[FieldTrip] Source analysis web_command

Thu Feb 20 08:53:05 CET 2025

Hi Zhen,

Well, my first idea is to contact your local IT support to help you with this. This e-mail list is not intended to debug this type of problems.

My second idea is to really try and interpret the error message you get, which states that workbench (I think that the error is thrown by workbench, but I am not sure because you did not include the relevant part of the error stack in your e-mails so far, for instance which line of the scripts throw an error, which command you executed exactly etc, but I am sure that your issue is not FieldTrip related, so actually on this discussion list discontinue it being discussed) cannot find a file, because it says: “File does not exist”. This means either that your Freesurfer results are incomplete, not located where you think you specified them to be located, or that the Freesurfer output is named in a different way than what you think that they should be named (for instance, mixing up ’sub-001’, and ’subject-001’)

Good luck,
Jan-Mathijs

On 20 Feb 2025, at 00:31, Ni, Zhen (NIH/NINDS) [C] <zhen.ni at nih.gov> wrote:

You don't often get email from zhen.ni at nih.gov<mailto:zhen.ni at nih.gov>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification>
Hi Jan-Mathijs,
I followed the instruction but still cannot run the script correctly.
For $1 <DIRNAME>, I input the directory containing the freesurfer results (>>7.4.1/subjects     in my computer).
For $2 <SUBJECTNAME>, I input the subject (>>sub-001    in my computer).
These were defined in the /.bashrc file. I think they are likely correct.

For $3 <TEMPLATE>, I setup a folder <template> on my desktop. First, I copied L/R.sphere.8k_fs_LR_surf.gii from fieldtrip into this folder. Second, I downloaded L/R.sphere.164k_fs_LR_surf.gii from workbench (>>HCPpipelines/global/templates/standard_mesh_atlases) into this folder. I added L/R.atlasroi.32_fs_LR_shape.gii from workbench (>>91282_Greyordinates) for the coordinates although I think this may not be necessary.

I also tried some other options for the third step ($3) but always got the same error message:

While running >>>>/workbench/subject-001.L.sulc.native.shape.gii CORTEX_LEFT

ERROR: NAME OF FILE: subject-001.L.sulc.native.shape.gii
PATH TO FILE: >>>>/sub-001/workbench File does not exist

I looked at the >>>/workbench directory, several files were created with very small size. It seems that the softwares were running ok but they cannot find the templates in the folder (<template>) I setup on the desktop.  Therefore, it cannot work with the “left cortex” from the very beginning.

I wonder if you have any ideas.
Thanks

Zhen

From: fieldtrip <fieldtrip-bounces at science.ru.nl> On Behalf Of Schoffelen, J.M. (Jan Mathijs) via fieldtrip
Sent: Thursday, February 6, 2025 2:39 AM
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Cc: Schoffelen, J.M. (Jan Mathijs) <janmathijs.schoffelen at donders.ru.nl>
Subject: [EXTERNAL] Re: [FieldTrip] Source analysis web_command

Hi Zhen,

Can you please consult the docstring of the ft_postfreesurferscript.sh?

Among others, it mentions:

# This script is adjusted from HCP's FS2CaretConvertRegisterNonlinear
# script, and creates sets of cortical meshes at various resolutions,
# which are surface-registered to a template, and which can be directly
# used for group-level averaging. The results will be stored in the
# directory 'workbench', in the subject-specific freesurfer folder.
#
# Use as:
#
#  ft_postfreesurferscript.sh <DIRNAME> <SUBJECTNAME> <TEMPLATEDIRNAME>
#
# 1. <DIRNAME> points to the directory which contains the subject specific
#     directory that contains the freesurfer results.
# 2. <SUBJECTNAME> is the name of the subject specific directory.
# 3. <TEMPLATEDIRNAME> is the directory that contains the required template
#     meshes.

This is indicating that you need to specify the location of the template meshes as an argument to the script.

Good luck,
Jan-Mathijs

On 4 Feb 2025, at 18:42, Ni, Zhen (NIH/NINDS) [C] <zhen.ni at nih.gov<mailto:zhen.ni at nih.gov>> wrote:

You don't often get email from zhen.ni at nih.gov<mailto:zhen.ni at nih.gov>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification>
Thank you, Jan-Mathijs,
Now the problem with the path was solved and the scripted was started running. Unfortunately, another problem occurred. The error message showed “Error: name of file: .L.sulc.native.shape.nii; path to file: >>>freesurfer/7.4.1/subjects//sub-001///workbench; file does not exist”

I copied the templates (MNI152….gii and L(R).4(8/164)K.gii) into the /surf (also /workbench, directory). I wonder if the templates should be copied into other directory or there are other problems with “path”.

Zhen

From: fieldtrip <fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>> On Behalf Of Schoffelen, J.M. (Jan Mathijs) via fieldtrip
Sent: Thursday, January 30, 2025 3:19 AM
To: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
Cc: Schoffelen, J.M. (Jan Mathijs) <janmathijs.schoffelen at donders.ru.nl<mailto:janmathijs.schoffelen at donders.ru.nl>>
Subject: [EXTERNAL] Re: [FieldTrip] Source analysis web_command

I agree, you need to sort out your path, and you need to ensure that the shell script has the executable permission flag switched on. Your system administrator/Stackoverflow/google/chatGPT/Deepseek should be able to help you on your way I think.

Good luck,
Jan-Mathijs

On 29 Jan 2025, at 21:07, Ni, Zhen (NIH/NINDS) [C] via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

I’m at the second step for creating a source model for source reconstruction: creation of mesh using HCP workbench. I installed Connectome Workbench on my Mac (M3). In the first step a series of products were generated by Freesurfer. The problem is that they cannot be read by the Workbench. I can open wb_view but when I input the command (ft_freesurferscript.sh) from the terminal, it showed "command cannot be found". I tested other commands from the terminal. Even wb_command does not work. I wonder if the environment setting is not correct.

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