subject:"Re\: \[Freesurfer\] if\: Expression Syntax"

Re: [Freesurfer] if: Expression Syntax - preproc-sess

2024-03-22 Thread 蒋文骥

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傻逼 别tm给我发消息了！退订 



 Replied Message 
| From | Stefano Delli Pizzi |
| Date | 03/22/2024 19:03 |
| To | Douglas N. Greve |
| Cc | Freesurfer support list |
| Subject | Re: [Freesurfer] if: Expression Syntax - preproc-sess |

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II have copied the f.nii.gz file (which contains the functional data filtered 
by AROMA) and renamed it as 'fmcpr.nii.gz’. 
Do you agree?
The scripts run fine.

Stefano





Il giorno 21 mar 2024, alle ore 17:01, Stefano Delli Pizzi 
 ha scritto:


My command line is
fcseed-sess -s 156484 -cfg wm.config. 
I do not understand where I'm making an error or if a change is needed.
Thanks
Stefano



Il giorno 21 mar 2024, alle ore 14:35, Douglas N. Greve 
 ha scritto:


-funcstem f.even



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Re: [Freesurfer] if: Expression Syntax - preproc-sess

2024-03-22 Thread Stefano Delli Pizzi

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II have copied the f.nii.gz file (which contains the functional data filtered 
by AROMA) and renamed it as 'fmcpr.nii.gz’. 
Do you agree?
The scripts run fine.
Stefano


> Il giorno 21 mar 2024, alle ore 17:01, Stefano Delli Pizzi 
>  ha scritto:
> 
> My command line is
> fcseed-sess -s 156484 -cfg wm.config. 
> I do not understand where I'm making an error or if a change is needed.
> Thanks
> Stefano
> 
>> Il giorno 21 mar 2024, alle ore 14:35, Douglas N. Greve 
>> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>> 
>> -funcstem f.even
> 

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Re: [Freesurfer] if: Expression Syntax - preproc-sess

2024-03-21 Thread Stefano Delli Pizzi

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My command line is
fcseed-sess -s 156484 -cfg wm.config. 
I do not understand where I'm making an error or if a change is needed.
Thanks
Stefano

> Il giorno 21 mar 2024, alle ore 14:35, Douglas N. Greve 
>  ha scritto:
> 
> -funcstem f.even

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 .
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Re: [Freesurfer] if: Expression Syntax - preproc-sess

2024-03-21 Thread Douglas N. Greve

What is your fcseed-config command line? If the input is not fmcpr, then 
you have to set the input when you config, eg, -funcstem f.even


On 3/19/2024 11:37 AM, Stefano Delli Pizzi wrote:


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Thank you Doug.
The preproc-sess command line runs fine.
An error occurs on:
fcseed-sess -s ID -cfg wm.config -overwrite
ERROR: could not determine file for rs-fMRI_AROMA/ID/rest/001/fmcpr

Best regards
Stefano

Il giorno 19 mar 2024, alle ore 15:54, Douglas N. Greve 
 ha scritto:


Hi Stefano, I think I found and fixed the problem. Can you try these?

On 3/19/2024 7:30 AM, Stefano Delli Pizzi wrote:


External Email - Use Caution

Hi Doug,

The raw functional file is firstly passed with motion correction 
(i.e., mc-sess -s ID -fsd rest -per-run) and AROMA filtering.

Next, I have renamed the ICA filtered file as f.nii.gz.
Then, I run:

preproc-sess -s ${1} -surface fsaverage lhrh -nomc -fwhm 0 -mni305 
-fsd rest -per-run -sliceorder even -force


There are issues with labels since excluding motion correction 
doesn't produce key files necessary for concatenating the files.
The preprocessing script is searching for the fmcpr.nii.gz file, 
which cannot be found because it is not created using the -nomc option.


When I duplicate and rename the file f.nii.gz as fmcpr.nii.gz and 
rerun preproc, the operation is done and the 
fmcpr.odd.sm0.fsaverage.lh is created.


However, when I run the next steps (fcseed-sess -s ID -cfg wm.config 
-overwrite), a second error occurs (reported below) because the 
script searches for fmcpr, which cannot be produced since I used -mc.


ERROR: could not determine file for 
/Volumes/mnu/MRI/PPMI/NIFTI/FreeSurfer/rs-fMRI_AROMA/ID/rest/001/fmcpr 
This error seems to be related to the script searching for the fmcpr 
file, which isn't available due to the use of -mc.


Thank you.

Best regards,


Stefano




Il giorno 18 mar 2024, alle ore 17:16, Stefano Delli Pizzi 
 ha scritto:


Hi Doug have you any news
Thank you very much!
Stefano

Il giorno 12 mar 2024, alle ore 10:26, Stefano Delli Pizzi 
 ha scritto:


Thank you.
I’m attaching the file.
Stefano


Il giorno 11 mar 2024, alle ore 22:20, Douglas N. Greve 
 ha scritto:


can you send me this file 
/Applications/freesurfer/7.4.1/fsfast/bin/preproc-sess



On 3/11/2024 3:58 AM, Stefano Delli Pizzi wrote:


External Email - Use Caution

It seems to me that I've done what you suggest. Attached is a 
new outputs.

Thanks
Stefano

Il giorno 10 mar 2024, alle ore 23:44, Douglas N. Greve 
 ha scritto:


Are you sure that you are using the new version that I gave 
you? It looks like the previous version. Also, it does not look 
like the entire terminal output.


On 3/8/2024 12:11 PM, Stefano Delli Pizzi wrote:


External Email - Use Caution

The entire terminal output is attached.
Thanks!

Il giorno 8 mar 2024, alle ore 15:56, Douglas N. Greve 
 ha scritto:


entire terminal output




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 .




The information in this e-mail is intended only for the person to 
whom it is addressed.  If you believe this e-mail was sent to you 
in error and the e-mail contains patient information, please 
contact the Mass General Brigham Compliance HelpLine at 
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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 
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Re: [Freesurfer] if: Expression Syntax - preproc-sess

2024-03-19 Thread Stefano Delli Pizzi

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Thank you Doug.
The preproc-sess command line runs fine.
An error occurs on:
fcseed-sess -s ID -cfg wm.config -overwrite
ERROR: could not determine file for rs-fMRI_AROMA/ID/rest/001/fmcpr

Best regards
Stefano

> Il giorno 19 mar 2024, alle ore 15:54, Douglas N. Greve 
>  ha scritto:
> 
> Hi Stefano, I think I found and fixed the problem. Can you try these? 
> 
> On 3/19/2024 7:30 AM, Stefano Delli Pizzi wrote:
>> External Email - Use Caution
>> 
>> Hi Doug,  
>> 
>> The raw functional file is firstly passed with motion correction (i.e., 
>> mc-sess -s ID -fsd rest -per-run) and AROMA filtering.
>> Next, I have renamed the ICA filtered file as f.nii.gz.
>> Then, I run:
>> 
>> preproc-sess -s ${1} -surface fsaverage lhrh -nomc -fwhm 0 -mni305 -fsd rest 
>> -per-run -sliceorder even -force
>> 
>> There are issues with labels since excluding motion correction doesn't 
>> produce key files necessary for concatenating the files. 
>> The preprocessing script is searching for the fmcpr.nii.gz file, which 
>> cannot be found because it is not created using the -nomc option. 
>> 
>> When I duplicate and rename the file f.nii.gz as fmcpr.nii.gz and rerun 
>> preproc, the operation is done and the fmcpr.odd.sm0.fsaverage.lh is 
>> created. 
>> 
>> However, when I run the next steps (fcseed-sess -s ID -cfg wm.config 
>> -overwrite), a second error occurs (reported below) because the script 
>> searches for fmcpr, which cannot be produced since I used -mc.  
>> 
>> ERROR: could not determine file for 
>> /Volumes/mnu/MRI/PPMI/NIFTI/FreeSurfer/rs-fMRI_AROMA/ID/rest/001/fmcpr This 
>> error seems to be related to the script searching for the fmcpr file, which 
>> isn't available due to the use of -mc.
>> 
>> Thank you.
>> 
>> Best regards,
>> 
>> 
>> Stefano
>> 
>> 
>> 
>> 
>>> Il giorno 18 mar 2024, alle ore 17:16, Stefano Delli Pizzi 
>>> mailto:sdellipi...@gmail.com>> ha scritto:
>>> 
>>> Hi Doug have you any news
>>> Thank you very much!
>>> Stefano
>>> 
 Il giorno 12 mar 2024, alle ore 10:26, Stefano Delli Pizzi 
 mailto:sdellipi...@gmail.com>> ha scritto:
 
 Thank you.
 I’m attaching the file.
 Stefano
 
 
> Il giorno 11 mar 2024, alle ore 22:20, Douglas N. Greve 
> mailto:dgr...@mgh.harvard.edu>> ha scritto:
> 
> can you send me this file 
> /Applications/freesurfer/7.4.1/fsfast/bin/preproc-sess
> 
> 
> On 3/11/2024 3:58 AM, Stefano Delli Pizzi wrote:
>> External Email - Use Caution
>> 
>> It seems to me that I've done what you suggest.
>> Attached is a new outputs.
>> Thanks
>> Stefano
>> 
>> 
>> 
>>> Il giorno 10 mar 2024, alle ore 23:44, Douglas N. Greve 
>>> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>>> 
>>> Are you sure that you are using the new version that I gave you? It 
>>> looks like the previous version. Also, it does not look like the entire 
>>> terminal output.
>>> 
>>> On 3/8/2024 12:11 PM, Stefano Delli Pizzi wrote:
 External Email - Use Caution
 
 The entire terminal output is attached.
 Thanks!
 
> Il giorno 8 mar 2024, alle ore 15:56, Douglas N. Greve 
> mailto:dgr...@mgh.harvard.edu>> ha scritto:
> 
> entire terminal output
 
>>> 
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu 
>>> https://secure-web.cisco.com/1sSUGeb2ig2jpdimRxpnmJD_858yb00GE2-WzBCOa7CcQFfAY_uUe6VtyA1oO8Lc0Kw-n6HgNBcX_q9Fo92L64wwFoPOprTCwcUtlLqdVLXhnUt12HQDTFp1XdiYzAVB9XJP93Xi87hPBy-LRGesgl0LjSBKXVr_zEvmciMMSWERkAc1EmD-QZxGd-MBynOOpPc2rMCITW58yJevb-F9NX-0XGTkYJkDscvs4CIz23OsRJHt8weLQ0mBoodfI3dKMrR8QiACirryiEF7kn4JCfluBWQkx_xQgR4XyiyE9D2VA6YvXsF95x9mv41HoHIBd/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 
>>>

Re: [Freesurfer] if: Expression Syntax - preproc-sess

2024-03-19 Thread Douglas N. Greve


Hi Stefano, I think I found and fixed the problem. Can you try these?

On 3/19/2024 7:30 AM, Stefano Delli Pizzi wrote:


External Email - Use Caution

Hi Doug,

The raw functional file is firstly passed with motion correction 
(i.e., mc-sess -s ID -fsd rest -per-run) and AROMA filtering.

Next, I have renamed the ICA filtered file as f.nii.gz.
Then, I run:

preproc-sess -s ${1} -surface fsaverage lhrh -nomc -fwhm 0 -mni305 
-fsd rest -per-run -sliceorder even -force


There are issues with labels since excluding motion correction doesn't 
produce key files necessary for concatenating the files.
The preprocessing script is searching for the fmcpr.nii.gz file, which 
cannot be found because it is not created using the -nomc option.


When I duplicate and rename the file f.nii.gz as fmcpr.nii.gz and 
rerun preproc, the operation is done and the 
fmcpr.odd.sm0.fsaverage.lh is created.


However, when I run the next steps (fcseed-sess -s ID -cfg wm.config 
-overwrite), a second error occurs (reported below) because the script 
searches for fmcpr, which cannot be produced since I used -mc.


ERROR: could not determine file for 
/Volumes/mnu/MRI/PPMI/NIFTI/FreeSurfer/rs-fMRI_AROMA/ID/rest/001/fmcpr 
This error seems to be related to the script searching for the fmcpr 
file, which isn't available due to the use of -mc.


Thank you.

Best regards,


Stefano




Il giorno 18 mar 2024, alle ore 17:16, Stefano Delli Pizzi 
 ha scritto:


Hi Doug have you any news
Thank you very much!
Stefano

Il giorno 12 mar 2024, alle ore 10:26, Stefano Delli Pizzi 
 ha scritto:


Thank you.
I’m attaching the file.
Stefano


Il giorno 11 mar 2024, alle ore 22:20, Douglas N. Greve 
 ha scritto:


can you send me this file 
/Applications/freesurfer/7.4.1/fsfast/bin/preproc-sess



On 3/11/2024 3:58 AM, Stefano Delli Pizzi wrote:


External Email - Use Caution

It seems to me that I've done what you suggest. Attached is a new 
outputs.

Thanks
Stefano

Il giorno 10 mar 2024, alle ore 23:44, Douglas N. Greve 
 ha scritto:


Are you sure that you are using the new version that I gave you? 
It looks like the previous version. Also, it does not look like 
the entire terminal output.


On 3/8/2024 12:11 PM, Stefano Delli Pizzi wrote:


External Email - Use Caution

The entire terminal output is attached.
Thanks!

Il giorno 8 mar 2024, alle ore 15:56, Douglas N. Greve 
 ha scritto:


entire terminal output




___
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The information in this e-mail is intended only for the person to 
whom it is addressed.  If you believe this e-mail was sent to you 
in error and the e-mail contains patient information, please 
contact the Mass General Brigham Compliance HelpLine at 
https://www.massgeneralbrigham.org/complianceline 
 .




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 
 
.






#! /bin/tcsh -f

#
# preproc-sess - runs preprocessing (mc, spatsmooth, mkbrainmask, inorm)
#
# Original Author: Doug Greve
#
# Copyright © 2021
# The General Hospital Corporation (Boston, MA). 
# All rights reserved.
#
# Distribution, usage and copying of this software is covered under the
# terms found in the License Agreement file named 'COPYING' found in the
# FreeSurfer source code root directory, and duplicated here:
# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOpenSourceLicense
#
# General inquiries: freesurfer@nmr.mgh.harvard.edu
# Bug reports: analysis-b...@nmr.mgh.harvard.edu
#

# To get per-run reg with smoothing, make sure -fwhm is after -per-run:
# preproc-sess -s risk001 -per-run -fwhm 5 -fsd bold 
# This creates fmcpr.sm5, then
# mkanalysis-sess -native -funcstem fmcpr.sm5 ...

set VERSION = 'preproc-sess @FS_VERSION@';

set inputargs = ($argv);
set DateStr = "`date '+%y%m%d%H%M'`"

set instem   = ();
set mcinstem   = ();
set mcoutstem  = ();
set stcinstem   = ();
set stcoutstem  = ();
set sminstem   = ();
set smoutstem  = ();
set inormstem  = ();
set maskdir= masks
set maskstem   = brain;
set UseSmoothMask = 0;
set fwhm = ();
set surffwhm = ();
set volsurffwhm  = (); # for testing
set SliceOrder = ();
set SliceDelayFile = ()
set nSliceGroups = 1;
set

Re: [Freesurfer] if: Expression Syntax - preproc-sess

2024-03-10 Thread Douglas N. Greve

Are you sure that you are using the new version that I gave you? It 
looks like the previous version. Also, it does not look like the entire 
terminal output.


On 3/8/2024 12:11 PM, Stefano Delli Pizzi wrote:


External Email - Use Caution

The entire terminal output is attached.
Thanks!

Il giorno 8 mar 2024, alle ore 15:56, Douglas N. Greve 
 ha scritto:


entire terminal output


___
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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
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] if: Expression Syntax - preproc-sess

2024-03-08 Thread Stefano Delli Pizzi

External Email - Use CautionThe entire terminal output is attached.Thanks!

preproc-141696-rest.log
Description: Binary data
Il giorno 8 mar 2024, alle ore 15:56, Douglas N. Greve  ha scritto:entire terminal output___
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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
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 
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Re: [Freesurfer] if: Expression Syntax - preproc-sess

2024-03-08 Thread Stefano Delli Pizzi

External Email - Use Caution

Thank you very much.
After the updata that you suggested, this error occurs:
could not determine file for 
/Volumes/mnu/MRI/PPMI/NIFTI/FreeSurfer/rs-fMRI/XXX/rest/001/fmcpr.even
Stefano

> Il giorno 5 mar 2024, alle ore 16:26, Douglas N. Greve 
>  ha scritto:
> 
> I've made a patch to try to fix this. I've attached 3 files. Copy them to 
> $FREESURFER/fsfast/bin. Make them executable by running
> cd $FREESURFER/fsfast/bin
> chmod a+x rawfunc2surf-sess rawfunc2tal-sess preproc-sess 
> Let me know if that works
> 
> 
> On 3/5/2024 2:28 AM, Stefano Delli Pizzi wrote:
>> External Email - Use Caution
>> 
>> Here -debug outputs
>> 
>> preproc-sess -s 091223sbj01m_tp1 -surface fsaverage lhrh -fwhm 0 -nomc 
>> -mni305 -fsd rest -per-run -sliceorder up -debug
>> set echo = 1 ;
>> breaksw
>> breaksw
>> 
>> end
>> end
>> while ( $#argv != 0 )
>> while ( 0 != 0 )
>> goto parse_args_return ;
>> goto parse_args_return
>> 
>> foreach grp ( $grpdefs )
>> foreach grp ( )
>> 
>> goto check_params ;
>> goto check_params
>> 
>> if ( $#SessList == 0 ) then
>> if ( 1 == 0 ) then
>> 
>> if ( $#SearchPathList == 0 ) then
>> if ( 0 == 0 ) then
>> set SearchPathList = "." ;
>> set SearchPathList = .
>> endif
>> endif
>> 
>> goto check_params_return ;
>> goto check_params_return
>> 
>> 
>> set UniqueList = ( ) ;
>> set UniqueList = ( )
>> foreach d ( $SearchPathList )
>> foreach d ( . )
>> if ( ! -e $d ) then
>> if ( ! -e . ) then
>> 
>> set IsUnique = 1 ;
>> set IsUnique = 1
>> foreach u ( $UniqueList )
>> foreach u ( )
>> if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ;
>> if ( 1 ) set UniqueList = ( . )
>> set UniqueList = ( . )
>> end
>> end
>> 
>> set SearchPathList = ( $UniqueList ) ;
>> set SearchPathList = ( . )
>> 
>> set errs = 0 ;
>> set errs = 0
>> 
>> 
>> set SessPath = ( ) ;
>> set SessPath = ( )
>> foreach sess ( $SessList )
>> foreach sess ( 091223sbj01m_tp1 )
>> set tmp = ( ) ;
>> set tmp = ( )
>> foreach d ( $SearchPathList )
>> foreach d ( . )
>> set stst = $d/$sess
>> set stst = ./091223sbj01m_tp1
>> if ( -d $stst ) then
>> if ( -d ./091223sbj01m_tp1 ) then
>> if ( ! -r $stst ) then
>> if ( ! -r ./091223sbj01m_tp1 ) then
>> pushd $stst > /dev/null ;
>> pushd ./091223sbj01m_tp1
>> set tmp = ( $tmp `$PWDCMD` ) ;
>> set tmp = ( `$PWDCMD` )
>> pwd
>> popd > /dev/null ;
>> popd
>> endif
>> endif
>> end
>> end
>> set nfound = ( $#tmp ) ;
>> set nfound = ( 1 )
>> if ( $nfound == 0 ) then
>> if ( 1 == 0 ) then
>> if ( $nfound > 1 ) then
>> if ( 1 > 1 ) then
>> set SessPath = ( $SessPath $tmp ) ;
>> set SessPath = ( 
>> /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1 )
>> end
>> end
>> 
>> 
>> set UniqueList = ( ) ;
>> set UniqueList = ( )
>> foreach s ( $SessPath )
>> foreach s ( /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1 )
>> set IsUnique = 1 ;
>> set IsUnique = 1
>> foreach u ( $UniqueList )
>> foreach u ( )
>> if ( ! $IsUnique && ! $AllowRedundant ) then
>> if ( ! 1 && ! 0 ) then
>> 
>> set UniqueList = ( $UniqueList $s ) ;
>> set UniqueList = ( 
>> /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1 )
>> endif
>> endif
>> end
>> end
>> 
>> 
>> echo $SessPath
>> echo /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1
>> 
>> exit $errs ;
>> exit 0
>> 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 ( $#instem == 0 ) set instem = "f" ;
>> if ( 0 == 0 ) set instem = f
>> set instem = f
>> 
>> if ( $#fsd == 0 ) then
>> if ( 1 == 0 ) then
>> 
>> if ( $DoMC || $DoReg ) then
>> if ( 0 || 1 ) then
>> if ( $PerRun == 0 && $PerSess == 0 ) then
>> if ( 1 == 0 && 0 == 0 ) then
>> endif
>> endif
>> 
>> if ( $DoMC ) then
>> if ( 0 ) then
>> 
>> set mcoutstem = $instem ;
>> set mcoutstem = f
>> endif
>> endif
>> 
>> if ( $DoSTC ) then
>> if ( 1 ) then
>> if ( $#stcinstem == 0 ) set stcinstem = $mcoutstem
>> if ( 0 == 0 ) set stcinstem = f
>> set stcinstem = f
>> if ( $#stcoutstem == 0 ) then
>> if ( 0 == 0 ) then
>> if ( $#SliceOrder ) set stcoutstem = $stcinstem.$SliceOrder
>> if ( 1 ) set stcoutstem = f.up
>> set stcoutstem = f.up
>> if ( $#SliceDelayFile ) set stcoutstem = $stcinstem.sdf
>> if ( 0 ) set stcoutstem = f.sdf
>> endif
>> endif
>> else
>> else
>> 
>> if ( $ToSurf || $ToMNI305 || $ToCVS ) then
>> if ( 1 || 1 || 0 ) then
>> if ( $#fwhm == 0 ) then
>> if ( 1 == 0 ) then
>> set DoVolSmooth = 0 ;
>> set DoVolSmooth = 0
>> set DoSurfSmooth = 0 ;
>> set DoSurfSmooth = 0
>> set DoSmooth = 0 ;
>> set DoSmooth = 0
>> endif
>> endif
>> 
>> if ( $DoSmooth ) then
>> if ( 0 ) then
>> 
>> if ( $DoInorm && $#inormstem == 0 ) then
>> if ( 0 && 0 == 0 ) then
>> 
>> if ( ! $DoMC && ! $DoSTC && ! $DoSmooth && ! $DoMask && ! $DoTemplate ) then
>> if ( ! 0 && ! 1 && ! 0 && ! 1 && ! 1 ) then
>> 
>> if ( $#ProjFrac && $DoProjAvg ) then
>> if ( 0 && 0 )

Re: [Freesurfer] if: Expression Syntax - preproc-sess

2024-03-04 Thread Stefano Delli Pizzi

External Email - Use Caution

Here -debug outputs

preproc-sess -s 091223sbj01m_tp1 -surface fsaverage lhrh -fwhm 0 -nomc -mni305 
-fsd rest -per-run -sliceorder up -debug
set echo = 1 ;
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 0 != 0 )
goto parse_args_return ;
goto parse_args_return

foreach grp ( $grpdefs )
foreach grp ( )

goto check_params ;
goto check_params

if ( $#SessList == 0 ) then
if ( 1 == 0 ) then

if ( $#SearchPathList == 0 ) then
if ( 0 == 0 ) then
set SearchPathList = "." ;
set SearchPathList = .
endif
endif

goto check_params_return ;
goto check_params_return


set UniqueList = ( ) ;
set UniqueList = ( )
foreach d ( $SearchPathList )
foreach d ( . )
if ( ! -e $d ) then
if ( ! -e . ) then

set IsUnique = 1 ;
set IsUnique = 1
foreach u ( $UniqueList )
foreach u ( )
if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ;
if ( 1 ) set UniqueList = ( . )
set UniqueList = ( . )
end
end

set SearchPathList = ( $UniqueList ) ;
set SearchPathList = ( . )

set errs = 0 ;
set errs = 0


set SessPath = ( ) ;
set SessPath = ( )
foreach sess ( $SessList )
foreach sess ( 091223sbj01m_tp1 )
set tmp = ( ) ;
set tmp = ( )
foreach d ( $SearchPathList )
foreach d ( . )
set stst = $d/$sess
set stst = ./091223sbj01m_tp1
if ( -d $stst ) then
if ( -d ./091223sbj01m_tp1 ) then
if ( ! -r $stst ) then
if ( ! -r ./091223sbj01m_tp1 ) then
pushd $stst > /dev/null ;
pushd ./091223sbj01m_tp1
set tmp = ( $tmp `$PWDCMD` ) ;
set tmp = ( `$PWDCMD` )
pwd
popd > /dev/null ;
popd
endif
endif
end
end
set nfound = ( $#tmp ) ;
set nfound = ( 1 )
if ( $nfound == 0 ) then
if ( 1 == 0 ) then
if ( $nfound > 1 ) then
if ( 1 > 1 ) then
set SessPath = ( $SessPath $tmp ) ;
set SessPath = ( 
/Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1 )
end
end


set UniqueList = ( ) ;
set UniqueList = ( )
foreach s ( $SessPath )
foreach s ( /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1 )
set IsUnique = 1 ;
set IsUnique = 1
foreach u ( $UniqueList )
foreach u ( )
if ( ! $IsUnique && ! $AllowRedundant ) then
if ( ! 1 && ! 0 ) then

set UniqueList = ( $UniqueList $s ) ;
set UniqueList = ( 
/Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1 )
endif
endif
end
end


echo $SessPath
echo /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1

exit $errs ;
exit 0
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 ( $#instem == 0 ) set instem = "f" ;
if ( 0 == 0 ) set instem = f
set instem = f

if ( $#fsd == 0 ) then
if ( 1 == 0 ) then

if ( $DoMC || $DoReg ) then
if ( 0 || 1 ) then
if ( $PerRun == 0 && $PerSess == 0 ) then
if ( 1 == 0 && 0 == 0 ) then
endif
endif

if ( $DoMC ) then
if ( 0 ) then

set mcoutstem = $instem ;
set mcoutstem = f
endif
endif

if ( $DoSTC ) then
if ( 1 ) then
if ( $#stcinstem == 0 ) set stcinstem = $mcoutstem
if ( 0 == 0 ) set stcinstem = f
set stcinstem = f
if ( $#stcoutstem == 0 ) then
if ( 0 == 0 ) then
if ( $#SliceOrder ) set stcoutstem = $stcinstem.$SliceOrder
if ( 1 ) set stcoutstem = f.up
set stcoutstem = f.up
if ( $#SliceDelayFile ) set stcoutstem = $stcinstem.sdf
if ( 0 ) set stcoutstem = f.sdf
endif
endif
else
else

if ( $ToSurf || $ToMNI305 || $ToCVS ) then
if ( 1 || 1 || 0 ) then
if ( $#fwhm == 0 ) then
if ( 1 == 0 ) then
set DoVolSmooth = 0 ;
set DoVolSmooth = 0
set DoSurfSmooth = 0 ;
set DoSurfSmooth = 0
set DoSmooth = 0 ;
set DoSmooth = 0
endif
endif

if ( $DoSmooth ) then
if ( 0 ) then

if ( $DoInorm && $#inormstem == 0 ) then
if ( 0 && 0 == 0 ) then

if ( ! $DoMC && ! $DoSTC && ! $DoSmooth && ! $DoMask && ! $DoTemplate ) then
if ( ! 0 && ! 1 && ! 0 && ! 1 && ! 1 ) then

if ( $#ProjFrac && $DoProjAvg ) then
if ( 0 && 0 ) then

if ( $UseB0DC && $#ProjFracExpKey ) then
if ( 0 && 0 ) then

if ( $#regfile == 0 ) then
if ( 0 == 0 ) then
if ( ! $UseB0DC ) set regfile = register.dof$RegDOF.lta
if ( ! 0 ) set regfile = register.dof6.lta
set regfile = register.dof6.lta
if ( $UseB0DC ) set regfile = register.dof$RegDOF.b0dc.lta
if ( 0 ) set regfile = register.dof6.b0dc.lta
endif
endif

if ( $#SliceDelayFile != 0 && $#SliceOrder != 0 ) then
if ( 0 != 0 && 1 != 0 ) then

goto check_params_return ;
goto check_params_return


if ( $nolog ) then
if ( 0 ) then

set logdir = log ;
set logdir = log
mkdir -p $logdir
mkdir -p log
if ( ! -e $logdir ) then
if ( ! -e log ) then

if ( $#SessList > 1 ) then
if ( 1 > 1 ) then

set sb = `basename $SessList`
set sb = `basename $SessList`
basename /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1
set LF = $logdir/preproc-sess.$sb.log
set LF = log/preproc-sess.091223sbj01m_tp1.log
endif
endif
if ( -e $LF ) mv $LF $LF.old
if ( -e log/preproc-sess.091223sbj01m_tp1.log ) mv 
log/preproc-sess.091223sbj01m_tp1.log log/preproc-sess.091223sbj01m_tp1.log.old
mv log/preproc-sess.091223sbj01m_tp1.log 
log/preproc-sess.091223sbj01m_tp1.log.old
endif
endif
endif
endif
echo

Re: [Freesurfer] if: Expression Syntax - preproc-sess

2024-02-23 Thread Douglas N. Greve

I cannot reproduce this locally. If you still want help, attach logs. 
You can also try running it with -debug as the first option and capture 
the copious terminal output.


On 2/6/2024 8:39 AM, Huang, Yujing wrote:


Not sure where this happened. Does it produce any log files that you 
can share? Maybe both logs with and without the -nomc option.


Best,

Yujing

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Stefano Delli 
Pizzi

*Sent:* Saturday, February 3, 2024 2:33 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] if: Expression Syntax - preproc-sess

*External Email - Use Caution *

Hello FreeSurfer Developers,
I'm attempting to run preproc-sess with -nomc option
preproc-sess -s subj -surface fsaverage lhrh -fwhm 0 -nomc -mni305 
-fsd rest

-per-run -sliceorder up -force
if: Expression Syntax.
This error occurred before to create the file with slice timing correction
The error did not occur when I run the preproc-sess command line 
without the

-nomc option.
I've searched the list and no similar errors have been reported. Does 
anyone

have any thoughts on how to trouble-shoot this one?
FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
Platform: Darwin Kernel Version 21.6.0

___
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Re: [Freesurfer] if: Expression Syntax - preproc-sess with -nomc option

2024-02-17 Thread Stefano Delli Pizzi

External Email - Use Caution

Thank you!

When I run:

stem2fname /Users/stefano/Desktop/XXX/rs-fMRI/003_S_6014/rest/001/f.even

I obtain this output:

/Users/stefano/Desktop/XXX/rs-fMRI/003_S_6014/rest/001/f.even.nii.gz


Anyway when I test also for other files, I found f.nii.gz ok, but an error that 
occurs on fmcpr.nii.gz, which is present in the folder after visual check.

stem2fname /Users/stefano/Desktop/XXX/rs-fMRI/003_S_6014/rest/001/fmcpr.nii.gz 
ERROR: could not determine file for 
/Users/stefano/Desktop/XXX/rs-fMRI/003_S_6014/rest/001/fmcpr.nii.gz

Kind regards


Stefano

> Il giorno 14 feb 2024, alle ore 21:28, Huang, Yujing 
>  ha scritto:
> 
> 
> Hi Stefano,
>  
> I looked at the log files that you sent in a separate email. I see 2 problems 
> here:
> 1. when running preproc-sess with -nomc option,  rawfunc2surf-sess couldn’t 
> find file fmcpr.up or fmcpr.even in the directory
> 2. I think the ‘if: Expression Syntax‘ error is from stem2fname
>  
> To confirm #2, can you try ‘stem2fname 
> /home/dylan/Documents/TRACULA/INPUTS/BIDS/derivatives/freesurfer/sub-01/mri/brainmask’
>  from your command line?
>  
> Best,
>  
> Yujing
>  
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  On Behalf Of Stefano Delli Pizzi
> Sent: Tuesday, February 13, 2024 4:32 AM
> To: Greve, Douglas N.,Ph.D. ; Freesurfer support list 
> 
> Subject: Re: [Freesurfer] if: Expression Syntax - preproc-sess with -nomc 
> option
>  
> External Email - Use Caution
> 
> Thank you.
> Stefano
> 
> 
> Binarizing based on threshold
> min1e-09
> max+infinity
> binval1
> binvalnot 0
> fstart = 0, fend = 0, nframes = 1
> Found 149926 values in range
> Counting number of voxels in first frame
> Found 149925 voxels in final mask
> Writing output to 
> /Users/stefano/Desktop/XXX/rs-fMRI/003_S_6014/rest/masks/brain.fsaverage.rh.pr.nii.gz
> Count: 149925 149925.00 163842 91.505841
> mri_binarize done
>   1/1 003_S_6014 001 lh -
> Mar 13 Feb 2024 10:28:12 CET
> ERROR: could not determine file for 
> /Users/stefano/Desktop/XXX/rs-fMRI/003_S_6014/rest/001/fmcpr.even
> if ( $status ) exit 1 ;
> if ( 1 ) exit 1
> exit 1
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/10UYWaHnqx4BENWI9xbmA4UTtoBV8-qeSvbi4Ygpl66AsqDp5jQhfgYnt8nhdklQlgisL8SMyMDGItqm1nm6aj4HLQ5A2cS2ruIkz77VKfqHTuzVKihDCJfTw_VvZM7RrLvHW4EpNNFCq8MJu7m0cSGKWwePlXzfQaQ555gFD2zSc4ic4CXGltAOQ0XZo9-tF9aF1MoM1CtniYpeabnzR4LXnk6_s3WC83t2f1EIVg-Z6LzzkgD6KBMY-j8AnAiDwp44K5lWJaPdOZ3pWCUxN6lYAtuSKHw5TYVjUtcjbQPK8ikT1owDwPD2ns6u7Rp2caDw9TI4rygEeFdExhrDRDQ/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 
> https://secure-web.cisco.com/19R-KHUg-mJTpyNchJK6kESVPGdGZ65kDU18vi0_YzFb4VNoMYqOU7qKpo4ChvJ7cJs2XXxMoSPzaoa2AKf_fqKXXaRWpCCnLInvVo-M4ybuv98pyMJfrFh7aHIEpNpNV4lV9RlTpFhS9QNGx97xiLzYjSl-zmHTF-uOGMLdzh7v_HVIpccjkbgCadGbh-TsO5NmsyCck9oO3IAnrxQP6t3eUB9xembmyJd9E8PP8FH7ZPMyen_c74UJCy-DmV6SnlHp-fZ1KT4O6MlRiOl0cQCgFbadwc_8J_ezXzrjumUrYiKjNyFdVt7H6bKf0ZLFoh1iPCOPe3jfgqgcj94UrcQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>  
> <https://secure-web.cisco.com/19R-KHUg-mJTpyNchJK6kESVPGdGZ65kDU18vi0_YzFb4VNoMYqOU7qKpo4ChvJ7cJs2XXxMoSPzaoa2AKf_fqKXXaRWpCCnLInvVo-M4ybuv98pyMJfrFh7aHIEpNpNV4lV9RlTpFhS9QNGx97xiLzYjSl-zmHTF-uOGMLdzh7v_HVIpccjkbgCadGbh-TsO5NmsyCck9oO3IAnrxQP6t3eUB9xembmyJd9E8PP8FH7ZPMyen_c74UJCy-DmV6SnlHp-fZ1KT4O6MlRiOl0cQCgFbadwc_8J_ezXzrjumUrYiKjNyFdVt7H6bKf0ZLFoh1iPCOPe3jfgqgcj94UrcQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>  .
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Re: [Freesurfer] if: Expression Syntax - preproc-sess with -nomc option

2024-02-14 Thread Huang, Yujing

Hi Stefano,

I looked at the log files that you sent in a separate email. I see 2 problems 
here:
1. when running preproc-sess with -nomc option,  rawfunc2surf-sess couldn't 
find file fmcpr.up or fmcpr.even in the directory
2. I think the 'if: Expression Syntax' error is from stem2fname

To confirm #2, can you try 'stem2fname 
/home/dylan/Documents/TRACULA/INPUTS/BIDS/derivatives/freesurfer/sub-01/mri/brainmask'
 from your command line?

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Stefano Delli Pizzi
Sent: Tuesday, February 13, 2024 4:32 AM
To: Greve, Douglas N.,Ph.D. ; Freesurfer support list 

Subject: Re: [Freesurfer] if: Expression Syntax - preproc-sess with -nomc option


External Email - Use Caution
Thank you.
Stefano


Binarizing based on threshold
min1e-09
max+infinity
binval1
binvalnot 0
fstart = 0, fend = 0, nframes = 1
Found 149926 values in range
Counting number of voxels in first frame
Found 149925 voxels in final mask
Writing output to 
/Users/stefano/Desktop/XXX/rs-fMRI/003_S_6014/rest/masks/brain.fsaverage.rh.pr.nii.gz
Count: 149925 149925.00 163842 91.505841
mri_binarize done
  1/1 003_S_6014 001 lh -
Mar 13 Feb 2024 10:28:12 CET
ERROR: could not determine file for 
/Users/stefano/Desktop/XXX/rs-fMRI/003_S_6014/rest/001/fmcpr.even
if ( $status ) exit 1 ;
if ( 1 ) exit 1
exit 1
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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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Re: [Freesurfer] if: Expression Syntax - preproc-sess with -nomc option

2024-02-13 Thread Stefano Delli Pizzi

External Email - Use Caution

Thank you.
Stefano

Binarizing based on threshold
min1e-09
max+infinity
binval1
binvalnot 0
fstart = 0, fend = 0, nframes = 1
Found 149926 values in range
Counting number of voxels in first frame
Found 149925 voxels in final mask
Writing output to 
/Users/stefano/Desktop/XXX/rs-fMRI/003_S_6014/rest/masks/brain.fsaverage.rh.pr.nii.gz
Count: 149925 149925.00 163842 91.505841
mri_binarize done
  1/1 003_S_6014 001 lh -
Mar 13 Feb 2024 10:28:12 CET
ERROR: could not determine file for 
/Users/stefano/Desktop/XXX/rs-fMRI/003_S_6014/rest/001/fmcpr.even
if ( $status ) exit 1 ;
if ( 1 ) exit 1
exit 1___
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Re: [Freesurfer] if: Expression Syntax - preproc-sess with -nomc option

2024-02-07 Thread Douglas N. Greve

Can you run it with -debug as the first option, capture the output, and 
send it to me? It will be a lot of output, so just capture it in a file 
and send the file, eg

preproc-sess -debug -s subj -surface fsaverage lhrh -fwhm 0 -nomc -mni305 -fsd 
rest -per-run -sliceorder up -force | tee pps.log

On 1/22/2024 11:20 AM, Stefano Delli Pizzi wrote:
>  External Email - Use Caution
>
> Hello FreeSurfer Developers,
>
> I'm attempting to run preproc-sess with -nomc option
>
> preproc-sess -s subj -surface fsaverage lhrh -fwhm 0 -nomc -mni305 -fsd rest 
> -per-run -sliceorder up -force
> if: Expression Syntax.
>
> This error occurred before to create the file with slice timing correction
>
> The error did not occur when I run the preproc-sess command line without the 
> -nomc option.
>
> I've searched the list and no similar errors have been reported. Does anyone 
> have any thoughts on how to trouble-shoot this one?
>
> FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
> Platform: Darwin Kernel Version 21.6.0
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
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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 
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Re: [Freesurfer] if: Expression Syntax - preproc-sess

2024-02-06 Thread Huang, Yujing

Not sure where this happened. Does it produce any log files that you can share? 
Maybe both logs with and without the -nomc option.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Stefano Delli Pizzi
Sent: Saturday, February 3, 2024 2:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] if: Expression Syntax - preproc-sess


External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to run preproc-sess with -nomc option



preproc-sess -s subj -surface fsaverage lhrh -fwhm 0 -nomc -mni305 -fsd rest

-per-run -sliceorder up -force

if: Expression Syntax.



This error occurred before to create the file with slice timing correction



The error did not occur when I run the preproc-sess command line without the

-nomc option.



I've searched the list and no similar errors have been reported. Does anyone

have any thoughts on how to trouble-shoot this one?



FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460

Platform: Darwin Kernel Version 21.6.0
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Re: [Freesurfer] if: Expression Syntax

2015-07-24 Thread Douglas Greve



can you run
register-sess -debug -s nmasa_031_130412 -d 
/autofs/cluster/iaslab/NMASA/mri/func/encoding -fsd bold -dof 6 -per-run 
-update | tee fordoug2.log


and send me fourdoug2.log

doug


On 7/24/15 10:22 AM, Morenikeji Adebayo wrote:

Hi there,

Attached is the log file from running:

preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface 
fsaverage lhrh -mni305 -fwhm 5 -per*-run*| tee fordoug.log


I got more errors when I ran:

preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface 
fsaverage lhrh -mni305 -fwhm 5 -per | tee fordoug.log



Thanks,
Keji



On Jul 23, 2015, at 6:05 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:


Yes, but you have a typo -min305 instead of -mni305



On 07/22/2015 05:30 PM, Morenikeji Adebayo wrote:

I sure can. Hopefully. Is the what you need?





On Jul 22, 2015, at 5:01 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
mailto:gr...@nmr.mgh.harvard.edu wrote:


can you just send the log and not put it into a doc file?

On 07/22/2015 04:46 PM, Morenikeji Adebayo wrote:

No problem! Here you go.




On Jul 22, 2015, at 4:30 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
mailto:gr...@nmr.mgh.harvard.edu

mailto:gr...@nmr.mgh.harvard.edu wrote:

Sorry, there should not be a * at the end of -per. I was just 
trying to

copy your command line with -debug as the first arg.

On 07/22/2015 04:02 PM, Morenikeji Adebayo wrote:

Hi Doug,

When I run:
preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface
fsaverage lhrh -min305 -fwhm 5 -per* | tee fordoug.log

I get:
preproc-sess: No match.

Thanks,
Keji



On Jul 22, 2015, at 3:37 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu 



wrote:

*
Can you run the following

preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface
fsaverage lhrh -min305 -fwhm 5 -per* | tee fordoug.log

and send me fordoug.log




On 07/22/2015 02:12 PM, Morenikeji Adebayo wrote:

Hi there,

I’m running stable:

source /usr/local/freesurfer/stable5_3_0

Thanks,
Keji


On Jul 21, 2015, at 4:56 PM, Douglas Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
mailto:gr...@nmr.mgh.harvard.edu

mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu wrote:

what environment are you running in? ie, dev or stable?

On 7/21/15 2:12 PM, Morenikeji Adebayo wrote:

Hi there,

*When running selxavg for the following session:*

nmasa_031_130412
*
*
*The following error message was generated:*
*
*
Error using MRIread (line 76)
ERROR: cannot determine format of
/autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm
(MRIread)

Error in fast_selxavg3 (line 146)
 runmask = MRIread(flac.maskfspec);
*
*
*I did some investigating and discovered that all the bold
runs for
this participant are missing the following files:*
*
*
.../func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm
.../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.lh.nii.gz
.../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.rh.nii.gz
*
*
*
So I ran:

preproc-sess -s nmasa_031_130412 -fsd bold -stc up -surface
fsaverage lhrh -min305 -fwhm 5 -per

*
*
*
*Which generated the following error message:*

if: Expression Syntax

**Do you have any idea what might be going wrong with this 
subject

or what this error message (**if: Expression Syntax) **means?**
*
*
*
*
Thanks,
Keji
---
Morenikeji Adebayo
Clinical Research Coordinator
Department of Psychiatric Neuroscience
Massachusetts General Hospital
(p) 617.643.6347
k...@nmr.mgh.harvard.edu mailto:k...@nmr.mgh.harvard.edu 
mailto:k...@nmr.mgh.harvard.edu

mailto:k...@nmr.mgh.harvard.edumailto:k...@nmr.mgh.harvard.edu
mailto:k...@nmr.mgh.harvard.edu



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---
Morenikeji Adebayo
Clinical Research Coordinator
Department of Psychiatric Neuroscience
Massachusetts General Hospital
(p) 617.643.6347
k...@nmr.mgh.harvard.edu mailto:k...@nmr.mgh.harvard.edu 
mailto:k...@nmr.mgh.harvard.edu

mailto:k...@nmr.mgh.harvard.edumailto:k...@nmr.mgh.harvard.edu
mailto:k...@nmr.mgh.harvard.edu

Re: [Freesurfer] if: Expression Syntax

2015-07-24 Thread Douglas Greve


I think there is something wrong with the contents of
/autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/subjectname

It looks like it is cd nmasa_031_130412, probably it should be 
nmasa_031_130412 ?




On 7/24/15 11:58 AM, Morenikeji Adebayo wrote:

Hi Doug,

fordoug2 is attached.

Thanks,
Keji




On Jul 24, 2015, at 11:17 AM, Douglas Greve 
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:



can you run
register-sess -debug -s nmasa_031_130412 -d 
/autofs/cluster/iaslab/NMASA/mri/func/encoding -fsd bold -dof 6 
-per-run -update | tee fordoug2.log


and send me fourdoug2.log

doug


On 7/24/15 10:22 AM, Morenikeji Adebayo wrote:

Hi there,

Attached is the log file from running:

preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface 
fsaverage lhrh -mni305 -fwhm 5 -per*-run*| tee fordoug.log


I got more errors when I ran:

preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface 
fsaverage lhrh -mni305 -fwhm 5 -per | tee fordoug.log



Thanks,
Keji



On Jul 23, 2015, at 6:05 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:


Yes, but you have a typo -min305 instead of -mni305



On 07/22/2015 05:30 PM, Morenikeji Adebayo wrote:

I sure can. Hopefully. Is the what you need?





On Jul 22, 2015, at 5:01 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
mailto:gr...@nmr.mgh.harvard.edu wrote:


can you just send the log and not put it into a doc file?

On 07/22/2015 04:46 PM, Morenikeji Adebayo wrote:

No problem! Here you go.




On Jul 22, 2015, at 4:30 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
mailto:gr...@nmr.mgh.harvard.edu

mailto:gr...@nmr.mgh.harvard.edu wrote:

Sorry, there should not be a * at the end of -per. I was just 
trying to

copy your command line with -debug as the first arg.

On 07/22/2015 04:02 PM, Morenikeji Adebayo wrote:

Hi Doug,

When I run:
preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface
fsaverage lhrh -min305 -fwhm 5 -per* | tee fordoug.log

I get:
preproc-sess: No match.

Thanks,
Keji



On Jul 22, 2015, at 3:37 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu 



wrote:

*
Can you run the following

preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up 
-surface

fsaverage lhrh -min305 -fwhm 5 -per* | tee fordoug.log

and send me fordoug.log




On 07/22/2015 02:12 PM, Morenikeji Adebayo wrote:

Hi there,

I’m running stable:

source /usr/local/freesurfer/stable5_3_0

Thanks,
Keji


On Jul 21, 2015, at 4:56 PM, Douglas Greve
gr...@nmr.mgh.harvard.edu 
mailto:gr...@nmr.mgh.harvard.edu 
mailto:gr...@nmr.mgh.harvard.edu

mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu wrote:

what environment are you running in? ie, dev or stable?

On 7/21/15 2:12 PM, Morenikeji Adebayo wrote:

Hi there,

*When running selxavg for the following session:*

nmasa_031_130412
*
*
*The following error message was generated:*
*
*
Error using MRIread (line 76)
ERROR: cannot determine format of
/autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm
(MRIread)

Error in fast_selxavg3 (line 146)
 runmask = MRIread(flac.maskfspec);
*
*
*I did some investigating and discovered that all the bold
runs for
this participant are missing the following files:*
*
*
.../func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm
.../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.lh.nii.gz
.../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.rh.nii.gz
*
*
*
So I ran:

preproc-sess -s nmasa_031_130412 -fsd bold -stc up -surface
fsaverage lhrh -min305 -fwhm 5 -per

*
*
*
*Which generated the following error message:*

if: Expression Syntax

**Do you have any idea what might be going wrong with this 
subject
or what this error message (**if: Expression Syntax) 
**means?**

*
*
*
*
Thanks,
Keji
---
Morenikeji Adebayo
Clinical Research Coordinator
Department of Psychiatric Neuroscience
Massachusetts General Hospital
(p) 617.643.6347
k...@nmr.mgh.harvard.edu mailto:k...@nmr.mgh.harvard.edu 
mailto:k...@nmr.mgh.harvard.edu

mailto:k...@nmr.mgh.harvard.edumailto:k...@nmr.mgh.harvard.edu
mailto:k...@nmr.mgh.harvard.edu



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Re: [Freesurfer] if: Expression Syntax

2015-07-24 Thread Morenikeji Adebayo

Hi Doug,fordoug2 is attached.Thanks,Keji

fordoug2.log
Description: Binary data
On Jul 24, 2015, at 11:17 AM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote:
  

  
  

can you run
register-sess -debug -s nmasa_031_130412 -d
/autofs/cluster/iaslab/NMASA/mri/func/encoding -fsd bold -dof 6
-per-run -update | tee fordoug2.log

and send me fourdoug2.log

doug


On 7/24/15 10:22 AM, Morenikeji Adebayo
  wrote:


  
  Hi there,
  
  
  Attached is the log file from running:
  
  
  preproc-sess
  -debug -s nmasa_031_130412 -fsd bold -stc up -surfacefsaverage lhrh -mni305
-fwhm 5 -per-run | tee fordoug.log
  

  I got more
  errors when I ran:
  

  preproc-sess
  -debug -s nmasa_031_130412 -fsd bold -stc up -surfacefsaverage lhrh -mni305 -fwhm 5
  -per | tee fordoug.log
  

  

  Thanks,
  Keji
  
  
  
  
  
  
  

  
On Jul 23, 2015, at 6:05 PM, Douglas N Greve
  gr...@nmr.mgh.harvard.edu
  wrote:

Yes, but you have a typo -min305 instead of
  -mni305
  
  
  
  On 07/22/2015 05:30 PM, Morenikeji Adebayo wrote:
  I sure can. Hopefully. Is
the what you need?




On Jul 22, 2015, at
  5:01 PM, Douglas N Greve 
  gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu
  wrote:
  
  can you just send the log and not put it into a doc
  file?
  
  On 07/22/2015 04:46 PM, Morenikeji Adebayo wrote:
  No problem! Here you
go.



On Jul 22, 2015, at
  4:30 PM, Douglas N Greve
  gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu
  
  mailto:gr...@nmr.mgh.harvard.edu
  wrote:
  
  Sorry, there should not be a * at the end of -per.
  I was just trying to
  copy your command line with -debug as the first
  arg.
  
  On 07/22/2015 04:02 PM, Morenikeji Adebayo wrote:
  Hi Doug,

When I run:
preproc-sess -debug -s nmasa_031_130412 -fsd
bold -stc up -surface
fsaverage lhrh -min305 -fwhm 5 -per* | tee
fordoug.log

I get:
preproc-sess: No match.

Thanks,
Keji


On Jul 22,
  2015, at 3:37 PM, Douglas N Greve
  gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
  
  
  wrote:
  
  *
  Can you run the following
  
  preproc-sess -debug -s nmasa_031_130412 -fsd
  bold -stc up -surface
  fsaverage lhrh -min305 -fwhm 5 -per* |
  tee fordoug.log
  
  and send me fordoug.log
  
  
  
  
  On 07/22/2015 02:12 PM, Morenikeji Adebayo
  wrote:
  Hi there,

I’m running stable:

source /usr/local/freesurfer/stable5_3_0

Thanks,
Keji

On Jul 21,
  2015, at 4:56 PM, Douglas Greve
  gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu
  wrote:

Re: [Freesurfer] if: Expression Syntax

2015-07-24 Thread Morenikeji Adebayo

Oh excellent, you are correct! I’ll update the file and try re-running selxavg.

Thanks,
Keji

 On Jul 24, 2015, at 12:06 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote:
 
 I think there is something wrong with the contents of 
 /autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/subjectname
 
 It looks like it is cd nmasa_031_130412, probably it should be 
 nmasa_031_130412 ?
 
 
 
 On 7/24/15 11:58 AM, Morenikeji Adebayo wrote:
 Hi Doug,
 
 fordoug2 is attached.
 
 Thanks,
 Keji
 
 
 
 
 On Jul 24, 2015, at 11:17 AM, Douglas Greve gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 
 can you run
 register-sess -debug -s nmasa_031_130412 -d 
 /autofs/cluster/iaslab/NMASA/mri/func/encoding -fsd bold -dof 6 -per-run 
 -update | tee fordoug2.log
 
 and send me fourdoug2.log
 
 doug
 
 
 On 7/24/15 10:22 AM, Morenikeji Adebayo wrote:
 Hi there,
 
 Attached is the log file from running:
 
 preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface 
 fsaverage lhrh -mni305 -fwhm 5 -per-run | tee fordoug.log
 
 I got more errors when I ran:
 
 preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface 
 fsaverage lhrh -mni305 -fwhm 5 -per | tee fordoug.log
 
 
 Thanks,
 Keji
 
 
 
 On Jul 23, 2015, at 6:05 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 Yes, but you have a typo -min305 instead of -mni305
 
 
 
 On 07/22/2015 05:30 PM, Morenikeji Adebayo wrote:
 I sure can. Hopefully. Is the what you need?
 
 
 
 
 On Jul 22, 2015, at 5:01 PM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
 wrote:
 
 can you just send the log and not put it into a doc file?
 
 On 07/22/2015 04:46 PM, Morenikeji Adebayo wrote:
 No problem! Here you go.
 
 
 
 On Jul 22, 2015, at 4:30 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 Sorry, there should not be a * at the end of -per. I was just trying 
 to
 copy your command line with -debug as the first arg.
 
 On 07/22/2015 04:02 PM, Morenikeji Adebayo wrote:
 Hi Doug,
 
 When I run:
 preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface
 fsaverage lhrh -min305 -fwhm 5 -per* | tee fordoug.log
 
 I get:
 preproc-sess: No match.
 
 Thanks,
 Keji
 
 
 On Jul 22, 2015, at 3:37 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu 
 
 wrote:
 
 *
 Can you run the following
 
 preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface
 fsaverage lhrh -min305 -fwhm 5 -per* | tee fordoug.log
 
 and send me fordoug.log
 
 
 
 
 On 07/22/2015 02:12 PM, Morenikeji Adebayo wrote:
 Hi there,
 
 I’m running stable:
 
 source /usr/local/freesurfer/stable5_3_0
 
 Thanks,
 Keji
 
 On Jul 21, 2015, at 4:56 PM, Douglas Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 what environment are you running in? ie, dev or stable?
 
 On 7/21/15 2:12 PM, Morenikeji Adebayo wrote:
 Hi there,
 
 *When running selxavg for the following session:*
 
 nmasa_031_130412
 *
 *
 *The following error message was generated:*
 *
 *
 Error using MRIread (line 76)
 ERROR: cannot determine format of
 /autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm
 (MRIread)
 
 Error in fast_selxavg3 (line 146)
  runmask = MRIread(flac.maskfspec);
 *
 *
 *I did some investigating and discovered that all the bold 
 runs for
 this participant are missing the following files:*
 *
 *
 .../func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm
 .../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.lh.nii.gz
 .../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.rh.nii.gz
 *
 *
 *
 So I ran:
 
 preproc-sess -s nmasa_031_130412 -fsd bold -stc up -surface
 fsaverage lhrh -min305 -fwhm 5 -per
 
 *
 *
 *
 *Which generated the following error message:* message:*
 
 if: Expression Syntax
 
 **Do you have any idea what might be going wrong with this 
 subject
 or what this error message (**if: Expression Syntax) **means?**
 *
 *
 *
 *
 Thanks,
 Keji
 ---
 Morenikeji Adebayo
 Clinical Research Coordinator
 Department of Psychiatric Neuroscience
 Massachusetts General Hospital
 (p) 617.643.6347
 k...@nmr.mgh.harvard.edu mailto:k...@nmr.mgh.harvard.edu

Re: [Freesurfer] if: Expression Syntax

2015-07-24 Thread Morenikeji Adebayo

Hi there,Attached is the log file from running:preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surfacefsaverage lhrh -mni305 -fwhm 5 -per-run | tee fordoug.logI got more errors when I ran:preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surfacefsaverage lhrh -mni305 -fwhm 5 -per | tee fordoug.logThanks,Keji

fordoug (3).log
Description: Binary data
On Jul 23, 2015, at 6:05 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:Yes, but you have a typo -min305 instead of -mni305On 07/22/2015 05:30 PM, Morenikeji Adebayo wrote:I sure can. Hopefully. Is the what you need?On Jul 22, 2015, at 5:01 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:can you just send the log and not put it into a doc file?On 07/22/2015 04:46 PM, Morenikeji Adebayo wrote:No problem! Here you go.On Jul 22, 2015, at 4:30 PM, Douglas N Grevegr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:Sorry, there should not be a * at the end of -per. I was just trying tocopy your command line with -debug as the first arg.On 07/22/2015 04:02 PM, Morenikeji Adebayo wrote:Hi Doug,When I run:preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surfacefsaverage lhrh -min305 -fwhm 5 -per* | tee fordoug.logI get:preproc-sess: No match.Thanks,KejiOn Jul 22, 2015, at 3:37 PM, Douglas N Grevegr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:*Can you run the followingpreproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surfacefsaverage lhrh -min305 -fwhm 5 -per* | tee fordoug.logand send me fordoug.logOn 07/22/2015 02:12 PM, Morenikeji Adebayo wrote:Hi there,I’m running stable:source /usr/local/freesurfer/stable5_3_0Thanks,KejiOn Jul 21, 2015, at 4:56 PM, Douglas Grevegr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:what environment are you running in? ie, dev or stable?On 7/21/15 2:12 PM, Morenikeji Adebayo wrote:Hi there,*When running selxavg for the following session:*nmasa_031_130412***The following error message was generated:***Error using MRIread (line 76)ERROR: cannot determine format of/autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm(MRIread)Error in fast_selxavg3 (line 146) runmask = MRIread(flac.maskfspec);***I did some investigating and discovered that all the bold runs forthis participant are missing the following files:***.../func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm.../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.lh.nii.gz.../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.rh.nii.gz***So I ran:preproc-sess -s nmasa_031_130412 -fsd bold -stc up -surfacefsaverage lhrh -min305 -fwhm 5 -perWhich generated the following error message:*if: _expression_ Syntax**Do you have any idea what might be going wrong with this subjector what this error message (**if: _expression_ Syntax) **means?**Thanks,Keji---Morenikeji AdebayoClinical Research CoordinatorDepartment of Psychiatric NeuroscienceMassachusetts General Hospital(p) 617.643.6347k...@nmr.mgh.harvard.edu mailto:k...@nmr.mgh.harvard.edumailto:k...@nmr.mgh.harvard.edumailto:k...@nmr.mgh.harvard.edumailto:k...@nmr.mgh.harvard.edu___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer---Morenikeji AdebayoClinical Research CoordinatorDepartment of Psychiatric NeuroscienceMassachusetts General Hospital(p) 617.643.6347k...@nmr.mgh.harvard.edu mailto:k...@nmr.mgh.harvard.edumailto:k...@nmr.mgh.harvard.edumailto:k...@nmr.mgh.harvard.edumailto:k...@nmr.mgh.harvard.edu___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer--Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax: 617-726-7422Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 http://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harvard.edu/facility/filedrop/index.html

Re: [Freesurfer] if: Expression Syntax

2015-07-24 Thread Morenikeji Adebayo

That fixed it! Thanks for all your help - I appreciate it.

Keji

 On Jul 24, 2015, at 12:17 PM, Morenikeji Adebayo k...@nmr.mgh.harvard.edu 
 wrote:
 
 Oh excellent, you are correct! I’ll update the file and try re-running 
 selxavg.
 
 Thanks,
 Keji
 
 On Jul 24, 2015, at 12:06 PM, Douglas Greve gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 I think there is something wrong with the contents of 
 /autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/subjectname
 
 It looks like it is cd nmasa_031_130412, probably it should be 
 nmasa_031_130412 ?
 
 
 
 On 7/24/15 11:58 AM, Morenikeji Adebayo wrote:
 Hi Doug,
 
 fordoug2 is attached.
 
 Thanks,
 Keji
 
 
 
 
 On Jul 24, 2015, at 11:17 AM, Douglas Greve gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 
 can you run
 register-sess -debug -s nmasa_031_130412 -d 
 /autofs/cluster/iaslab/NMASA/mri/func/encoding -fsd bold -dof 6 -per-run 
 -update | tee fordoug2.log
 
 and send me fourdoug2.log
 
 doug
 
 
 On 7/24/15 10:22 AM, Morenikeji Adebayo wrote:
 Hi there,
 
 Attached is the log file from running:
 
 preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface 
 fsaverage lhrh -mni305 -fwhm 5 -per-run | tee fordoug.log
 
 I got more errors when I ran:
 
 preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface 
 fsaverage lhrh -mni305 -fwhm 5 -per | tee fordoug.log
 
 
 Thanks,
 Keji
 
 
 
 On Jul 23, 2015, at 6:05 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 Yes, but you have a typo -min305 instead of -mni305
 
 
 
 On 07/22/2015 05:30 PM, Morenikeji Adebayo wrote:
 I sure can. Hopefully. Is the what you need?
 
 
 
 
 On Jul 22, 2015, at 5:01 PM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
 wrote:
 
 can you just send the log and not put it into a doc file?
 
 On 07/22/2015 04:46 PM, Morenikeji Adebayo wrote:
 No problem! Here you go.
 
 
 
 On Jul 22, 2015, at 4:30 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 Sorry, there should not be a * at the end of -per. I was just trying 
 to
 copy your command line with -debug as the first arg.
 
 On 07/22/2015 04:02 PM, Morenikeji Adebayo wrote:
 Hi Doug,
 
 When I run:
 preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface
 fsaverage lhrh -min305 -fwhm 5 -per* | tee fordoug.log
 
 I get:
 preproc-sess: No match.
 
 Thanks,
 Keji
 
 
 On Jul 22, 2015, at 3:37 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu 
 
 wrote:
 
 *
 Can you run the following
 
 preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface
 fsaverage lhrh -min305 -fwhm 5 -per* | tee fordoug.log
 
 and send me fordoug.log
 
 
 
 
 On 07/22/2015 02:12 PM, Morenikeji Adebayo wrote:
 Hi there,
 
 I’m running stable:
 
 source /usr/local/freesurfer/stable5_3_0
 
 Thanks,
 Keji
 
 On Jul 21, 2015, at 4:56 PM, Douglas Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 what environment are you running in? ie, dev or stable?
 
 On 7/21/15 2:12 PM, Morenikeji Adebayo wrote:
 Hi there,
 
 *When running selxavg for the following session:*
 
 nmasa_031_130412
 *
 *
 *The following error message was generated:*
 *
 *
 Error using MRIread (line 76)
 ERROR: cannot determine format of
 /autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm
 (MRIread)
 
 Error in fast_selxavg3 (line 146)
  runmask = MRIread(flac.maskfspec);
 *
 *
 *I did some investigating and discovered that all the bold 
 runs for
 this participant are missing the following files:*
 *
 *
 .../func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm
 .../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.lh.nii.gz
 .../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.rh.nii.gz
 *
 *
 *
 So I ran:
 
 preproc-sess -s nmasa_031_130412 -fsd bold -stc up -surface
 fsaverage lhrh -min305 -fwhm 5 -per
 
 *
 *
 *
 *Which generated the following error message:* message:*
 
 if: Expression Syntax
 
 **Do you have any idea what might be going wrong with this 
 subject
 or what this error message (**if: Expression Syntax) **means?**
 *
 *
 *
 *
 Thanks,
 Keji
 ---
 Morenikeji Adebayo

Re: [Freesurfer] if: Expression Syntax

2015-07-23 Thread Douglas N Greve

Yes, but you have a typo -min305 instead of -mni305



On 07/22/2015 05:30 PM, Morenikeji Adebayo wrote:
 I sure can. Hopefully. Is the what you need?




 On Jul 22, 2015, at 5:01 PM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:

 can you just send the log and not put it into a doc file?

 On 07/22/2015 04:46 PM, Morenikeji Adebayo wrote:
 No problem! Here you go.



 On Jul 22, 2015, at 4:30 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu wrote:

 Sorry, there should not be a * at the end of -per. I was just trying to
 copy your command line with -debug as the first arg.

 On 07/22/2015 04:02 PM, Morenikeji Adebayo wrote:
 Hi Doug,

 When I run:
 preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface
 fsaverage lhrh -min305 -fwhm 5 -per* | tee fordoug.log

 I get:
 preproc-sess: No match.

 Thanks,
 Keji


 On Jul 22, 2015, at 3:37 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu 

 wrote:

 *
 Can you run the following

 preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface
 fsaverage lhrh -min305 -fwhm 5 -per* | tee fordoug.log

 and send me fordoug.log




 On 07/22/2015 02:12 PM, Morenikeji Adebayo wrote:
 Hi there,

 I’m running stable:

 source /usr/local/freesurfer/stable5_3_0

 Thanks,
 Keji

 On Jul 21, 2015, at 4:56 PM, Douglas Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu wrote:

 what environment are you running in? ie, dev or stable?

 On 7/21/15 2:12 PM, Morenikeji Adebayo wrote:
 Hi there,

 *When running selxavg for the following session:*

 nmasa_031_130412
 *
 *
 *The following error message was generated:*
 *
 *
 Error using MRIread (line 76)
 ERROR: cannot determine format of
 /autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm
 (MRIread)

 Error in fast_selxavg3 (line 146)
   runmask = MRIread(flac.maskfspec);
 *
 *
 *I did some investigating and discovered that all the bold 
 runs for
 this participant are missing the following files:*
 *
 *
 .../func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm
 .../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.lh.nii.gz
 .../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.rh.nii.gz
 *
 *
 *
 So I ran:

 preproc-sess -s nmasa_031_130412 -fsd bold -stc up -surface
 fsaverage lhrh -min305 -fwhm 5 -per

 *
 *
 *
 *Which generated the following error message:*

 if: Expression Syntax

 **Do you have any idea what might be going wrong with this subject
 or what this error message (**if: Expression Syntax) **means?**
 *
 *
 *
 *
 Thanks,
 Keji
 ---
 Morenikeji Adebayo
 Clinical Research Coordinator
 Department of Psychiatric Neuroscience
 Massachusetts General Hospital
 (p) 617.643.6347
 k...@nmr.mgh.harvard.edu mailto:k...@nmr.mgh.harvard.edu
 mailto:k...@nmr.mgh.harvard.edumailto:k...@nmr.mgh.harvard.edu
 mailto:k...@nmr.mgh.harvard.edu



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 ---
 Morenikeji Adebayo
 Clinical Research Coordinator
 Department of Psychiatric Neuroscience
 Massachusetts General Hospital
 (p) 617.643.6347
 k...@nmr.mgh.harvard.edu mailto:k...@nmr.mgh.harvard.edu
 mailto:k...@nmr.mgh.harvard.edumailto:k...@nmr.mgh.harvard.edu
 mailto:k...@nmr.mgh.harvard.edu



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

 Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 
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Re: [Freesurfer] if: Expression Syntax

2015-07-23 Thread Morenikeji Adebayo

Just following up. Did i send the log in the correct format?

Thanks,
Keji

On Jul 22, 2015, at 5:30 PM, Morenikeji Adebayo wrote:

 I sure can. Hopefully. Is the what you need?
 
 fordoug.log
 
 On Jul 22, 2015, at 5:01 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu 
 wrote:
 
 can you just send the log and not put it into a doc file?
 
 On 07/22/2015 04:46 PM, Morenikeji Adebayo wrote:
 No problem! Here you go.
 
 
 
 On Jul 22, 2015, at 4:30 PM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 Sorry, there should not be a * at the end of -per. I was just trying to
 copy your command line with -debug as the first arg.
 
 On 07/22/2015 04:02 PM, Morenikeji Adebayo wrote:
 Hi Doug,
 
 When I run:
 preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface
 fsaverage lhrh -min305 -fwhm 5 -per* | tee fordoug.log
 
 I get:
 preproc-sess: No match.
 
 Thanks,
 Keji
 
 
 On Jul 22, 2015, at 3:37 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu 
 wrote:
 
 *
 Can you run the following
 
 preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface
 fsaverage lhrh -min305 -fwhm 5 -per* | tee fordoug.log
 
 and send me fordoug.log
 
 
 
 
 On 07/22/2015 02:12 PM, Morenikeji Adebayo wrote:
 Hi there,
 
 I’m running stable:
 
 source /usr/local/freesurfer/stable5_3_0
 
 Thanks,
 Keji
 
 On Jul 21, 2015, at 4:56 PM, Douglas Greve
 gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 what environment are you running in? ie, dev or stable?
 
 On 7/21/15 2:12 PM, Morenikeji Adebayo wrote:
 Hi there,
 
 *When running selxavg for the following session:*
 
 nmasa_031_130412
 *
 *
 *The following error message was generated:*
 *
 *
 Error using MRIread (line 76)
 ERROR: cannot determine format of
 /autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm
 (MRIread)
 
 Error in fast_selxavg3 (line 146)
   runmask = MRIread(flac.maskfspec);
 *
 *
 *I did some investigating and discovered that all the bold runs for
 this participant are missing the following files:*
 *
 *
 .../func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm
 .../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.lh.nii.gz
 .../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.rh.nii.gz
 *
 *
 *
 So I ran:
 
 preproc-sess -s nmasa_031_130412 -fsd bold -stc up -surface
 fsaverage lhrh -min305 -fwhm 5 -per
 
 *
 *
 *
 *Which generated the following error message:*
 
 if: Expression Syntax
 
 **Do you have any idea what might be going wrong with this subject
 or what this error message (**if: Expression Syntax) **means?**
 *
 *
 *
 *
 Thanks,
 Keji
 ---
 Morenikeji Adebayo
 Clinical Research Coordinator
 Department of Psychiatric Neuroscience
 Massachusetts General Hospital
 (p) 617.643.6347
 k...@nmr.mgh.harvard.edu 
 mailto:k...@nmr.mgh.harvard.edumailto:k...@nmr.mgh.harvard.edu
 mailto:k...@nmr.mgh.harvard.edu
 
 
 
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 ---
 Morenikeji Adebayo
 Clinical Research Coordinator
 Department of Psychiatric Neuroscience
 Massachusetts General Hospital
 (p) 617.643.6347
 k...@nmr.mgh.harvard.edu 
 mailto:k...@nmr.mgh.harvard.edumailto:k...@nmr.mgh.harvard.edu
 mailto:k...@nmr.mgh.harvard.edu
 
 
 
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 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422
 
 Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2
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 ---
 Morenikeji Adebayo
 Clinical Research Coordinator
 Department of Psychiatric Neuroscience

Re: [Freesurfer] if: Expression Syntax

2015-07-22 Thread Morenikeji Adebayo

Hi there,

I’m running stable:

source /usr/local/freesurfer/stable5_3_0

Thanks,
Keji

 On Jul 21, 2015, at 4:56 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote:
 
 what environment are you running in? ie, dev or stable?
 
 On 7/21/15 2:12 PM, Morenikeji Adebayo wrote:
 Hi there,
 
 When running selxavg for the following session:
 
 
 
 nmasa_031_130412
 
 
   
 The following
 error message was generated:
 
 
   
  Error using MRIread (line 76)
 ERROR: cannot determine format of
 /autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm
 (MRIread)
 
 
 
 Error in fast_selxavg3 (line 146)
   runmask = MRIread(flac.maskfspec);
 
 I did some investigating and discovered that all the bold runs for this 
 participant are missing the following files:
 
 .../func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm
 
 .../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.lh.nii.gz
 .../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.rh.nii.gz
 
 
 
  So I ran:
 
 
 
 preproc-sess -s
   nmasa_031_130412 -fsd bold -stc up -surface
   fsaverage lhrh -min305 -fwhm 5 -per
 
 
   
 
 
 
 Which generated the following error
   message:
 
 
 
 if: Expression Syntax
 
 Do you have any idea
   what might be going wrong with this subject or what
   this error message (if: Expression Syntax) means?
 
 
 
 
 
 
 Thanks,
 Keji
 ---
 Morenikeji Adebayo
 Clinical Research Coordinator
 Department of Psychiatric Neuroscience
 Massachusetts General Hospital
 (p) 617.643.6347
 k...@nmr.mgh.harvard.edu mailto:k...@nmr.mgh.harvard.edu
 
 
 ___
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---
Morenikeji Adebayo
Clinical Research Coordinator
Department of Psychiatric Neuroscience
Massachusetts General Hospital
(p) 617.643.6347
k...@nmr.mgh.harvard.edu

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Re: [Freesurfer] if: Expression Syntax

2015-07-22 Thread Douglas N Greve

*
Can you run the following

preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface 
fsaverage lhrh -min305 -fwhm 5 -per* | tee fordoug.log

and send me fordoug.log




On 07/22/2015 02:12 PM, Morenikeji Adebayo wrote:
 Hi there,

 I’m running stable:

 source /usr/local/freesurfer/stable5_3_0

 Thanks,
 Keji

 On Jul 21, 2015, at 4:56 PM, Douglas Greve gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu wrote:

 what environment are you running in? ie, dev or stable?

 On 7/21/15 2:12 PM, Morenikeji Adebayo wrote:
 Hi there,

 *When running selxavg for the following session:*

 nmasa_031_130412
 *
 *
 *The following error message was generated:*
 *
 *
 Error using MRIread (line 76)
 ERROR: cannot determine format of
 /autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm
 (MRIread)

 Error in fast_selxavg3 (line 146)
  runmask = MRIread(flac.maskfspec);
 *
 *
 *I did some investigating and discovered that all the bold runs for 
 this participant are missing the following files:*
 *
 *
 .../func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm
 .../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.lh.nii.gz
 .../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.rh.nii.gz
 *
 *
 *
 So I ran:

 preproc-sess -s nmasa_031_130412 -fsd bold -stc up -surface 
 fsaverage lhrh -min305 -fwhm 5 -per

 *
 *
 *
 *Which generated the following error message:*

 if: Expression Syntax

 **Do you have any idea what might be going wrong with this subject 
 or what this error message (**if: Expression Syntax) **means?**
 *
 *
 *
 *
 Thanks,
 Keji
 ---
 Morenikeji Adebayo
 Clinical Research Coordinator
 Department of Psychiatric Neuroscience
 Massachusetts General Hospital
 (p) 617.643.6347
 k...@nmr.mgh.harvard.edu mailto:k...@nmr.mgh.harvard.edu



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 Freesurfer mailing list
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 ---
 Morenikeji Adebayo
 Clinical Research Coordinator
 Department of Psychiatric Neuroscience
 Massachusetts General Hospital
 (p) 617.643.6347
 k...@nmr.mgh.harvard.edu mailto:k...@nmr.mgh.harvard.edu



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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.

Re: [Freesurfer] if: Expression Syntax

2015-07-22 Thread Douglas N Greve

Sorry, there should not be a * at the end of -per. I was just trying to 
copy your command line with -debug as the first arg.

On 07/22/2015 04:02 PM, Morenikeji Adebayo wrote:
 Hi Doug,

 When I run:
 preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface 
 fsaverage lhrh -min305 -fwhm 5 -per* | tee fordoug.log

 I get:
 preproc-sess: No match.

 Thanks,
 Keji


 On Jul 22, 2015, at 3:37 PM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:

 *
 Can you run the following

 preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface
 fsaverage lhrh -min305 -fwhm 5 -per* | tee fordoug.log

 and send me fordoug.log




 On 07/22/2015 02:12 PM, Morenikeji Adebayo wrote:
 Hi there,

 I’m running stable:

 source /usr/local/freesurfer/stable5_3_0

 Thanks,
 Keji

 On Jul 21, 2015, at 4:56 PM, Douglas Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu wrote:

 what environment are you running in? ie, dev or stable?

 On 7/21/15 2:12 PM, Morenikeji Adebayo wrote:
 Hi there,

 *When running selxavg for the following session:*

 nmasa_031_130412
 *
 *
 *The following error message was generated:*
 *
 *
 Error using MRIread (line 76)
 ERROR: cannot determine format of
 /autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm
 (MRIread)

 Error in fast_selxavg3 (line 146)
 runmask = MRIread(flac.maskfspec);
 *
 *
 *I did some investigating and discovered that all the bold runs for
 this participant are missing the following files:*
 *
 *
 .../func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm
 .../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.lh.nii.gz
 .../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.rh.nii.gz
 *
 *
 *
 So I ran:

 preproc-sess -s nmasa_031_130412 -fsd bold -stc up -surface
 fsaverage lhrh -min305 -fwhm 5 -per

 *
 *
 *
 *Which generated the following error message:*

 if: Expression Syntax

 **Do you have any idea what might be going wrong with this subject
 or what this error message (**if: Expression Syntax) **means?**
 *
 *
 *
 *
 Thanks,
 Keji
 ---
 Morenikeji Adebayo
 Clinical Research Coordinator
 Department of Psychiatric Neuroscience
 Massachusetts General Hospital
 (p) 617.643.6347
 k...@nmr.mgh.harvard.edu mailto:k...@nmr.mgh.harvard.edu 
 mailto:k...@nmr.mgh.harvard.edu



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

 ---
 Morenikeji Adebayo
 Clinical Research Coordinator
 Department of Psychiatric Neuroscience
 Massachusetts General Hospital
 (p) 617.643.6347
 k...@nmr.mgh.harvard.edu mailto:k...@nmr.mgh.harvard.edu 
 mailto:k...@nmr.mgh.harvard.edu



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



 ---
 Morenikeji Adebayo
 Clinical Research Coordinator
 Department of Psychiatric Neuroscience
 Massachusetts General Hospital
 (p) 617.643.6347
 k...@nmr.mgh.harvard.edu mailto:k...@nmr.mgh.harvard.edu



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 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: 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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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners

Re: [Freesurfer] if: Expression Syntax

2015-07-22 Thread Morenikeji Adebayo

Hi Doug,

When I run: 
preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface fsaverage 
lhrh -min305 -fwhm 5 -per* | tee fordoug.log

I get:
preproc-sess: No match.

Thanks,
Keji


 On Jul 22, 2015, at 3:37 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu 
 wrote:
 
 *
 Can you run the following
 
 preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface 
 fsaverage lhrh -min305 -fwhm 5 -per* | tee fordoug.log
 
 and send me fordoug.log
 
 
 
 
 On 07/22/2015 02:12 PM, Morenikeji Adebayo wrote:
 Hi there,
 
 I’m running stable:
 
 source /usr/local/freesurfer/stable5_3_0
 
 Thanks,
 Keji
 
 On Jul 21, 2015, at 4:56 PM, Douglas Greve gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 what environment are you running in? ie, dev or stable?
 
 On 7/21/15 2:12 PM, Morenikeji Adebayo wrote:
 Hi there,
 
 *When running selxavg for the following session:*
 
 nmasa_031_130412
 *
 *
 *The following error message was generated:*
 *
 *
 Error using MRIread (line 76)
 ERROR: cannot determine format of
 /autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm
 (MRIread)
 
 Error in fast_selxavg3 (line 146)
 runmask = MRIread(flac.maskfspec);
 *
 *
 *I did some investigating and discovered that all the bold runs for 
 this participant are missing the following files:*
 *
 *
 .../func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm
 .../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.lh.nii.gz
 .../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.rh.nii.gz
 *
 *
 *
 So I ran:
 
 preproc-sess -s nmasa_031_130412 -fsd bold -stc up -surface 
 fsaverage lhrh -min305 -fwhm 5 -per
 
 *
 *
 *
 *Which generated the following error message:*
 
 if: Expression Syntax
 
 **Do you have any idea what might be going wrong with this subject 
 or what this error message (**if: Expression Syntax) **means?**
 *
 *
 *
 *
 Thanks,
 Keji
 ---
 Morenikeji Adebayo
 Clinical Research Coordinator
 Department of Psychiatric Neuroscience
 Massachusetts General Hospital
 (p) 617.643.6347
 k...@nmr.mgh.harvard.edu mailto:k...@nmr.mgh.harvard.edu
 
 
 
 ___
 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 mailto:Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 ---
 Morenikeji Adebayo
 Clinical Research Coordinator
 Department of Psychiatric Neuroscience
 Massachusetts General Hospital
 (p) 617.643.6347
 k...@nmr.mgh.harvard.edu mailto:k...@nmr.mgh.harvard.edu
 
 
 
 ___
 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: 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/
 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 

---
Morenikeji Adebayo
Clinical Research Coordinator
Department of Psychiatric Neuroscience
Massachusetts General Hospital
(p) 617.643.6347
k...@nmr.mgh.harvard.edu

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] if: Expression Syntax

2015-07-22 Thread Douglas N Greve

can you just send the log and not put it into a doc file?

On 07/22/2015 04:46 PM, Morenikeji Adebayo wrote:
 No problem! Here you go.



 On Jul 22, 2015, at 4:30 PM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:

 Sorry, there should not be a * at the end of -per. I was just trying to
 copy your command line with -debug as the first arg.

 On 07/22/2015 04:02 PM, Morenikeji Adebayo wrote:
 Hi Doug,

 When I run:
 preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface
 fsaverage lhrh -min305 -fwhm 5 -per* | tee fordoug.log

 I get:
 preproc-sess: No match.

 Thanks,
 Keji


 On Jul 22, 2015, at 3:37 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu 
 wrote:

 *
 Can you run the following

 preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surface
 fsaverage lhrh -min305 -fwhm 5 -per* | tee fordoug.log

 and send me fordoug.log




 On 07/22/2015 02:12 PM, Morenikeji Adebayo wrote:
 Hi there,

 I’m running stable:

 source /usr/local/freesurfer/stable5_3_0

 Thanks,
 Keji

 On Jul 21, 2015, at 4:56 PM, Douglas Greve
 gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu wrote:

 what environment are you running in? ie, dev or stable?

 On 7/21/15 2:12 PM, Morenikeji Adebayo wrote:
 Hi there,

 *When running selxavg for the following session:*

 nmasa_031_130412
 *
 *
 *The following error message was generated:*
 *
 *
 Error using MRIread (line 76)
 ERROR: cannot determine format of
 /autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm
 (MRIread)

 Error in fast_selxavg3 (line 146)
runmask = MRIread(flac.maskfspec);
 *
 *
 *I did some investigating and discovered that all the bold runs for
 this participant are missing the following files:*
 *
 *
 .../func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm
 .../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.lh.nii.gz
 .../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.rh.nii.gz
 *
 *
 *
 So I ran:

 preproc-sess -s nmasa_031_130412 -fsd bold -stc up -surface
 fsaverage lhrh -min305 -fwhm 5 -per

 *
 *
 *
 *Which generated the following error message:*

 if: Expression Syntax

 **Do you have any idea what might be going wrong with this subject
 or what this error message (**if: Expression Syntax) **means?**
 *
 *
 *
 *
 Thanks,
 Keji
 ---
 Morenikeji Adebayo
 Clinical Research Coordinator
 Department of Psychiatric Neuroscience
 Massachusetts General Hospital
 (p) 617.643.6347
 k...@nmr.mgh.harvard.edu 
 mailto:k...@nmr.mgh.harvard.edumailto:k...@nmr.mgh.harvard.edu
 mailto:k...@nmr.mgh.harvard.edu



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

 ---
 Morenikeji Adebayo
 Clinical Research Coordinator
 Department of Psychiatric Neuroscience
 Massachusetts General Hospital
 (p) 617.643.6347
 k...@nmr.mgh.harvard.edu 
 mailto:k...@nmr.mgh.harvard.edumailto:k...@nmr.mgh.harvard.edu
 mailto:k...@nmr.mgh.harvard.edu



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

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

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

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 ---
 Morenikeji Adebayo
 Clinical Research Coordinator
 Department of Psychiatric Neuroscience
 Massachusetts General Hospital
 (p) 617.643.6347
 k...@nmr.mgh.harvard.edu 
 mailto:k...@nmr.mgh.harvard.edumailto:k...@nmr.mgh.harvard.edu



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Re: [Freesurfer] if: Expression Syntax

2015-07-22 Thread Morenikeji Adebayo

I sure can. Hopefully. Is the what you need?

fordoug.log
Description: Binary data
On Jul 22, 2015, at 5:01 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:can you just send the log and not put it into a doc file?On 07/22/2015 04:46 PM, Morenikeji Adebayo wrote:No problem! Here you go.On Jul 22, 2015, at 4:30 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:Sorry, there should not be a * at the end of -per. I was just trying tocopy your command line with -debug as the first arg.On 07/22/2015 04:02 PM, Morenikeji Adebayo wrote:Hi Doug,When I run:preproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surfacefsaverage lhrh -min305 -fwhm 5 -per* | tee fordoug.logI get:preproc-sess: No match.Thanks,KejiOn Jul 22, 2015, at 3:37 PM, Douglas N Grevegr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:*Can you run the followingpreproc-sess -debug -s nmasa_031_130412 -fsd bold -stc up -surfacefsaverage lhrh -min305 -fwhm 5 -per* | tee fordoug.logand send me fordoug.logOn 07/22/2015 02:12 PM, Morenikeji Adebayo wrote:Hi there,I’m running stable:source /usr/local/freesurfer/stable5_3_0Thanks,KejiOn Jul 21, 2015, at 4:56 PM, Douglas Grevegr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:what environment are you running in? ie, dev or stable?On 7/21/15 2:12 PM, Morenikeji Adebayo wrote:Hi there,*When running selxavg for the following session:*nmasa_031_130412***The following error message was generated:***Error using MRIread (line 76)ERROR: cannot determine format of/autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm(MRIread)Error in fast_selxavg3 (line 146) runmask = MRIread(flac.maskfspec);***I did some investigating and discovered that all the bold runs forthis participant are missing the following files:***.../func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm.../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.lh.nii.gz.../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.rh.nii.gz***So I ran:preproc-sess -s nmasa_031_130412 -fsd bold -stc up -surfacefsaverage lhrh -min305 -fwhm 5 -perWhich generated the following error message:*if: _expression_ Syntax**Do you have any idea what might be going wrong with this subjector what this error message (**if: _expression_ Syntax) **means?**Thanks,Keji---Morenikeji AdebayoClinical Research CoordinatorDepartment of Psychiatric NeuroscienceMassachusetts General Hospital(p) 617.643.6347k...@nmr.mgh.harvard.edu mailto:k...@nmr.mgh.harvard.edumailto:k...@nmr.mgh.harvard.edumailto:k...@nmr.mgh.harvard.edu___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer---Morenikeji AdebayoClinical Research CoordinatorDepartment of Psychiatric NeuroscienceMassachusetts General Hospital(p) 617.643.6347k...@nmr.mgh.harvard.edu mailto:k...@nmr.mgh.harvard.edumailto:k...@nmr.mgh.harvard.edumailto:k...@nmr.mgh.harvard.edu___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer--Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax: 617-726-7422Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlOutgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer---Morenikeji AdebayoClinical Research CoordinatorDepartment of Psychiatric NeuroscienceMassachusetts General Hospital(p) 617.643.6347k...@nmr.mgh.harvard.edu mailto:k...@nmr.mgh.harvard.edumailto:k...@nmr.mgh.harvard.edu___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer--Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax:

Re: [Freesurfer] if: Expression Syntax

2015-07-21 Thread Douglas Greve


what environment are you running in? ie, dev or stable?

On 7/21/15 2:12 PM, Morenikeji Adebayo wrote:

Hi there,

*When running selxavg for the following session:*

nmasa_031_130412
*
*
*The following error message was generated:*
*
*
Error using MRIread (line 76)
ERROR: cannot determine format of
/autofs/cluster/iaslab/NMASA/mri/func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm
(MRIread)

Error in fast_selxavg3 (line 146)
 runmask = MRIread(flac.maskfspec);
*
*
*I did some investigating and discovered that all the bold runs for 
this participant are missing the following files:*

*
*
.../func/encoding/nmasa_031_130412/bold/015/masks/brain.mni305.2mm
.../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.lh.nii.gz
.../func/encoding/nmasa_031_130412/bold/015/masks/brain.fsaverage.rh.nii.gz
*
*
*
So I ran:

preproc-sess -s nmasa_031_130412 -fsd bold -stc up -surface fsaverage 
lhrh -min305 -fwhm 5 -per


*
*
*
*Which generated the following error message:*

if: Expression Syntax

**Do you have any idea what might be going wrong with this subject or 
what this error message (**if: Expression Syntax) **means?**

*
*
*
*
Thanks,
Keji
---
Morenikeji Adebayo
Clinical Research Coordinator
Department of Psychiatric Neuroscience
Massachusetts General Hospital
(p) 617.643.6347
k...@nmr.mgh.harvard.edu mailto:k...@nmr.mgh.harvard.edu



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