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

2024-03-22 Thread 蒋文骥 
External Email - Use Caution

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 |

External Email - Use Caution

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



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the 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 
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

2024-03-22 Thread Stefano Delli Pizzi 
External Email - Use Caution

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
> 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the 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

2024-03-21 Thread Stefano Delli Pizzi 
External Email - Use Caution

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

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the 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

2024-03-21 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:


External Email - Use Caution

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




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person 
to whom it is addressed.  If you believe this e-mail was sent 
to you in error and the e-mail contains patient information, 
please contact the 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 
 
.








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 
 
.





___
Freesurfer mailing l

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

2024-03-19 Thread Stefano Delli Pizzi 
External Email - Use Caution

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 
>>> https://secure-web.cisco.com/19VAVeGTK_0MwuD_e9Lge1KBTUyFgZiB_0wQtNJdmJyQ5Pz7G9Qzu06HKJe_TQNblI_rTEgsefznJY_Mv2nn5SAOCFfifoqeVafVaF0xfn7KdgFSuhX1tSPv_xNheB6sOj_FHFmVbXpyyzlPlVQv4K34ssoCmGdsznLPw5vunmHF_z8m3E4Cc0lBsBisF4cV8G87EAGZDbRpLRtFargovc2nJK3KJ

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




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to 
whom it is addressed.  If you believe this e-mail was sent to you 
in error and the e-mail contains patient information, please 
contact the 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 f

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


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the 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___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the 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 
efano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject 
>> fsaverage -stc up -update )
>> if ( $UseB0DC ) set cmd = ( $cmd -b0dc )
>> if ( 0 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d 
>> /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject 
>> fsaverage -stc up -update -b0dc )
>> if ( $RegDOF != 6 ) set cmd = ( $cmd -dof $RegDOF )
>> if ( 6 != 6 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d 
>> /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject 
>> fsaverage -stc up -update -dof 6 )
>> if ( $PerRun ) set cmd = ( $cmd -per-run )
>> if ( 1 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d 
>> /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject 
>> fsaverage -stc up -update -per-run )
>> set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d 
>> /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject 
>> fsaverage -stc up -update -per-run )
>> if ( $PerSess ) set cmd = ( $cmd -per-session )
>> if ( 0 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d 
>> /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject 
>> fsaverage -stc up -update -per-run -per-session )
>> if ( $#ProjFrac ) set cmd = ( $cmd -projfrac $ProjFrac -expkey 
>> $ProjFracExpKey )
>> if ( 0 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d 
>> /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject 
>> fsaverage -stc up -update -per-run -projfrac -expkey )
>> if ( $#volsurffwhm ) set cmd = ( $cmd -volsurffwhm $volsurffwhm )
>> if ( 0 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d 
>> /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject 
>> fsaverage -stc up -update -per-run -volsurffwhm )
>> if ( ! $UseCortexLabel ) set cmd = ( $cmd -no-cortex-label )
>> if ( ! 1 ) set cmd = ( rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d 
>> /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject 
>> fsaverage -stc up -update -per-run -no-cortex-label )
>> echo "$sessid To Surface -" | & tee -a $LF
>> echo 091223sbj01m_tp1 To Surface -
>> tee -a 
>> /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log
>> 091223sbj01m_tp1 To Surface -
>> echo $cmd | & tee -a $LF
>> echo rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d 
>> /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject 
>> fsaverage -stc up -update -per-run
>> tee -a 
>> /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log
>> rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d 
>> /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject 
>> fsaverage -stc up -update -per-run
>> $cmd | & tee -a $LF
>> rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d 
>> /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject 
>> fsaverage -stc up -update -per-run
>> tee -a 
>> /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log
>> instem fmcpr.up
>> outstem fmcpr.up.sm0.fsaverage.hemi
>> -- 
>> 1/1 091223sbj01m_tp1
>>   1/1 091223sbj01m_tp1 001 lh -
>> Lun 26 Feb 2024 18:46:32 CET
>> /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/001/masks/brain.fsaverage.lh.pr.nii.gz
>>  does not need updating
>>   1/1 091223sbj01m_tp1 002 lh -
>> Lun 26 Feb 2024 18:46:32 CET
>> /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/002/masks/brain.fsaverage.lh.pr.nii.gz
>>  does not need updating
>>   1/1 091223sbj01m_tp1 003 lh -
>> Lun 26 Feb 2024 18:46:32 CET
>> /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/003/masks/brain.fsaverage.lh.pr.nii.gz
>>  does not need updating
>> /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/masks/brain.fsaverage.lh.pr.nii.gz
>>  does not need updating
>>   1/1 091223sbj01m_tp1 001 rh -
>> Lun 26 Feb 2024 18:46:32 CET
>> /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/001/masks/brain.fsaverage.rh.pr.nii.gz
>>  does not need updating
>>   1/1 091223sbj01m_tp1 002 rh -
>> Lun 26 Feb 2024 18:46:32 CET
>> /Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/002/masks/brain.fsaverage.rh.pr.nii.gz
>>  does not need updating
>>   1/1 091223sbj01m_tp1 003 rh -
>>

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

2024-03-04 Thread Stefano Delli Pizzi 
fano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log
rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d 
/Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage 
-stc up -update -per-run
$cmd | & tee -a $LF
rawfunc2surf-sess -fwhm 0 -s 091223sbj01m_tp1 -d 
/Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA -fsd rest -trgsubject fsaverage 
-stc up -update -per-run
tee -a 
/Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/log/preproc-091223sbj01m_tp1-rest.log
instem fmcpr.up
outstem fmcpr.up.sm0.fsaverage.hemi
-- 
1/1 091223sbj01m_tp1
  1/1 091223sbj01m_tp1 001 lh -
Lun 26 Feb 2024 18:46:32 CET
/Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/001/masks/brain.fsaverage.lh.pr.nii.gz
 does not need updating
  1/1 091223sbj01m_tp1 002 lh -
Lun 26 Feb 2024 18:46:32 CET
/Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/002/masks/brain.fsaverage.lh.pr.nii.gz
 does not need updating
  1/1 091223sbj01m_tp1 003 lh -
Lun 26 Feb 2024 18:46:32 CET
/Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/003/masks/brain.fsaverage.lh.pr.nii.gz
 does not need updating
/Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/masks/brain.fsaverage.lh.pr.nii.gz
 does not need updating
  1/1 091223sbj01m_tp1 001 rh -
Lun 26 Feb 2024 18:46:32 CET
/Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/001/masks/brain.fsaverage.rh.pr.nii.gz
 does not need updating
  1/1 091223sbj01m_tp1 002 rh -
Lun 26 Feb 2024 18:46:32 CET
/Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/002/masks/brain.fsaverage.rh.pr.nii.gz
 does not need updating
  1/1 091223sbj01m_tp1 003 rh -
Lun 26 Feb 2024 18:46:32 CET
/Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/003/masks/brain.fsaverage.rh.pr.nii.gz
 does not need updating
/Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/masks/brain.fsaverage.rh.pr.nii.gz
 does not need updating
  1/1 091223sbj01m_tp1 001 lh -
Lun 26 Feb 2024 18:46:32 CET
ERROR: could not determine file for 
/Users/stefano/Desktop/MODAFINIL/rs-fMRI_AROMA/091223sbj01m_tp1/rest/001/fmcpr.up
if ( $status ) exit 1 ;
if ( 1 ) exit 1
exit 1



> Il giorno 23 feb 2024, alle ore 18:32, Stefano Delli Pizzi 
>  ha scritto:
> 
> Thank you!
>  I have already sent it to you (probabile to Yujing) some days ago. Were they 
> not okay?
> Could it be because I'm running data on MacOS? 
> If you do preprocessing with -nomc, does it work on your dataset? I've tried 
> it with three different databases.
> Regards
> Stefano 
> 
>> Il giorno 23 feb 2024, alle ore 17:32, Douglas N. Greve 
>>  ha scritto:
>> 
>>  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 
>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
>>>  
>>> <mailto: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 <mailto: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
>>> 
>>> 
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harv

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

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the 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 
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 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>
>  .
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the 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 
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 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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the 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 
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 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___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the 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 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

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the 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

2024-02-06 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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the 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 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

[Freesurfer] if: Expression Syntax - preproc-sess

2024-02-03 Thread Stefano Delli Pizzi 
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
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

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

2024-01-22 Thread Stefano Delli Pizzi 
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
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.