Re: [Freesurfer] mri_glmfit-sim error

[Douglas N. Greve]

Yes, all the 7.X versions will give the same answer unless you 
explicitly use a new feature


On 3/20/2023 2:45 PM, mariangela asimina wrote:


External Email - Use Caution

I see now this is an issue addressed stable 7.2.0 version of FreeSurfer:
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes 
<https://secure-web.cisco.com/1_0nM8kQPAwlCZzUFPKYxFeyxAfrBfjVnMbuFBgpiLtOtAz0Rcg2ns0AHK0Z-UuAC0K-jylD0ZM1hP4emJWrKoCvyUwJv4VVaznUFGMKUwg5OuApejYTaxHdKuzNe5HOOGskw2aVkgC0HOeyCPniLzoA5MSfRjpv1RfRJdNli3dKvwIjsY48WuxJT69HBkSXeu374bWB2rlhnP3OpNcmqdmIzR2dm46aiVRBcm3JvbkQLgtvhZeadmj2hfxQUQPDJYVfkQcP70pazbHOft-_rcNzvPKYmvvAAelzNeTuwNBoa1gQT-rqipRmHUXA8AhgFoON7c7sEJ06rpAXxn2QgBw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes>


mri_glmfit-sim

  * Fixed locale issue to handle cases where decimal points are
represented by commas.


Is it ok to install the newest version (7.3.2) and run mri_glmfit-sim 
on data made with the version I used?
Is it ok to troubleshoot the recon-all output that I already have, 
after installing the newer version? Or would I have to run the 
recon-all again?


Lastly, if the answer to the above is negative, is it possible to 
solve the issue with the commas on the version I am using?


Thank you!
Mariangela




*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of mariangela 
asimina 

*Sent:* Monday, March 20, 2023 8:13 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* [Freesurfer] mri_glmfit-sim error

External Email - Use Caution

Hello FreeSurfer developers and experts,

I am trying to do cluster correction with mri_glmfit-sim after running 
mri_glmfit.


The command I ran:
  mri_glmfit-sim --glmdir lh.volume.SCNStudyTest.10.glmdir --cache 
3.0 abs --cwp 0.05 --2spaces


produces the following error:
  ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0

FreeSurfer version: 
freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b

Operating System: Ubuntu 22.04.2 LTS
Kernel: Linux 5.19.0-35-generic


I have searched the archive and cannot find a similar error.
I would appreciate your help.


Mariangela Asimina


I also ran the command with the --debug flag and I get the following 
output, but I'm afraid I can't interpret it:

set echo = 1 ;
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 8 != 0 )

set flag = $argv[1] ; shift ;
set flag = --glmdir
shift

switch ( $flag )
switch ( --glmdir )
if ( $#argv < 0 ) goto arg1err ;
if ( 7 < 0 ) goto arg1err
set glmdir = $argv[1] ; shift ;
set glmdir = lh.volume.SCNStudyTest.10.glmdir
shift
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 6 != 0 )

set flag = $argv[1] ; shift ;
set flag = --cache
shift

switch ( $flag )
switch ( --cache )
if ( $#argv < 2 ) goto arg2err ;
if ( 5 < 2 ) goto arg2err
set thresh = $argv[1] ; shift ;
set thresh = 3.0
shift
set simsign = $argv[1] ; shift ;
set simsign = abs
shift
set UseCache = 1 ;
set UseCache = 1
set DoSim = 0 ;
set DoSim = 0

set thresh = `echo $thresh | sed 's/,/./g'`
set thresh = `echo $thresh | sed 's/,/./g'`
sed s/,/./g
echo 3.0
set thresh = `printf %2.1f $thresh`
set thresh = `printf %2.1f $thresh`
printf %2.1f 3.0
if ( $thresh != 1.3 && $thresh != 2.0 && $thresh != 2.3 && $thresh != 
3.0 && $thresh != 3.3 && $thresh != 4.0 ) then
if ( 3,0 != 1.3 && 3,0 != 2.0 && 3,0 != 2.3 && 3,0 != 3.0 && 3,0 != 
3.3 && 3,0 != 4.0 ) then

echo "ERROR: thresh = $thresh, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0"
echo ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
exit 1 ;
exit 1


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Re: [Freesurfer] mri_glmfit-sim error

[mariangela asimina]

External Email - Use Caution

I see now this is an issue addressed stable 7.2.0 version of FreeSurfer:
https://secure-web.cisco.com/1_0nM8kQPAwlCZzUFPKYxFeyxAfrBfjVnMbuFBgpiLtOtAz0Rcg2ns0AHK0Z-UuAC0K-jylD0ZM1hP4emJWrKoCvyUwJv4VVaznUFGMKUwg5OuApejYTaxHdKuzNe5HOOGskw2aVkgC0HOeyCPniLzoA5MSfRjpv1RfRJdNli3dKvwIjsY48WuxJT69HBkSXeu374bWB2rlhnP3OpNcmqdmIzR2dm46aiVRBcm3JvbkQLgtvhZeadmj2hfxQUQPDJYVfkQcP70pazbHOft-_rcNzvPKYmvvAAelzNeTuwNBoa1gQT-rqipRmHUXA8AhgFoON7c7sEJ06rpAXxn2QgBw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes


mri_glmfit-sim

  *   Fixed locale issue to handle cases where decimal points are represented 
by commas.

Is it ok to install the newest version (7.3.2) and run mri_glmfit-sim on data 
made with the version I used?
Is it ok to troubleshoot the recon-all output that I already have, after 
installing the newer version? Or would I have to run the recon-all again?

Lastly, if the answer to the above is negative, is it possible to solve the 
issue with the commas on the version I am using?

Thank you!
Mariangela




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

Sent: Monday, March 20, 2023 8:13 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] mri_glmfit-sim error


External Email - Use Caution

Hello FreeSurfer developers and experts,

I am trying to do cluster correction with mri_glmfit-sim after running 
mri_glmfit.

The command I ran:
  mri_glmfit-sim --glmdir lh.volume.SCNStudyTest.10.glmdir --cache 3.0 abs 
--cwp 0.05 --2spaces

produces the following error:
  ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0

FreeSurfer version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
Operating System: Ubuntu 22.04.2 LTS
Kernel: Linux 5.19.0-35-generic


I have searched the archive and cannot find a similar error.
I would appreciate your help.


Mariangela Asimina


I also ran the command with the --debug flag and I get the following output, 
but I'm afraid I can't interpret it:
set echo = 1 ;
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 8 != 0 )

set flag = $argv[1] ; shift ;
set flag = --glmdir
shift

switch ( $flag )
switch ( --glmdir )
if ( $#argv < 0 ) goto arg1err ;
if ( 7 < 0 ) goto arg1err
set glmdir = $argv[1] ; shift ;
set glmdir = lh.volume.SCNStudyTest.10.glmdir
shift
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 6 != 0 )

set flag = $argv[1] ; shift ;
set flag = --cache
shift

switch ( $flag )
switch ( --cache )
if ( $#argv < 2 ) goto arg2err ;
if ( 5 < 2 ) goto arg2err
set thresh = $argv[1] ; shift ;
set thresh = 3.0
shift
set simsign = $argv[1] ; shift ;
set simsign = abs
shift
set UseCache = 1 ;
set UseCache = 1
set DoSim = 0 ;
set DoSim = 0

set thresh = `echo $thresh | sed 's/,/./g'`
set thresh = `echo $thresh | sed 's/,/./g'`
sed s/,/./g
echo 3.0
set thresh = `printf %2.1f $thresh`
set thresh = `printf %2.1f $thresh`
printf %2.1f 3.0
if ( $thresh != 1.3 && $thresh != 2.0 && $thresh != 2.3 && $thresh != 3.0 && 
$thresh != 3.3 && $thresh != 4.0 ) then
if ( 3,0 != 1.3 && 3,0 != 2.0 && 3,0 != 2.3 && 3,0 != 3.0 && 3,0 != 3.3 && 3,0 
!= 4.0 ) then
echo "ERROR: thresh = $thresh, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0"
echo ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
exit 1 ;
exit 1

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[Freesurfer] mri_glmfit-sim error

[mariangela asimina]

External Email - Use Caution

Hello FreeSurfer developers and experts,

I am trying to do cluster correction with mri_glmfit-sim after running 
mri_glmfit.

The command I ran:
  mri_glmfit-sim --glmdir lh.volume.SCNStudyTest.10.glmdir --cache 3.0 abs 
--cwp 0.05 --2spaces

produces the following error:
  ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0

FreeSurfer version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
Operating System: Ubuntu 22.04.2 LTS
Kernel: Linux 5.19.0-35-generic


I have searched the archive and cannot find a similar error.
I would appreciate your help.


Mariangela Asimina


I also ran the command with the --debug flag and I get the following output, 
but I'm afraid I can't interpret it:
set echo = 1 ;
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 8 != 0 )

set flag = $argv[1] ; shift ;
set flag = --glmdir
shift

switch ( $flag )
switch ( --glmdir )
if ( $#argv < 0 ) goto arg1err ;
if ( 7 < 0 ) goto arg1err
set glmdir = $argv[1] ; shift ;
set glmdir = lh.volume.SCNStudyTest.10.glmdir
shift
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 6 != 0 )

set flag = $argv[1] ; shift ;
set flag = --cache
shift

switch ( $flag )
switch ( --cache )
if ( $#argv < 2 ) goto arg2err ;
if ( 5 < 2 ) goto arg2err
set thresh = $argv[1] ; shift ;
set thresh = 3.0
shift
set simsign = $argv[1] ; shift ;
set simsign = abs
shift
set UseCache = 1 ;
set UseCache = 1
set DoSim = 0 ;
set DoSim = 0

set thresh = `echo $thresh | sed 's/,/./g'`
set thresh = `echo $thresh | sed 's/,/./g'`
sed s/,/./g
echo 3.0
set thresh = `printf %2.1f $thresh`
set thresh = `printf %2.1f $thresh`
printf %2.1f 3.0
if ( $thresh != 1.3 && $thresh != 2.0 && $thresh != 2.3 && $thresh != 3.0 && 
$thresh != 3.3 && $thresh != 4.0 ) then
if ( 3,0 != 1.3 && 3,0 != 2.0 && 3,0 != 2.3 && 3,0 != 3.0 && 3,0 != 3.3 && 3,0 
!= 4.0 ) then
echo "ERROR: thresh = $thresh, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0"
echo ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
exit 1 ;
exit 1

___
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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. 

Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized

[Tarumi Takashi]

External Email - Use Caution

Dear Dr. Yendiki,

Thank you so much for this additional explanation. It’s clear now.

Best regards,
Taka

> 2022/01/21 2:13、Yendiki, Anastasia のメール:
> 
> 
> Yes, the tutorial was written when the 7.2 release was in the last stages of 
> development. What happened between then and the final, released 7.2 was that 
> it now just figures out that the input is 1D by checking the dimensions of 
> the input, so you don't have to specify it on the command line.
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Tarumi Takashi 
> 
> Sent: Thursday, January 20, 2022 7:59 AM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized
>  
> External Email - Use Caution
> 
> Dear Dr. Yendiki,
> 
> Thank you so much for your reply. Yes, the command can run without the "--1d" 
> flag. But, I thought that the flag is "required for any along-tract analysis" 
> as stated in your TraculaStatistics instruction and highlighted in the 
> release notes for v7.2 (added 1D capability for mri_glmfit-sim). I would 
> greatly appreciate for your further clarifications. Thank you so much for 
> your help.
> 
> Best regards,
> Taka
> 
> On Thu, Jan 20, 2022 at 1:09 PM Yendiki, Anastasia  
> wrote:
> Hi Taka - Does it work when you remove the "--1d" from the command line? I 
> think that must be an error in the documentation.
> 
> Anastasia.
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Tarumi Takashi 
> 
> Sent: Wednesday, January 12, 2022 7:04 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized
>  
> External Email - Use Caution
> 
> Dear FreeSurfer Developers:
> 
> I am attempting to perform cluster-wise correction for the along-tract 
> measures, as described on the Tract statistics tutorial (MailScanner has 
> detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 
> https://secure-web.cisco.com/1MfvOB_RivuZacGakSlQntFiJmL3ek2B3qow_L8RuzHu3IW5D2fREF-sQi1qv3m9fC5W8DqHpEr5GP3uI86jIs2FGSd2j6oZRwohX-JENNPLRPc1VueNVOsfVQ-Zy9tMJj23fNN-DUylXWCYZAJaiLvJbv6rizKfL45IJHJmwMXF2rcaRSytczC1HEMx-iBASyUjg4tmaD1b3MkLdCNNjyoJzAT7YEsXcT29Xs3Y5St9-dVPp0Q7Efrl2W05gAQsXxeECJ0y-XlTJctTicvJTzQcUtrp_uchiT7Ejjv0qInvQQYLfdtEqXyzQoo7C6ieDj6X2RTmEIfP0Ig28orvLuA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTraculaStatistics
>  But, when I run the command below, the flag --1d is not recognized.
> 
> Command: mri_glmfit-sim --glmdir cc.bodyp.FA_Avg.glmdir --1d --cwp .05 --perm 
> 1000 1.3 pos
> Error: Flag --1d unrecognized.
> 
> I could not find similar errors reported. Does anyone have any thoughts on 
> how to trouble-shoot this? The FreeSurfer version I'm using is 7.2.0 on an M1 
> Mac machine with macOS 12.1. Thank you so much for your help.
> 
> Sincerely,
> Taka
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
> claiming to be 
> https://secure-web.cisco.com/1JIjyXSqrn8YrXsDtjtj0cK2WrsAOTGEAkFWJvZVr1dC2qHtos6IyBIsz1Pf0Iqa2P2guNAHlc3KkgGVVxTzj_m82ageBpz_oj7ISRBYYudY02_tDEwxxXvF5lVXONUkpg4zkewj0jH4TQE4weXIs18pQwO5E3hUuF02CBUNopytCxfl2s41Xrl5xSm4yD6Rjb3rLZr5DumDOGfy9E4BIfRvEt2Ar6ufDnCLpVzpywI5VHbmqnvRn_JD0OXTvHwRoQYCwbsXzpvrDSYZKCS-O45H8OsQv1WIbODbIcAurDKsKXEOz0uC8CjVJv8tprMh9wJ9pGzDhu46F2c59qG7s1A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> 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 MailScanner has detected a possible fraud attempt from 
> "secure-web.cisco.com" claiming to be 
> http://secure-web.cisco.com/1k-3-r_MrjlGx2tXOpq55YLid6LmRVdQXU5A6ST8MojcEtAP0o2uKfif3yXL07PurH84lRIF0DHdGjpX-1ZGcTb2hs4sx25IAK8eZ2LAo_-_p6McwSfV7Y8qSBI11MFROnynmNzZWP0RvPErHJVUEO2DPv333tFCmTKiiFFJ8YRtiUqsX2dsI14jkpgY4LndQZRIa2ofkPmHicOVaCgphYq0R2WCk-rRBckKcUcXKBFhPvHGM2Eld-ebhVIo_-VGlfVxC_aG4ZY0g-bHnt4lCvDRiNMbplmzRLh3ZyIbYKjHi2v0VHlcFwlESnLsz9T7CpalSK_6wbnKP3Ocj938L4g/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>  . If the e-mail was sent to you in error but does not contain patient 
> information, please contact the sender and properly dispose of the e-mail.
> 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.  C

Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized

[Yendiki, Anastasia]

Yes, the tutorial was written when the 7.2 release was in the last stages of 
development. What happened between then and the final, released 7.2 was that it 
now just figures out that the input is 1D by checking the dimensions of the 
input, so you don't have to specify it on the command line.

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

Sent: Thursday, January 20, 2022 7:59 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized


External Email - Use Caution

Dear Dr. Yendiki,

Thank you so much for your reply. Yes, the command can run without the "--1d" 
flag. But, I thought that the flag is "required for any along-tract analysis" 
as stated in your TraculaStatistics instruction and highlighted in the release 
notes for v7.2 (added 1D capability for mri_glmfit-sim). I would greatly 
appreciate for your further clarifications. Thank you so much for your help.

Best regards,
Taka

On Thu, Jan 20, 2022 at 1:09 PM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Taka - Does it work when you remove the "--1d" from the command line? I 
think that must be an error in the documentation.

Anastasia.

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Tarumi Takashi mailto:tak...@gmail.com>>
Sent: Wednesday, January 12, 2022 7:04 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized


External Email - Use Caution

Dear FreeSurfer Developers:

I am attempting to perform cluster-wise correction for the along-tract 
measures, as described on the Tract statistics tutorial (MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics<https://secure-web.cisco.com/1k_UHTgDkMyztiBV5VO6PazEUkIHIp4tFCos8o1vMfT5XasrL80AhnLun3nO3SbemuhiScR_HhzrdGaw0p1j5nK5lhe10k7-lPaCijiC0Vh7MQ0yuekVDkLDVrJqmG8Iv7dJngPrQuEM0Hi8ZnXXatPZFWA1aWQoWHkUSICt5kTu0nJuvpZHOUVg_RNMdlWUhH2kGUUGxeihwX0Nt22xOH5wPY2jNspczuzK2y2bSu-wVlXPvrnE1NXoh1Xk07_LOqY3hqWmAMeIEzH8SYeketuWolK-kKBMySEzU8Qcf85MkxF8ulxY7sh4wOn1doxI61CJ2S55Gnkqug92Kav4Oew/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTraculaStatistics>).
 But, when I run the command below, the flag --1d is not recognized.

Command: mri_glmfit-sim --glmdir cc.bodyp.FA_Avg.glmdir --1d --cwp .05 --perm 
1000 1.3 pos
Error: Flag --1d unrecognized.

I could not find similar errors reported. Does anyone have any thoughts on how 
to trouble-shoot this? The FreeSurfer version I'm using is 7.2.0 on an M1 Mac 
machine with macOS 12.1. Thank you so much for your help.

Sincerely,
Taka
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
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Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized

[Tarumi Takashi]

External Email - Use Caution

Dear Dr. Yendiki,

Thank you so much for your reply. Yes, the command can run without the
"--1d" flag. But, I thought that the flag is "required for any along-tract
analysis" as stated in your TraculaStatistics instruction and highlighted
in the release notes for v7.2 (added 1D capability for mri_glmfit-sim). I
would greatly appreciate for your further clarifications. Thank you so much
for your help.

Best regards,
Taka

On Thu, Jan 20, 2022 at 1:09 PM Yendiki, Anastasia 
wrote:

> Hi Taka - Does it work when you remove the "--1d" from the command line? I
> think that must be an error in the documentation.
>
> Anastasia.
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Tarumi Takashi <
> tak...@gmail.com>
> *Sent:* Wednesday, January 12, 2022 7:04 PM
> *To:* freesurfer@nmr.mgh.harvard.edu 
> *Subject:* [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized
>
>
> External Email - Use Caution
>
> Dear FreeSurfer Developers:
>
> I am attempting to perform cluster-wise correction for the along-tract
> measures, as described on the Tract statistics tutorial (*MailScanner has
> detected a possible fraud attempt from "secure-web.cisco.com" claiming to
> be* 
> https://secure-web.cisco.com/14xTl-nXfhrT5s1HVQuP9A9vkMOy3hcNKfB2a4mLefQS6dl6-aqoECeHaosa2LFWdLTjGO9Fy1kpdjM631BpxovShFWZZnQP-Dhdr006lWhdN-X6ybWNDqx6uSWRU5YWSDVYXJgieK0q39yS1emZyDSqxj6jNaEcWN-5cwAEmoIVCE7D3-RJanSNI6Y0iBm7_FJQA64D0dGcvdndr0MX26xv_TB1PK0yL_ZbmoLx7M03L4-QTP3ky_P2xLnlWnkIdLXLbDrDPUsHQCR_om50OzamOsL2Xoz19qWPFmM38lhRQh0eJesWJzbQwhwh0WQyEAY2SL9gQ06L1NaykAWbh0Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTraculaStatistics
> <https://secure-web.cisco.com/1k_UHTgDkMyztiBV5VO6PazEUkIHIp4tFCos8o1vMfT5XasrL80AhnLun3nO3SbemuhiScR_HhzrdGaw0p1j5nK5lhe10k7-lPaCijiC0Vh7MQ0yuekVDkLDVrJqmG8Iv7dJngPrQuEM0Hi8ZnXXatPZFWA1aWQoWHkUSICt5kTu0nJuvpZHOUVg_RNMdlWUhH2kGUUGxeihwX0Nt22xOH5wPY2jNspczuzK2y2bSu-wVlXPvrnE1NXoh1Xk07_LOqY3hqWmAMeIEzH8SYeketuWolK-kKBMySEzU8Qcf85MkxF8ulxY7sh4wOn1doxI61CJ2S55Gnkqug92Kav4Oew/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTraculaStatistics>).
> But, when I run the command below, the flag --1d is not recognized.
>
> Command: mri_glmfit-sim --glmdir cc.bodyp.FA_Avg.glmdir --1d --cwp .05
> --perm 1000 1.3 pos
> Error: Flag --1d unrecognized.
>
> I could not find similar errors reported. Does anyone have any thoughts on
> how to trouble-shoot this? The FreeSurfer version I'm using is 7.2.0 on an
> M1 Mac machine with macOS 12.1. Thank you so much for your help.
>
> Sincerely,
> Taka
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized

[Yendiki, Anastasia]

Hi Taka - Does it work when you remove the "--1d" from the command line? I 
think that must be an error in the documentation.

Anastasia.

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

Sent: Wednesday, January 12, 2022 7:04 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized


External Email - Use Caution

Dear FreeSurfer Developers:

I am attempting to perform cluster-wise correction for the along-tract 
measures, as described on the Tract statistics tutorial (MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics<https://secure-web.cisco.com/1k_UHTgDkMyztiBV5VO6PazEUkIHIp4tFCos8o1vMfT5XasrL80AhnLun3nO3SbemuhiScR_HhzrdGaw0p1j5nK5lhe10k7-lPaCijiC0Vh7MQ0yuekVDkLDVrJqmG8Iv7dJngPrQuEM0Hi8ZnXXatPZFWA1aWQoWHkUSICt5kTu0nJuvpZHOUVg_RNMdlWUhH2kGUUGxeihwX0Nt22xOH5wPY2jNspczuzK2y2bSu-wVlXPvrnE1NXoh1Xk07_LOqY3hqWmAMeIEzH8SYeketuWolK-kKBMySEzU8Qcf85MkxF8ulxY7sh4wOn1doxI61CJ2S55Gnkqug92Kav4Oew/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTraculaStatistics>).
 But, when I run the command below, the flag --1d is not recognized.

Command: mri_glmfit-sim --glmdir cc.bodyp.FA_Avg.glmdir --1d --cwp .05 --perm 
1000 1.3 pos
Error: Flag --1d unrecognized.

I could not find similar errors reported. Does anyone have any thoughts on how 
to trouble-shoot this? The FreeSurfer version I'm using is 7.2.0 on an M1 Mac 
machine with macOS 12.1. Thank you so much for your help.

Sincerely,
Taka
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[Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized

[Tarumi Takashi]

External Email - Use Caution

Dear FreeSurfer Developers:

I am attempting to perform cluster-wise correction for the along-tract
measures, as described on the Tract statistics tutorial (
https://secure-web.cisco.com/1k_UHTgDkMyztiBV5VO6PazEUkIHIp4tFCos8o1vMfT5XasrL80AhnLun3nO3SbemuhiScR_HhzrdGaw0p1j5nK5lhe10k7-lPaCijiC0Vh7MQ0yuekVDkLDVrJqmG8Iv7dJngPrQuEM0Hi8ZnXXatPZFWA1aWQoWHkUSICt5kTu0nJuvpZHOUVg_RNMdlWUhH2kGUUGxeihwX0Nt22xOH5wPY2jNspczuzK2y2bSu-wVlXPvrnE1NXoh1Xk07_LOqY3hqWmAMeIEzH8SYeketuWolK-kKBMySEzU8Qcf85MkxF8ulxY7sh4wOn1doxI61CJ2S55Gnkqug92Kav4Oew/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTraculaStatistics
But, when I run the command below, the flag --1d is not recognized.

Command: mri_glmfit-sim --glmdir cc.bodyp.FA_Avg.glmdir --1d --cwp .05
--perm 1000 1.3 pos
Error: Flag --1d unrecognized.

I could not find similar errors reported. Does anyone have any thoughts on
how to trouble-shoot this? The FreeSurfer version I'm using is 7.2.0 on an
M1 Mac machine with macOS 12.1. Thank you so much for your help.

Sincerely,
Taka
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] mri_glmfit-sim error

[Douglas N. Greve]

This happens because the cached p-values were generated from a 
simulation that only went up to 30mm FWHM of smoothing. lGI has lots of 
internal smoothness which often pushes it over this level. You can try 
not using any smoothing, or, even better, try using permutation instead. 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm


On 8/3/2021 11:56 AM, Harriet Cornwell wrote:


External Email - Use Caution

External Email - Use Caution

Hi FreeSurfer team,

I am currently trying to run a correlational analysis in FreeSurfer. I 
am able to run the preproc and mri_glmfit commands successfully, but I 
am getting error messages when running mri_glmfit-sim for lGI, 
thickness and area. An example error message is: ERROR: cannot find 
/usr/local/freesurfer6/freesurfer//average/mult-comp-cor/fsaverage/rh/cortex/fwhm55/abs/th40/mc-z.csd. 
I have attached the full terminal output so that you can see the 
variations of this error message that I am getting. Are you able to 
advise what the issue might be and how I might go about fixing the 
issue? Just for reference, I am using a smoothing value of 10 for 
volume, area and thickness, and 5 for lGI. I would also be happy to 
share my design matrix and scripts if that would make the 
troubleshooting easier.


Thank you in advance for any help you can offer.

Best wishes,

*Harriet Cornwell*

PhD Student | Department of Psychology

University of Bath | 10 West 2.08


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The information in this e-mail is intended only for the person to whom it is 
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contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If 
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Re: [Freesurfer] mri_glmfit-sim error with no csd files generated

[Na, Xiaoxu]

External Email - Use Caution

Thank you for your confirmation! I tried the -perm as well and this error 
wouldn't show after using the csd files generated from permutation.

However, I have one more question. Shall I use -perm first in order to use 
-cache? If this is the case, the pial_lgi features went through well using the 
permutation, but once I tried -cache afterward, it showed the error as below 
with fwhm larger than 30, is there something wrong with the design? I don't 
understand quite much how this fwhm became this large by the way.
Thank you so much!


cmdline mri_glmfit --y sAnalysis/rh.pial_lgi.g2v2DSleepiness.10.mgh --fsgd 
sAnalysis/g2v2DSleepiness.fsgd dods --C sAnalysis/g1g2.sleepscore.mtx --surf 
fsaverage rh --cortex --glmdir sAnalysis/rh.pial_lgi.g2v2DSleepiness.10.glmdir 
--eres-save
SURFACE: fsaverage rh
log file is 
sAnalysis/rh.pial_lgi.g2v2DSleepiness.10.glmdir/cache.mri_glmfit-sim.log

cd /home/xiaoxu/8YearOldNiiB1
/home/xiaoxu/freesurfer/bin/mri_glmfit-sim
--glmdir sAnalysis/rh.pial_lgi.g2v2DSleepiness.10.glmdir --cache 4 pos --cwp 
0.05 --2spaces

mri_glmfit-sim 7.1.0
Wed Jan 13 14:08:23 CST 2021
Linux xnVMUbuntu18 5.4.0-59-generic #65~18.04.1-Ubuntu SMP Mon Dec 14 15:59:40 
UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
xiaoxu
setenv SUBJECTS_DIR /home/xiaoxu/8YearOldNiiB1
FREESURFER_HOME /home/xiaoxu/freesurfer

Original mri_glmfit command line:
cmdline mri_glmfit --y sAnalysis/rh.pial_lgi.g2v2DSleepiness.10.mgh --fsgd 
sAnalysis/g2v2DSleepiness.fsgd dods --C sAnalysis/g1g2.sleepscore.mtx --surf 
fsaverage rh --cortex --glmdir sAnalysis/rh.pial_lgi.g2v2DSleepiness.10.glmdir 
--eres-save

DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 36.436322
ERROR: cannot find 
/home/xiaoxu/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm36/pos/th40/mc-z.csd


Regards,
Xiaoxu


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Greve, Douglas N.,Ph.D.
Sent: Wednesday, January 13, 2021 9:16 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_glmfit-sim error with no csd files generated

When you use --cache, mri_glmfit-sim will use precomputed (ie, "cached") CSD 
files as found in  $FREESURFER_HOME/average/mult-comp-cor
On 1/5/2021 4:55 PM, Na, Xiaoxu wrote:

External Email - Use Caution
Dear Freesurfer Experts,

I've all the subjects successfully done recon-all, lgi before coming to the 
group analysis. The following group analysis will use the 10mm smoothing as 
generated in previous recon-all.  Mris_preproc were implemented successfully 
and mri_glmfit as well. However, while coming to the mri_glmfit-sim, it showed 
done finally, but when going back to the directory, I found out no csd files 
have ever been generated, and this was reported as well during the 
mri_glmfit-sim run. Please kindly see the log as below for details. The error 
was reported in the middle, so I changed it into red. It's quite appreciated it 
you may help on this. Thanks a lot!


$ mri_glmfit-sim \
>  --glmdir s/lh.area.g2v3gaCSHQ.10.glmdir \
>  --cache 4 neg \
>  --cwp 0.05  \
>  --2spaces
cmdline mri_glmfit --y sAnalysis/lh.area.g2v3gaCSHQ.10.mgh --fsgd 
sAnalysis/g2v3gaCSHQ.fsgd --C sAnalysis/g1g2.sscorewithBMI.mtx --surf fsaverage 
lh --cortex --glmdir sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir
SURFACE: fsaverage lh
log file is sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/cache.mri_glmfit-sim.log

cd /home/xiaoxu/8YearOldNiiB1
/home/xiaoxu/freesurfer/bin/mri_glmfit-sim
--glmdir sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir --cache 4 neg --cwp 0.05 
--2spaces

mri_glmfit-sim 7.1.0
Tue Jan  5 15:11:00 CST 2021
Linux xnVMUbuntu18 5.4.0-58-generic #64~18.04.1-Ubuntu SMP Wed Dec 9 17:11:11 
UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
xiaoxu
setenv SUBJECTS_DIR /home/xiaoxu/8YearOldNiiB1
FREESURFER_HOME /home/xiaoxu/freesurfer

Original mri_glmfit command line:
cmdline mri_glmfit --y sAnalysis/lh.area.g2v3gaCSHQ.10.mgh --fsgd 
sAnalysis/g2v3gaCSHQ.fsgd --C sAnalysis/g1g2.sscorewithBMI.mtx --surf fsaverage 
lh --cortex --glmdir sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir

DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 20.731766
CSD 
/home/xiaoxu/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm21/neg/th40/mc-z.csd
mri_surfcluster --in 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/sig.mgh --mask 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/mask.mgh --cwsig 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.mgh
 --sum 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.summary
 --ocn 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.ocn.mgh
 --annot aparc --cwpvalthresh 0.05 --o 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.masked.mgh
 --no-fixmni --csd-out 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/csd/all.cache.th40.neg-

Re: [Freesurfer] mri_glmfit-sim error with no csd files generated

[Greve, Douglas N.,Ph.D.]

When you use --cache, mri_glmfit-sim will use precomputed (ie, "cached") CSD 
files as found in  $FREESURFER_HOME/average/mult-comp-cor

On 1/5/2021 4:55 PM, Na, Xiaoxu wrote:

External Email - Use Caution
Dear Freesurfer Experts,

I’ve all the subjects successfully done recon-all, lgi before coming to the 
group analysis. The following group analysis will use the 10mm smoothing as 
generated in previous recon-all.  Mris_preproc were implemented successfully 
and mri_glmfit as well. However, while coming to the mri_glmfit-sim, it showed 
done finally, but when going back to the directory, I found out no csd files 
have ever been generated, and this was reported as well during the 
mri_glmfit-sim run. Please kindly see the log as below for details. The error 
was reported in the middle, so I changed it into red. It’s quite appreciated it 
you may help on this. Thanks a lot!


$ mri_glmfit-sim \
>  --glmdir s/lh.area.g2v3gaCSHQ.10.glmdir \
>  --cache 4 neg \
>  --cwp 0.05  \
>  --2spaces
cmdline mri_glmfit --y sAnalysis/lh.area.g2v3gaCSHQ.10.mgh --fsgd 
sAnalysis/g2v3gaCSHQ.fsgd --C sAnalysis/g1g2.sscorewithBMI.mtx --surf fsaverage 
lh --cortex --glmdir sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir
SURFACE: fsaverage lh
log file is sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/cache.mri_glmfit-sim.log

cd /home/xiaoxu/8YearOldNiiB1
/home/xiaoxu/freesurfer/bin/mri_glmfit-sim
--glmdir sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir --cache 4 neg --cwp 0.05 
--2spaces

mri_glmfit-sim 7.1.0
Tue Jan  5 15:11:00 CST 2021
Linux xnVMUbuntu18 5.4.0-58-generic #64~18.04.1-Ubuntu SMP Wed Dec 9 17:11:11 
UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
xiaoxu
setenv SUBJECTS_DIR /home/xiaoxu/8YearOldNiiB1
FREESURFER_HOME /home/xiaoxu/freesurfer

Original mri_glmfit command line:
cmdline mri_glmfit --y sAnalysis/lh.area.g2v3gaCSHQ.10.mgh --fsgd 
sAnalysis/g2v3gaCSHQ.fsgd --C sAnalysis/g1g2.sscorewithBMI.mtx --surf fsaverage 
lh --cortex --glmdir sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir

DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 20.731766
CSD 
/home/xiaoxu/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm21/neg/th40/mc-z.csd
mri_surfcluster --in 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/sig.mgh --mask 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/mask.mgh --cwsig 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.mgh
 --sum 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.summary
 --ocn 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.ocn.mgh
 --annot aparc --cwpvalthresh 0.05 --o 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.masked.mgh
 --no-fixmni --csd-out 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/csd/all.cache.th40.neg-g1g2.sscorewithBMI.csd
 --csd 
/home/xiaoxu/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm21/neg/th40/mc-z.csd
 --csdpdf 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.pdf.dat
 --vwsig 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.voxel.mgh
 --vwsigmax 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.voxel.max.dat
 --oannot 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.ocn.annot
 --bonferroni 2 --surf white
Merging CSD files
ERROR: could not open 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/csd/all.cache.th40.neg-g1g2.sscorewithBMI.csd
Creating CDFs from CSD files
csd->threshsign = -1
thsign = neg, id = -1
version 7.1.0
hemi   = lh
srcid  = 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/sig.mgh
srcsubjid  = fsaverage
srcsurf= white
srcframe   = 0
thsign = neg
thmin  = 4
thmax  = -1
fdr= -1
minarea= 0
Bonferroni  = 2
xfmfile= talairach.xfm
nth = -1
outid= 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.masked.mgh
 MGH
ocnid= 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.ocn.mgh
 MGH
sumfile  = 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.summary
subjectsdir= /home/xiaoxu/8YearOldNiiB1
FixMNI = 0
Found 148772 vertices in mask
Found 148772 vertices in mask
Found 148772 points in clabel.
- XFM matrix (RAS2RAS) ---
/home/xiaoxu/8YearOldNiiB1/fsaverage/mri/transforms/talairach.xfm
1.0   0.0   0.0   0.0;
0.0   1.0   0.0   0.0;
0.0   0.0   1.0   0.0;
0.0   0.0   0.0   1.0;

Reading source surface /home/xiaoxu/8YearOldNiiB1/fsaverage/surf/lh.white
Done reading source surface
Reading annotation /home/xiaoxu/8YearOldNiiB1/fsaverage/label/lh.aparc.annot
mri_surfcluster supposed to be reproducible but seed not set
reading colortable from annotation 

[Freesurfer] mri_glmfit-sim error with no csd files generated

[Na, Xiaoxu]

External Email - Use Caution

Dear Freesurfer Experts,

I've all the subjects successfully done recon-all, lgi before coming to the 
group analysis. The following group analysis will use the 10mm smoothing as 
generated in previous recon-all.  Mris_preproc were implemented successfully 
and mri_glmfit as well. However, while coming to the mri_glmfit-sim, it showed 
done finally, but when going back to the directory, I found out no csd files 
have ever been generated, and this was reported as well during the 
mri_glmfit-sim run. Please kindly see the log as below for details. The error 
was reported in the middle, so I changed it into red. It's quite appreciated it 
you may help on this. Thanks a lot!


$ mri_glmfit-sim \
>  --glmdir s/lh.area.g2v3gaCSHQ.10.glmdir \
>  --cache 4 neg \
>  --cwp 0.05  \
>  --2spaces
cmdline mri_glmfit --y sAnalysis/lh.area.g2v3gaCSHQ.10.mgh --fsgd 
sAnalysis/g2v3gaCSHQ.fsgd --C sAnalysis/g1g2.sscorewithBMI.mtx --surf fsaverage 
lh --cortex --glmdir sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir
SURFACE: fsaverage lh
log file is sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/cache.mri_glmfit-sim.log

cd /home/xiaoxu/8YearOldNiiB1
/home/xiaoxu/freesurfer/bin/mri_glmfit-sim
--glmdir sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir --cache 4 neg --cwp 0.05 
--2spaces

mri_glmfit-sim 7.1.0
Tue Jan  5 15:11:00 CST 2021
Linux xnVMUbuntu18 5.4.0-58-generic #64~18.04.1-Ubuntu SMP Wed Dec 9 17:11:11 
UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
xiaoxu
setenv SUBJECTS_DIR /home/xiaoxu/8YearOldNiiB1
FREESURFER_HOME /home/xiaoxu/freesurfer

Original mri_glmfit command line:
cmdline mri_glmfit --y sAnalysis/lh.area.g2v3gaCSHQ.10.mgh --fsgd 
sAnalysis/g2v3gaCSHQ.fsgd --C sAnalysis/g1g2.sscorewithBMI.mtx --surf fsaverage 
lh --cortex --glmdir sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir

DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 20.731766
CSD 
/home/xiaoxu/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm21/neg/th40/mc-z.csd
mri_surfcluster --in 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/sig.mgh --mask 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/mask.mgh --cwsig 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.mgh
 --sum 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.summary
 --ocn 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.ocn.mgh
 --annot aparc --cwpvalthresh 0.05 --o 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.masked.mgh
 --no-fixmni --csd-out 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/csd/all.cache.th40.neg-g1g2.sscorewithBMI.csd
 --csd 
/home/xiaoxu/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm21/neg/th40/mc-z.csd
 --csdpdf 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.pdf.dat
 --vwsig 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.voxel.mgh
 --vwsigmax 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.voxel.max.dat
 --oannot 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.ocn.annot
 --bonferroni 2 --surf white
Merging CSD files
ERROR: could not open 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/csd/all.cache.th40.neg-g1g2.sscorewithBMI.csd
Creating CDFs from CSD files
csd->threshsign = -1
thsign = neg, id = -1
version 7.1.0
hemi   = lh
srcid  = 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/sig.mgh
srcsubjid  = fsaverage
srcsurf= white
srcframe   = 0
thsign = neg
thmin  = 4
thmax  = -1
fdr= -1
minarea= 0
Bonferroni  = 2
xfmfile= talairach.xfm
nth = -1
outid= 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.masked.mgh
 MGH
ocnid= 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.ocn.mgh
 MGH
sumfile  = 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.summary
subjectsdir= /home/xiaoxu/8YearOldNiiB1
FixMNI = 0
Found 148772 vertices in mask
Found 148772 vertices in mask
Found 148772 points in clabel.
- XFM matrix (RAS2RAS) ---
/home/xiaoxu/8YearOldNiiB1/fsaverage/mri/transforms/talairach.xfm
1.0   0.0   0.0   0.0;
0.0   1.0   0.0   0.0;
0.0   0.0   1.0   0.0;
0.0   0.0   0.0   1.0;

Reading source surface /home/xiaoxu/8YearOldNiiB1/fsaverage/surf/lh.white
Done reading source surface
Reading annotation /home/xiaoxu/8YearOldNiiB1/fsaverage/label/lh.aparc.annot
mri_surfcluster supposed to be reproducible but seed not set
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
Computing metric properties

Re: [Freesurfer] mri_glmfit-sim error CSDs have the same seed

[Meaghan Perdue]

External Email - Use Caution

Hi Doug,

Deleting the .csd files and re-running worked.
Thank you!
Meaghan

On Tue, Sep 15, 2020 at 11:30 AM Douglas N. Greve 
wrote:

> *Message sent from a system outside of UConn.*
>
> Hmm, there should have been a lot more terminal output than that.
> Try this, delete the CSD files:
> rm lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j*-osgm.csd
> Then re-run. If it fails, then send me the perm.th20.abs.j*-osgm.csd files
>
> On 9/14/2020 2:58 PM, Meaghan Perdue wrote:
>
> External Email - Use Caution
> Hi Doug,
>
> Here is the command:
>
> mri_glmfit-sim --glmdir lh.rs6980093.thickness10.glmdir --perm 1000 2.0
> abs --cwp 0.05 --2spaces --bg 4
>
> And here is the output:
>
> mri_glmfit simulation done 4.78645
>
>
> mri_glmfit simulation done 4.806
>
>
> mri_glmfit simulation done 4.81553
>
>
> mri_glmfit simulation done 4.81997
>
>
> mri_surfcluster --in
> lh.rs6980093.thickness10.glmdir/rs6980093_thickness/sig.mgh --mask
> lh.rs6980093.thickness10.glmdir/mask.mgh --cwsig
> lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.cluster.mgh
> --sum
> lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.cluster.summary
> --ocn
> lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.ocn.mgh
> --annot aparc --cwpvalthresh 0.05 --o
> lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.masked.mgh
> --no-fixmni --csd
> lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j001-rs6980093_thickness.csd
> --csd
> lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j002-rs6980093_thickness.csd
> --csd
> lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j003-rs6980093_thickness.csd
> --csd
> lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j004-rs6980093_thickness.csd
> --csdpdf
> lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.pdf.dat
> --vwsig
> lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.voxel.mgh
> --vwsigmax
> lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.voxel.max.dat
> --oannot
> lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.ocn.annot
> --bonferroni 2 --surf white
> ERROR: CSDmerge: CSDs have same seed
>
>
> Thank you!
> Meaghan
>
> On Wed, Sep 9, 2020 at 4:28 PM Douglas N. Greve 
> wrote:
>
>> *Message sent from a system outside of UConn.*
>>
>> please send the full command line and terminal output
>>
>> On 9/9/2020 3:19 PM, Meaghan Perdue wrote:
>>
>> External Email - Use Caution
>> Hello Freesurfer experts,
>>
>> We're receiving the following error message when trying to run
>> mri_glmfit-sim:
>> ERROR: CSDmerge: CSDs have same seed
>>
>> This only occurs when we try to run the permutation on the LH for
>> thickness. We've been able to run the simulation successfully on LH surface
>> area and RH thickness and area.
>>
>> How can we troubleshoot this problem?
>>
>> Thank you,
>> Meaghan Perdue
>>
>> --
>> Meaghan Perdue
>> she | her | hers
>>
>> PhD Student
>> Developmental Psychology
>> Neurobiology of Language
>> University of Connecticut
>> Bousfield A302
>> Visit my website 
>>
>> ___
>> 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
>
>
>
> --
> Meaghan Perdue
> she | her | hers
>
> PhD Student
> Developmental Psychology
> Neurobiology of Language
> University of Connecticut
> Bousfield A302
> Visit my website 
>
> ___
> 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



-- 
Meaghan Perdue
she | her | hers

PhD Student
Developmental Psychology
Neurobiology of Language
University of Connecticut
Bousfield A302
Visit my website 
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] mri_glmfit-sim error CSDs have the same seed

[Douglas N. Greve]

Hmm, there should have been a lot more terminal output than that.
Try this, delete the CSD files:
rm lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j*-osgm.csd
Then re-run. If it fails, then send me the perm.th20.abs.j*-osgm.csd files

On 9/14/2020 2:58 PM, Meaghan Perdue wrote:


External Email - Use Caution

Hi Doug,

Here is the command:

mri_glmfit-sim --glmdir lh.rs6980093.thickness10.glmdir --perm 1000 
2.0 abs --cwp 0.05 --2spaces --bg 4


And here is the output:

mri_glmfit simulation done 4.78645


mri_glmfit simulation done 4.806


mri_glmfit simulation done 4.81553


mri_glmfit simulation done 4.81997


mri_surfcluster --in 
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/sig.mgh --mask 
lh.rs6980093.thickness10.glmdir/mask.mgh --cwsig 
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.cluster.mgh 
--sum 
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.cluster.summary 
--ocn 
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.ocn.mgh 
--annot aparc --cwpvalthresh 0.05 --o 
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.masked.mgh 
--no-fixmni --csd 
lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j001-rs6980093_thickness.csd 
--csd 
lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j002-rs6980093_thickness.csd 
--csd 
lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j003-rs6980093_thickness.csd 
--csd 
lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j004-rs6980093_thickness.csd 
--csdpdf 
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.pdf.dat 
--vwsig 
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.voxel.mgh 
--vwsigmax 
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.voxel.max.dat 
--oannot 
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.ocn.annot 
--bonferroni 2 --surf white

ERROR: CSDmerge: CSDs have same seed


Thank you!
Meaghan

On Wed, Sep 9, 2020 at 4:28 PM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


*Message sent from a system outside of UConn.*

please send the full command line and terminal output

On 9/9/2020 3:19 PM, Meaghan Perdue wrote:


External Email - Use Caution

Hello Freesurfer experts,

We're receiving the following error message when trying to run
mri_glmfit-sim:
ERROR: CSDmerge: CSDs have same seed

This only occurs when we try to run the permutation on the LH for
thickness. We've been able to run the simulation successfully on
LH surface area and RH thickness and area.

How can we troubleshoot this problem?

Thank you,
Meaghan Perdue

-- 
Meaghan Perdue

she | her | hers

PhD Student
Developmental Psychology
Neurobiology of Language
University of Connecticut
Bousfield A302
Visit my website 

___
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



--
Meaghan Perdue
she | her | hers

PhD Student
Developmental Psychology
Neurobiology of Language
University of Connecticut
Bousfield A302
Visit my website 

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


___
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Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] mri_glmfit-sim error CSDs have the same seed

[Meaghan Perdue]

External Email - Use Caution

Hi Doug,

Here is the command:

mri_glmfit-sim --glmdir lh.rs6980093.thickness10.glmdir --perm 1000 2.0 abs
--cwp 0.05 --2spaces --bg 4

And here is the output:

mri_glmfit simulation done 4.78645


mri_glmfit simulation done 4.806


mri_glmfit simulation done 4.81553


mri_glmfit simulation done 4.81997


mri_surfcluster --in
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/sig.mgh --mask
lh.rs6980093.thickness10.glmdir/mask.mgh --cwsig
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.cluster.mgh
--sum
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.cluster.summary
--ocn
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.ocn.mgh
--annot aparc --cwpvalthresh 0.05 --o
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.masked.mgh
--no-fixmni --csd
lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j001-rs6980093_thickness.csd
--csd
lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j002-rs6980093_thickness.csd
--csd
lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j003-rs6980093_thickness.csd
--csd
lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j004-rs6980093_thickness.csd
--csdpdf
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.pdf.dat
--vwsig
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.voxel.mgh
--vwsigmax
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.voxel.max.dat
--oannot
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.ocn.annot
--bonferroni 2 --surf white
ERROR: CSDmerge: CSDs have same seed


Thank you!
Meaghan

On Wed, Sep 9, 2020 at 4:28 PM Douglas N. Greve 
wrote:

> *Message sent from a system outside of UConn.*
>
> please send the full command line and terminal output
>
> On 9/9/2020 3:19 PM, Meaghan Perdue wrote:
>
> External Email - Use Caution
> Hello Freesurfer experts,
>
> We're receiving the following error message when trying to run
> mri_glmfit-sim:
> ERROR: CSDmerge: CSDs have same seed
>
> This only occurs when we try to run the permutation on the LH for
> thickness. We've been able to run the simulation successfully on LH surface
> area and RH thickness and area.
>
> How can we troubleshoot this problem?
>
> Thank you,
> Meaghan Perdue
>
> --
> Meaghan Perdue
> she | her | hers
>
> PhD Student
> Developmental Psychology
> Neurobiology of Language
> University of Connecticut
> Bousfield A302
> Visit my website 
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



-- 
Meaghan Perdue
she | her | hers

PhD Student
Developmental Psychology
Neurobiology of Language
University of Connecticut
Bousfield A302
Visit my website 
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Re: [Freesurfer] mri_glmfit-sim error CSDs have the same seed

[Douglas N. Greve]

please send the full command line and terminal output

On 9/9/2020 3:19 PM, Meaghan Perdue wrote:


External Email - Use Caution

Hello Freesurfer experts,

We're receiving the following error message when trying to run 
mri_glmfit-sim:

ERROR: CSDmerge: CSDs have same seed

This only occurs when we try to run the permutation on the LH for 
thickness. We've been able to run the simulation successfully on LH 
surface area and RH thickness and area.


How can we troubleshoot this problem?

Thank you,
Meaghan Perdue

--
Meaghan Perdue
she | her | hers

PhD Student
Developmental Psychology
Neurobiology of Language
University of Connecticut
Bousfield A302
Visit my website 

___
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[Freesurfer] mri_glmfit-sim error CSDs have the same seed

[Meaghan Perdue]

External Email - Use Caution

Hello Freesurfer experts,

We're receiving the following error message when trying to run
mri_glmfit-sim:
ERROR: CSDmerge: CSDs have same seed

This only occurs when we try to run the permutation on the LH for
thickness. We've been able to run the simulation successfully on LH surface
area and RH thickness and area.

How can we troubleshoot this problem?

Thank you,
Meaghan Perdue

-- 
Meaghan Perdue
she | her | hers

PhD Student
Developmental Psychology
Neurobiology of Language
University of Connecticut
Bousfield A302
Visit my website 
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Re: [Freesurfer] mri_glmfit-sim error

[Douglas N. Greve]

See this page
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm

On 2/7/2020 9:52 PM, Kim, Gwang-Won wrote:


Hi there,

I ran “mri_glmfit-sim –glmdir g2v3.wls –2spaces –perm 1000 1.3 abs”.

But, there was error message as follow: “design matrix is not 
orthogonal, cannot be used with permutation. If this something you 
really want to do, run with –perm-force”


Please let me know how to process mri_glmfit-sim.

Thank you,

Gwang-Won


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[Freesurfer] mri_glmfit-sim error

[Kim, Gwang-Won]

Hi there,

I ran “mri_glmfit-sim -glmdir g2v3.wls -2spaces -perm 1000 1.3 abs”.

But, there was error message as follow: “design matrix is not orthogonal, 
cannot be used with permutation. If this something you really want to do, run 
with -perm-force”
Please let me know how to process mri_glmfit-sim.

Thank you,
Gwang-Won
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Re: [Freesurfer] mri_glmfit-sim error correcting for MC for LGI analysis

[amirhossein manzouri]

External Email - Use Caution

Hi Freesurfer,
I am also experiencing the same problem and everything regarding FREESURFER
path looks ok just getting error that says:
Reading source surface
/storage/affective/ume2/confined/Amir/FS/fsaverage/surf/rh.white
MRISread(): could not open file
No such file or directory
mri_surfcluster: could not read surface
/storage/affective/ume2/confined/Amir/FS/fsaverage/surf/rh.white
No such file or directory
I wonder if you found the reason and solution?

Best regards,
Amirhossein Manzouri





On Thu, Dec 6, 2018 at 6:57 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

>
>
> On 11/27/2018 06:46 AM, C.P.E. Rollins wrote:
> > External Email - Use Caution
> > Hi Douglas,
> >
> > Thanks a lot for your answers.
> >
> > 1) For the permutations, would you recommend using this for
> > controlling for MC in cortical thickness analyses too?
> Yes
> > Why is it recommended to use permutation simulation as opposed to Z
> > Monte Carlo simulation for an LGI analysis?
> Because the spatial correlations are very high (which makes MCZ less
> accurate)
> >
> > 2) I've attached here the output from ls -Rl
> > $FREESURFER_HOME/subjects/fsaverage.
> It looks like there is a difference in where you think FREESURFER_HOME
> is. Below, you say it is in /home/cper2/BeneMin/Freesurfer, but the
> attached file says it is in /applications/freesurfer/freesurfer_6.0.0.
> Which one is it?
>
>
> >
> > Thanks again,
> > Colleen
> >
> > On 2018-11-23 16:26, C.P.E. Rollins wrote:
> >> Dear Freesurfer Developers,
> >> I have a 2-part question:
> >> 1) I was advised to use permutation to control for multiple
> >> comparisons in an LGI analysis, would you mind elaborating how to do
> >> this in command line (in terms of command and parameters)?
> >> 2) In running "mri_glmfit-sim --glmdir lh.5.lgi_MAN_new.glmdir --cache
> >> 1.3 pos --cwp 0.05 --2spaces --debug", I receive the following error
> >> (attached). I was wondering if you might have any advice? The file
> >> /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white exists and I can
> >> view it in freeview.
> >>
> >> Many thanks,
> >> Colleen
> >
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] mri_glmfit-sim error correcting for MC for LGI analysis

[Greve, Douglas N.,Ph.D.]

On 11/27/2018 06:46 AM, C.P.E. Rollins wrote:
> External Email - Use Caution
> Hi Douglas,
>
> Thanks a lot for your answers.
>
> 1) For the permutations, would you recommend using this for 
> controlling for MC in cortical thickness analyses too? 
Yes
> Why is it recommended to use permutation simulation as opposed to Z 
> Monte Carlo simulation for an LGI analysis?
Because the spatial correlations are very high (which makes MCZ less 
accurate)
>
> 2) I've attached here the output from ls -Rl 
> $FREESURFER_HOME/subjects/fsaverage.
It looks like there is a difference in where you think FREESURFER_HOME 
is. Below, you say it is in /home/cper2/BeneMin/Freesurfer, but the 
attached file says it is in /applications/freesurfer/freesurfer_6.0.0. 
Which one is it?


>
> Thanks again,
> Colleen
>
> On 2018-11-23 16:26, C.P.E. Rollins wrote:
>> Dear Freesurfer Developers,
>> I have a 2-part question:
>> 1) I was advised to use permutation to control for multiple
>> comparisons in an LGI analysis, would you mind elaborating how to do
>> this in command line (in terms of command and parameters)?
>> 2) In running "mri_glmfit-sim --glmdir lh.5.lgi_MAN_new.glmdir --cache
>> 1.3 pos --cwp 0.05 --2spaces --debug", I receive the following error
>> (attached). I was wondering if you might have any advice? The file
>> /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white exists and I can
>> view it in freeview.
>>
>> Many thanks,
>> Colleen
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] mri_glmfit-sim error correcting for MC for LGI analysis

[C.P.E. Rollins]

   External Email - Use Caution


Hi Douglas,

Thanks a lot for your answers.

1) For the permutations, would you recommend using this for controlling 
for MC in cortical thickness analyses too? Why is it recommended to use 
permutation simulation as opposed to Z Monte Carlo simulation for an LGI 
analysis?


2) I've attached here the output from ls -Rl 
$FREESURFER_HOME/subjects/fsaverage.


Thanks again,
Colleen

On 2018-11-23 16:26, C.P.E. Rollins wrote:

Dear Freesurfer Developers,
I have a 2-part question:
1) I was advised to use permutation to control for multiple
comparisons in an LGI analysis, would you mind elaborating how to do
this in command line (in terms of command and parameters)?
2) In running "mri_glmfit-sim --glmdir lh.5.lgi_MAN_new.glmdir --cache
1.3 pos --cwp 0.05 --2spaces --debug", I receive the following error
(attached). I was wondering if you might have any advice? The file
/home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white exists and I can
view it in freeview.

Many thanks,
Colleen/applications/freesurfer/freesurfer_6.0.0/subjects/fsaverage:
total 169
drwxrwsr-x  2 pfb29 sysadmin 125 Dec 21  2015 label
drwxrwsr-x  4 pfb29 sysadmin  21 Nov 27  2012 mri
drwxrwsr-x  2 pfb29 sysadmin  13 Apr 11  2013 mri.2mm
drwxrwsr-x  2 pfb29 sysadmin  18 Nov 13  2015 scripts
drwxrwsr-x  2 pfb29 sysadmin  68 Nov 13  2015 surf
drwxrwsr-x 12 pfb29 sysadmin  16 Nov 13  2015 xhemi

/applications/freesurfer/freesurfer_6.0.0/subjects/fsaverage/label:
total 110485
-rwxrwxr-x 1 pfb29 sysadmin 1314302 Aug 14  2007 lh.aparc.a2005s.annot
-rwxrwxr-x 1 pfb29 sysadmin 1314060 Dec 30  2010 lh.aparc.a2009s.annot
-rwxrwxr-x 1 pfb29 sysadmin 1312250 Dec 30  2010 lh.aparc.annot
-rwxrwxr-x 1 pfb29 sysadmin 6636682 Mar 19  2010 lh.aparc.label
-rwxrwxr-x 1 pfb29 sysadmin  166374 Jun 28  2007 lh.BA1_exvivo.label
-rwxrwxr-x 1 pfb29 sysadmin   46008 Jan 15  2013 lh.BA1_exvivo.thresh.label
-rwxrwxr-x 1 pfb29 sysadmin  320897 Jun 28  2007 lh.BA2_exvivo.label
-rwxrwxr-x 1 pfb29 sysadmin   94863 Jan 15  2013 lh.BA2_exvivo.thresh.label
-rwxrwxr-x 1 pfb29 sysadmin  163588 Jun 28  2007 lh.BA3a_exvivo.label
-rwxrwxr-x 1 pfb29 sysadmin   68084 Jan 15  2013 lh.BA3a_exvivo.thresh.label
-rwxrwxr-x 1 pfb29 sysadmin  239495 Jun 28  2007 lh.BA3b_exvivo.label
-rwxrwxr-x 1 pfb29 sysadmin   90376 Jan 15  2013 lh.BA3b_exvivo.thresh.label
-rwxrwxr-x 1 pfb29 sysadmin  167585 Jun 28  2007 lh.BA44_exvivo.label
-rwxrwxr-x 1 pfb29 sysadmin   83185 Jan 15  2013 lh.BA44_exvivo.thresh.label
-rwxrwxr-x 1 pfb29 sysadmin  137141 Jun 28  2007 lh.BA45_exvivo.label
-rwxrwxr-x 1 pfb29 sysadmin   50422 Jan 15  2013 lh.BA45_exvivo.thresh.label
-rwxrwxr-x 1 pfb29 sysadmin  231744 Jun 28  2007 lh.BA4a_exvivo.label
-rwxrwxr-x 1 pfb29 sysadmin  103857 Jan 15  2013 lh.BA4a_exvivo.thresh.label
-rwxrwxr-x 1 pfb29 sysadmin  163313 Jun 28  2007 lh.BA4p_exvivo.label
-rwxrwxr-x 1 pfb29 sysadmin   69838 Jan 15  2013 lh.BA4p_exvivo.thresh.label
-rwxrwxr-x 1 pfb29 sysadmin  538881 Jun 28  2007 lh.BA6_exvivo.label
-rwxrwxr-x 1 pfb29 sysadmin  311318 Jan 15  2013 lh.BA6_exvivo.thresh.label
-rwxrwxr-x 1 pfb29 sysadmin 6117569 Aug 14  2007 lh.cortex.label
-rwxrwxr-x 1 pfb29 sysadmin   57500 May 19  2009 lh.entorhinal_exvivo.label
-rwxrwxr-x 1 pfb29 sysadmin   21693 Apr 30  2015 
lh.entorhinal_exvivo.thresh.label
-rwxrwxr-x 1 pfb29 sysadmin  559985 Aug 14  2007 lh.Medial_wall.label
-rwxrwxr-x 1 pfb29 sysadmin   85306 Jun 28  2007 lh.MT_exvivo.label
-rwxrwxr-x 1 pfb29 sysadmin   23084 Jan 15  2013 lh.MT_exvivo.thresh.label
-rwxrwxr-x 1 pfb29 sysadmin 1311209 Sep  6  2011 lh.oasis.chubs.annot
-rwxrwxr-x 1 pfb29 sysadmin   14343 Sep  6  2011 lh.oasis.chubs.ifc.label
-rwxrwxr-x 1 pfb29 sysadmin   23011 Sep  6  2011 lh.oasis.chubs.ipc.label
-rwxrwxr-x 1 pfb29 sysadmin9280 Sep  6  2011 lh.oasis.chubs.ips.label
-rwxrwxr-x 1 pfb29 sysadmin   45063 Sep  6  2011 
lh.oasis.chubs.lateraltemporal.label
-rwxrwxr-x 1 pfb29 sysadmin   18804 Sep  6  2011 lh.oasis.chubs.medialpfc.label
-rwxrwxr-x 1 pfb29 sysadmin   23996 Sep  6  2011 lh.oasis.chubs.mtl.label
-rwxrwxr-x 1 pfb29 sysadmin   23082 Sep  6  2011 
lh.oasis.chubs.retrosplenial.label
-rwxrwxr-x 1 pfb29 sysadmin   19132 Sep  6  2011 lh.oasis.chubs.tp.label
-rwxrwxr-x 1 pfb29 sysadmin 1316686 Mar 11  2010 lh.PALS_B12_Brodmann.annot
-rwxrwxr-x 1 pfb29 sysadmin  282993 Mar 11  2010 lh.PALS_B12.labels.gii
-rwxrwxr-x 1 pfb29 sysadmin 1316686 Mar 11  2010 lh.PALS_B12_Lobes.annot
-rwxrwxr-x 1 pfb29 sysadmin 1316686 Mar 11  2010 lh.PALS_B12_OrbitoFrontal.annot
-rwxrwxr-x 1 pfb29 sysadmin 1316686 Mar 11  2010 lh.PALS_B12_Visuotopic.annot
-rwxrwxr-x 1 pfb29 sysadmin   55014 Oct 23  2012 lh.perirhinal_exvivo.label
-rwxrwxr-x 1 pfb29 sysadmin   20742 Apr 30  2015 
lh.perirhinal_exvivo.thresh.label
-rwxrwxr-x 1 pfb29 sysadmin  192278 Jun 28  2007 lh.V1_exvivo.label
-rwxrwxr-x 1 pfb29 sysadmin  151679 Jan 15  2013 lh.V1_exvivo.thresh.label
-rwxrwxr-x 1 pfb29 sysadmin  337758 Jun 28  2007 lh.V2_exvivo.label
-rwxrwxr-x 1 pfb29 

Re: [Freesurfer] mri_glmfit-sim error correcting for MC for LGI analysis

[Greve, Douglas N.,Ph.D.]

On 11/23/2018 11:26 AM, C.P.E. Rollins wrote:
> External Email - Use Caution
> Dear Freesurfer Developers,
> I have a 2-part question:
> 1) I was advised to use permutation to control for multiple 
> comparisons in an LGI analysis, would you mind elaborating how to do 
> this in command line (in terms of command and parameters)?
It is very similar to running with MCZ. See 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
> 2) In running "mri_glmfit-sim --glmdir lh.5.lgi_MAN_new.glmdir --cache 
> 1.3 pos --cwp 0.05 --2spaces --debug", I receive the following error 
> (attached). I was wondering if you might have any advice? The file
> /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white exists and I can
> view it in freeview.
I don't know  what is going on there.  Can you send me the result of
ls -Rl $FREESURFER_HOME/subjects/fsaverage

>
> Many thanks,
> Colleen
>
>
> set echo = 1 ;
> breaksw
> breaksw
>
> end
> end
> while ( $#argv != 0 )
> while ( 0 != 0 )
>
> goto parse_args_return ;
> goto parse_args_return
>
> goto check_params ;
> goto check_params
> if ( $#glmdir == 0 ) then
> if ( 1 == 0 ) then
> if ( $DoSim ) then
> if ( 0 ) then
> set residual = ( )
> set residual = ( )
> if ( $nulltype == perm && $PermResid ) then
> if ( == perm && 1 ) then
> if ( $DiagCluster && $DoBackground ) then
> if ( 0 && 0 ) then
> if ( $DiagCluster && $DoPBSubmit ) then
> if ( 0 && 0 ) then
> if ( $DiagCluster && $DoSim == 0 ) then
> if ( 0 && 0 == 0 ) then
>
> goto check_params_return ;
> goto check_params_return
>
> if ( ! -e $glmdir ) then
> if ( ! -e lh.5.lgi_MAN_new.glmdir ) then
>
> set glmfitlog = $glmdir/mri_glmfit.log
> set glmfitlog = lh.5.lgi_MAN_new.glmdir/mri_glmfit.log
> if ( ! -e $glmfitlog ) then
> if ( ! -e lh.5.lgi_MAN_new.glmdir/mri_glmfit.log ) then
>
> if ( $nulltype != perm ) then
> if ( != perm ) then
> set fwhmfile = $glmdir/fwhm.dat
> set fwhmfile = lh.5.lgi_MAN_new.glmdir/fwhm.dat
> if ( ! -e $fwhmfile ) then
> if ( ! -e lh.5.lgi_MAN_new.glmdir/fwhm.dat ) then
>
> set fwhm = `cat $fwhmfile` ;
> set fwhm = `cat $fwhmfile`
> cat lh.5.lgi_MAN_new.glmdir/fwhm.dat
> else
> else
>
> set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
> set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
> awk {if($1 == "cwd") print $2}
> cat lh.5.lgi_MAN_new.glmdir/mri_glmfit.log
> if ( 0 && ! -e $glmfitcwd ) then
> if ( 0 && ! -e /home/cper2/BeneMin/Freesurfer ) then
> set glmfitcwd = `pwd` ;
> set glmfitcwd = `pwd`
> pwd
>
> set anattype = volume ;
> set anattype = volume
> set subject = ( ) ;
> set subject = ( )
> set hemi = ( ) ;
> set hemi = ( )
> set surf = "white" ;
> set surf = white
> set wls = ( ) ;
> set wls = ( )
>
> set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
> set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
> awk {if($1 == "cwd") print $2}
> cat lh.5.lgi_MAN_new.glmdir/mri_glmfit.log
>
>
> set glmfitcmd0 = `cat $glmfitlog | awk '{if($1 == "cmdline") print $0}'`
> set glmfitcmd0 = `cat $glmfitlog | awk '{if($1 == "cmdline") print $0}'`
> awk {if($1 == "cmdline") print $0}
> cat lh.5.lgi_MAN_new.glmdir/mri_glmfit.log
> set glmfitcmd = ( $glmfitcmd0 ) ;
> set glmfitcmd = ( cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd 
> FSGD_MAN_new.txt dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh 
> --C contrast_dods.txt )
> echo $glmfitcmd
> echo cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt 
> dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C 
> contrast_dods.txt
> cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt dods 
> --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C contrast_dods.txt
> set gd2mtx = dods
> set gd2mtx = dods
> set UseTable = 0 ;
> set UseTable = 0
> set label = ( ) ;
> set label = ( )
> while ( $#glmfitcmd )
> while ( 14 )
> set flag = $glmfitcmd[1] ; shift glmfitcmd ;
> set flag = cmdline
> shift glmfitcmd
>
> switch ( $flag )
> switch ( cmdline )
> case "mri_glmfit"
> case mri_glmfit
> case "--prune"
> case --prune
> case "--no-prune"
> case --no-prune
> case "--pca"
> case --pca
> case "--synth"
> case --synth
> case "--allowsubjrep"
> case --allowsubjrep
> case "--illcond"
> case --illcond
> case "--debug"
> case --debug
> case "--synth"
> case --synth
> case "--cortex"
> case --cortex
> case "--kurtosis"
> case --kurtosis
> case "--nii"
> case --nii
> case "--nii.gz"
> case --nii.gz
> case "--rescale-x"
> case --rescale-x
> case "--no-rescale-x"
> case --no-rescale-x
> case "--fisher"
> case --fisher
> case "--no-pcc"
> case --no-pcc
> case "dods"
> case dods
> case "mri_glmfit.bin"
> case mri_glmfit.bin
> case "--save-eres"
> case --save-eres
> breaksw
> breaksw
> end
> end
> while ( $#glmfitcmd )
> while ( 13 )
> set flag = $glmfitcmd[1] ; shift glmfitcmd ;
> set flag = mri_glmfit.bin
> shift glmfitcmd
>
> switch ( $flag )
> switch ( mri_glmfit.bin )
> case "--save-eres"
> case --save-eres
> 

[Freesurfer] mri_glmfit-sim error correcting for MC for LGI analysis

[C.P.E. Rollins]

   External Email - Use Caution


Dear Freesurfer Developers,
I have a 2-part question:
1) I was advised to use permutation to control for multiple comparisons 
in an LGI analysis, would you mind elaborating how to do this in command 
line (in terms of command and parameters)?
2) In running "mri_glmfit-sim --glmdir lh.5.lgi_MAN_new.glmdir --cache 
1.3 pos --cwp 0.05 --2spaces --debug", I receive the following error 
(attached). I was wondering if you might have any advice? The file

/home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white exists and I can
view it in freeview.

Many thanks,
Colleenset echo = 1 ;
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 0 != 0 )

goto parse_args_return ;
goto parse_args_return

goto check_params ;
goto check_params
if ( $#glmdir == 0 ) then
if ( 1 == 0 ) then
if ( $DoSim ) then
if ( 0 ) then
set residual = ( )
set residual = ( )
if ( $nulltype == perm && $PermResid ) then
if ( == perm && 1 ) then
if ( $DiagCluster && $DoBackground ) then
if ( 0 && 0 ) then
if ( $DiagCluster && $DoPBSubmit ) then
if ( 0 && 0 ) then
if ( $DiagCluster && $DoSim == 0 ) then
if ( 0 && 0 == 0 ) then

goto check_params_return ;
goto check_params_return

if ( ! -e $glmdir ) then
if ( ! -e lh.5.lgi_MAN_new.glmdir ) then

set glmfitlog = $glmdir/mri_glmfit.log
set glmfitlog = lh.5.lgi_MAN_new.glmdir/mri_glmfit.log
if ( ! -e $glmfitlog ) then
if ( ! -e lh.5.lgi_MAN_new.glmdir/mri_glmfit.log ) then

if ( $nulltype != perm ) then
if ( != perm ) then
set fwhmfile = $glmdir/fwhm.dat
set fwhmfile = lh.5.lgi_MAN_new.glmdir/fwhm.dat
if ( ! -e $fwhmfile ) then
if ( ! -e lh.5.lgi_MAN_new.glmdir/fwhm.dat ) then

set fwhm = `cat $fwhmfile` ;
set fwhm = `cat $fwhmfile`
cat lh.5.lgi_MAN_new.glmdir/fwhm.dat
else
else

set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
awk {if($1 == "cwd") print $2}
cat lh.5.lgi_MAN_new.glmdir/mri_glmfit.log
if ( 0 && ! -e $glmfitcwd ) then
if ( 0 && ! -e /home/cper2/BeneMin/Freesurfer ) then
set glmfitcwd = `pwd` ;
set glmfitcwd = `pwd`
pwd

set anattype = volume ;
set anattype = volume
set subject = ( ) ;
set subject = ( )
set hemi = ( ) ;
set hemi = ( )
set surf = "white" ;
set surf = white
set wls = ( ) ;
set wls = ( )

set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
awk {if($1 == "cwd") print $2}
cat lh.5.lgi_MAN_new.glmdir/mri_glmfit.log


set glmfitcmd0 = `cat $glmfitlog | awk '{if($1 == "cmdline") print $0}'`
set glmfitcmd0 = `cat $glmfitlog | awk '{if($1 == "cmdline") print $0}'`
awk {if($1 == "cmdline") print $0}
cat lh.5.lgi_MAN_new.glmdir/mri_glmfit.log
set glmfitcmd = ( $glmfitcmd0 ) ;
set glmfitcmd = ( cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd 
FSGD_MAN_new.txt dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C 
contrast_dods.txt )
echo $glmfitcmd
echo cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt 
dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C contrast_dods.txt
cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt dods 
--glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C contrast_dods.txt
set gd2mtx = dods
set gd2mtx = dods
set UseTable = 0 ;
set UseTable = 0
set label = ( ) ;
set label = ( )
while ( $#glmfitcmd )
while ( 14 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = cmdline
shift glmfitcmd

switch ( $flag )
switch ( cmdline )
case "mri_glmfit"
case mri_glmfit
case "--prune"
case --prune
case "--no-prune"
case --no-prune
case "--pca"
case --pca
case "--synth"
case --synth
case "--allowsubjrep"
case --allowsubjrep
case "--illcond"
case --illcond
case "--debug"
case --debug
case "--synth"
case --synth
case "--cortex"
case --cortex
case "--kurtosis"
case --kurtosis
case "--nii"
case --nii
case "--nii.gz"
case --nii.gz
case "--rescale-x"
case --rescale-x
case "--no-rescale-x"
case --no-rescale-x
case "--fisher"
case --fisher
case "--no-pcc"
case --no-pcc
case "dods"
case dods
case "mri_glmfit.bin"
case mri_glmfit.bin
case "--save-eres"
case --save-eres
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 13 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = mri_glmfit.bin
shift glmfitcmd

switch ( $flag )
switch ( mri_glmfit.bin )
case "--save-eres"
case --save-eres
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 12 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = --y
shift glmfitcmd

switch ( $flag )
switch ( --y )
if ( $#y == 0 ) set y = $glmfitcmd[1] ;
if ( 0 == 0 ) set y = lh.5.lgi_MAN_new.mgh
set y = lh.5.lgi_MAN_new.mgh
shift glmfitcmd ;
shift glmfitcmd
if ( $DoClusterMean ) then
if ( 1 ) then
if ( ! -e $y ) then
if ( ! -e lh.5.lgi_MAN_new.mgh ) then
endif
endif
if ( "$flag" == "--table" ) set UseTable = 1 ;
if ( --y == --table ) set UseTable = 1
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 10 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;

[Freesurfer] mri_glmfit-sim error

[C.P.E. Rollins]

External Email - Use Caution

Dear Freesurfer Developers,

I'm trying to run mri_glmfit-sim to correct for multiple comparisons but 
am receiving the following error:

cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt 
dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C 
contrast_dods.txt
SURFACE: fsaverage lh
log file is lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log

cd /home/cper2/BeneMin/Freesurfer
/applications/freesurfer/freesurfer_6.0.0/bin/mri_glmfit-sim
--glmdir lh.5.lgi_MAN_new.glmdir --cache 2 neg --cwp 0.05 --2spaces

$Id: mri_glmfit-sim,v 1.66 2016/11/16 20:52:22 greve Exp $
Fri Nov 16 09:38:40 GMT 2018
Linux wbic-gate-2 3.16.0-6-amd64 #1 SMP Debian 3.16.57-2 (2018-07-14) 
x86_64 GNU/Linux
cper2
setenv SUBJECTS_DIR /home/cper2/BeneMin/Freesurfer
FREESURFER_HOME /applications/freesurfer/freesurfer_6.0.0

Original mri_glmfit command line:
cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt 
dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C 
contrast_dods.txt

DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 26.134985
CSD 
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/neg/th20/mc-z.csd
mri_surfcluster --in lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh 
--mask lh.5.lgi_MAN_new.glmdir/mask.mgh --cwsig 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.cluster.mgh 
--sum 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.cluster.summary 
--ocn 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.ocn.mgh 
--annot aparc --cwpvalthresh 0.05 --o 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.masked.mgh 
--no-fixmni --csd 
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/neg/th20/mc-z.csd
 
--csdpdf 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.pdf.dat --vwsig 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.voxel.mgh 
--vwsigmax 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.voxel.max.dat 
--oannot 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.ocn.annot 
--bonferroni 2 --surf white
Creating CDFs from CSD files
csd->threshsign = -1
thsign = neg, id = -1
version $Id: mri_surfcluster.c,v 1.60 2016/11/01 19:49:22 greve Exp $
hemi   = lh
srcid  = lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh
srcsubjid  = fsaverage
srcsurf= white
srcframe   = 0
thsign = neg
thmin  = 2
thmax  = -1
fdr= -1
minarea= 0
Bonferroni  = 2
xfmfile= talairach.xfm
nth = -1
outid= 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.masked.mgh 
MGH
ocnid= 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.ocn.mgh MGH
sumfile  = 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.cluster.summary
subjectsdir= /home/cper2/BeneMin/Freesurfer
FixMNI = 0
Found 149955 vertices in mask
Found 149955 vertices in mask
Found 149955 points in clabel.
- XFM matrix (RAS2RAS) ---
/home/cper2/BeneMin/Freesurfer/fsaverage/mri/transforms/talairach.xfm
  1.0   0.0   0.0   0.0;
  0.0   1.0   0.0   0.0;
  0.0   0.0   1.0   0.0;
  0.0   0.0   0.0   1.0;
MRISread(?): could not open file
No such file or directory

Reading source surface 
/home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white
mri_surfcluster.bin: could not read surface 
/home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white
No such file or directory

However, the files 
/home/cper2/BeneMin/Freesurfer/fsaverage/mri/transforms/talairach.xfm 
and /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white both exist 
and I can read them looking at the permissions.

I was wondering if you might have any advice for this.

Many thanks,
Colleen

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Re: [Freesurfer] mri_glmfit-sim error

[C.P.E. Rollins]

External Email - Use Caution

Hi Douglas,
Yes, the file 
(/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/surf/rh.white) 
exists, I can view it in Freeview and have read permissions.

I had recently tried downloading this patch: 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/ as I 
was equally having issues with make_average_subject and had found this 
forum post: 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg57023.html

Not sure if the problem might then be with mri_surfcluster.bin ?
Thanks again,
Colleen

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Re: [Freesurfer] mri_glmfit-sim error

[Greve, Douglas N.,Ph.D.]

Can you verify that the followign file exists, that you have read permission, 
and that you can successfully load it into freeview? 
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/surf/rh.white

On 9/21/18 11:41 AM, C.P.E. Rollins wrote:
   External Email - Use Caution
Hello Freesurfer Developpers,

I'm trying to use mri_glmfit-sim to make clusterwise corrections but am running 
into the following error:
- XFM matrix (RAS2RAS) ---
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/mri/transforms/talairach.xfm
 1.0   0.0   0.0   0.0;
 0.0   1.0   0.0   0.0;
 0.0   0.0   1.0   0.0;
 0.0   0.0   0.0   1.0;
MRISread('\ufffd\ufffd): could not open file
No such file or directory

Reading source surface 
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/surf/rh.white
mri_surfcluster.bin: could not read surface 
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/surf/rh.white
No such file or directory

I've attached here the log file. I was wondering if you had any insights into 
the error?

Thanks a lot for your help.

Colleen



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[Freesurfer] mri_glmfit-sim error

[C.P.E. Rollins]

   External Email - Use Caution


Hello Freesurfer Developpers,

I'm trying to use mri_glmfit-sim to make clusterwise corrections but am 
running into the following error:

- XFM matrix (RAS2RAS) ---
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/mri/transforms/talairach.xfm
 1.0   0.0   0.0   0.0;
 0.0   1.0   0.0   0.0;
 0.0   0.0   1.0   0.0;
 0.0   0.0   0.0   1.0;
MRISread('\ufffd\ufffd): could not open file
No such file or directory

Reading source surface 
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/surf/rh.white
mri_surfcluster.bin: could not read surface 
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/surf/rh.white

No such file or directory

I've attached here the log file. I was wondering if you had any insights 
into the error?


Thanks a lot for your help.

Colleen
cd /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer
/applications/freesurfer/freesurfer_6.0.0/bin/mri_glmfit-sim
--glmdir rh.10.thickness.glmdir --cache 2 abs --cwp 0.05 --2spaces

$Id: mri_glmfit-sim,v 1.60.2.4 2016/11/17 18:01:28 zkaufman Exp $
Fri Sep 21 16:21:47 BST 2018
Linux wbic-gate-1 3.16.0-6-amd64 #1 SMP Debian 3.16.57-2 (2018-07-14) x86_64 
GNU/Linux
cper2
setenv SUBJECTS_DIR /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer
FREESURFER_HOME /applications/freesurfer/freesurfer_6.0.0

Original mri_glmfit command line:
cmdline mri_glmfit.bin --y rh.10.thickness.post.mgh --fsgd FSGD.txt doss --C 
contrast_doss.txt --surf fsaverage rh --cortex --glmdir rh.10.thickness.glmdir

DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = doss
fwhm = 14.003044
CSD 
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/rh/cortex/fwhm14/abs/th20/mc-z.csd
mri_surfcluster --in rh.10.thickness.glmdir/contrast_doss.txt/sig.mgh --mask 
rh.10.thickness.glmdir/mask.mgh --cwsig 
rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.cluster.mgh --sum 
rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.cluster.summary 
--ocn rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.ocn.mgh 
--annot aparc --cwpvalthresh 0.05 --o 
rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.masked.mgh 
--no-fixmni --csd 
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/rh/cortex/fwhm14/abs/th20/mc-z.csd
 --csdpdf rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.pdf.dat 
--vwsig rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.voxel.mgh 
--vwsigmax 
rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.voxel.max.dat 
--oannot rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.ocn.annot 
--bonferroni 2 --surf white
Creating CDFs from CSD files
csd->threshsign = 0
thsign = abs, id = 0
version $Id: mri_surfcluster.c,v 1.60 2016/11/01 19:49:22 greve Exp $
hemi   = rh
srcid  = rh.10.thickness.glmdir/contrast_doss.txt/sig.mgh 
srcsubjid  = fsaverage
srcsurf= white
srcframe   = 0
thsign = abs
thmin  = 2
thmax  = -1
fdr= -1
minarea= 0
Bonferroni  = 2
xfmfile= talairach.xfm
nth = -1
outid= 
rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.masked.mgh MGH
ocnid= rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.ocn.mgh 
MGH
sumfile  = 
rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.cluster.summary
subjectsdir= /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer
FixMNI = 0
Found 148285 vertices in mask
Found 148285 vertices in mask
Found 148285 points in clabel.
- XFM matrix (RAS2RAS) ---
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/mri/transforms/talairach.xfm
 1.0   0.0   0.0   0.0;
 0.0   1.0   0.0   0.0;
 0.0   0.0   1.0   0.0;
 0.0   0.0   0.0   1.0;

Reading source surface 
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/surf/rh.white
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Re: [Freesurfer] mri_glmfit-sim ERROR cannot find mc-z.csd file

[Douglas N Greve]

Is  this for a volume analysis? If so, then you'll need to use the --grf 
option instead of using the mcz simulations (those are just for surface)


On 07/08/2017 01:03 PM, Aly Negreira wrote:
> Hi Doug!
>
> Thank you for the reply! Re-ran w/ --debug as first option. Below is 
> the output. Not sure if this is helpful, but when I cd to 
> /Applications/freesurfer/average/mult-comp-cor/fsaverage
> there are only directories for lh and rh, nothing for mni.
>
> Thanks for the help!
>
> Aly
>
>  Alysons-iMac:~/analyses/EMOT_REG_FX_DISS] aneg% mri_glmfit-sim \  
> --debug \
>
>   --glmdir 
> GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/
>  
> \
>
>   --cache 1.3 abs \
>
>   --cwp  0.05\
>
>   --3spaces \? --debug \
>
> ?   --glmdir 
> GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/
>  
> \
>
> ?   --cache 1.3 abs \
>
> ?   --cwp  0.05\
>
> ?   --3spaces \
>
> ?
>
> set echo = 1 ;
>
> breaksw
>
> breaksw
>
>
> end
>
> end
>
> while ( $#argv != 0 )
>
> while ( 8 != 0 )
>
>
> set flag = $argv[1] ; shift ;
>
> set flag = --glmdir
>
> shift
>
>
> switch ( $flag )
>
> switch ( --glmdir )
>
> if ( $#argv < 0 ) goto arg1err ;
>
> if ( 7 < 0 ) goto arg1err
>
> set glmdir = $argv[1] ; shift ;
>
> set glmdir = 
> GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/
>
> shift
>
> breaksw
>
> breaksw
>
>
> end
>
> end
>
> while ( $#argv != 0 )
>
> while ( 6 != 0 )
>
>
> set flag = $argv[1] ; shift ;
>
> set flag = --cache
>
> shift
>
>
> switch ( $flag )
>
> switch ( --cache )
>
> if ( $#argv < 2 ) goto arg2err ;
>
> if ( 5 < 2 ) goto arg2err
>
> set thresh = $argv[1] ; shift ;
>
> set thresh = 1.3
>
> shift
>
> set simsign = $argv[1] ; shift ;
>
> set simsign = abs
>
> shift
>
> set UseCache = 1 ;
>
> set UseCache = 1
>
> set DoSim = 0 ;
>
> set DoSim = 0
>
> set thresh = `printf %2.1f $thresh`
>
> set thresh = `printf %2.1f $thresh`
>
> printf %2.1f 1.3
>
> if ( $thresh != 1.3 && $thresh != 2.0 && $thresh != 2.3 && $thresh != 
> 3.0 && $thresh != 3.3 && $thresh != 4.0 ) then
>
> if ( 1.3 != 1.3 && 1.3 != 2.0 && 1.3 != 2.3 && 1.3 != 3.0 && 1.3 != 
> 3.3 && 1.3 != 4.0 ) then
>
> breaksw
>
> breaksw
>
>
> end
>
> end
>
> while ( $#argv != 0 )
>
> while ( 3 != 0 )
>
>
> set flag = $argv[1] ; shift ;
>
> set flag = --cwp
>
> shift
>
>
> switch ( $flag )
>
> switch ( --cwp )
>
> case "--cwpvalthresh":
>
> case --cwpvalthresh:
>
> if ( $#argv < 1 ) goto arg1err ;
>
> if ( 2 < 1 ) goto arg1err
>
> set cwpvalthresh = $argv[1] ; shift ;
>
> set cwpvalthresh = 0.05
>
> shift
>
> breaksw
>
> breaksw
>
>
> end
>
> end
>
> while ( $#argv != 0 )
>
> while ( 1 != 0 )
>
>
> set flag = $argv[1] ; shift ;
>
> set flag = --3spaces
>
> shift
>
>
> switch ( $flag )
>
> switch ( --3spaces )
>
> set Bonferroni = 3 ;
>
> set Bonferroni = 3
>
> breaksw
>
> breaksw
>
>
> end
>
> end
>
> while ( $#argv != 0 )
>
> while ( 0 != 0 )
>
>
> goto parse_args_return ;
>
> goto parse_args_return
>
>
> goto check_params ;
>
> goto check_params
>
> if ( $#glmdir == 0 ) then
>
> if ( 1 == 0 ) then
>
> if ( $DoSim ) then
>
> if ( 0 ) then
>
>
> if ( $DiagCluster && $DoBackground ) then
>
> if ( 0 && 0 ) then
>
> if ( $DiagCluster && $DoPBSubmit ) then
>
> if ( 0 && 0 ) then
>
> if ( $DiagCluster && $DoSim == 0 ) then
>
> if ( 0 && 0 == 0 ) then
>
>
> goto check_params_return ;
>
> goto check_params_return
>
>
> if ( ! -e $glmdir ) then
>
> if ( ! -e 
> GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/
>  
> ) then
>
>
> set glmfitlog = $glmdir/mri_glmfit.log
>
> set glmfitlog = 
> GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log
>
> if ( ! -e $glmfitlog ) then
>
> if ( ! -e 
> GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log
>  
> ) then
>
>
> set mask = `stem2fname $glmdir/mask`
>
> set mask = `stem2fname $glmdir/mask`
>
> stem2fname 
> GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mask
>
> if ( $status ) then
>
> if ( 0 ) then
>
>
> if ( $nulltype != perm ) then
>
> if ( != perm ) then
>
> set fwhmfile = $glmdir/fwhm.dat
>
> set fwhmfile = 
> GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//fwhm.dat
>
> if ( ! -e $fwhmfile ) then
>
> if ( ! -e 
> GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//fwhm.dat
>  
> ) then
>
>
> set fwhm = `cat $fwhmfile` ;
>
> set fwhm = `cat $fwhmfile`
>
> cat 
> 

Re: [Freesurfer] mri_glmfit-sim ERROR cannot find mc-z.csd file

[Aly Negreira]

Hi Doug!

Thank you for the reply! Re-ran w/ --debug as first option. Below is the
output. Not sure if this is helpful, but when I cd to
/Applications/freesurfer/average/mult-comp-cor/fsaverage
there are only directories for lh and rh, nothing for mni.

Thanks for the help!

Aly

 Alysons-iMac:~/analyses/EMOT_REG_FX_DISS] aneg% mri_glmfit-sim \  --debug \

  --glmdir
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/
\

  --cache 1.3 abs \

  --cwp  0.05\

  --3spaces \?   --debug \

?   --glmdir
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/
\

?   --cache 1.3 abs \

?   --cwp  0.05\

?   --3spaces \

?

set echo = 1 ;

breaksw

breaksw


end

end

while ( $#argv != 0 )

while ( 8 != 0 )


set flag = $argv[1] ; shift ;

set flag = --glmdir

shift


switch ( $flag )

switch ( --glmdir )

if ( $#argv < 0 ) goto arg1err ;

if ( 7 < 0 ) goto arg1err

set glmdir = $argv[1] ; shift ;

set glmdir =
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/

shift

breaksw

breaksw


end

end

while ( $#argv != 0 )

while ( 6 != 0 )


set flag = $argv[1] ; shift ;

set flag = --cache

shift


switch ( $flag )

switch ( --cache )

if ( $#argv < 2 ) goto arg2err ;

if ( 5 < 2 ) goto arg2err

set thresh = $argv[1] ; shift ;

set thresh = 1.3

shift

set simsign = $argv[1] ; shift ;

set simsign = abs

shift

set UseCache = 1 ;

set UseCache = 1

set DoSim = 0 ;

set DoSim = 0

set thresh = `printf %2.1f $thresh`

set thresh = `printf %2.1f $thresh`

printf %2.1f 1.3

if ( $thresh != 1.3 && $thresh != 2.0 && $thresh != 2.3 && $thresh != 3.0
&& $thresh != 3.3 && $thresh != 4.0 ) then

if ( 1.3 != 1.3 && 1.3 != 2.0 && 1.3 != 2.3 && 1.3 != 3.0 && 1.3 != 3.3 &&
1.3 != 4.0 ) then

breaksw

breaksw


end

end

while ( $#argv != 0 )

while ( 3 != 0 )


set flag = $argv[1] ; shift ;

set flag = --cwp

shift


switch ( $flag )

switch ( --cwp )

case "--cwpvalthresh":

case --cwpvalthresh:

if ( $#argv < 1 ) goto arg1err ;

if ( 2 < 1 ) goto arg1err

set cwpvalthresh = $argv[1] ; shift ;

set cwpvalthresh = 0.05

shift

breaksw

breaksw


end

end

while ( $#argv != 0 )

while ( 1 != 0 )


set flag = $argv[1] ; shift ;

set flag = --3spaces

shift


switch ( $flag )

switch ( --3spaces )

set Bonferroni = 3 ;

set Bonferroni = 3

breaksw

breaksw


end

end

while ( $#argv != 0 )

while ( 0 != 0 )


goto parse_args_return ;

goto parse_args_return


goto check_params ;

goto check_params

if ( $#glmdir == 0 ) then

if ( 1 == 0 ) then

if ( $DoSim ) then

if ( 0 ) then


if ( $DiagCluster && $DoBackground ) then

if ( 0 && 0 ) then

if ( $DiagCluster && $DoPBSubmit ) then

if ( 0 && 0 ) then

if ( $DiagCluster && $DoSim == 0 ) then

if ( 0 && 0 == 0 ) then


goto check_params_return ;

goto check_params_return


if ( ! -e $glmdir ) then

if ( ! -e
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/
) then


set glmfitlog = $glmdir/mri_glmfit.log

set glmfitlog =
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log

if ( ! -e $glmfitlog ) then

if ( ! -e
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log
) then


set mask = `stem2fname $glmdir/mask`

set mask = `stem2fname $glmdir/mask`

stem2fname
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mask

if ( $status ) then

if ( 0 ) then


if ( $nulltype != perm ) then

if ( != perm ) then

set fwhmfile = $glmdir/fwhm.dat

set fwhmfile =
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//fwhm.dat

if ( ! -e $fwhmfile ) then

if ( ! -e
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//fwhm.dat
) then


set fwhm = `cat $fwhmfile` ;

set fwhm = `cat $fwhmfile`

cat
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//fwhm.dat

else

else


set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`

set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`

cat
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log

awk {if($1 == "cwd") print $2}

if ( ! -e $glmfitcwd ) then

if ( ! -e /Users/aneg/analyses/EMOT_REG_FX_DISS ) then


set anattype = volume ;

set anattype = volume

set subject = ( ) ;

set subject = ( )

set hemi = ( ) ;

set hemi = ( )

set surf = "white" ;

set surf = white

set y = ( ) ;

set y = ( )

set wls = ( ) ;

set wls = ( )


set glmfitcwd = `cat $glmfitlog | awk '{if($1 

Re: [Freesurfer] mri_glmfit-sim ERROR cannot find mc-z.csd file

[Douglas Greve]

Hi Aly, it is not creating the path correctly, not sure why. Can you run 
it again with --debug as the first option and send me the terminal output?


doug



On 7/1/17 1:57 PM, Aly Negreira wrote:

Hi Freesurfer Community,

I'm using FsFast on my dissertation data and trying to run a monte 
carlo correction on my functional data in the volume. I keep running 
into the below error. In attempting to troubleshoot, it looks like 
Yuko ran into a similiar issue (see archived email from Fri Dec 9 @ 
12:26:46 EST in 2011) just not sure how to fix it! Please adviceI 
just want my PhD already!


Thank you!

Aly


ERROR: cannot find 
/Applications/freesurfer/average/mult-comp-cor///cortex/fwhm10/abs/th13/mc-z.csd

COMMAND:
mri_glmfit-sim \
--glmdir 
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ 
\

  --cache 1.3 abs \
  --cwp  0.05\
  --3spaces


MAC INFO:
OS X El Capitan Version 10.11.6


FREESURFER VERSION:
 freesurfer-Darwin-lion-stable-pub-v5.3.0 




___
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


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 Partners Compliance HelpLine at
http://www.partners.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 the e-mail.

[Freesurfer] mri_glmfit-sim ERROR cannot find mc-z.csd file

[Aly Negreira]

Hi Freesurfer Community,

I'm using FsFast on my dissertation data and trying to run a monte carlo
correction on my functional data in the volume. I keep running into the
below error. In attempting to troubleshoot, it looks like Yuko ran into a
similiar issue (see archived email from Fri Dec 9 @ 12:26:46 EST in 2011)
just not sure how to fix it! Please adviceI just want my PhD already!

Thank you!

Aly


ERROR: cannot find
/Applications/freesurfer/average/mult-comp-cor///cortex/fwhm10/abs/th13/mc-z.csd
COMMAND:
mri_glmfit-sim \
--glmdir
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/
\
  --cache 1.3 abs \
  --cwp  0.05\
  --3spaces


MAC INFO:
OS X El Capitan Version 10.11.6


FREESURFER VERSION:
 freesurfer-Darwin-lion-stable-pub-v5.3.0 
___
Freesurfer mailing list
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 Partners Compliance HelpLine at
http://www.partners.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 the e-mail.

Re: [Freesurfer] mri_glmfit-sim error

[Douglas Greve]

how did you compute the difference? Can you send the mris_preproc and 
mri_surf2surf command lines?

On 5/9/16 10:26 PM, Govindarajan, Koushik Athreya wrote:
> First did the mris_preproc and then the mri_surf2surf. Followed the group 
> analysis wiki basically.
>
> Thanks
> Koushik
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, May 09, 2016 5:30 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_glmfit-sim error
>
> It looks like over half your voxels have been pruned because they have
> value identical to 0 in at least one subject
>
> Found 149926 points in label.
> Pruning voxels by thr: 0.00
> Found 65950 voxels in mask
>
> How did you create rh.paired-diff.thickness.sm05.mgh?
>
>
>
> On 05/09/2016 10:24 AM, Govindarajan, Koushik Athreya wrote:
>> This is the command line output for mri_glmfit:
>>
>> 
>> [adits123@localhost projectoutputdata]$ mri_glmfit --glmdir 
>> rh.paired-diff.glmdir --y rh.paired-diff.thickness.sm05.mgh --fsgd 
>> paireddifftp1tp2.txt --C contrastpaired.mtx --surf fsaverage rh
>> gdfReadHeader: reading paireddifftp1tp2.txt
>> INFO: gd2mtx_method is dods
>> Reading source surface 
>> /home/adits123/Desktop/projectoutputdata/fsaverage/surf/rh.white
>> Number of vertices 163842
>> Number of faces327680
>> Total area 65020.765625
>> AvgVtxArea   0.396850
>> AvgVtxDist   0.717994
>> StdVtxDist   0.193566
>>
>> $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
>> cwd /home/adits123/Desktop/projectoutputdata
>> cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y 
>> rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C 
>> contrastpaired.mtx --surf fsaverage rh
>> sysname  Linux
>> hostname localhost.localdomain
>> machine  x86_64
>> user adits123
>> FixVertexAreaFlag = 1
>> UseMaskWithSmoothing 1
>> OneSampleGroupMean 0
>> y
>> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh
>> logyflag 0
>> usedti  0
>> FSGD paireddifftp1tp2.txt
>> labelmask  
>> /home/adits123/Desktop/projectoutputdata/fsaverage/label/rh.cortex.label
>> maskinv 0
>> glmdir rh.paired-diff.glmdir
>> IllCondOK 0
>> ReScaleX 1
>> DoFFx 0
>> Creating output directory rh.paired-diff.glmdir
>> Loading y from 
>> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh
>> INFO: gd2mtx_method is dods
>> Saving design matrix to rh.paired-diff.glmdir/Xg.dat
>> Normalized matrix condition is 1
>> Matrix condition is 1
>> Found 149926 points in label.
>> Pruning voxels by thr: 0.00
>> Found 65950 voxels in mask
>> Saving mask to rh.paired-diff.glmdir/mask.mgh
>> Reshaping mriglm->mask...
>> search space = 32101.581527
>> DOF = 364
>> Starting fit and test
>> Fit completed in 0.03265 minutes
>> Computing spatial AR1 on surface
>> Residual: ar1mn=inf, ar1std=-nan, gstd=-nan, fwhm=-nan
>> Writing results
>> contrastpaired
>>   maxvox sig=4.51832  F=17.8453  at  index 50390 0 0seed=1463164810
>> mri_glmfit done
>>
>> ---
>>
>>
>> This is mri_glmfit-sim:
>> ---
>> [adits123@localhost projectoutputdata]$ mri_glmfit-sim --glmdir 
>> $SUBJECTS_DIR/rh.paired-diff.glmdir --sim mc-z 1 1.3 mc-z.pos.1.3 
>> --sim-sign pos --cwpvalthresh 0.05
>> cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y 
>> rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C 
>> contrastpaired.mtx --surf fsaverage rh
>> SURFACE: fsaverage rh
>> log file is 
>> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/mc-z.pos.1.3.mri_glmfit-sim.log
>>
>> cd /home/adits123/Desktop/projectoutputdata
>> /usr/local/freesurfer/bin/mri_glmfit-sim
>> --glmdir /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir 
>> --sim mc-z 1 1.3 mc-z.pos.1.3 --sim-sign pos --cwpvalthresh 0.05
>>
>> $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
>> Mon May  9 09:11:28 CDT 2016
>> 

Re: [Freesurfer] mri_glmfit-sim error

[Govindarajan, Koushik Athreya]

First did the mris_preproc and then the mri_surf2surf. Followed the group 
analysis wiki basically.

Thanks
Koushik


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, May 09, 2016 5:30 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_glmfit-sim error

It looks like over half your voxels have been pruned because they have
value identical to 0 in at least one subject

Found 149926 points in label.
Pruning voxels by thr: 0.00
Found 65950 voxels in mask

How did you create rh.paired-diff.thickness.sm05.mgh?



On 05/09/2016 10:24 AM, Govindarajan, Koushik Athreya wrote:
> This is the command line output for mri_glmfit:
>
> 
> [adits123@localhost projectoutputdata]$ mri_glmfit --glmdir 
> rh.paired-diff.glmdir --y rh.paired-diff.thickness.sm05.mgh --fsgd 
> paireddifftp1tp2.txt --C contrastpaired.mtx --surf fsaverage rh
> gdfReadHeader: reading paireddifftp1tp2.txt
> INFO: gd2mtx_method is dods
> Reading source surface 
> /home/adits123/Desktop/projectoutputdata/fsaverage/surf/rh.white
> Number of vertices 163842
> Number of faces327680
> Total area 65020.765625
> AvgVtxArea   0.396850
> AvgVtxDist   0.717994
> StdVtxDist   0.193566
>
> $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
> cwd /home/adits123/Desktop/projectoutputdata
> cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y 
> rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C 
> contrastpaired.mtx --surf fsaverage rh
> sysname  Linux
> hostname localhost.localdomain
> machine  x86_64
> user adits123
> FixVertexAreaFlag = 1
> UseMaskWithSmoothing 1
> OneSampleGroupMean 0
> y
> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh
> logyflag 0
> usedti  0
> FSGD paireddifftp1tp2.txt
> labelmask  
> /home/adits123/Desktop/projectoutputdata/fsaverage/label/rh.cortex.label
> maskinv 0
> glmdir rh.paired-diff.glmdir
> IllCondOK 0
> ReScaleX 1
> DoFFx 0
> Creating output directory rh.paired-diff.glmdir
> Loading y from 
> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh
> INFO: gd2mtx_method is dods
> Saving design matrix to rh.paired-diff.glmdir/Xg.dat
> Normalized matrix condition is 1
> Matrix condition is 1
> Found 149926 points in label.
> Pruning voxels by thr: 0.00
> Found 65950 voxels in mask
> Saving mask to rh.paired-diff.glmdir/mask.mgh
> Reshaping mriglm->mask...
> search space = 32101.581527
> DOF = 364
> Starting fit and test
> Fit completed in 0.03265 minutes
> Computing spatial AR1 on surface
> Residual: ar1mn=inf, ar1std=-nan, gstd=-nan, fwhm=-nan
> Writing results
>contrastpaired
>  maxvox sig=4.51832  F=17.8453  at  index 50390 0 0seed=1463164810
> mri_glmfit done
>
> ---
>
>
> This is mri_glmfit-sim:
> ---
> [adits123@localhost projectoutputdata]$ mri_glmfit-sim --glmdir 
> $SUBJECTS_DIR/rh.paired-diff.glmdir --sim mc-z 1 1.3 mc-z.pos.1.3 
> --sim-sign pos --cwpvalthresh 0.05
> cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y 
> rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C 
> contrastpaired.mtx --surf fsaverage rh
> SURFACE: fsaverage rh
> log file is 
> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/mc-z.pos.1.3.mri_glmfit-sim.log
>
> cd /home/adits123/Desktop/projectoutputdata
> /usr/local/freesurfer/bin/mri_glmfit-sim
> --glmdir /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir --sim 
> mc-z 1 1.3 mc-z.pos.1.3 --sim-sign pos --cwpvalthresh 0.05
>
> $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
> Mon May  9 09:11:28 CDT 2016
> Linux localhost.localdomain 2.6.32-250.el6.x86_64 #1 SMP Tue Mar 6 23:00:19 
> EST 2012 x86_64 x86_64 x86_64 GNU/Linux
> adits123
> setenv SUBJECTS_DIR /home/adits123/Desktop/projectoutputdata
> FREESURFER_HOME /usr/local/freesurfer
>
> Original mri_glmfit command line:
> cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y 
> rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C 
> contrastpaired.mtx --surf fsaverage rh
>
> DoSim = 1
> UseCache = 0
> DoPoll = 0
> DoPBSubmit = 0
> DoBackground = 0
> DiagCluster = 0
> gd2mtx = dods
> fwhm = -nan
> nSimPerJ

Re: [Freesurfer] mri_glmfit-sim error

[Douglas N Greve]

top/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001
>  --sim-sign pos --fwhm -nan --fsgd 
> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/y.fsgd dods 
> --surf fsaverage rh white
> simbase 
> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001
> FWHM = -nan
> ERROR: input FWHM is NaN (not a number).
>Check the mask in the glm directory.
> Mon May  9 09:11:28 CDT 2016
> ERROR: cannot find any csd files
>
> -------------
>
> Many thanks for helping me with this Doug.
>
> Regards
> Koushik
>
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, May 06, 2016 3:21 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_glmfit-sim error
>
> something is going wrong because the FWHM is not-a-number (nan). Can you
> send the actual terminal output and not just the log file?
>
> On 05/06/2016 11:55 AM, Govindarajan, Koushik Athreya wrote:
>> Thanks for the reply Doug. This is content of my mri_glmfit.log:
>>
>> ---
>> $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
>> cwd /home/adits123/Desktop/projectoutputdata
>> cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y 
>> rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C 
>> contrastpaired.mtx --surf fsaverage rh
>> sysname  Linux
>> hostname localhost.localdomain
>> machine  x86_64
>> user adits123
>> FixVertexAreaFlag = 1
>> UseMaskWithSmoothing 1
>> OneSampleGroupMean 0
>> y
>> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh
>> logyflag 0
>> usedti  0
>> FSGD paireddifftp1tp2.txt
>> labelmask  
>> /home/adits123/Desktop/projectoutputdata/fsaverage/label/rh.cortex.label
>> maskinv 0
>> glmdir rh.paired-diff.glmdir
>> IllCondOK 0
>> ReScaleX 1
>> DoFFx 0
>> ResidualFWHM -nan
>> SearchSpace 32101.581527
>> anattype surface
>> -
>>
>> The left hemisphere says pretty much the same thing, with the ResidualFWHM 
>> 0.00 and SearchSpace 44094.721767
>>
>> Thanks
>> Koushik
>>
>> ___
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Friday, May 06, 2016 10:46 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] mri_glmfit-sim error
>>
>> The problem is with the estimate of the FWHM for that run. Can you
>> re-run mri_glmfit and send me the command line and terminal output?
>>
>> On 05/06/2016 10:27 AM, Govindarajan, Koushik Athreya wrote:
>>> Dear FS experts,
>>>
>>>   I ran into an error with one of my mri_glmfit-sim execution
>>> and was not sure what was going on. The same simulation is currently
>>> running for the left hemisphere without any hiccups but I get this
>>> following error for the right hemisphere:
>>> ---
>>> cd /home/adits123/Desktop/projectoutputdata
>>> /usr/local/freesurfer/bin/mri_glmfit-sim
>>> --glmdir
>>> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir --sim
>>> mc-z 1 1.3 mc-z.pos.1.3 --sim-sign pos --cwpvalthresh 0.05
>>>
>>> $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
>>> Thu May  5 13:16:51 CDT 2016
>>> Linux localhost.localdomain 2.6.32-250.el6.x86_64 #1 SMP Tue Mar 6
>>> 23:00:19 EST 2012 x86_64 x86_64 x86_64 GNU/Linux
>>> adits123
>>> setenv SUBJECTS_DIR /home/adits123/Desktop/projectoutputdata
>>> FREESURFER_HOME /usr/local/freesurfer
>>>
>>> Original mri_glmfit command line:
>>> cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y
>>> rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C
>>> contrastpaired.mtx --surf fsaverage rh
>>>
>>> DoSim = 1
>>> UseCache = 0
>>> DoPoll 

Re: [Freesurfer] mri_glmfit-sim error

[Govindarajan, Koushik Athreya]

 Re: [Freesurfer] mri_glmfit-sim error

something is going wrong because the FWHM is not-a-number (nan). Can you
send the actual terminal output and not just the log file?

On 05/06/2016 11:55 AM, Govindarajan, Koushik Athreya wrote:
> Thanks for the reply Doug. This is content of my mri_glmfit.log:
>
> ---
> $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
> cwd /home/adits123/Desktop/projectoutputdata
> cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y 
> rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C 
> contrastpaired.mtx --surf fsaverage rh
> sysname  Linux
> hostname localhost.localdomain
> machine  x86_64
> user adits123
> FixVertexAreaFlag = 1
> UseMaskWithSmoothing 1
> OneSampleGroupMean 0
> y
> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh
> logyflag 0
> usedti  0
> FSGD paireddifftp1tp2.txt
> labelmask  
> /home/adits123/Desktop/projectoutputdata/fsaverage/label/rh.cortex.label
> maskinv 0
> glmdir rh.paired-diff.glmdir
> IllCondOK 0
> ReScaleX 1
> DoFFx 0
> ResidualFWHM -nan
> SearchSpace 32101.581527
> anattype surface
> -
>
> The left hemisphere says pretty much the same thing, with the ResidualFWHM 
> 0.00 and SearchSpace 44094.721767
>
> Thanks
> Koushik
>
> ___
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, May 06, 2016 10:46 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_glmfit-sim error
>
> The problem is with the estimate of the FWHM for that run. Can you
> re-run mri_glmfit and send me the command line and terminal output?
>
> On 05/06/2016 10:27 AM, Govindarajan, Koushik Athreya wrote:
>> Dear FS experts,
>>
>>  I ran into an error with one of my mri_glmfit-sim execution
>> and was not sure what was going on. The same simulation is currently
>> running for the left hemisphere without any hiccups but I get this
>> following error for the right hemisphere:
>> ---
>> cd /home/adits123/Desktop/projectoutputdata
>> /usr/local/freesurfer/bin/mri_glmfit-sim
>> --glmdir
>> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir --sim
>> mc-z 1 1.3 mc-z.pos.1.3 --sim-sign pos --cwpvalthresh 0.05
>>
>> $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
>> Thu May  5 13:16:51 CDT 2016
>> Linux localhost.localdomain 2.6.32-250.el6.x86_64 #1 SMP Tue Mar 6
>> 23:00:19 EST 2012 x86_64 x86_64 x86_64 GNU/Linux
>> adits123
>> setenv SUBJECTS_DIR /home/adits123/Desktop/projectoutputdata
>> FREESURFER_HOME /usr/local/freesurfer
>>
>> Original mri_glmfit command line:
>> cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y
>> rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C
>> contrastpaired.mtx --surf fsaverage rh
>>
>> DoSim = 1
>> UseCache = 0
>> DoPoll = 0
>> DoPBSubmit = 0
>> DoBackground = 0
>> DiagCluster = 0
>> gd2mtx = dods
>> fwhm = -nan
>> nSimPerJob = 1
>> 1/1 Thu May  5 13:16:51 CDT 2016
>> mri_glmfit --y
>> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh
>> --C
>> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/tmp.mri_glmfit-sim-931/contrastpaired.mtx
>> --mask
>> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/mask.mgh --sim
>> mc-z 1 1.3
>> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001
>> --sim-sign pos --fwhm -nan --fsgd
>> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/y.fsgd
>> dods --surf fsaverage rh white
>> simbase
>> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001
>> FWHM = -nan
>> ERROR: input FWHM is NaN (not a number).
>>Check the mask in the glm directory.
>> Thu May  5 13:16:51 CDT 2016
>> ERROR: cannot find any csd files
>> 
>>
>> I am not sure what the fwhm is NaN error is and also why it is only
>> showing up for one hemisphere. Any help is appreciated.
>>
>> Thanks
>> Ko

Re: [Freesurfer] mri_glmfit-sim error

[Douglas N Greve]

something is going wrong because the FWHM is not-a-number (nan). Can you 
send the actual terminal output and not just the log file?

On 05/06/2016 11:55 AM, Govindarajan, Koushik Athreya wrote:
> Thanks for the reply Doug. This is content of my mri_glmfit.log:
>
> ---
> $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
> cwd /home/adits123/Desktop/projectoutputdata
> cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y 
> rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C 
> contrastpaired.mtx --surf fsaverage rh
> sysname  Linux
> hostname localhost.localdomain
> machine  x86_64
> user adits123
> FixVertexAreaFlag = 1
> UseMaskWithSmoothing 1
> OneSampleGroupMean 0
> y
> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh
> logyflag 0
> usedti  0
> FSGD paireddifftp1tp2.txt
> labelmask  
> /home/adits123/Desktop/projectoutputdata/fsaverage/label/rh.cortex.label
> maskinv 0
> glmdir rh.paired-diff.glmdir
> IllCondOK 0
> ReScaleX 1
> DoFFx 0
> ResidualFWHM -nan
> SearchSpace 32101.581527
> anattype surface
> -
>
> The left hemisphere says pretty much the same thing, with the ResidualFWHM 
> 0.00 and SearchSpace 44094.721767
>
> Thanks
> Koushik
>
> ___
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, May 06, 2016 10:46 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_glmfit-sim error
>
> The problem is with the estimate of the FWHM for that run. Can you
> re-run mri_glmfit and send me the command line and terminal output?
>
> On 05/06/2016 10:27 AM, Govindarajan, Koushik Athreya wrote:
>> Dear FS experts,
>>
>>  I ran into an error with one of my mri_glmfit-sim execution
>> and was not sure what was going on. The same simulation is currently
>> running for the left hemisphere without any hiccups but I get this
>> following error for the right hemisphere:
>> ---
>> cd /home/adits123/Desktop/projectoutputdata
>> /usr/local/freesurfer/bin/mri_glmfit-sim
>> --glmdir
>> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir --sim
>> mc-z 1 1.3 mc-z.pos.1.3 --sim-sign pos --cwpvalthresh 0.05
>>
>> $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
>> Thu May  5 13:16:51 CDT 2016
>> Linux localhost.localdomain 2.6.32-250.el6.x86_64 #1 SMP Tue Mar 6
>> 23:00:19 EST 2012 x86_64 x86_64 x86_64 GNU/Linux
>> adits123
>> setenv SUBJECTS_DIR /home/adits123/Desktop/projectoutputdata
>> FREESURFER_HOME /usr/local/freesurfer
>>
>> Original mri_glmfit command line:
>> cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y
>> rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C
>> contrastpaired.mtx --surf fsaverage rh
>>
>> DoSim = 1
>> UseCache = 0
>> DoPoll = 0
>> DoPBSubmit = 0
>> DoBackground = 0
>> DiagCluster = 0
>> gd2mtx = dods
>> fwhm = -nan
>> nSimPerJob = 1
>> 1/1 Thu May  5 13:16:51 CDT 2016
>> mri_glmfit --y
>> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh
>> --C
>> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/tmp.mri_glmfit-sim-931/contrastpaired.mtx
>> --mask
>> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/mask.mgh --sim
>> mc-z 1 1.3
>> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001
>> --sim-sign pos --fwhm -nan --fsgd
>> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/y.fsgd
>> dods --surf fsaverage rh white
>> simbase
>> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001
>> FWHM = -nan
>> ERROR: input FWHM is NaN (not a number).
>>Check the mask in the glm directory.
>> Thu May  5 13:16:51 CDT 2016
>> ERROR: cannot find any csd files
>> 
>>
>> I am not sure what the fwhm is NaN error is and also why it is only
>> showing up for one hemisphere. Any help is appreciated.
>>
>> Thanks
>> Koushik Govindarajan
>>
>>

Re: [Freesurfer] mri_glmfit-sim error

[Govindarajan, Koushik Athreya]

Thanks for the reply Doug. This is content of my mri_glmfit.log:

---
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /home/adits123/Desktop/projectoutputdata
cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y 
rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C 
contrastpaired.mtx --surf fsaverage rh 
sysname  Linux
hostname localhost.localdomain
machine  x86_64
user adits123
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y/home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh
logyflag 0
usedti  0
FSGD paireddifftp1tp2.txt
labelmask  
/home/adits123/Desktop/projectoutputdata/fsaverage/label/rh.cortex.label
maskinv 0
glmdir rh.paired-diff.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
ResidualFWHM -nan
SearchSpace 32101.581527
anattype surface
-

The left hemisphere says pretty much the same thing, with the ResidualFWHM 
0.00 and SearchSpace 44094.721767

Thanks
Koushik

___
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, May 06, 2016 10:46 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_glmfit-sim error

The problem is with the estimate of the FWHM for that run. Can you
re-run mri_glmfit and send me the command line and terminal output?

On 05/06/2016 10:27 AM, Govindarajan, Koushik Athreya wrote:
> Dear FS experts,
>
> I ran into an error with one of my mri_glmfit-sim execution
> and was not sure what was going on. The same simulation is currently
> running for the left hemisphere without any hiccups but I get this
> following error for the right hemisphere:
> ---
> cd /home/adits123/Desktop/projectoutputdata
> /usr/local/freesurfer/bin/mri_glmfit-sim
> --glmdir
> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir --sim
> mc-z 1 1.3 mc-z.pos.1.3 --sim-sign pos --cwpvalthresh 0.05
>
> $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
> Thu May  5 13:16:51 CDT 2016
> Linux localhost.localdomain 2.6.32-250.el6.x86_64 #1 SMP Tue Mar 6
> 23:00:19 EST 2012 x86_64 x86_64 x86_64 GNU/Linux
> adits123
> setenv SUBJECTS_DIR /home/adits123/Desktop/projectoutputdata
> FREESURFER_HOME /usr/local/freesurfer
>
> Original mri_glmfit command line:
> cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y
> rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C
> contrastpaired.mtx --surf fsaverage rh
>
> DoSim = 1
> UseCache = 0
> DoPoll = 0
> DoPBSubmit = 0
> DoBackground = 0
> DiagCluster = 0
> gd2mtx = dods
> fwhm = -nan
> nSimPerJob = 1
> 1/1 Thu May  5 13:16:51 CDT 2016
> mri_glmfit --y
> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh
> --C
> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/tmp.mri_glmfit-sim-931/contrastpaired.mtx
> --mask
> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/mask.mgh --sim
> mc-z 1 1.3
> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001
> --sim-sign pos --fwhm -nan --fsgd
> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/y.fsgd
> dods --surf fsaverage rh white
> simbase
> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001
> FWHM = -nan
> ERROR: input FWHM is NaN (not a number).
>   Check the mask in the glm directory.
> Thu May  5 13:16:51 CDT 2016
> ERROR: cannot find any csd files
> 
>
> I am not sure what the fwhm is NaN error is and also why it is only
> showing up for one hemisphere. Any help is appreciated.
>
> Thanks
> Koushik Govindarajan
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=BQIBAg=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ=1HhXPfHvKTUOPuOoWPyLoNkxq8sndV0W50bRj0rR6UU=BggIQggY76Oebm525cL3bUb9izcgjTD6_4vfkjef8D8=3c7uri11bRrp6EP-VQMGPCg9-aReCCqRqnleGrzIu60=

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: 
https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2=

Re: [Freesurfer] mri_glmfit-sim error

[Douglas N Greve]

The problem is with the estimate of the FWHM for that run. Can you 
re-run mri_glmfit and send me the command line and terminal output?

On 05/06/2016 10:27 AM, Govindarajan, Koushik Athreya wrote:
> Dear FS experts,
>
> I ran into an error with one of my mri_glmfit-sim execution 
> and was not sure what was going on. The same simulation is currently 
> running for the left hemisphere without any hiccups but I get this 
> following error for the right hemisphere:
> ---
> cd /home/adits123/Desktop/projectoutputdata
> /usr/local/freesurfer/bin/mri_glmfit-sim
> --glmdir 
> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir --sim 
> mc-z 1 1.3 mc-z.pos.1.3 --sim-sign pos --cwpvalthresh 0.05
>
> $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
> Thu May  5 13:16:51 CDT 2016
> Linux localhost.localdomain 2.6.32-250.el6.x86_64 #1 SMP Tue Mar 6 
> 23:00:19 EST 2012 x86_64 x86_64 x86_64 GNU/Linux
> adits123
> setenv SUBJECTS_DIR /home/adits123/Desktop/projectoutputdata
> FREESURFER_HOME /usr/local/freesurfer
>
> Original mri_glmfit command line:
> cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y 
> rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C 
> contrastpaired.mtx --surf fsaverage rh
>
> DoSim = 1
> UseCache = 0
> DoPoll = 0
> DoPBSubmit = 0
> DoBackground = 0
> DiagCluster = 0
> gd2mtx = dods
> fwhm = -nan
> nSimPerJob = 1
> 1/1 Thu May  5 13:16:51 CDT 2016
> mri_glmfit --y 
> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh 
> --C 
> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/tmp.mri_glmfit-sim-931/contrastpaired.mtx
>  
> --mask 
> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/mask.mgh --sim 
> mc-z 1 1.3 
> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001
>  
> --sim-sign pos --fwhm -nan --fsgd 
> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/y.fsgd 
> dods --surf fsaverage rh white
> simbase 
> /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001
> FWHM = -nan
> ERROR: input FWHM is NaN (not a number).
>   Check the mask in the glm directory.
> Thu May  5 13:16:51 CDT 2016
> ERROR: cannot find any csd files
> 
>
> I am not sure what the fwhm is NaN error is and also why it is only 
> showing up for one hemisphere. Any help is appreciated.
>
> Thanks
> Koushik Govindarajan
>
>
>
>
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[Freesurfer] mri_glmfit-sim error

[Govindarajan, Koushik Athreya]

Dear FS experts,

I ran into an error with one of my mri_glmfit-sim execution and was not 
sure what was going on. The same simulation is currently running for the left 
hemisphere without any hiccups but I get this following error for the right 
hemisphere:
---
cd /home/adits123/Desktop/projectoutputdata
/usr/local/freesurfer/bin/mri_glmfit-sim
--glmdir /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir --sim 
mc-z 1 1.3 mc-z.pos.1.3 --sim-sign pos --cwpvalthresh 0.05

$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
Thu May  5 13:16:51 CDT 2016
Linux localhost.localdomain 2.6.32-250.el6.x86_64 #1 SMP Tue Mar 6 23:00:19 EST 
2012 x86_64 x86_64 x86_64 GNU/Linux
adits123
setenv SUBJECTS_DIR /home/adits123/Desktop/projectoutputdata
FREESURFER_HOME /usr/local/freesurfer

Original mri_glmfit command line:
cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y 
rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C 
contrastpaired.mtx --surf fsaverage rh

DoSim = 1
UseCache = 0
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = -nan
nSimPerJob = 1
1/1 Thu May  5 13:16:51 CDT 2016
mri_glmfit --y 
/home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh --C 
/home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/tmp.mri_glmfit-sim-931/contrastpaired.mtx
 --mask /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/mask.mgh 
--sim mc-z 1 1.3 
/home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001
 --sim-sign pos --fwhm -nan --fsgd 
/home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/y.fsgd dods 
--surf fsaverage rh white
simbase 
/home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001
FWHM = -nan
ERROR: input FWHM is NaN (not a number).
  Check the mask in the glm directory.
Thu May  5 13:16:51 CDT 2016
ERROR: cannot find any csd files


I am not sure what the fwhm is NaN error is and also why it is only showing up 
for one hemisphere. Any help is appreciated.

Thanks
Koushik Govindarajan


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Re: [Freesurfer] mri_glmfit-sim error

[Douglas N Greve]

Use "abs" not ""

On 09/04/2015 03:20 PM, Xiaomin Yue wrote:
> Hi,
>
> I got this error when run mri_glmfit-sim: missing name for redirect. 
>  I am running freesurfer 5.3.  the command is: mri_glmfit --glmdir 
> ces.nii --cache 2 --sim-sign .  The ces.nii was generated from 
> group level analysis (isxconcat-sess).
>
> Thanks for your help.
>
> Xiaomin
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] mri_glmfit-sim error

[Xiaomin Yue]

Thanks

Xiaomin




On Tue, Sep 8, 2015 at 2:03 PM -0700, "Douglas N Greve" 
 wrote:
Use "abs" not ""

On 09/04/2015 03:20 PM, Xiaomin Yue wrote:
> Hi,
>
> I got this error when run mri_glmfit-sim: missing name for redirect.
>  I am running freesurfer 5.3.  the command is: mri_glmfit --glmdir
> ces.nii --cache 2 --sim-sign .  The ces.nii was generated from
> group level analysis (isxconcat-sess).
>
> Thanks for your help.
>
> Xiaomin
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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[Freesurfer] mri_glmfit-sim error

[Xiaomin Yue]

Hi,
I got this error when run mri_glmfit-sim: missing name for redirect.  I am 
running freesurfer 5.3.  the command is: mri_glmfit --glmdir ces.nii --cache 2 
--sim-sign .  The ces.nii was generated from group level analysis 
(isxconcat-sess).  
Thanks for your help.
Xiaomin   ___
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[Freesurfer] mri_glmfit-sim Error

[Eiran Vadim Harel]

Hello Freesurfers,
I use freesurfer v5.3.0
When I do group analysis correction for multiple comparisons for lh as follows: 
mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm 
--nii.gz --surface fsaverage lh
mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166
I get this error message:
ERROR: cannot find 
/Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm00/pos/th30/mc-z.csd
For the mkanalysis-sess i used fwhm = 5.
When i do the same for mni305 and use:
mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm 
--nii.gz 
mri_glmfit-sim --glmdir group.glm --grf 3 pos --cwpvalthresh .0166

It works well without an error.
Thanks,Eiran___
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Re: [Freesurfer] mri_glmfit-sim error

[Douglas Greve]

Can you run mri_glmfit-sim with --debug as the first option, then 
capture the output by putting | tee new.log (no quotes) and post new.log

doug

On 10/24/14 9:33 PM, wrz891...@163.com wrote:
Thanks   a lot !  It just stopped woking  at the  last line and it 
didn't generate the  results ,so I didn't konw how to deal whit it .



wrz891...@163.com

*From:* Douglas N Greve mailto:gr...@nmr.mgh.harvard.edu
*Date:* 2014-10-25 00:32
*To:* freesurfer mailto:freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] mri_glmfit-sim error
what is the error? I did not see anything in the log file.
On 10/24/2014 04:18 AM, wrz891...@163.com wrote:

 Dear Freesurfer Experts,
 I'm a new freesurfer, it comes some errors whendoing mri_glmfit-sim
 analysis. I don't konw what is wrong about it ,it just never
work when
 # doning at mri_glmfit-sim ,and my
 commandsas follwing.


 mris_preproc --fsgd advsnc.fsgd \
 --cache-in thickness.fwhm10.fsaverage \
 --target fsaverage --hemi lh \
 --out lh.advsnc.thickness.10.mgh

 mri_glmfit --y lh.advsnc.thickness.10.mgh --fsgd advsnc.fsgd --C
 AD-NC.interecpt.mtx --surf fsaverage lh --cortex --glmdir
 lh.advsnc.glmdir

 mri_glmfit-sim \
 --glmdir lh.advsnc.glmdir \
 --cache 4 neg\
 --cwp 0.05\
 --2spaces

 Many thanks!


 wrz891...@163.com mailto:wrz891...@163.com





 ___
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 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 
Douglas N. Greve, Ph.D.

MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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but does not contain patient information, please contact the
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dispose of the e-mail.



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[Freesurfer] mri_glmfit-sim error

[wrz891...@163.com]

Dear Freesurfer Experts, 
I'm a new freesurfer ,  it comes some errors when doing  
mri_glmfit-sim analysis. I don't konw  what is wrong about it ,it just never 
work when doning at  mri_glmfit-sim ,and  my  
commands  as follwing. 


mris_preproc --fsgd advsnc.fsgd \ 
--cache-in thickness.fwhm10.fsaverage \ 
--target fsaverage --hemi lh \ 
--out lh.advsnc.thickness.10.mgh 

mri_glmfit --y lh.advsnc.thickness.10.mgh --fsgd advsnc.fsgd --C 
AD-NC.interecpt.mtx --surf fsaverage lh --cortex --glmdir lh.advsnc.glmdir  

 mri_glmfit-sim \ 
--glmdir lh.advsnc.glmdir \ 
--cache 4 neg\ 
--cwp 0.05\ 
--2spaces

Many thanks!


wrz891...@163.com 





cache.mri_glmfit-sim.log
Description: Binary data
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Re: [Freesurfer] mri_glmfit-sim error

[Douglas N Greve]

what is the error? I did not see anything in the log file.

On 10/24/2014 04:18 AM, wrz891...@163.com wrote:

 Dear Freesurfer Experts,
 I'm a new freesurfer, it comes some errors whendoing mri_glmfit-sim 
 analysis. I don't konw what is wrong about it ,it just never work when 
 # doning at mri_glmfit-sim ,and my
 commandsas follwing.


 mris_preproc --fsgd advsnc.fsgd \
 --cache-in thickness.fwhm10.fsaverage \
 --target fsaverage --hemi lh \
 --out lh.advsnc.thickness.10.mgh

 mri_glmfit --y lh.advsnc.thickness.10.mgh --fsgd advsnc.fsgd --C 
 AD-NC.interecpt.mtx --surf fsaverage lh --cortex --glmdir 
 lh.advsnc.glmdir

 mri_glmfit-sim \
 --glmdir lh.advsnc.glmdir \
 --cache 4 neg\
 --cwp 0.05\
 --2spaces

 Many thanks!
 
 wrz891...@163.com mailto:wrz891...@163.com





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

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] mri_glmfit-sim error

[wrz891...@163.com]

Thanks   a lot !  It just stopped woking  at the  last line and it didn't 
generate the  results ,so I didn't konw how to deal whit it .



wrz891...@163.com
 
From: Douglas N Greve
Date: 2014-10-25 00:32
To: freesurfer
Subject: Re: [Freesurfer] mri_glmfit-sim error
what is the error? I did not see anything in the log file.
 
On 10/24/2014 04:18 AM, wrz891...@163.com wrote:

 Dear Freesurfer Experts,
 I'm a new freesurfer, it comes some errors whendoing mri_glmfit-sim 
 analysis. I don't konw what is wrong about it ,it just never work when 
 # doning at mri_glmfit-sim ,and my
 commandsas follwing.


 mris_preproc --fsgd advsnc.fsgd \
 --cache-in thickness.fwhm10.fsaverage \
 --target fsaverage --hemi lh \
 --out lh.advsnc.thickness.10.mgh

 mri_glmfit --y lh.advsnc.thickness.10.mgh --fsgd advsnc.fsgd --C 
 AD-NC.interecpt.mtx --surf fsaverage lh --cortex --glmdir 
 lh.advsnc.glmdir

 mri_glmfit-sim \
 --glmdir lh.advsnc.glmdir \
 --cache 4 neg\
 --cwp 0.05\
 --2spaces

 Many thanks!
 
 wrz891...@163.com mailto:wrz891...@163.com





 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
 
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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[Freesurfer] MRI_glmfit-sim error

[Jon Alan Wieser]

I'm running a monte carlo sim and am getting an error:


command line:


 mri_glmfit-sim   \
--glmdir   MTA_persistanceCP  \
--sim mc-z 1000 1.3 mc-z.negative   \
--sim-sign abs --cwpvalthresh 0.999  \
--overwrite



output:

cmdline mri_glmfit --y /Studies/MTA/qdec/MTA_persistanceCP/y.mgh --fsgd 
/Studies/MTA/qdec/MTA_persistanceCP/qdec.fsgd dods --glmdir 
/Studies/MTA/qdec/MTA_persistanceCP --surf fsaverage rh --label 
/Studies/MTA/fsaverage/label/rh.aparc.label --C 
/Studies/MTA/qdec/MTA_persistanceCP/contrasts/rh-Avg-Intercept-thickness.mat 
--C 
/Studies/MTA/qdec/MTA_persistanceCP/contrasts/rh-Diff-F-M-Intercept-thickness.mat
SURFACE: fsaverage rh
log file is MTA_persistanceCP/mc-z.negative.mri_glmfit-sim.log

cd /Studies/MTA/qdec
/Applications/freesurfer/bin/mri_glmfit-sim
--glmdir MTA_persistanceCP --sim mc-z 1000 1.3 mc-z.negative --sim-sign abs 
--cwpvalthresh 0.999 --overwrite

$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
Tue Jul 29 14:08:52 CDT 2014
Darwin psy-blackbird.ad.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun  7 
16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
wieser
setenv SUBJECTS_DIR /Applications/freesurfer/subjects
FREESURFER_HOME /Applications/freesurfer

Original mri_glmfit command line:
cmdline mri_glmfit --y /Studies/MTA/qdec/MTA_persistanceCP/y.mgh --fsgd 
/Studies/MTA/qdec/MTA_persistanceCP/qdec.fsgd dods --glmdir 
/Studies/MTA/qdec/MTA_persistanceCP --surf fsaverage rh --label 
/Studies/MTA/fsaverage/label/rh.aparc.label --C 
/Studies/MTA/qdec/MTA_persistanceCP/contrasts/rh-Avg-Intercept-thickness.mat 
--C 
/Studies/MTA/qdec/MTA_persistanceCP/contrasts/rh-Diff-F-M-Intercept-thickness.mat

DoSim = 1
UseCache = 0
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 14.370530
nSimPerJob = 1000
1/1 Tue Jul 29 14:08:52 CDT 2014
mri_glmfit --y MTA_persistanceCP/y.mgh --C 
MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Avg-Intercept-thickness.mtx --C 
MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Avg-thickness-Gender-Cor.mtx --C 
MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-C-P-Cor-thickness-Gender.mtx 
--C 
MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-C-P-Intercept-thickness.mtx 
--C 
MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-Control-MJuser-Cor-thickness-Gender.mtx
 --C 
MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-Control-MJuser-Intercept-thickness.mtx
 --C 
MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-F-M-Intercept-thickness.mtx 
--C 
MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-X-ADHD_Persist-MJ_group-Cor-thickness-Gender.mtx
 --C 
MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-X-ADHD_Persist-MJ_group-Intercept-thickness.mtx
 --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Avg-Intercept-thickness.mtx 
--C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Avg-thickness-Gender-Cor.mtx 
--C 
MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-C-P-Cor-thickness-Gender.mtx 
--C 
MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-C-P-Intercept-thickness.mtx 
--C 
MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-Control-MJuser-Cor-thickness-Gender.mtx
 --C 
MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-Control-MJuser-Intercept-thickness.mtx
 --C 
MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-F-M-Intercept-thickness.mtx 
--C 
MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-X-ADHD_Persist-MJ_group-Cor-thickness-Gender.mtx
 --C 
MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-X-ADHD_Persist-MJ_group-Intercept-thickness.mtx
 --mask MTA_persistanceCP/mask.mgh --sim mc-z 1000 1.3 
MTA_persistanceCP/csd/mc-z.negative.j001 --sim-sign abs --fwhm 14.370530 --fsgd 
MTA_persistanceCP/y.fsgd dods --label 
/Studies/MTA/fsaverage/label/rh.aparc.label --surf fsaverage rh white
INFO: ignoring tag Creator
INFO: ignoring tag SUBJECTS_DIR
INFO: ignoring tag SynthSeed
simbase MTA_persistanceCP/csd/mc-z.negative.j001
FWHM = 14.370530
gdfReadHeader: reading MTA_persistanceCP/y.fsgd
INFO: NOT demeaning continuous variables
Continuous Variable Means (all subjects)
0 Age 23.9348 1.40499
Class Means of each Continuous Variable
1 Gender_MFF  23.8000
2 Gender_MFM  23.9722
INFO: gd2mtx_method is dods
Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/rh.white
Number of vertices 163842
Number of faces327680
Total area 65020.765625
AvgVtxArea   0.396850
AvgVtxDist   0.717994
StdVtxDist   0.193566
Surface smoothing by fwhm=14.370530, niters=152.00

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /Studies/MTA/Qdec
cmdline mri_glmfit --y MTA_persistanceCP/y.mgh --C 
MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Avg-Intercept-thickness.mtx --C 
MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Avg-thickness-Gender-Cor.mtx --C 
MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-C-P-Cor-thickness-Gender.mtx 
--C 
MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-C-P-Intercept-thickness.mtx 
--C 

Re: [Freesurfer] MRI_glmfit-sim error

[Douglas N Greve]

I'm not sure how that could have happened. Did you run mri_glmfit 
multiple times by any chance?

On 07/29/2014 03:10 PM, Jon Alan Wieser wrote:


 I'm running a monte carlo sim and am getting an error:


 command line:


  mri_glmfit-sim   \
 --glmdir   MTA_persistanceCP  \
 --sim mc-z 1000 1.3 mc-z.negative   \
 --sim-sign abs --cwpvalthresh 0.999  \
 --overwrite



 output:

 cmdline mri_glmfit --y /Studies/MTA/qdec/MTA_persistanceCP/y.mgh 
 --fsgd /Studies/MTA/qdec/MTA_persistanceCP/qdec.fsgd dods --glmdir 
 /Studies/MTA/qdec/MTA_persistanceCP --surf fsaverage rh --label 
 /Studies/MTA/fsaverage/label/rh.aparc.label --C 
 /Studies/MTA/qdec/MTA_persistanceCP/contrasts/rh-Avg-Intercept-thickness.mat 
 --C 
 /Studies/MTA/qdec/MTA_persistanceCP/contrasts/rh-Diff-F-M-Intercept-thickness.mat
 SURFACE: fsaverage rh
 log file is MTA_persistanceCP/mc-z.negative.mri_glmfit-sim.log

 cd /Studies/MTA/qdec
 /Applications/freesurfer/bin/mri_glmfit-sim
 --glmdir MTA_persistanceCP --sim mc-z 1000 1.3 mc-z.negative 
 --sim-sign abs --cwpvalthresh 0.999 --overwrite

 $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
 Tue Jul 29 14:08:52 CDT 2014
 Darwin psy-blackbird.ad.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: 
 Tue Jun  7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
 wieser
 setenv SUBJECTS_DIR /Applications/freesurfer/subjects
 FREESURFER_HOME /Applications/freesurfer

 Original mri_glmfit command line:
 cmdline mri_glmfit --y /Studies/MTA/qdec/MTA_persistanceCP/y.mgh 
 --fsgd /Studies/MTA/qdec/MTA_persistanceCP/qdec.fsgd dods --glmdir 
 /Studies/MTA/qdec/MTA_persistanceCP --surf fsaverage rh --label 
 /Studies/MTA/fsaverage/label/rh.aparc.label --C 
 /Studies/MTA/qdec/MTA_persistanceCP/contrasts/rh-Avg-Intercept-thickness.mat 
 --C 
 /Studies/MTA/qdec/MTA_persistanceCP/contrasts/rh-Diff-F-M-Intercept-thickness.mat

 DoSim = 1
 UseCache = 0
 DoPoll = 0
 DoPBSubmit = 0
 DoBackground = 0
 DiagCluster = 0
 gd2mtx = dods
 fwhm = 14.370530
 nSimPerJob = 1000
 1/1 Tue Jul 29 14:08:52 CDT 2014
 mri_glmfit --y MTA_persistanceCP/y.mgh --C 
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Avg-Intercept-thickness.mtx 
 --C 
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Avg-thickness-Gender-Cor.mtx 
 --C 
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-C-P-Cor-thickness-Gender.mtx
  
 --C 
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-C-P-Intercept-thickness.mtx
  
 --C 
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-Control-MJuser-Cor-thickness-Gender.mtx
  
 --C 
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-Control-MJuser-Intercept-thickness.mtx
  
 --C 
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-F-M-Intercept-thickness.mtx
  
 --C 
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-X-ADHD_Persist-MJ_group-Cor-thickness-Gender.mtx
  
 --C 
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-X-ADHD_Persist-MJ_group-Intercept-thickness.mtx
  
 --C 
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Avg-Intercept-thickness.mtx 
 --C 
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Avg-thickness-Gender-Cor.mtx 
 --C 
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-C-P-Cor-thickness-Gender.mtx
  
 --C 
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-C-P-Intercept-thickness.mtx
  
 --C 
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-Control-MJuser-Cor-thickness-Gender.mtx
  
 --C 
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-Control-MJuser-Intercept-thickness.mtx
  
 --C 
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-F-M-Intercept-thickness.mtx
  
 --C 
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-X-ADHD_Persist-MJ_group-Cor-thickness-Gender.mtx
  
 --C 
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-X-ADHD_Persist-MJ_group-Intercept-thickness.mtx
  
 --mask MTA_persistanceCP/mask.mgh --sim mc-z 1000 1.3 
 MTA_persistanceCP/csd/mc-z.negative.j001 --sim-sign abs --fwhm 
 14.370530 --fsgd MTA_persistanceCP/y.fsgd dods --label 
 /Studies/MTA/fsaverage/label/rh.aparc.label --surf fsaverage rh white
 INFO: ignoring tag Creator
 INFO: ignoring tag SUBJECTS_DIR
 INFO: ignoring tag SynthSeed
 simbase MTA_persistanceCP/csd/mc-z.negative.j001
 FWHM = 14.370530
 gdfReadHeader: reading MTA_persistanceCP/y.fsgd
 INFO: NOT demeaning continuous variables
 Continuous Variable Means (all subjects)
 0 Age 23.9348 1.40499
 Class Means of each Continuous Variable
 1 Gender_MFF  23.8000
 2 Gender_MFM  23.9722
 INFO: gd2mtx_method is dods
 Reading source surface 
 /Applications/freesurfer/subjects/fsaverage/surf/rh.white
 Number of vertices 163842
 Number of faces327680
 Total area 65020.765625
 AvgVtxArea   0.396850
 AvgVtxDist   0.717994
 StdVtxDist   0.193566
 Surface smoothing by fwhm=14.370530, niters=152.00

 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
 cwd /Studies/MTA/Qdec
 cmdline mri_glmfit --y MTA_persistanceCP/y.mgh --C 
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Avg-Intercept-thickness.mtx 
 --C 
 

Re: [Freesurfer] MRI_glmfit-sim error

[Jon Alan Wieser]

I ran the analysis in qdec, not mri_glmfit  . I did a few analyses in qdec

Jon

From: freesurfer-boun...@nmr.mgh.harvard.edu 
freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve 
gr...@nmr.mgh.harvard.edu
Sent: Tuesday, July 29, 2014 3:48 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] MRI_glmfit-sim error

I'm not sure how that could have happened. Did you run mri_glmfit
multiple times by any chance?

On 07/29/2014 03:10 PM, Jon Alan Wieser wrote:


 I'm running a monte carlo sim and am getting an error:


 command line:


  mri_glmfit-sim   \
 --glmdir   MTA_persistanceCP  \
 --sim mc-z 1000 1.3 mc-z.negative   \
 --sim-sign abs --cwpvalthresh 0.999  \
 --overwrite



 output:

 cmdline mri_glmfit --y /Studies/MTA/qdec/MTA_persistanceCP/y.mgh
 --fsgd /Studies/MTA/qdec/MTA_persistanceCP/qdec.fsgd dods --glmdir
 /Studies/MTA/qdec/MTA_persistanceCP --surf fsaverage rh --label
 /Studies/MTA/fsaverage/label/rh.aparc.label --C
 /Studies/MTA/qdec/MTA_persistanceCP/contrasts/rh-Avg-Intercept-thickness.mat
 --C
 /Studies/MTA/qdec/MTA_persistanceCP/contrasts/rh-Diff-F-M-Intercept-thickness.mat
 SURFACE: fsaverage rh
 log file is MTA_persistanceCP/mc-z.negative.mri_glmfit-sim.log

 cd /Studies/MTA/qdec
 /Applications/freesurfer/bin/mri_glmfit-sim
 --glmdir MTA_persistanceCP --sim mc-z 1000 1.3 mc-z.negative
 --sim-sign abs --cwpvalthresh 0.999 --overwrite

 $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
 Tue Jul 29 14:08:52 CDT 2014
 Darwin psy-blackbird.ad.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0:
 Tue Jun  7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
 wieser
 setenv SUBJECTS_DIR /Applications/freesurfer/subjects
 FREESURFER_HOME /Applications/freesurfer

 Original mri_glmfit command line:
 cmdline mri_glmfit --y /Studies/MTA/qdec/MTA_persistanceCP/y.mgh
 --fsgd /Studies/MTA/qdec/MTA_persistanceCP/qdec.fsgd dods --glmdir
 /Studies/MTA/qdec/MTA_persistanceCP --surf fsaverage rh --label
 /Studies/MTA/fsaverage/label/rh.aparc.label --C
 /Studies/MTA/qdec/MTA_persistanceCP/contrasts/rh-Avg-Intercept-thickness.mat
 --C
 /Studies/MTA/qdec/MTA_persistanceCP/contrasts/rh-Diff-F-M-Intercept-thickness.mat

 DoSim = 1
 UseCache = 0
 DoPoll = 0
 DoPBSubmit = 0
 DoBackground = 0
 DiagCluster = 0
 gd2mtx = dods
 fwhm = 14.370530
 nSimPerJob = 1000
 1/1 Tue Jul 29 14:08:52 CDT 2014
 mri_glmfit --y MTA_persistanceCP/y.mgh --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Avg-Intercept-thickness.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Avg-thickness-Gender-Cor.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-C-P-Cor-thickness-Gender.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-C-P-Intercept-thickness.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-Control-MJuser-Cor-thickness-Gender.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-Control-MJuser-Intercept-thickness.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-F-M-Intercept-thickness.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-X-ADHD_Persist-MJ_group-Cor-thickness-Gender.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-X-ADHD_Persist-MJ_group-Intercept-thickness.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Avg-Intercept-thickness.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Avg-thickness-Gender-Cor.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-C-P-Cor-thickness-Gender.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-C-P-Intercept-thickness.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-Control-MJuser-Cor-thickness-Gender.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-Control-MJuser-Intercept-thickness.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-F-M-Intercept-thickness.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-X-ADHD_Persist-MJ_group-Cor-thickness-Gender.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-X-ADHD_Persist-MJ_group-Intercept-thickness.mtx
 --mask MTA_persistanceCP/mask.mgh --sim mc-z 1000 1.3
 MTA_persistanceCP/csd/mc-z.negative.j001 --sim-sign abs --fwhm
 14.370530 --fsgd MTA_persistanceCP/y.fsgd dods --label
 /Studies/MTA/fsaverage/label/rh.aparc.label --surf fsaverage rh white
 INFO: ignoring tag Creator
 INFO: ignoring tag SUBJECTS_DIR
 INFO: ignoring tag SynthSeed
 simbase MTA_persistanceCP/csd/mc-z.negative.j001
 FWHM = 14.370530
 gdfReadHeader: reading MTA_persistanceCP/y.fsgd
 INFO: NOT demeaning continuous variables
 Continuous Variable Means (all subjects)
 0 Age 23.9348 1.40499
 Class Means of each Continuous Variable
 1 Gender_MFF  23.8000
 2 Gender_MFM  23.9722
 INFO: gd2mtx_method is dods
 Reading source surface
 /Applications/freesurfer/subjects/fsaverage/surf/rh.white
 Number of vertices 163842
 Number of faces327680
 Total area 65020.765625
 AvgVtxArea   0.396850
 AvgVtxDist   0.717994
 StdVtxDist

Re: [Freesurfer] MRI_glmfit-sim error

[Douglas N Greve]

I think that could be the problem. I don't think that qdec cleans up 
after itself, so that is probably a contrast from another analysis. Try 
rerunning qdec using a different output folder, or just delete that 
contrast.

doug

On 07/29/2014 04:52 PM, Jon Alan Wieser wrote:
 I ran the analysis in qdec, not mri_glmfit  . I did a few analyses in qdec

 Jon
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve 
 gr...@nmr.mgh.harvard.edu
 Sent: Tuesday, July 29, 2014 3:48 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] MRI_glmfit-sim error

 I'm not sure how that could have happened. Did you run mri_glmfit
 multiple times by any chance?

 On 07/29/2014 03:10 PM, Jon Alan Wieser wrote:

 I'm running a monte carlo sim and am getting an error:


 command line:


   mri_glmfit-sim   \
 --glmdir   MTA_persistanceCP  \
 --sim mc-z 1000 1.3 mc-z.negative   \
 --sim-sign abs --cwpvalthresh 0.999  \
 --overwrite



 output:

 cmdline mri_glmfit --y /Studies/MTA/qdec/MTA_persistanceCP/y.mgh
 --fsgd /Studies/MTA/qdec/MTA_persistanceCP/qdec.fsgd dods --glmdir
 /Studies/MTA/qdec/MTA_persistanceCP --surf fsaverage rh --label
 /Studies/MTA/fsaverage/label/rh.aparc.label --C
 /Studies/MTA/qdec/MTA_persistanceCP/contrasts/rh-Avg-Intercept-thickness.mat
 --C
 /Studies/MTA/qdec/MTA_persistanceCP/contrasts/rh-Diff-F-M-Intercept-thickness.mat
 SURFACE: fsaverage rh
 log file is MTA_persistanceCP/mc-z.negative.mri_glmfit-sim.log

 cd /Studies/MTA/qdec
 /Applications/freesurfer/bin/mri_glmfit-sim
 --glmdir MTA_persistanceCP --sim mc-z 1000 1.3 mc-z.negative
 --sim-sign abs --cwpvalthresh 0.999 --overwrite

 $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
 Tue Jul 29 14:08:52 CDT 2014
 Darwin psy-blackbird.ad.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0:
 Tue Jun  7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
 wieser
 setenv SUBJECTS_DIR /Applications/freesurfer/subjects
 FREESURFER_HOME /Applications/freesurfer

 Original mri_glmfit command line:
 cmdline mri_glmfit --y /Studies/MTA/qdec/MTA_persistanceCP/y.mgh
 --fsgd /Studies/MTA/qdec/MTA_persistanceCP/qdec.fsgd dods --glmdir
 /Studies/MTA/qdec/MTA_persistanceCP --surf fsaverage rh --label
 /Studies/MTA/fsaverage/label/rh.aparc.label --C
 /Studies/MTA/qdec/MTA_persistanceCP/contrasts/rh-Avg-Intercept-thickness.mat
 --C
 /Studies/MTA/qdec/MTA_persistanceCP/contrasts/rh-Diff-F-M-Intercept-thickness.mat

 DoSim = 1
 UseCache = 0
 DoPoll = 0
 DoPBSubmit = 0
 DoBackground = 0
 DiagCluster = 0
 gd2mtx = dods
 fwhm = 14.370530
 nSimPerJob = 1000
 1/1 Tue Jul 29 14:08:52 CDT 2014
 mri_glmfit --y MTA_persistanceCP/y.mgh --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Avg-Intercept-thickness.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Avg-thickness-Gender-Cor.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-C-P-Cor-thickness-Gender.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-C-P-Intercept-thickness.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-Control-MJuser-Cor-thickness-Gender.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-Control-MJuser-Intercept-thickness.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-F-M-Intercept-thickness.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-X-ADHD_Persist-MJ_group-Cor-thickness-Gender.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-X-ADHD_Persist-MJ_group-Intercept-thickness.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Avg-Intercept-thickness.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Avg-thickness-Gender-Cor.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-C-P-Cor-thickness-Gender.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-C-P-Intercept-thickness.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-Control-MJuser-Cor-thickness-Gender.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-Control-MJuser-Intercept-thickness.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-F-M-Intercept-thickness.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-X-ADHD_Persist-MJ_group-Cor-thickness-Gender.mtx
 --C
 MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-X-ADHD_Persist-MJ_group-Intercept-thickness.mtx
 --mask MTA_persistanceCP/mask.mgh --sim mc-z 1000 1.3
 MTA_persistanceCP/csd/mc-z.negative.j001 --sim-sign abs --fwhm
 14.370530 --fsgd MTA_persistanceCP/y.fsgd dods --label
 /Studies/MTA/fsaverage/label/rh.aparc.label --surf fsaverage rh white
 INFO: ignoring tag Creator
 INFO: ignoring tag SUBJECTS_DIR
 INFO: ignoring tag SynthSeed
 simbase MTA_persistanceCP/csd/mc-z.negative.j001
 FWHM = 14.370530
 gdfReadHeader: reading MTA_persistanceCP/y.fsgd
 INFO: NOT demeaning continuous variables
 Continuous Variable Means (all subjects)
 0 Age 23.9348 1.40499
 Class Means of each Continuous Variable
 1 Gender_MFF  23.8000
 2

[Freesurfer] mri_glmfit-sim error

[yd li]

Hello list,
I'm working with FS 5.0.3. When I used 'mri_glmfit-sim --glmdir
/home/a/freesurfer/g2.lh/C1 --sim mc-z 5000 4 mc-z.abs
--sim-sign  abs  --cwpvalthresh 0.05 --overwrite' for multiple comparison
correction, i got an error message 'cannot find /.../g2.lh/C1/mri_glmfit.log'.
I found a mri_glmfit.log in folder  /.../g2.lh, and copied this file to
folder /.../g2.lh/C1/.But i still got an error 'fwhm: Undefined variable.'
Can anybody help me settle this problem? Thank you!

 -

FREESURFER_HOME: /usr/local/freesurfer

Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

Debian version: wheezy/sid

Kernel info: Linux 3.5.0-23-generic x86_64
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[Freesurfer] mri_glmfit-sim Error

[Jon Wieser]

After running a group comparison using qdec I wanted to use mc-z   
for multiple comparison correction 
I tried running:


mri_glmfit-sim   \
--glmdir MTA_ADHD_MJ2   \
--sim mc-z 1000 2.0 mc-z.negative   \
--sim-sign abs --cwpvalthresh 0.999  \
--overwrite


ERROR: dimension mismatch between X and contrast 
MTA_ADHD_MJ2/tmp.mri_glmfit-sim-9440/lh-Avg-thickness-Age-Cor.mtx   X has 4 
cols, C has 8 cols


What does this mean and how to fix it? 
-- 
Jon Wieser
Research Specialist
UW-Milwaukee
Psychology Department, Pearse Hall Rm 366
2441 East Hartford Ave
Milwaukee, WI 53211
Phone: 414-229-7145
Fax: 414-229-5219
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Re: [Freesurfer] mri_glmfit-sim error

[Glen Lee]

Doug --
Sorry for asking your help again as I can't seem to resolve this on my own.

I looked up the mri_glmfit-sim --help and added the path of csd file in the
argument, but it still fails to find .csd file.
Can you let me know once again what I did wrong? (see the command line
below).

mri_glmfit-sim --cwpvalthresh 0.99 --glmdir GLM --no-sim
/csd/mc-z.negative.j001-osgm.csd  --overwrite

Also see the output below.

Original mri_glmfit command line:
cmdline mri_glmfit --y Bb_Bp_sm8_i6_n13_L.mgh --osgm --glmdir GLM --surf
fsaverage_sym lh

DoSim = 0
UseCache = 0
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 5.124509
ERROR: cannot find any csd files





On Tue, Jun 4, 2013 at 11:25 AM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:


 --no-sim takes an argument. Run mri_glmfit-sim with --help to get more info
 doug


 On 06/04/2013 09:11 AM, Glen Lee wrote:

 Hi Doug,
 I tried as you suggested, but i've got the following error:  e.g.,cannot
 find any csd files.
 However, I can see them stored in csd folder as shown below:

 /2D/results/LH/GLM/csd ls
 mc-z.negative.j001-osgm.csd  perm.abs.2.j001-osgm.csd

 I'm guessing that I need to define the path for this csd folder?

  Here is the command line that I typed in:
  mri_glmfit-sim --cwpvalthresh 0.99 --glmdir GLM --no-sim  --overwrite

  -Glen








 On Mon, Jun 3, 2013 at 11:03 PM, Douglas Greve 
 gr...@nmr.mgh.harvard.edumailto:
 gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote:


 hi Glen, no cluster will show up if the p-value for all clusters
 is above .05. You can change this with --cwpvalthresh to something
 like .99. That should give you all the clusters. Also, you don't
 have to run the full simulation again; you can use the --no-sim
 option and it will use the simulation that you already did.
 doug



 On 6/3/13 9:45 PM, Glen Lee wrote:

 Indeed, I initially tried 10,000 iterations and got nothing.
 What else then could have gone wrong?

 FYI, I use v5.1.0.


 On Mon, Jun 3, 2013 at 5:32 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu
 wrote:

 You will need more like 1 iterations instead of 100.
 doug

 On 06/03/2013 04:49 PM, Glen Lee wrote:
  Hello Freesurfer experts--
 
  I ran mri_glmfit-sim to validate the group level GLM result
 (which was
  already done using mri_glmfit), but I was not able to get
 any result
  out of it.
 
   Even with a quite liberal threshold (2), no vertices came
 out (below
  is what I typed in for the random permutation).
 
   mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2
  --sim-sign
  abs --overwrite
 
  What is strange is that I was clearly see a number of
 clusters when I
  overlaid sig.mgh at a matched threshold (e.g., p2), but no
 cluster
  shows up in  perm.abs.2.sig.cluster.mgh.
  I should be able to see the identical map between those right?
 
  FYI, I also pasted the content in
 perm.abs.2.sig.cluster.summary below.
  As can be seen, nothing is listed in the stats table.
 
  Any of your help would be greatly appreciated.
  -Glen
 
 
 
 
 
 
  # Cluster Growing Summary (mri_surfcluster)
  # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36
 greve Exp $
  # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
  # CreationTime 2013/06/03-20:19:31-GMT
  # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd
  GLM/csd/perm.abs.2.j001-osgm.**csd --mask GLM/mask.mgh --cwsig
  GLM/osgm/perm.abs.2.sig.**cluster.mgh --vwsig
  GLM/osgm/perm.abs.2.sig.voxel.**mgh --sum
  GLM/osgm/perm.abs.2.sig.**cluster.summary --ocn
  GLM/osgm/perm.abs.2.sig.ocn.**mgh --oannot
  GLM/osgm/perm.abs.2.sig.ocn.**annot --annot aparc --csdpdf
  GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o
  GLM/osgm/perm.abs.2.sig.**masked.mgh --no-fixmni --surf white
  # cwd /glen/2D/results/LH
  # sysname  Linux
  # hostname sumo.uphs.upenn.edu http://sumo.uphs.upenn.edu
 http://sumo.uphs.upenn.edu
  # machine  x86_64
  # FixVertexAreaFlag 1
  # FixSurfClusterArea 1
  #
  # Input  GLM/osgm/sig.mgh
  # Frame Number  0
  # srcsubj fsaverage_sym
  # hemi lh
  # surface white
  # annot aparc
  # SUBJECTS_DIR /usr/local/freesurfer5-1/**subjects
  # SearchSpace_mm2 59961.4
  # SearchSpace_vtx 82070
  # Bonferroni 0
  # Minimum Threshold 2
  # Maximum Threshold infinity
  # Threshold Sign  

Re: [Freesurfer] mri_glmfit-sim error

[Glen Lee]

Hi Doug,
I tried as you suggested, but i've got the following error:  e.g.,cannot
find any csd files.
However, I can see them stored in csd folder as shown below:

/2D/results/LH/GLM/csd ls
mc-z.negative.j001-osgm.csd  perm.abs.2.j001-osgm.csd

I'm guessing that I need to define the path for this csd folder?

 Here is the command line that I typed in:
 mri_glmfit-sim --cwpvalthresh 0.99 --glmdir GLM --no-sim  --overwrite

 -Glen









On Mon, Jun 3, 2013 at 11:03 PM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote:


 hi Glen, no cluster will show up if the p-value for all clusters is above
 .05. You can change this with --cwpvalthresh to something like .99. That
 should give you all the clusters. Also, you don't have to run the full
 simulation again; you can use the --no-sim option and it will use the
 simulation that you already did.
 doug



 On 6/3/13 9:45 PM, Glen Lee wrote:

 Indeed, I initially tried 10,000 iterations and got nothing.
 What else then could have gone wrong?

 FYI, I use v5.1.0.


  On Mon, Jun 3, 2013 at 5:32 PM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu wrote:

 You will need more like 1 iterations instead of 100.
 doug

 On 06/03/2013 04:49 PM, Glen Lee wrote:
  Hello Freesurfer experts--
 
  I ran mri_glmfit-sim to validate the group level GLM result (which was
  already done using mri_glmfit), but I was not able to get any result
  out of it.
 
   Even with a quite liberal threshold (2), no vertices came out (below
  is what I typed in for the random permutation).
 
   mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2  --sim-sign
  abs --overwrite
 
  What is strange is that I was clearly see a number of clusters when I
  overlaid sig.mgh at a matched threshold (e.g., p2), but no cluster
  shows up in  perm.abs.2.sig.cluster.mgh.
  I should be able to see the identical map between those right?
 
  FYI, I also pasted the content in perm.abs.2.sig.cluster.summary below.
  As can be seen, nothing is listed in the stats table.
 
  Any of your help would be greatly appreciated.
  -Glen
 
 
 
 
 
 
  # Cluster Growing Summary (mri_surfcluster)
  # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $
  # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
  # CreationTime 2013/06/03-20:19:31-GMT
  # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd
  GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig
  GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig
  GLM/osgm/perm.abs.2.sig.voxel.mgh --sum
  GLM/osgm/perm.abs.2.sig.cluster.summary --ocn
  GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot
  GLM/osgm/perm.abs.2.sig.ocn.annot --annot aparc --csdpdf
  GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o
  GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white
  # cwd /glen/2D/results/LH
  # sysname  Linux
   # hostname sumo.uphs.upenn.edu http://sumo.uphs.upenn.edu
   # machine  x86_64
  # FixVertexAreaFlag 1
  # FixSurfClusterArea 1
  #
  # Input  GLM/osgm/sig.mgh
  # Frame Number  0
  # srcsubj fsaverage_sym
  # hemi lh
  # surface white
  # annot aparc
  # SUBJECTS_DIR /usr/local/freesurfer5-1/subjects
  # SearchSpace_mm2 59961.4
  # SearchSpace_vtx 82070
  # Bonferroni 0
  # Minimum Threshold 2
  # Maximum Threshold infinity
  # Threshold Signabs
  # AdjustThreshWhenOneTail 1
  # CW PValue Threshold: 0.05
  # Area Threshold0 mm^2
  # CSD thresh  2.00
  # CSD nreps100
  # CSD simtype  perm
  # CSD contrast osgm
  # CSD confint  90.00
  # Overall max 3.495 at vertex 61659
  # Overall min -4.18843 at vertex 73402
  # NClusters  0
  # Total Cortical Surface Area 59961.4 (mm^2)
  # FixMNI = 0
  #
  # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZ  CWP
   CWPLowCWPHi   NVtxs   Annot
 
 
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 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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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 Partners Compliance
 HelpLine at
 http://www.partners.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 the e-mail.




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Re: [Freesurfer] mri_glmfit-sim error

[Douglas N Greve]

--no-sim takes an argument. Run mri_glmfit-sim with --help to get more info
doug

On 06/04/2013 09:11 AM, Glen Lee wrote:
 Hi Doug,
 I tried as you suggested, but i've got the following error: 
  e.g.,cannot find any csd files.
 However, I can see them stored in csd folder as shown below:

 /2D/results/LH/GLM/csd ls
 mc-z.negative.j001-osgm.csd  perm.abs.2.j001-osgm.csd

 I'm guessing that I need to define the path for this csd folder?

  Here is the command line that I typed in:
  mri_glmfit-sim --cwpvalthresh 0.99 --glmdir GLM --no-sim  --overwrite

  -Glen








 On Mon, Jun 3, 2013 at 11:03 PM, Douglas Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:


 hi Glen, no cluster will show up if the p-value for all clusters
 is above .05. You can change this with --cwpvalthresh to something
 like .99. That should give you all the clusters. Also, you don't
 have to run the full simulation again; you can use the --no-sim
 option and it will use the simulation that you already did.
 doug



 On 6/3/13 9:45 PM, Glen Lee wrote:
 Indeed, I initially tried 10,000 iterations and got nothing.
 What else then could have gone wrong?

 FYI, I use v5.1.0.


 On Mon, Jun 3, 2013 at 5:32 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:

 You will need more like 1 iterations instead of 100.
 doug

 On 06/03/2013 04:49 PM, Glen Lee wrote:
  Hello Freesurfer experts--
 
  I ran mri_glmfit-sim to validate the group level GLM result
 (which was
  already done using mri_glmfit), but I was not able to get
 any result
  out of it.
 
   Even with a quite liberal threshold (2), no vertices came
 out (below
  is what I typed in for the random permutation).
 
   mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2
  --sim-sign
  abs --overwrite
 
  What is strange is that I was clearly see a number of
 clusters when I
  overlaid sig.mgh at a matched threshold (e.g., p2), but no
 cluster
  shows up in  perm.abs.2.sig.cluster.mgh.
  I should be able to see the identical map between those right?
 
  FYI, I also pasted the content in
 perm.abs.2.sig.cluster.summary below.
  As can be seen, nothing is listed in the stats table.
 
  Any of your help would be greatly appreciated.
  -Glen
 
 
 
 
 
 
  # Cluster Growing Summary (mri_surfcluster)
  # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36
 greve Exp $
  # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
  # CreationTime 2013/06/03-20:19:31-GMT
  # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd
  GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig
  GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig
  GLM/osgm/perm.abs.2.sig.voxel.mgh --sum
  GLM/osgm/perm.abs.2.sig.cluster.summary --ocn
  GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot
  GLM/osgm/perm.abs.2.sig.ocn.annot --annot aparc --csdpdf
  GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o
  GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white
  # cwd /glen/2D/results/LH
  # sysname  Linux
  # hostname sumo.uphs.upenn.edu http://sumo.uphs.upenn.edu
 http://sumo.uphs.upenn.edu
  # machine  x86_64
  # FixVertexAreaFlag 1
  # FixSurfClusterArea 1
  #
  # Input  GLM/osgm/sig.mgh
  # Frame Number  0
  # srcsubj fsaverage_sym
  # hemi lh
  # surface white
  # annot aparc
  # SUBJECTS_DIR /usr/local/freesurfer5-1/subjects
  # SearchSpace_mm2 59961.4
  # SearchSpace_vtx 82070
  # Bonferroni 0
  # Minimum Threshold 2
  # Maximum Threshold infinity
  # Threshold Signabs
  # AdjustThreshWhenOneTail 1
  # CW PValue Threshold: 0.05
  # Area Threshold0 mm^2
  # CSD thresh  2.00
  # CSD nreps100
  # CSD simtype  perm
  # CSD contrast osgm
  # CSD confint  90.00
  # Overall max 3.495 at vertex 61659
  # Overall min -4.18843 at vertex 73402
  # NClusters  0
  # Total Cortical Surface Area 59961.4 (mm^2)
  # FixMNI = 0
  #
  # ClusterNo  Max   VtxMax Size(mm^2)  MNIX   MNIY   MNIZ  CWP
   CWPLowCWPHi   NVtxs   Annot
 
 
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[Freesurfer] mri_glmfit-sim error

[Glen Lee]

Hello Freesurfer experts--

I ran mri_glmfit-sim to validate the group level GLM result (which was
already done using mri_glmfit), but I was not able to get any result out of
it.

 Even with a quite liberal threshold (2), no vertices came out (below is
what I typed in for the random permutation).

 mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2  --sim-sign abs
--overwrite

What is strange is that I was clearly see a number of clusters when I
overlaid sig.mgh at a matched threshold (e.g., p2), but no cluster shows
up in  perm.abs.2.sig.cluster.mgh.
I should be able to see the identical map between those right?

FYI, I also pasted the content in perm.abs.2.sig.cluster.summary below.
As can be seen, nothing is listed in the stats table.

Any of your help would be greatly appreciated.
-Glen






# Cluster Growing Summary (mri_surfcluster)
# $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $
# $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
# CreationTime 2013/06/03-20:19:31-GMT
# cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd
GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig
GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig
GLM/osgm/perm.abs.2.sig.voxel.mgh --sum
GLM/osgm/perm.abs.2.sig.cluster.summary --ocn
GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot GLM/osgm/perm.abs.2.sig.ocn.annot
--annot aparc --csdpdf GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o
GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white
# cwd /glen/2D/results/LH
# sysname  Linux
# hostname sumo.uphs.upenn.edu
# machine  x86_64
# FixVertexAreaFlag 1
# FixSurfClusterArea 1
#
# Input  GLM/osgm/sig.mgh
# Frame Number  0
# srcsubj fsaverage_sym
# hemi lh
# surface white
# annot aparc
# SUBJECTS_DIR /usr/local/freesurfer5-1/subjects
# SearchSpace_mm2 59961.4
# SearchSpace_vtx 82070
# Bonferroni 0
# Minimum Threshold 2
# Maximum Threshold infinity
# Threshold Signabs
# AdjustThreshWhenOneTail 1
# CW PValue Threshold: 0.05
# Area Threshold0 mm^2
# CSD thresh  2.00
# CSD nreps100
# CSD simtype  perm
# CSD contrast osgm
# CSD confint  90.00
# Overall max 3.495 at vertex 61659
# Overall min -4.18843 at vertex 73402
# NClusters  0
# Total Cortical Surface Area 59961.4 (mm^2)
# FixMNI = 0
#
# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow
   CWPHi   NVtxs   Annot
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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 Partners Compliance HelpLine at
http://www.partners.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 the e-mail.

Re: [Freesurfer] mri_glmfit-sim error

[Glen Lee]

Indeed, I initially tried 10,000 iterations and got nothing.
What else then could have gone wrong?

FYI, I use v5.1.0.


On Mon, Jun 3, 2013 at 5:32 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:

 You will need more like 1 iterations instead of 100.
 doug

 On 06/03/2013 04:49 PM, Glen Lee wrote:
  Hello Freesurfer experts--
 
  I ran mri_glmfit-sim to validate the group level GLM result (which was
  already done using mri_glmfit), but I was not able to get any result
  out of it.
 
   Even with a quite liberal threshold (2), no vertices came out (below
  is what I typed in for the random permutation).
 
   mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2  --sim-sign
  abs --overwrite
 
  What is strange is that I was clearly see a number of clusters when I
  overlaid sig.mgh at a matched threshold (e.g., p2), but no cluster
  shows up in  perm.abs.2.sig.cluster.mgh.
  I should be able to see the identical map between those right?
 
  FYI, I also pasted the content in perm.abs.2.sig.cluster.summary below.
  As can be seen, nothing is listed in the stats table.
 
  Any of your help would be greatly appreciated.
  -Glen
 
 
 
 
 
 
  # Cluster Growing Summary (mri_surfcluster)
  # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $
  # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
  # CreationTime 2013/06/03-20:19:31-GMT
  # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd
  GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig
  GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig
  GLM/osgm/perm.abs.2.sig.voxel.mgh --sum
  GLM/osgm/perm.abs.2.sig.cluster.summary --ocn
  GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot
  GLM/osgm/perm.abs.2.sig.ocn.annot --annot aparc --csdpdf
  GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o
  GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white
  # cwd /glen/2D/results/LH
  # sysname  Linux
  # hostname sumo.uphs.upenn.edu http://sumo.uphs.upenn.edu
  # machine  x86_64
  # FixVertexAreaFlag 1
  # FixSurfClusterArea 1
  #
  # Input  GLM/osgm/sig.mgh
  # Frame Number  0
  # srcsubj fsaverage_sym
  # hemi lh
  # surface white
  # annot aparc
  # SUBJECTS_DIR /usr/local/freesurfer5-1/subjects
  # SearchSpace_mm2 59961.4
  # SearchSpace_vtx 82070
  # Bonferroni 0
  # Minimum Threshold 2
  # Maximum Threshold infinity
  # Threshold Signabs
  # AdjustThreshWhenOneTail 1
  # CW PValue Threshold: 0.05
  # Area Threshold0 mm^2
  # CSD thresh  2.00
  # CSD nreps100
  # CSD simtype  perm
  # CSD contrast osgm
  # CSD confint  90.00
  # Overall max 3.495 at vertex 61659
  # Overall min -4.18843 at vertex 73402
  # NClusters  0
  # Total Cortical Surface Area 59961.4 (mm^2)
  # FixMNI = 0
  #
  # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZ  CWP
   CWPLowCWPHi   NVtxs   Annot
 
 
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Re: [Freesurfer] mri_glmfit-sim error

[Douglas Greve]

hi Glen, no cluster will show up if the p-value for all clusters is 
above .05. You can change this with --cwpvalthresh to something like 
.99. That should give you all the clusters. Also, you don't have to run 
the full simulation again; you can use the --no-sim option and it will 
use the simulation that you already did.

doug


On 6/3/13 9:45 PM, Glen Lee wrote:

Indeed, I initially tried 10,000 iterations and got nothing.
What else then could have gone wrong?

FYI, I use v5.1.0.


On Mon, Jun 3, 2013 at 5:32 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:


You will need more like 1 iterations instead of 100.
doug

On 06/03/2013 04:49 PM, Glen Lee wrote:
 Hello Freesurfer experts--

 I ran mri_glmfit-sim to validate the group level GLM result
(which was
 already done using mri_glmfit), but I was not able to get any result
 out of it.

  Even with a quite liberal threshold (2), no vertices came out
(below
 is what I typed in for the random permutation).

  mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2  --sim-sign
 abs --overwrite

 What is strange is that I was clearly see a number of clusters
when I
 overlaid sig.mgh at a matched threshold (e.g., p2), but no cluster
 shows up in  perm.abs.2.sig.cluster.mgh.
 I should be able to see the identical map between those right?

 FYI, I also pasted the content in perm.abs.2.sig.cluster.summary
below.
 As can be seen, nothing is listed in the stats table.

 Any of your help would be greatly appreciated.
 -Glen






 # Cluster Growing Summary (mri_surfcluster)
 # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $
 # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
 # CreationTime 2013/06/03-20:19:31-GMT
 # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd
 GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig
 GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig
 GLM/osgm/perm.abs.2.sig.voxel.mgh --sum
 GLM/osgm/perm.abs.2.sig.cluster.summary --ocn
 GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot
 GLM/osgm/perm.abs.2.sig.ocn.annot --annot aparc --csdpdf
 GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o
 GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white
 # cwd /glen/2D/results/LH
 # sysname  Linux
 # hostname sumo.uphs.upenn.edu http://sumo.uphs.upenn.edu
http://sumo.uphs.upenn.edu
 # machine  x86_64
 # FixVertexAreaFlag 1
 # FixSurfClusterArea 1
 #
 # Input  GLM/osgm/sig.mgh
 # Frame Number  0
 # srcsubj fsaverage_sym
 # hemi lh
 # surface white
 # annot aparc
 # SUBJECTS_DIR /usr/local/freesurfer5-1/subjects
 # SearchSpace_mm2 59961.4
 # SearchSpace_vtx 82070
 # Bonferroni 0
 # Minimum Threshold 2
 # Maximum Threshold infinity
 # Threshold Signabs
 # AdjustThreshWhenOneTail 1
 # CW PValue Threshold: 0.05
 # Area Threshold0 mm^2
 # CSD thresh  2.00
 # CSD nreps100
 # CSD simtype  perm
 # CSD contrast osgm
 # CSD confint  90.00
 # Overall max 3.495 at vertex 61659
 # Overall min -4.18843 at vertex 73402
 # NClusters  0
 # Total Cortical Surface Area 59961.4 (mm^2)
 # FixMNI = 0
 #
 # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZ  CWP
  CWPLowCWPHi   NVtxs   Annot


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[Freesurfer] mri_glmfit-sim - error of fwhm

[Sophie Maingault]

Dear experts, 

I have a error message when I use the command : mdi_glmfit-sim ‹glmdir X
‹cwpvalthresh 0,001 ‹cache 3 abs

ERROR : cannot find
/usr/local/freesurfer/average/mult-comp-cor/fsaverage_sym/lh/cortex/fwhm00/a
bs/th20/mc-z.csd

I don't understand why because to create this glmdir I use a file with fwhm
= 5 mm and in the directory
/usr/local/freesurfer/average/mult-comp-cor/fsaverage_sym/lh/cortex there
are all values of fwhm (from 1 to 30) but not 0. I have to add an argument
to specify fwhm used ?

Thank you for your help !

Best regards.

Sophie



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Re: [Freesurfer] mri_glmfit-sim - error of fwhm

[Douglas N Greve]

Hi Sophie, the problem may be that you have used 0,001 instead of 
0.001.
doug


On 05/02/2013 10:40 AM, Sophie Maingault wrote:
 Dear experts,

 I have a error message when I use the command : mdi_glmfit-sim —glmdir 
 X —cwpvalthresh 0,001 —cache 3 abs

 ERROR : cannot find 
 /usr/local/freesurfer/average/mult-comp-cor/fsaverage_sym/lh/cortex/fwhm00/abs/th20/mc-z.csd

 I don't understand why because to create this glmdir I use a file with 
 fwhm = 5 mm and in the directory 
 /usr/local/freesurfer/average/mult-comp-cor/fsaverage_sym/lh/cortex 
 there are all values of fwhm (from 1 to 30) but not 0. I have to add 
 an argument to specify fwhm used ?

 Thank you for your help !

 Best regards.

 Sophie



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[Freesurfer] mri_glmfit-sim error

[Juke Cha]

Hi all,

I've got an error while running mri_glmfit-sim. I ran this for several
measures, and only for 'volume' and 'area' the function complained about
missing CSD files stating ERROR: cannot find any csd files
I don't know if this is a known issue. I saw several threads posted
regarding this issue, but did not see a solution. Any suggestion?


Best,
Juke
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Re: [Freesurfer] mri_glmfit-sim error

[Douglas N Greve]

Can you send your command line and terminal output?

On 05/14/2012 09:26 AM, Juke Cha wrote:

 Hi all,

 I've got an error while running mri_glmfit-sim. I ran this for several 
 measures, and only for 'volume' and 'area' the function complained 
 about missing CSD files stating ERROR: cannot find any csd files
 I don't know if this is a known issue. I saw several threads posted 
 regarding this issue, but did not see a solution. Any suggestion?


 Best,
 Juke


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Re: [Freesurfer] mri_glmfit-sim error

[Douglas N Greve]

Hi Mingxia, use
--cache 1.3 neg

you have it the other way around
doug

zhang mingxia wrote:
 Hi, every one,

 I just run the flag mri_glmfit-sim for Surface-based Correction for 
 Multiple Comparisons as below:

 mri_glmfit-sim \
 --glmdir lh.Chinese_fastreading_thickness.glmdir \
 --cache neg 1.3 \
 --cwpvalthresh .025

  lh.Chinese_fastreading_thickness.glmdir is the pre-cached simulation 
 results. There is error:printf: neg: expected a numeric value
 ERROR: thresh = 0.0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0

 What is the problem? Thank you in advance.

 Sincerely,
 Mingxia Zhang
 

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Re: [Freesurfer] mri_glmfit-sim error

[zhang mingxia]

Thank you very much!!

On Wed, Jan 4, 2012 at 11:55 PM, zhang mingxia
zhangmingxia1...@gmail.comwrote:

 Hi, every one,

 I just run the flag mri_glmfit-sim for Surface-based Correction for
 Multiple Comparisons as below:

 mri_glmfit-sim \
 --glmdir lh.Chinese_fastreading_thickness.glmdir \
 --cache neg 1.3 \
 --cwpvalthresh .025

  lh.Chinese_fastreading_thickness.glmdir is the pre-cached simulation
 results. There is error:printf: neg: expected a numeric value
 ERROR: thresh = 0.0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0

 What is the problem? Thank you in advance.

 Sincerely,
 Mingxia Zhang

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[Freesurfer] mri_glmfit-sim error

[zhang mingxia]

Hi, every one,

I just run the flag mri_glmfit-sim for Surface-based Correction for
Multiple Comparisons as below:

mri_glmfit-sim \
--glmdir lh.Chinese_fastreading_thickness.glmdir \
--cache neg 1.3 \
--cwpvalthresh .025

 lh.Chinese_fastreading_thickness.glmdir is the pre-cached simulation
results. There is error:printf: neg: expected a numeric value
ERROR: thresh = 0.0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0

What is the problem? Thank you in advance.

Sincerely,
Mingxia Zhang
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Re: [Freesurfer] mri_glmfit-sim error

[Douglas N Greve]

Hi Joost, the precomputed tables only go up to 30mm FWHM. The 25 mm you 
apply adds to some that is already there to cause it to be 31mm, so the 
table does not exist. I would say that 25mm is a lot to smooth by. Do 
you really need that much?
doug

j janssen wrote:
 Hi,

 - FS version: 5.1
 - system: Linux neuro3 2.6.27.41-170.2.117.fc10.x86_64 #1 SMP Thu Dec
 10 10:36:29 EST 2009 x86_64 x86_64 x86_64 GNU/Linux
 - on-screen error output:
 cmdline mri_glmfit --glmdir
 rh_thickness_men_20fwhm_asp_vs_con_controlling_for_IQ_AGE --y
 rh.thickness.fwhm20.men.age.iq.mgh --fsgd FSGD_1F3L_2C.txt dods --C
 asp_vs_con_controlling_for_IQ_AGE.txt --surface fsaverage rh
 SURFACE: fsaverage rh
 log file is 
 rh_thickness_men_20fwhm_asp_vs_con_controlling_for_IQ_AGE/cache.mri_glmfit-sim.log

 cd 
 /home/neuro/asperger_psychosis_study/freesurfer51/qdec/3groups/DIAGNOSE_CI_AGE
 /usr/local/freesurfer/bin/mri_glmfit-sim
 --glmdir rh_thickness_men_20fwhm_asp_vs_con_controlling_for_IQ_AGE
 --cache 1.3 abs

 $Id: mri_glmfit-sim,v 1.36.2.1 2011/03/28 15:46:10 greve Exp $
 Wed Dec 21 15:58:23 CET 2011
 Linux neuro3 2.6.27.41-170.2.117.fc10.x86_64 #1 SMP Thu Dec 10
 10:36:29 EST 2009 x86_64 x86_64 x86_64 GNU/Linux
 neuro
 setenv SUBJECTS_DIR /home/neuro/asperger_psychosis_study/freesurfer51
 FREESURFER_HOME /usr/local/freesurfer

 Original mri_glmfit command line:
 cmdline mri_glmfit --glmdir
 rh_thickness_men_20fwhm_asp_vs_con_controlling_for_IQ_AGE --y
 rh.thickness.fwhm20.men.age.iq.mgh --fsgd FSGD_1F3L_2C.txt dods --C
 asp_vs_con_controlling_for_IQ_AGE.txt --surface fsaverage rh

 DoSim = 0
 UseCache = 1
 DoPoll = 0
 DoPBSubmit = 0
 DoBackground = 0
 DiagCluster = 0
 gd2mtx = dods
 fwhm = 31.421003
 ERROR: cannot find
 /usr/local/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm31/abs/th13/mc-z.csd

 rh.thickness.fwhm20.men.age.iq.mgh was created by (i've attached the
 pertaining preproc log file):
 /usr/local/freesurfer/bin/mris_preproc --out
 rh.thickness.fwhm20.men.age.iq.mgh --target fsaverage --hemi rh --meas
 thickness --fsgd FSGD_1F3L_2C.txt --fwhm 20

 when i create rh.thickness.fwhm25.men.age.iq.mgh (i've attached the
 pertaining preproc log file) the following command:
 mri_glmfit-sim --glmdir
 rh_thickness_men_25fwhm_asp_vs_con_controlling_for_IQ_AGE --cache 1.3
 abs

 *does* work with output fwhm = 3.015979

 what am i doing wrong?
 thanks,
 -joost
 

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Re: [Freesurfer] mri_glmfit-sim error with v5.0

[Douglas N Greve]

Can you tar up your glmdir and drop it to me?
doug

Yuko Yotsumoto wrote:
 Thank you Doug,

 Hi Yuko, I think you must have an older version of glmfit-sim some  how. 
 I've put a newer version here:

 I replaced the /bin/mri_glmfit-sim, but got the same error.

 [ERROR 1]
 In line 292:
 set csdCache = 
 $CacheDir/$subject/$hemi/$CacheLabel/fwhm$fwhmStr/$simsign/th$threshStr/mc-z.csd

 In stead of making 
 csdCache 
 = 
 /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th30/mc-z.csd
 it did
 csdCache 
 = 
 /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm15/pos/th30/mc-z.csd

 It looks like I failed to tell freesurfer that $subject=fsaverage and 
 $hemi=lh.

 I changed this line to:
 set csdCache = 
 $CacheDir/fsaverage/lh/$CacheLabel/fwhm$fwhmStr/$simsign/th$threshStr/mc-z.csd

 and this worked. But I still don't understand why I got the error with 
 mri_glmfit-sim.

 [ERROR 2]
 In line 93, anattype is set to volume, but I'm doing surface analysis.
 set anattype = volume;
 Changing this to set anattype = surface; worked, but does this mean 
 mri_glmfit-sim is specialized for volume analysis only?
 Is there a way to change this in the command line not in the original 
 code?

 Best,
 Yuko


 Hi Yuko, I think you must have an older version of glmfit-sim some  how. 
 I've put a newer version here:
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim-v5.0
 copy this to your $FREESURFER_HOME/bin/mri_glmfit-sim (ie, change the 
 name; and make a backup copy).
 doug

 On Nov 23, 2011, at 2:07 PM, yukoyy wrote:

 Hello

 I'm having a trouble with mri_glmfit-sim with v5.0, which is locally 
 installed on Mac 10.6.8.

 Whan I ran:
 mri_glmfit-sim --glmdir MPglm.wls --cache 3.0 pos --cwpvalthresh .0166

 I got:
 ERROR: cannot find 
 /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm15/pos/th30/mc-z.csd

 I have
 /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th30/mc-z.csd
 in my directory.

 It looks like I need to somehow tell freesurfer /fsaverage/lh/, but 
 how?

 Before mri_glmfit-sim, I did the followings:
 isxconcat-sess -df sessdirfile -sf sessidlist -analysis PreL -hemi lh 
 -c 16vs4 -o MPgroup
 mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface 
 fsaverage lh --glmdir MPglm.wls --nii.gz


 % 
 -
 Also, when I did:
 mri_glmfit-sim --glmdir MPglm.wls --sim mc-z 100 2 mc-z.abs.2 
 --sim-sign abs --overwrite

 I got several warnings and errors (full error message pasted at the 
 end of this email):
 cmdline mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm 
 --surface fsaverage lh --glmdir MPglm.wls --nii.gz
 WARNING: unrecognized mri_glmfit cmd option --surface
 WARNING: unrecognized mri_glmfit cmd option fsaverage
 WARNING: unrecognized mri_glmfit cmd option lh
 WARNING: unrecognized mri_glmfit cmd option --nii.gz
 
 mri_glmfit --y 
 /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4/ces.008.nii
  
 --C
 MPglm.wls/tmp.mri_glmfit-sim-6456/osgm.mtx --mask 
 MPglm.wls/mask.nii.gz --sim mc-z 100 2 MPglm.wls/csd
 /mc-z.abs.2.j001 --sim-sign abs --fwhm 15.248189 --X 
 MPglm.wls/Xg.dat --wls /Users/kawabata/Documents/freesurfer
 /sessions/MP/MEAN/MPgroup/PreL/16vs4/cesvar.008.nii
 Bus error

 I don't understand why mri_glmfit-sim calls mri_glmfit, and gives 
 warnings? When I paste mri_glmfit --y ces.008.nii --wls 
 cesvar.008.nii --osgm --surface fsaverage lh --glmdir MPglm.wls 
 --nii.gz in the command line, it works without any error.

 Thanks in advance!
 Yuko Yotsumoto


 % full error message regarding the second question 
 ---
 cmdline mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm 
 --surface fsaverage lh --glmdir MPglm.wls --nii.gz
 WARNING: unrecognized mri_glmfit cmd option --surface
 WARNING: unrecognized mri_glmfit cmd option fsaverage
 WARNING: unrecognized mri_glmfit cmd option lh
 WARNING: unrecognized mri_glmfit cmd option --nii.gz
 log file is MPglm.wls/mc-z.abs.2.mri_glmfit-sim.log
 cd 
 /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4
 /Applications/freesurfer/bin/mri_glmfit-sim
 --glmdir MPglm.wls --sim mc-z 100 2 mc-z.abs.2 --sim-sign abs --overwrite

 $Id: mri_glmfit-sim,v 1.24.2.5 2010/07/27 22:49:00 greve Exp $
 Wed Nov 23 13:55:01 JST 2011
 Darwin Hideaki-Kawabata-no-MacBook-Pro.local 10.8.0 Darwin Kernel 
 Version 10.8.0: Tue Jun  7 16:32:41 PDT 2011; 
 root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
 kawabata
 setenv SUBJECTS_DIR /Users/kawabata/Documents/freesurfer/subjects
 FREESURFER_HOME /Applications/freesurfer
 DoSim = 1
 UseCache = 0
 DoPoll = 0
 DoPBSubmit = 0
 DoBackground = 0
 DiagCluster = 0
 gd2mtx = dods
 fwhm = 15.248189
 nSimPerJob = 100
 1/1 Wed Nov 23 13:55:01 JST 2011
 mri_glmfit --y 
 /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4/ces.008.nii
  
 --C 

Re: [Freesurfer] mri_glmfit-sim error with v5.0

[Yuko Yotsumoto]

Thank you Doug,

 Hi Yuko, I think you must have an older version of glmfit-sim some  how. 
 I've put a newer version here:

I replaced the /bin/mri_glmfit-sim, but got the same error.

[ERROR 1]
In line 292:
set csdCache = 
$CacheDir/$subject/$hemi/$CacheLabel/fwhm$fwhmStr/$simsign/th$threshStr/mc-z.csd

In stead of making 
csdCache = 
/Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th30/mc-z.csd
it did
csdCache = 
/Applications/freesurfer/average/mult-comp-cor///cortex/fwhm15/pos/th30/mc-z.csd

It looks like I failed to tell freesurfer that $subject=fsaverage and $hemi=lh.

I changed this line to:
set csdCache = 
$CacheDir/fsaverage/lh/$CacheLabel/fwhm$fwhmStr/$simsign/th$threshStr/mc-z.csd

and this worked. But I still don't understand why I got the error with 
mri_glmfit-sim.

[ERROR 2]
In line 93, anattype is set to volume, but I'm doing surface analysis.
set anattype = volume;
Changing this to set anattype = surface; worked, but does this mean 
mri_glmfit-sim is specialized for volume analysis only?
Is there a way to change this in the command line not in the original code?

Best,
Yuko


 Hi Yuko, I think you must have an older version of glmfit-sim some  how. 
 I've put a newer version here:
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim-v5.0
 copy this to your $FREESURFER_HOME/bin/mri_glmfit-sim (ie, change the 
 name; and make a backup copy).
 doug

On Nov 23, 2011, at 2:07 PM, yukoyy wrote:

 Hello
 
 I'm having a trouble with mri_glmfit-sim with v5.0, which is locally 
 installed on Mac 10.6.8.
 
 Whan I ran:
 mri_glmfit-sim --glmdir MPglm.wls --cache 3.0 pos --cwpvalthresh .0166
 
 I got:
 ERROR: cannot find 
 /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm15/pos/th30/mc-z.csd
 
 I have 
 /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th30/mc-z.csd
 in my directory.
 
 It looks like I need to somehow tell freesurfer /fsaverage/lh/, but how?
 
 Before mri_glmfit-sim, I did the followings:
 isxconcat-sess -df sessdirfile -sf sessidlist -analysis PreL -hemi lh -c 
 16vs4 -o MPgroup
 mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface fsaverage lh 
 --glmdir MPglm.wls --nii.gz
 
 
 % -
 Also, when I did:
 mri_glmfit-sim --glmdir MPglm.wls --sim mc-z 100 2 mc-z.abs.2 --sim-sign abs 
 --overwrite
 
 I got several warnings and errors (full error message pasted at the end of 
 this email):
 cmdline mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface 
 fsaverage lh --glmdir MPglm.wls --nii.gz
 WARNING: unrecognized mri_glmfit cmd option --surface
 WARNING: unrecognized mri_glmfit cmd option fsaverage
 WARNING: unrecognized mri_glmfit cmd option lh
 WARNING: unrecognized mri_glmfit cmd option --nii.gz
 
 mri_glmfit --y 
 /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4/ces.008.nii
  --C 
 MPglm.wls/tmp.mri_glmfit-sim-6456/osgm.mtx --mask MPglm.wls/mask.nii.gz 
 --sim mc-z 100 2 MPglm.wls/csd
 /mc-z.abs.2.j001 --sim-sign abs --fwhm 15.248189 --X MPglm.wls/Xg.dat --wls 
 /Users/kawabata/Documents/freesurfer
 /sessions/MP/MEAN/MPgroup/PreL/16vs4/cesvar.008.nii
 Bus error 
 
 I don't understand why mri_glmfit-sim calls mri_glmfit, and gives warnings? 
 When I paste mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm 
 --surface fsaverage lh --glmdir MPglm.wls --nii.gz in the command line, it 
 works without any error. 
 
 Thanks in advance!
 Yuko Yotsumoto
 
 
 % full error message regarding the second question 
 ---
 cmdline mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface 
 fsaverage lh --glmdir MPglm.wls --nii.gz
 WARNING: unrecognized mri_glmfit cmd option --surface
 WARNING: unrecognized mri_glmfit cmd option fsaverage
 WARNING: unrecognized mri_glmfit cmd option lh
 WARNING: unrecognized mri_glmfit cmd option --nii.gz
 log file is MPglm.wls/mc-z.abs.2.mri_glmfit-sim.log
 cd /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4
 /Applications/freesurfer/bin/mri_glmfit-sim
 --glmdir MPglm.wls --sim mc-z 100 2 mc-z.abs.2 --sim-sign abs --overwrite
 
 $Id: mri_glmfit-sim,v 1.24.2.5 2010/07/27 22:49:00 greve Exp $
 Wed Nov 23 13:55:01 JST 2011
 Darwin Hideaki-Kawabata-no-MacBook-Pro.local 10.8.0 Darwin Kernel Version 
 10.8.0: Tue Jun  7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 
 x86_64
 kawabata
 setenv SUBJECTS_DIR /Users/kawabata/Documents/freesurfer/subjects
 FREESURFER_HOME /Applications/freesurfer
 DoSim = 1
 UseCache = 0
 DoPoll = 0
 DoPBSubmit = 0
 DoBackground = 0
 DiagCluster = 0
 gd2mtx = dods
 fwhm = 15.248189
 nSimPerJob = 100
 1/1 Wed Nov 23 13:55:01 JST 2011
 mri_glmfit --y 
 /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4/ces.008.nii
  --C MPglm.wls/tmp.mri_glmfit-sim-6456/osgm.mtx --mask MPglm.wls/mask.nii.gz 
 --sim mc-z 100 2 

Re: [Freesurfer] mri_glmfit-sim error with v5.0

[Douglas N Greve]

Hi Yuko, I think you must have an older version of glmfit-sim some  how. 
I've put a newer version here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim-v5.0
copy this to your $FREESURFER_HOME/bin/mri_glmfit-sim (ie, change the 
name; and make a backup copy).
doug

yukoyy wrote:
 Hello

 I'm having a trouble with mri_glmfit-sim with v5.0, which is locally 
 installed on Mac 10.6.8.

 Whan I ran:
 mri_glmfit-sim --glmdir MPglm.wls --cache 3.0 pos --cwpvalthresh .0166

 I got:
 ERROR: cannot find 
 /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm15/pos/th30/mc-z.csd

 I have 
 /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th30/mc-z.csd
 in my directory.

 It looks like I need to somehow tell freesurfer /fsaverage/lh/, but how?

 Before mri_glmfit-sim, I did the followings:
 isxconcat-sess -df sessdirfile -sf sessidlist -analysis PreL -hemi lh -c 
 16vs4 -o MPgroup
 mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface fsaverage lh 
 --glmdir MPglm.wls --nii.gz


 % -
 Also, when I did:
 mri_glmfit-sim --glmdir MPglm.wls --sim mc-z 100 2 mc-z.abs.2 --sim-sign abs 
 --overwrite

 I got several warnings and errors (full error message pasted at the end of 
 this email):
   
 cmdline mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface 
 fsaverage lh --glmdir MPglm.wls --nii.gz
 WARNING: unrecognized mri_glmfit cmd option --surface
 WARNING: unrecognized mri_glmfit cmd option fsaverage
 WARNING: unrecognized mri_glmfit cmd option lh
 WARNING: unrecognized mri_glmfit cmd option --nii.gz
 
 
   
 mri_glmfit --y 
 /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4/ces.008.nii
  --C 
 MPglm.wls/tmp.mri_glmfit-sim-6456/osgm.mtx --mask MPglm.wls/mask.nii.gz 
 --sim mc-z 100 2 MPglm.wls/csd
 /mc-z.abs.2.j001 --sim-sign abs --fwhm 15.248189 --X MPglm.wls/Xg.dat --wls 
 /Users/kawabata/Documents/freesurfer
 /sessions/MP/MEAN/MPgroup/PreL/16vs4/cesvar.008.nii
 Bus error 
 

 I don't understand why mri_glmfit-sim calls mri_glmfit, and gives warnings? 
 When I paste mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm 
 --surface fsaverage lh --glmdir MPglm.wls --nii.gz in the command line, it 
 works without any error. 

 Thanks in advance!
 Yuko Yotsumoto


 % full error message regarding the second question 
 ---
 cmdline mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface 
 fsaverage lh --glmdir MPglm.wls --nii.gz
 WARNING: unrecognized mri_glmfit cmd option --surface
 WARNING: unrecognized mri_glmfit cmd option fsaverage
 WARNING: unrecognized mri_glmfit cmd option lh
 WARNING: unrecognized mri_glmfit cmd option --nii.gz
 log file is MPglm.wls/mc-z.abs.2.mri_glmfit-sim.log
 cd /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4
 /Applications/freesurfer/bin/mri_glmfit-sim
 --glmdir MPglm.wls --sim mc-z 100 2 mc-z.abs.2 --sim-sign abs --overwrite

 $Id: mri_glmfit-sim,v 1.24.2.5 2010/07/27 22:49:00 greve Exp $
 Wed Nov 23 13:55:01 JST 2011
 Darwin Hideaki-Kawabata-no-MacBook-Pro.local 10.8.0 Darwin Kernel Version 
 10.8.0: Tue Jun  7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 
 x86_64
 kawabata
 setenv SUBJECTS_DIR /Users/kawabata/Documents/freesurfer/subjects
 FREESURFER_HOME /Applications/freesurfer
 DoSim = 1
 UseCache = 0
 DoPoll = 0
 DoPBSubmit = 0
 DoBackground = 0
 DiagCluster = 0
 gd2mtx = dods
 fwhm = 15.248189
 nSimPerJob = 100
 1/1 Wed Nov 23 13:55:01 JST 2011
 mri_glmfit --y 
 /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4/ces.008.nii
  --C MPglm.wls/tmp.mri_glmfit-sim-6456/osgm.mtx --mask MPglm.wls/mask.nii.gz 
 --sim mc-z 100 2 MPglm.wls/csd/mc-z.abs.2.j001 --sim-sign abs --fwhm 
 15.248189 --X MPglm.wls/Xg.dat --wls 
 /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4/cesvar.008.nii
 Bus error 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


   

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

___
Freesurfer mailing list
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 Partners Compliance HelpLine at
http://www.partners.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 the e-mail.

[Freesurfer] mri_glmfit-sim error with v5.0

[yukoyy]

Hello

I'm having a trouble with mri_glmfit-sim with v5.0, which is locally installed 
on Mac 10.6.8.

Whan I ran:
mri_glmfit-sim --glmdir MPglm.wls --cache 3.0 pos --cwpvalthresh .0166

I got:
ERROR: cannot find 
/Applications/freesurfer/average/mult-comp-cor///cortex/fwhm15/pos/th30/mc-z.csd

I have 
/Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th30/mc-z.csd
in my directory.

It looks like I need to somehow tell freesurfer /fsaverage/lh/, but how?

Before mri_glmfit-sim, I did the followings:
isxconcat-sess -df sessdirfile -sf sessidlist -analysis PreL -hemi lh -c 16vs4 
-o MPgroup
mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface fsaverage lh 
--glmdir MPglm.wls --nii.gz


% -
Also, when I did:
mri_glmfit-sim --glmdir MPglm.wls --sim mc-z 100 2 mc-z.abs.2 --sim-sign abs 
--overwrite

I got several warnings and errors (full error message pasted at the end of this 
email):
 cmdline mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface 
 fsaverage lh --glmdir MPglm.wls --nii.gz
 WARNING: unrecognized mri_glmfit cmd option --surface
 WARNING: unrecognized mri_glmfit cmd option fsaverage
 WARNING: unrecognized mri_glmfit cmd option lh
 WARNING: unrecognized mri_glmfit cmd option --nii.gz

 mri_glmfit --y 
 /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4/ces.008.nii
  --C 
 MPglm.wls/tmp.mri_glmfit-sim-6456/osgm.mtx --mask MPglm.wls/mask.nii.gz --sim 
 mc-z 100 2 MPglm.wls/csd
 /mc-z.abs.2.j001 --sim-sign abs --fwhm 15.248189 --X MPglm.wls/Xg.dat --wls 
 /Users/kawabata/Documents/freesurfer
 /sessions/MP/MEAN/MPgroup/PreL/16vs4/cesvar.008.nii
 Bus error 

I don't understand why mri_glmfit-sim calls mri_glmfit, and gives warnings? 
When I paste mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface 
fsaverage lh --glmdir MPglm.wls --nii.gz in the command line, it works without 
any error. 

Thanks in advance!
Yuko Yotsumoto


% full error message regarding the second question 
---
cmdline mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface 
fsaverage lh --glmdir MPglm.wls --nii.gz
WARNING: unrecognized mri_glmfit cmd option --surface
WARNING: unrecognized mri_glmfit cmd option fsaverage
WARNING: unrecognized mri_glmfit cmd option lh
WARNING: unrecognized mri_glmfit cmd option --nii.gz
log file is MPglm.wls/mc-z.abs.2.mri_glmfit-sim.log
cd /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4
/Applications/freesurfer/bin/mri_glmfit-sim
--glmdir MPglm.wls --sim mc-z 100 2 mc-z.abs.2 --sim-sign abs --overwrite

$Id: mri_glmfit-sim,v 1.24.2.5 2010/07/27 22:49:00 greve Exp $
Wed Nov 23 13:55:01 JST 2011
Darwin Hideaki-Kawabata-no-MacBook-Pro.local 10.8.0 Darwin Kernel Version 
10.8.0: Tue Jun  7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
kawabata
setenv SUBJECTS_DIR /Users/kawabata/Documents/freesurfer/subjects
FREESURFER_HOME /Applications/freesurfer
DoSim = 1
UseCache = 0
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 15.248189
nSimPerJob = 100
1/1 Wed Nov 23 13:55:01 JST 2011
mri_glmfit --y 
/Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4/ces.008.nii
 --C MPglm.wls/tmp.mri_glmfit-sim-6456/osgm.mtx --mask MPglm.wls/mask.nii.gz 
--sim mc-z 100 2 MPglm.wls/csd/mc-z.abs.2.j001 --sim-sign abs --fwhm 15.248189 
--X MPglm.wls/Xg.dat --wls 
/Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4/cesvar.008.nii
Bus error 
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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 Partners Compliance HelpLine at
http://www.partners.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 the e-mail.

[Freesurfer] mri_glmfit-sim error

[GREGORY R KIRK]

hi folks,

when i run mri_glmfit-sim --glmdir rh.measure_t7cort.glmdir --cache 2.0 neg
i get an error message ERROR: cannot find 
/apps/x86_64_sci5/freesurfer-latest/average/mult-comp-cor/average/rh/cortex/fwhm14/neg/th20/mc-z.csd

there is fsaverage... should i just make a soft link ?
also when i run the mri_glmfit-sim with or without --cache i get
WARNING: unrecognized mri_glmfit cmd option doss, the glm fit anal was -doss 
and went without problem or complaints.
and using sim without --cache the simulations are running.

is this a nuisance error message that i should just ignore ?

thanks

greg
___
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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 Partners Compliance HelpLine at
http://www.partners.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 the e-mail.

Re: [Freesurfer] mri_glmfit-sim error

[Douglas N Greve]

You can make a soft link. Don't worry about that warning (it's not 
important, and I've fixed it for the next version).
doug

GREGORY R KIRK wrote:
 hi folks,

 when i run mri_glmfit-sim --glmdir rh.measure_t7cort.glmdir --cache 2.0 neg
 i get an error message ERROR: cannot find 
 /apps/x86_64_sci5/freesurfer-latest/average/mult-comp-cor/average/rh/cortex/fwhm14/neg/th20/mc-z.csd

 there is fsaverage... should i just make a soft link ?
 also when i run the mri_glmfit-sim with or without --cache i get
 WARNING: unrecognized mri_glmfit cmd option doss, the glm fit anal was -doss 
 and went without problem or complaints.
 and using sim without --cache the simulations are running.

 is this a nuisance error message that i should just ignore ?

 thanks

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


   

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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