[FieldTrip] Source analysis web_command

Thu Feb 20 00:31:52 CET 2025

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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