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
@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 -
? 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
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.
>>>
>>> Be
verage -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 -trg
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_
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!
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.
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,
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 occ
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
__
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:
>
> M
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
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
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
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
: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
t;
> 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
18 matches
Mail list logo