Re: [Freesurfer] Exited with errors, segmentation fault

[Julia Lam]

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



101_recon-all.error
Description: 101_recon-all.error


101_recon-all.log
Description: 101_recon-all.log


102_recon-all.error
Description: 102_recon-all.error


102_recon-all.log
Description: 102_recon-all.log


104_recon-all.error
Description: 104_recon-all.error


104_recon-all.log
Description: 104_recon-all.log
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] question about PETSurfer

[蒋袁芳]

External Email - Use Caution

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

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

[Shanika Jayakody]

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 
emails. Please click on the “Phish Alert” button on the top right of the 
Outlook dashboard to report any suspicious emails.

External Email - Use Caution

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, but I keep 
getting the error "run list is longer than subject list"
I have created a configuration file setting sublist and runlist to just one 
subject so I am not sure what the error is about.
I wonder if anyone can help me figure out a solution.

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

Re: [Freesurfer] Exited with errors, segmentation fault

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


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


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

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

[Hoopes, Andrew]

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).

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

Re: [Freesurfer] please help me

[Fischl, Bruce]

Not sure, cortical thickness maybe?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of saman fouladi
Sent: Saturday, October 24, 2020 11:57 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] please help me


External Email - Use Caution
thank Bruce

I read several articles and got a little confused.

Can you help me a little if you have any information?

On Saturday, October 24, 2020, 6:04:07 PM GMT+3:30, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:



Hi Saman



That’s really a scientific question and up to you!
Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of saman fouladi
Sent: Saturday, October 24, 2020 7:17 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] please help me



External Email - Use Caution

hi



Which output can I use to predict age after recon-all?



On Friday, October 23, 2020, 11:46:09 PM GMT+3:30, saman fouladi 
mailto:smnfoul...@yahoo.com>> wrote:





yes and replacing -sdir with -sd



thank you very much

On Friday, October 23, 2020, 5:58:11 PM GMT+3:30, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:





You need a -s before the “subj1”



Cheers

Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of saman fouladi
Sent: Friday, October 23, 2020 2:44 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] please help me



External Email - Use Caution

hi



my code is:



recon-all -i /home/MRI/Training/99060003/T1-image/39501.dcm  subj1 -sdir  
/home/MRI4 -all



ERROR: Flag subj1 unrecognized.
-i /home/nbml-challenge/Training/99060003/T1-image/39501.dcm subj1 -sdir 
/home/team33/MRI4 -all



what is ??





On Thursday, October 22, 2020, 5:40:05 PM GMT+3:30, saman fouladi 
mailto:smnfoul...@yahoo.com>> wrote:





hi Bruce



thank you very very much



On Wednesday, October 21, 2020, 9:05:36 PM GMT+3:30, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:





Nifty is a format that a lot of people use (including us) but it is not needed 
for our processing. Pick *one* file in your dicom series and pass it to 
recon-all:





recon-all -i  -s  -sdir  -all



cheers

Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of saman fouladi
Sent: Wednesday, October 21, 2020 11:57 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] please help me



External Email - Use Caution

hi



Thank you for your response



I have 60 subject MRI that each  contains 174 dcm file. and i want predict age 
of these subjects. in step one i want extract morphology features and in step2 
create a deep learning model that predict age.



According to what I said, what should I do?



If I have to use recon-all with what code can I do this? And what is the use of 
nifty?



On Wednesday, October 21, 2020, 1:06:50 AM GMT+3:30, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:





Hi Saman



Recon-all will give you a comprehensive assessment of most macroscopically 
visible structures in the brain. You don’t have to convert to nifty first – 
just point recon-all at a single slice in the proper dicom series (for your 3D 
T1-weighted scan), and it will spend a few hours doing stuff



Cheers

Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of saman fouladi
Sent: Tuesday, October 20, 2020 4:12 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] please help me



External Email - Use Caution

hi



I want to process MRI images to extract Morphology features.



I convert my dcm file to nii format by mri-convert command and then  I used FSL 
software and BET(Best extraction Tool).



Next I do not know what to do to extract morphological features?



My other question is what is the difference between recon-all and use FEAT( in 
FSL software)? What are the uses of each?



Thank you





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

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

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

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

[Yendiki, Anastasia]

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 
emails. Please click on the “Phish Alert” button on the top right of the 
Outlook dashboard to report any suspicious emails.

External Email - Use Caution

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, but I keep 
getting the error "run list is longer than subject list"
I have created a configuration file setting sublist and runlist to just one 
subject so I am not sure what the error is about.
I wonder if anyone can help me figure out a solution.

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

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

[Shanika Jayakody]

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 
emails. Please click on the “Phish Alert” button on the top right of the 
Outlook dashboard to report any suspicious emails.

External Email - Use Caution

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, but I keep 
getting the error "run list is longer than subject list"
I have created a configuration file setting sublist and runlist to just one 
subject so I am not sure what the error is about.
I wonder if anyone can help me figure out a solution.

Many thanks
Oshadi


Configurationfile
Description: Configurationfile


bvecs_Oshadi
Description: bvecs_Oshadi


bvals_Oshadi
Description: bvals_Oshadi


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

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

[Basavaraju, Rakshathi]

External Email - Use Caution

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  1094774   2285  3.234 0.889 
0.129 0.031   15 1.3

Is the lGI of caudal anterior cingulate 3.234 or 1.3?

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!

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

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

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

[Park, James]

External Email - Use Caution

Hello,

Sorry for the rapid follow up email, I just noticed I left some personal 
contact information on the previous email.

Could you please remove my signature from the archives?

Thank you so much.

Sincerely,
James Park

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

Date: Monday, October 26, 2020 at 3:01 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [External] [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
Research Specialist
Dpt. of Neurosurgery, Emory
james.kunwoo.p...@emory.edu
732-589-4215



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

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

[fsbuild]

External Email - Use Caution

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 Ubuntu18.04 LTS machine, until 
that doomsday where I installed updates asrecommended 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-genericI think it used to be 49 
instead of 52 before the upgrade, but I am notsure.Do you know of any patch 
fixing this, by any chance?Thanks for your lightsAntonin RovaiHôpital Erasme - 
ULBCliniques universitaires de BruxellesRoute de Lennik 808 - B - 1070 
BruxellesS www.erasme.ulb.ac.beDisclaimer : 
http://www.erasme.ulb.ac.be/email-disclaimer___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Re: [Freesurfer] segmentHA on Human Connectome Project

[Iglesias Gonzalez, Juan E.]

Glad to hear; thanks for sharing! It’s nice to see success stories here and 
there among all the questions  


Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com



From: AmirHussein Abdolalizadeh 
Date: Sunday, October 25, 2020 at 06:33
To: "Iglesias Gonzalez, Juan E." 
Cc: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: segmentHA on Human Connectome Project


External Email - Use Caution
I applied the change you suggested. It took me a while to run both segmentHA_T1 
and segmentHA_T2 on all my subjects (n = 145), to see whether I'll encounter 
any kind of errors, which I didn't. Thanks a lot!

Bests,
Amir

On Tue, Oct 20, 2020 at 5:35 PM Iglesias Gonzalez, Juan E. 
mailto:jiglesiasgonza...@mgh.harvard.edu>> 
wrote:
This is most likely a problema with wmparc.mgz which is still at 1mm.
Can you please try these commands from the mri directory of a subject and 
rerunning? The first one renames wmparc to wmparc.1mm and the second upscales 
it to the resolution of the other high resolution volumes using aseg.mgz as a 
references (you could also use any other high res volume like norm.mgz, etc).
mv wmparc.mgz wmparc.1mm.mgz
mri_convert wmparc.1mm.mgz wmparc.mgz -rl aseg.mgz -odt float -rt nearest


Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com



From: AmirHussein Abdolalizadeh 
mailto:amirhussei...@gmail.com>>
Date: Tuesday, October 20, 2020 at 02:40
To: "Iglesias Gonzalez, Juan E." 
mailto:jiglesiasgonza...@mgh.harvard.edu>>
Cc: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: segmentHA on Human Connectome Project


External Email - Use Caution
Thanks for your reply Eugenio. I renamed a few files in the /mri folder:



aseg.mgz → aseg.1mm.mgz

aseg.hires.mgz → aseg.mgz

brain.mgz → brain.1mm.mgz

brain.hires.mgz → brain.mgz

filled.mgz → filled.1mm.mgz

filled.hires.mgz → filled.mgz

norm.mgz → norm.1mm.mgz

T1w_hires.masked.norm.mgz → norm.mgz

T1.mgz → T1.1mm.mgz

T1w_hires.norm.mgz → T1.mgz

wm.mgz → wm.1mm.mgz

wm.hires.mgz → wm.mgz

However, it exits with this error:
Error in segmentSubjectT1_autoEstimateAlveusML (line 822)
MATLAB:sizeDimensionsMustMatch

It seems there was a file that I did not have to rename or a file that I have 
forgotten to rename, and two files in the process are based on different 
resolutions causing mismatch. Any ideas?

Bests,
Amir

p.s. The pipeline works fine with the same subject in which I haven't applied 
any changes to filenames.

On Sun, Oct 18, 2020 at 6:43 PM Iglesias Gonzalez, Juan E. 
mailto:jiglesiasgonza...@mgh.harvard.edu>> 
wrote:
Dear Amir,

  1.  By default, FS will use norm.mgz, aseg.mgz, etc. You will have to eg 
rename norm.mgz to norm.1mm.mgz and copy / symlink / rename the _hires 
equivalents to get FS to use the highres T1s.
  2.  That sounds appropriate!
  3.  That sounds about right 
Cheers,
/Eugenio




Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com



From: AmirHussein Abdolalizadeh 
mailto:amirhussei...@gmail.com>>
Date: Sunday, October 18, 2020 at 02:48
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: "Iglesias Gonzalez, Eugenio" 
mailto:e.igles...@ucl.ac.uk>>
Subject: segmentHA on Human Connectome Project

Hi,

I am trying to run segmentHA pipeline on HCP data. To do so, I have downloaded 
FS processed-extended structural data, manually made "scripts", "trash", and 
"stats" folders in each subject's folder [HCP output does not have these 
folders]. A few notes and questions:

1. segmentHA_T1 runs smoothly. However, I do not know which T1 does segmentHA 
use, since there are also a few "_hires" (high resolution) files resulting from 
HCP's structural analysis pipeline 
(https://github.com/Washington-University/HCPpipelines).

2. segmentHA_T2 also runs smoothly. However, I didn't know which T2 file is the 
most suitable to be given to this command. I did give T2w_hires.nii.gz 
(Voxelsize = 0.7 mm isotropic) in the /mri folder of each subject.

3. I statistically checked the correlation between HCP FS generated values of 
whole hippocampus/amygdala, and segmentHA generated ones. Of note, they were 
highly correlated (all p-values < 0.001, all r ~ 0.9).

I will be glad to know whether the pipeline I used to analyze HCP data is 
correct or any further steps are required.

Bests,
Amir
The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If 
the e-mail was sent to you in error but does not contain patient information, 
please contact the sender and properly dispose of 

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

[Yendiki, Anastasia]

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


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

Re: [Freesurfer] Traculina availability

[Yendiki, Anastasia]

Hi Zhen - We do not have a date for the next FreeSurfer release yet. The code 
for the infant stream has been merged into the main TRACULA code base, but 
there is some work still to be done to finalize the new atlas that we've been 
working on. In the meantime, you can try running the infant T1 segmentation 
stream, which you'd need to do before running our tract tools:
https://surfer.nmr.mgh.harvard.edu/fswiki/infantFS

Best,
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ngoh Zhen Ming 

Sent: Wednesday, October 21, 2020 2:24 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Traculina availability


External Email - Use Caution

Good Morning!

I understand that the stable release of TRACULInA will be included in the next 
version of freesurfer. Is there an estimate of when that will be? Or if there 
are any versions that are currently openly available for trial?

Thank you and look forward to hearing back!

Zhen Ming, NGOH
This e-mail and any attachments are only for the use of the intended recipient 
and may contain material that is confidential, privileged and/or protected by 
the Official Secrets Act. If you are not the intended recipient, please delete 
it or notify the sender immediately. Please do not copy or use it for any 
purpose or disclose the contents to any other person.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] freeview Core Dumped Error after upgrade in ubuntu

[Rovai Antonin]

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

Re: [Freesurfer] Contents of Freesurfer digest Vol 200, Issue 28 error trac all prep (Yendiki, Anastasia)

[Yendiki, Anastasia]

Hi Ileana - You can set the "pathlist" to include a specific set of pathways. 
In the example config file the pathlist includes all 18 pathways, but you can 
change it, e.g., to only include the rh ones:
https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc

That said, TRACULA doesn't use the conventional type of streamline tractography 
that would "stop" in the middle of a tract (e.g., due to a lesion), so I'd be 
interested in what you find. If you continue to have issues after running these 
tests, you can upload an example subject for me to look at here:
https://gate.nmr.mgh.harvard.edu/filedrop2/

Thanks,
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Camerino, I.L. (Ileana) 

Sent: Monday, October 26, 2020 7:08 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Contents of Freesurfer digest Vol 200, Issue 28 error 
trac all prep (Yendiki, Anastasia)

External Email - Use Caution

Hi Anastasia,

Thank you so much for your reply.
I omitted a very important information. I am working with left hemisphere 
stroke data. On a visual check I see that recon all worked well on all the 
participants (big and small lesions).  Although trac all worked for some 
participants with a smaller lesion, I suspect this failure may be due to the 
presence of a bigger lesion. In order to test if this is the case, I could 
perform trac all only on the right hemisphere.  Can you tell me how to perform 
tracall only on the right hemisphere? I tried to edit the config file but it 
did not work.
Please,  let me know if you have other suggestions on what can go wrong as well.

Thank you in advance
Best regards
Ileana

Ileana Camerino

PhD candidate
Donders Institute for Brain, Cognition and Behaviour

Centre for Cognition
Spinozabuilding
Room B02.25
Montessorilaan 3, 6525 HR Nijmegen
The Netherlands
Tel. +31-24 3612618





On 14/10/2020, 18:01, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
freesurfer-requ...@nmr.mgh.harvard.edu"  wrote:

Send Freesurfer mailing list submissions to
 freesurfer@nmr.mgh.harvard.edu

To subscribe or unsubscribe via the World Wide Web, visit
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
 freesurfer-requ...@nmr.mgh.harvard.edu

You can reach the person managing the list at
 freesurfer-ow...@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

   1. Re: error trac all prep (Yendiki, Anastasia)
   2. Postdoc and PhD positions @ BrainLENS Lab w/ Fumiko   Hoeft
  {Disarmed} (Jieyin Feng)
   3. Help with creating contrast matrix - 6 classes and 3
  variables (Paul Dhami)
   4. Reliability and sensitivity of two whole-brain segmentation
  approaches ? ASEG and SAMSEG (Donatas Sederevicius)
   5. tk applications failing to launch on VM (Windows)
  (Mcnorgan, Christopher)


--

Message: 1
Date: Tue, 13 Oct 2020 20:20:03 +
From: "Yendiki, Anastasia" 
Subject: Re: [Freesurfer] error trac all prep
To: "Freesurfer@nmr.mgh.harvard.edu" 
Message-ID:
 


Content-Type: text/plain; charset="us-ascii"

Hi Ileana - It looks like it fails on the left uncinate. Is there any 
artifact or missing part of the brain or brain mask, either in the diffusion 
scan or the T1 scan, in a location that would affect the uncinate?

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Camerino, I.L. (Ileana) 

Sent: Tuesday, October 13, 2020 11:12 AM
To: Freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] error trac all prep


External Email - Use Caution





Hello FreeSurfer Developers,

I'm attempting to run the tractography analyses as described on the Tracula 
tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula), I 
tried the all pipeline for one subject and it worked. I tried to run in 
parallel for the rest of the subjects and for three of them I get the following 
error when I run the trac all -prep command:

#!/bin/bash
export FREESURFER_HOME=/opt/freesurfer/6.0;
source $FREESURFER_HOME/SetUpFreeSurfer.sh;
export SUBJECT_DIR=$/project/3015068.01/ilecam/Reolang/Freesurfer
for i in `cat 
/project/3015068.01/ilecam/Reolang/scripts/list_trac_all_prep2.txt`; do 
trac-all -prep -c 
/project/3015068.01/ilecam/Reolang/Freesurfer/${i}/Tracula_out/tracula_config.txt;
 done


here below the content of trac-all.eror
--
SUBJECT sub-056
DATE Fri Oct  9 16:18:01 CEST 2020
USER ilecam
HOST dccn-c029.dccn.nl
PROCESSOR x86_64
OS Linux
Linux dccn-c029.dccn.nl 

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

[Shanika Jayakody]

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 
emails. Please click on the “Phish Alert” button on the top right of the 
Outlook dashboard to report any suspicious emails.

External Email - Use Caution

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, but I keep 
getting the error "run list is longer than subject list"
I have created a configuration file setting sublist and runlist to just one 
subject so I am not sure what the error is about.
I wonder if anyone can help me figure out a solution.

Many thanks
Oshadi


Tracula_logfile_Oshadi Jayakody
Description: Tracula_logfile_Oshadi Jayakody


Configurationfile
Description: Configurationfile


20190911_600196579_1002_DIFF_SAG_bvals
Description: 20190911_600196579_1002_DIFF_SAG_bvals


20190911_600196579_1002_DIFF_SAG_bvecs
Description: 20190911_600196579_1002_DIFF_SAG_bvecs
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurferdata=04%7C01%7Cshanika.jayakody%40einsteinmed.org%7C3f19f9b2955c4512f02308d875000ca5%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637387990364745770%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=THiAYaN8fjNBzyGCbtdS5b1kcTeIUrQPUkfyAjhKw64%3Dreserved=0___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

[Shanika Jayakody]

External Email - Use Caution


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, but I keep 
getting the error "run list is longer than subject list"
I have created a configuration file setting sublist and runlist to just one 
subject so I am not sure what the error is about.
I wonder if anyone can help me figure out a solution.

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

Re: [Freesurfer] Contents of Freesurfer digest Vol 200, Issue 28 error trac all prep (Yendiki, Anastasia)

[Camerino, I.L. (Ileana)]

External Email - Use Caution

Hi Anastasia,

Thank you so much for your reply.
I omitted a very important information. I am working with left hemisphere 
stroke data. On a visual check I see that recon all worked well on all the 
participants (big and small lesions).  Although trac all worked for some 
participants with a smaller lesion, I suspect this failure may be due to the 
presence of a bigger lesion. In order to test if this is the case, I could 
perform trac all only on the right hemisphere.  Can you tell me how to perform 
tracall only on the right hemisphere? I tried to edit the config file but it 
did not work. 
Please,  let me know if you have other suggestions on what can go wrong as well.

Thank you in advance
Best regards
Ileana

Ileana Camerino
 
PhD candidate 
Donders Institute for Brain, Cognition and Behaviour
 
Centre for Cognition
Spinozabuilding 
Room B02.25
Montessorilaan 3, 6525 HR Nijmegen
The Netherlands
Tel. +31-24 3612618
 
 
 
 

On 14/10/2020, 18:01, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
freesurfer-requ...@nmr.mgh.harvard.edu"  wrote:

Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu

To subscribe or unsubscribe via the World Wide Web, visit
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
freesurfer-requ...@nmr.mgh.harvard.edu

You can reach the person managing the list at
freesurfer-ow...@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

   1. Re: error trac all prep (Yendiki, Anastasia)
   2. Postdoc and PhD positions @ BrainLENS Lab w/ Fumiko   Hoeft
  {Disarmed} (Jieyin Feng)
   3. Help with creating contrast matrix - 6 classes and 3
  variables (Paul Dhami)
   4. Reliability and sensitivity of two whole-brain segmentation
  approaches ? ASEG and SAMSEG (Donatas Sederevicius)
   5. tk applications failing to launch on VM (Windows)
  (Mcnorgan, Christopher)


--

Message: 1
Date: Tue, 13 Oct 2020 20:20:03 +
From: "Yendiki, Anastasia" 
Subject: Re: [Freesurfer] error trac all prep
To: "Freesurfer@nmr.mgh.harvard.edu" 
Message-ID:



Content-Type: text/plain; charset="us-ascii"

Hi Ileana - It looks like it fails on the left uncinate. Is there any 
artifact or missing part of the brain or brain mask, either in the diffusion 
scan or the T1 scan, in a location that would affect the uncinate?

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Camerino, I.L. (Ileana) 

Sent: Tuesday, October 13, 2020 11:12 AM
To: Freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] error trac all prep


External Email - Use Caution





Hello FreeSurfer Developers,

I'm attempting to run the tractography analyses as described on the Tracula 
tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula), I 
tried the all pipeline for one subject and it worked. I tried to run in 
parallel for the rest of the subjects and for three of them I get the following 
error when I run the trac all -prep command:

#!/bin/bash
export FREESURFER_HOME=/opt/freesurfer/6.0;
source $FREESURFER_HOME/SetUpFreeSurfer.sh;
export SUBJECT_DIR=$/project/3015068.01/ilecam/Reolang/Freesurfer
for i in `cat 
/project/3015068.01/ilecam/Reolang/scripts/list_trac_all_prep2.txt`; do 
trac-all -prep -c 
/project/3015068.01/ilecam/Reolang/Freesurfer/${i}/Tracula_out/tracula_config.txt;
 done


here below the content of trac-all.eror
--
SUBJECT sub-056
DATE Fri Oct  9 16:18:01 CEST 2020
USER ilecam
HOST dccn-c029.dccn.nl
PROCESSOR x86_64
OS Linux
Linux dccn-c029.dccn.nl 4.19.94-300.el7.x86_64 #1 SMP Thu Jan 9 16:15:13 
UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
$Id: trac-preproc,v 1.54.2.2 2016/12/27 16:47:14 zkaufman Exp $
/opt/freesurfer/6.0/bin/trac-preproc
PWD /project/3015068.01/ilecam/Reolang/scripts
CMD /opt/freesurfer/6.0/bin/dmri_train --outdir 
/project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/Tracula_out/sub-056/dlabel/mni
 --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr 
rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr 
fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr 
rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr 
lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr 
rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr 

[Freesurfer] Subject cluster mean values from ocn.dat do not show the expected group difference

[Julian Macoveanu]

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?

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?

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 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

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

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

[Julian Macoveanu]

External Email - Use Caution

Sorry I had to re-posted this since since it quickly moved down the
list without an answer

Julian Macoveanu Thu, 22 Oct 2020 00:59:50 -0700

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?

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?

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 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

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