 8:20 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list


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I am double checking so the command is trac-all -prep -c /path/to/configuration 
file- is that what you meant?

Thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yendiki, Anastasia 

Sent: Monday, October 26, 2020 5:12 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list

What goes after "-c" in the trac-all command should be the configuration file, 
not the nifti file.

From: Shanika Jayakody 
Sent: Monday, October 26, 2020 5:01 PM
To: Yendiki, Anastasia 
Subject: Fw: Tracula error: run list is longer than subject list


External Email - Use Caution


Hi Anastasia

Thanks for your reply.

That file was a Dicom but it was named as "IM_0017". Anyways I tried with the 
extension (renamed the file too as IM_007.dcm)
Just to see if there is a different outcome, I ran trac-all on another subject 
too but still I get the same error.
I have two things to double check with you
1) our pre-processed files are nii, not dcm-I have changed the configuration 
file, bvals and bvec files as instructed in FreeSurfer wiki (attached) and did 
trac-all- this way the first error I get is illigal variable name. I am not 
sure if nii files won't work or if there is something wrong with my 
configuration file.
2) I ran trac-all on the same subjects dicom files (changed the configuration 
file accordingly)

Either way I get the same error (log file attached). It would be really great 
if you can suggest something-looking forward to hear from you.

Many thanks,
Oshadi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on beha