[Freesurfer] Updated Ubuntu 18 VM image with Freesurfer 7.2.0 release pre-installed

[fsbuild]

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The Ubuntu 18 VM image with the terminal shell environment set out of the box 
to use the pre-installed freesurfer 7.2.0 release - is back online. While 
the functionality of the release is unchanged, the new image is:- named with 
7_2_0 to distinguish it from future releases- a bit smaller in size and may run 
faster depending upon your hardware- expanded a bit differently

Please see the wiki page for details, 
https://secure-web.cisco.com/1yIC-PbRjEF1VSkLF8fML6h4gueEGDMqWNEbYP-pGBkGm0FvN9DvXgvUICkwog0XvCqXfhOj7VoHGkadyze4yTWAz04uiWSHaJStdGjuASLPL5cOw8rLny2aV6iNLaoOmjbN9-PU3-zcEC3qX3KoNoySg3In7eK8N8ZMMBvI-mLDdrq9jD4rTIk-ez6LtKc4foECsmyTjGX7J--lntItTSN8DPj0QrIua0tHTgy8H6hGp91PAFbMzxfBeFqCz46xtkdvrhV7IMsZnRiGYkHjyYQBhICdo4a-TN5tZXjRqwLMRyWAkIoJJfqY5QAzuU-cPtBY8y8imMSLdylBhm2ghdg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67
Happy to address any inquiries.
- R.

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[Freesurfer] mri_vol2vol anatomical to functional

[Manenti, Giorgio]

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Dear Freesurfer experts, 

I am getting problems to transform my xh.ribbon.mgh from anatomical 256x256x256 
to functional 104x104x69 space. 

When converting the ribbon via “ mri_vol2vol —reg REGfile —mov INPUT —targ 
funcTEMPLATE —o OUTPUT “ and checking via freeview, i am getting the right 
functional space dimensions but the INPUT and OUTPUT .mgz are never 
overlapping. Why am i getting this misplacement ? Is this problem due to the 
register file i provide or maybe it is just a visualisation error (perhaps 
freeview is not the best way to check the conversion). 

I tried to change REGfile by providing the 1) init.register.dof6.dat and 2) 
register.dof6.lta (changing “—reg with —lta”). I am getting an almost perfect 
merge when using the .lta file but still the two volumes are misaligned. 
I tried mri_label2vol as well, but as expected i got worse results. 

To provide a minimum more detail, after recon-all i process the anatomy with 
the longitudinal recon. At that point i use the longitudinal anatomy to 
register the functional data, which i process by 1) mk-template 2) topup & 
applytopup. 

Many thanks in advance 
Warm regards

Giorgio

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Re: [Freesurfer] bedpostx error inside trac-all

[Yendiki, Anastasia]

If you want to run it locally, then yes, running plain bedpostx should work.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Mirro, Amy 

Sent: Wednesday, March 23, 2022 11:17 AM
To: Freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] bedpostx error inside trac-all


External Email - Use Caution

Thanks so much for the quick response!

Mimicking the behavior of a local run was my goal. Right now, I run all three 
"portions" of trac-all in one script (using the python code shown below):

 # call each step in tracula
trac_all_prep_call = ["trac-all", "-prep", "-c", f"{config_file}", "-log", 
f"{prep_log_file}"]
trac_all_bed_call = ["trac-all", "-bedp", "-c", f"{config_file}", "-log", 
f"{bed_log_file}"]
trac_all_path_call = ["trac-all", "-path", "-c" , f"{config_file}", "-log", 
f"{path_log_file}"]
for trac_call in [trac_all_prep_call, trac_all_bed_call, 
trac_all_path_call]:
o= subprocess.run(trac_call)

So my goal when suggesting that change was to have the trac-all -bedp command 
work when the onpbs variable is False. However, it sounds like you are saying 
that in order to run bedpost not on a cluster I need to do so "outside" of 
trac-all. So, should I replace the trac_all_bed_call above with something like:

bedpost -n $nstick -model 1 /path/to/subjects/dmri/directory

Would that work? Sorry if I am misunderstanding. Thanks so much for your help!

Thanks,
Amy



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

Sent: Wednesday, March 23, 2022 9:10 AM
To: Freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] bedpostx error inside trac-all


* External Email - Caution *

Hi Amy - This will have the same effect as running it locally. All the the 
*_mgh version does is submit each slice as a separate job on a certain type of 
cluster. If you run trac-all with --jobs  , it will save a text file 
with the commands that would've been submitted as jobs, instead of actually 
trying to submit them. Then you can submit them to a cluster yourself, using 
the syntax that's specific to your cluster.

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Mirro, Amy 

Sent: Wednesday, March 23, 2022 10:04 AM
To: Freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] bedpostx error inside trac-all


External Email - Use Caution

Hello,

I am trying to run trac-all -bedp and I am running into the following error:


/opt/freesurfer/bin/bedpostx_mgh: 128: /opt/freesurfer/bin/bedpostx_mgh: Syntax 
error: "(" unexpected

Others have encountered this error previously, and you had advised running 
bedpostx locally (as oppsoed to bedpostx_mgh). I was wondering, however, if 
there is a way to still run bedpostx inside trac-all.

I was looking at the source code for trac-all in your github (branch 7.2), and 
I noticed that line 611 calls bedpostx_mgh despite being within the "if (! 
$onpbs)" conditional. Would changing line 611 from:

  set cmd = (bedpostx_mgh -n $nstick -model 1 $dtdir/dmri)
to
  set cmd = (bedpostx -n $nstick -model 1 $dtdir/dmri)

fix the problem?

If it's helpful:
I am running on centos7 and my build stamp is: 
freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b

Thanks,
Amy





The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.





The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
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Re: [Freesurfer] bedpostx error inside trac-all

[Mirro, Amy]

External Email - Use Caution

Thanks so much for the quick response!

Mimicking the behavior of a local run was my goal. Right now, I run all three 
"portions" of trac-all in one script (using the python code shown below):

 # call each step in tracula
trac_all_prep_call = ["trac-all", "-prep", "-c", f"{config_file}", "-log", 
f"{prep_log_file}"]
trac_all_bed_call = ["trac-all", "-bedp", "-c", f"{config_file}", "-log", 
f"{bed_log_file}"]
trac_all_path_call = ["trac-all", "-path", "-c" , f"{config_file}", "-log", 
f"{path_log_file}"]
for trac_call in [trac_all_prep_call, trac_all_bed_call, 
trac_all_path_call]:
o= subprocess.run(trac_call)

So my goal when suggesting that change was to have the trac-all -bedp command 
work when the onpbs variable is False. However, it sounds like you are saying 
that in order to run bedpost not on a cluster I need to do so "outside" of 
trac-all. So, should I replace the trac_all_bed_call above with something like:

bedpost -n $nstick -model 1 /path/to/subjects/dmri/directory

Would that work? Sorry if I am misunderstanding. Thanks so much for your help!

Thanks,
Amy



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

Sent: Wednesday, March 23, 2022 9:10 AM
To: Freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] bedpostx error inside trac-all


* External Email - Caution *

Hi Amy - This will have the same effect as running it locally. All the the 
*_mgh version does is submit each slice as a separate job on a certain type of 
cluster. If you run trac-all with --jobs  , it will save a text file 
with the commands that would've been submitted as jobs, instead of actually 
trying to submit them. Then you can submit them to a cluster yourself, using 
the syntax that's specific to your cluster.

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Mirro, Amy 

Sent: Wednesday, March 23, 2022 10:04 AM
To: Freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] bedpostx error inside trac-all


External Email - Use Caution

Hello,

I am trying to run trac-all -bedp and I am running into the following error:


/opt/freesurfer/bin/bedpostx_mgh: 128: /opt/freesurfer/bin/bedpostx_mgh: Syntax 
error: "(" unexpected

Others have encountered this error previously, and you had advised running 
bedpostx locally (as oppsoed to bedpostx_mgh). I was wondering, however, if 
there is a way to still run bedpostx inside trac-all.

I was looking at the source code for trac-all in your github (branch 7.2), and 
I noticed that line 611 calls bedpostx_mgh despite being within the "if (! 
$onpbs)" conditional. Would changing line 611 from:

  set cmd = (bedpostx_mgh -n $nstick -model 1 $dtdir/dmri)
to
  set cmd = (bedpostx -n $nstick -model 1 $dtdir/dmri)

fix the problem?

If it's helpful:
I am running on centos7 and my build stamp is: 
freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b

Thanks,
Amy





The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
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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 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
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receiving this message means you understand and accept this risk and wish to 
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Re: [Freesurfer] mri_segment_hypothalamic_subunits error: Illegal instruction 4

[Iglesias Gonzalez, Juan E.]

Dear Alice,

Can you please send us your full command line and output?

Cheers,

/E


Juan Eugenio Iglesias
http://www.jeiglesias.com

On Mar 23, 2022, at 10:41, Alice Tao 
mailto:ajt4...@med.cornell.edu>> wrote:

External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to use the mri_segment_hypothalamic_subunits tool on subjects 
that have been analyzed with recon-all as described on the wiki page 
(https://surfer.nmr.mgh.harvard.edu/fswiki/HypothalamicSubunits), but I 
received the following error when I run the mri_segment_hypothalamic_subunits 
command (mri_segment_hypothalamic_subunits--s):

  Illegal instruction: 4

Does anyone have any suggestions on how to trouble-shoot this problem? 
recon-all does not seem to have any issues.

1) FreeSurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
2) Platform: macOS Monterey, version 12.2.1

Thank you!
Alice
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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 https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] bedpostx error inside trac-all

[Yendiki, Anastasia]

Hi Amy - This will have the same effect as running it locally. All the the 
*_mgh version does is submit each slice as a separate job on a certain type of 
cluster. If you run trac-all with --jobs  , it will save a text file 
with the commands that would've been submitted as jobs, instead of actually 
trying to submit them. Then you can submit them to a cluster yourself, using 
the syntax that's specific to your cluster.

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Mirro, Amy 

Sent: Wednesday, March 23, 2022 10:04 AM
To: Freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] bedpostx error inside trac-all


External Email - Use Caution

Hello,

I am trying to run trac-all -bedp and I am running into the following error:


/opt/freesurfer/bin/bedpostx_mgh: 128: /opt/freesurfer/bin/bedpostx_mgh: Syntax 
error: "(" unexpected

Others have encountered this error previously, and you had advised running 
bedpostx locally (as oppsoed to bedpostx_mgh). I was wondering, however, if 
there is a way to still run bedpostx inside trac-all.

I was looking at the source code for trac-all in your github (branch 7.2), and 
I noticed that line 611 calls bedpostx_mgh despite being within the "if (! 
$onpbs)" conditional. Would changing line 611 from:

  set cmd = (bedpostx_mgh -n $nstick -model 1 $dtdir/dmri)
to
  set cmd = (bedpostx -n $nstick -model 1 $dtdir/dmri)

fix the problem?

If it's helpful:
I am running on centos7 and my build stamp is: 
freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b

Thanks,
Amy





The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] bedpostx error inside trac-all

[Mirro, Amy]

External Email - Use Caution

Hello,

I am trying to run trac-all -bedp and I am running into the following error:


/opt/freesurfer/bin/bedpostx_mgh: 128: /opt/freesurfer/bin/bedpostx_mgh: Syntax 
error: "(" unexpected

Others have encountered this error previously, and you had advised running 
bedpostx locally (as oppsoed to bedpostx_mgh). I was wondering, however, if 
there is a way to still run bedpostx inside trac-all.

I was looking at the source code for trac-all in your github (branch 7.2), and 
I noticed that line 611 calls bedpostx_mgh despite being within the "if (! 
$onpbs)" conditional. Would changing line 611 from:

  set cmd = (bedpostx_mgh -n $nstick -model 1 $dtdir/dmri)
to
  set cmd = (bedpostx -n $nstick -model 1 $dtdir/dmri)

fix the problem?

If it's helpful:
I am running on centos7 and my build stamp is: 
freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b

Thanks,
Amy


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
___
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Freesurfer@nmr.mgh.harvard.edu
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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 https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
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[Freesurfer] qdec analysis error

[David]

External Email - Use Caution

Hello FreeSurfer Developers,

I have a problem. Can you help me

freesurfer version : 6.0.0

Load qdec when I run qdec.table.dat, the data is loaded correctly, but when I 
design, I choose discrete and continuous factors for analysis
The error log is as follows
：

Input table: /media/root/Backup_Plus2/new/RECON/qdec/qdec5.table.dat
Subj#, SubjID, Data...
1 bd1 d Male 15.00 8.00
2 bd2 d Female 19.00 13.00
3 bd3 d Male 25.00 9.00
4 bd4 d Male 17.00 12.00
5 bd5 d Male 16.00 10.00
6 bd6 m Female 22.00 12.00
7 bd7 d Male 17.00 11.00
8 bd8 d Female 19.00 13.00
9 bd9 m Female 26.00 7.00
   10 bd10 m Male 53.00 15.00
   11 bd11 m Female 56.00 4.00
   12 bd12 d Female 21.00 14.00
   13 bd13 m Female 19.00 12.00
   14 bd14 m Female 32.00 15.00
   15 bd15 d Male 21.00 9.00
   16 bd16 d Male 16.00 10.00
   17 bd17 d Male 15.00 11.00
   18 bd18 d Female 32.00 10.00
   19 bd19 d Female 20.00 15.00
   20 bd20 d Female 17.00 11.00
   21 bd22 m Male 22.00 11.00
   22 bd23 m Female 28.00 6.00
   23 bd24 d Male 26.00 11.00
   24 bd25 m Female 24.00 9.00
   25 bd26 m Female 30.00 6.00
   26 bd27 m Female 20.00 12.00
   27 bd28 d Female 28.00 16.00
   28 bd29 m Female 18.00 12.00
   29 bd30 d Male 21.00 15.00
   30 bd31 d Female 30.00 16.00
   31 bd32 d Male 18.00 11.00
   32 bd33 d Female 16.00 10.00
   33 bd34 d Male 21.00 11.00
   34 bd35 d Female 15.00 10.00
   35 bd36 d Female 16.00 10.00
   36 bd37 d Male 19.00 14.00
   37 bd39 d Male 16.00 10.00
   38 bd40 m Female 20.00 14.00
   39 bd41 m Female 21.00 15.00
   40 bd42 d Male 23.00 9.00
   41 bd43 m Male 27.00 9.00
   42 bd44 d Female 15.00 8.00
   43 bd45 m Male 19.00 9.00
   44 bd46 d Female 16.00 11.00
   45 bd47 m Female 23.00 15.00
   46 bd48 m Male 18.00 13.00
   47 bd49 d Female 22.00 15.00
   48 bd50 d Female 17.00 11.00
   49 bd51 d Male 17.00 10.00
   50 bd52 d Male 27.00 15.00
   51 bd53 m Male 16.00 9.00
   52 bd54 d Male 18.00 12.00
   53 bd55 d Female 18.00 11.00
   54 bd56 m Female 16.00 10.00
   55 bd57 d Male 16.00 9.00
   56 bd58 m Male 22.00 9.00
   57 bd59 m Male 16.00 8.00
   58 bd60 d Male 16.00 9.00
   59 bd61 m Female 18.00 10.00
   60 bd62 d Female 15.00 9.00
   61 hc1 h Male 52.00 7.00
   62 hc2 h Female 24.00 10.00
   63 hc3 h Male 45.00 7.00
   64 hc4 h Female 18.00 13.00
   65 hc5 h Female 19.00 10.00
   66 hc6 h Female 17.00 12.00
   67 hc7 h Female 19.00 7.00
   68 hc8 h Male 48.00 5.00
   69 hc9 h Female 53.00 6.00
   70 hc10 h Female 52.00 15.00
   71 hc11 h Female 19.00 12.00
   72 hc12 h Female 18.00 12.00
   73 hc13 h Female 20.00 12.00
   74 hc14 h Female 18.00 12.00
   75 hc15 h Female 19.00 13.00
   76 hc16 h Female 18.00 11.00
   77 hc17 h Female 19.00 12.00
   78 hc18 h Female 19.00 12.00
   79 hc19 h Female 19.00 12.00
   80 hc20 h Female 19.00 12.00
   81 hc21 h Female 18.00 12.00
   82 hc22 h Female 18.00 12.00
   83 hc23 h Female 18.00 11.00
   84 hc24 h Female 18.00 12.00
   85 hc25 h Female 18.00 12.00
   86 hc26 h Female 18.00 11.00
   87 hc27 h Female 18.00 12.00
   88 hc28 h Female 18.00 12.00
   89 hc29 h Female 18.00 11.00
   90 hc30 h Male 20.00 12.00
   91 hc31 h Female 29.00 17.00
   92 hc32 h Female 16.00 10.00
   93 hc33 h Female 17.00 10.00
   94 hc34 h Female 26.00 14.00
   95 hc35 h Female 24.00 17.00
   96 hc36 h Female 22.00 17.00
   97 hc37 h Male 25.00 17.00
   98 hc38 h Male 24.00 17.00
   99 hc39 h Male 25.00 17.00
1  groups  discrete 3
1  d
2  m
3  h
2  gender  discrete 2
1  Male
2  Female
3  age  continuous 0
4  edu  continuous 0
Continuous Factors: Mean:   StdDev:
--- -   ---
age22.293 9.015
edu11.374 2.827

Number of subjects:   99
Number of factors:4 (2 discrete, 2 continuous)
Number of classes:6
Number of regressors: 18

Data table loading completed successfully.
SUBJECTS_DIR is '/media/root/Backup_Plus2/new/RECON'
ERROR: QdecGlmDesign::GenerateContrasts: factor 1 

[Freesurfer] Negative eTIV

[lqcheng2017]

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Dear experts,I extracted the eTIV using the mri_segstats, but it showed negative value. How could I solve this problem?Thank you very much.cmdline mri_segstats --subject Gelb --etiv-only UseRobust  0atlas_icv (eTIV) = -2105 mm^3    (det: -925.465454 )Best,Luqi




 



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