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<p class="MsoNormal">Hi Jan-Mathijs,<o:p></o:p></p>
<p class="MsoNormal">I followed the instruction but still cannot run the script correctly.<o:p></o:p></p>
<p class="MsoNormal">For $1 <DIRNAME>, I input the directory containing the freesurfer results (>>7.4.1/subjects in my computer).<o:p></o:p></p>
<p class="MsoNormal">For $2 <SUBJECTNAME>, I input the subject (>>sub-001 in my computer).<o:p></o:p></p>
<p class="MsoNormal">These were defined in the /.bashrc file. I think they are likely correct.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I also tried some other options for the third step ($3) but always got the same error message:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">While running >>>>/workbench/subject-001.L.sulc.native.shape.gii CORTEX_LEFT<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">ERROR: NAME OF FILE: subject-001.L.sulc.native.shape.gii<o:p></o:p></p>
<p class="MsoNormal">PATH TO FILE: >>>>/sub-001/workbench File does not exist<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I wonder if you have any ideas.<o:p></o:p></p>
<p class="MsoNormal">Thanks<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Zhen<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> fieldtrip <fieldtrip-bounces@science.ru.nl>
<b>On Behalf Of </b>Schoffelen, J.M. (Jan Mathijs) via fieldtrip<br>
<b>Sent:</b> Thursday, February 6, 2025 2:39 AM<br>
<b>To:</b> FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Cc:</b> Schoffelen, J.M. (Jan Mathijs) <janmathijs.schoffelen@donders.ru.nl><br>
<b>Subject:</b> [EXTERNAL] Re: [FieldTrip] Source analysis web_command<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Zhen, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Can you please consult the docstring of the ft_postfreesurferscript.sh?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Among others, it mentions: <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"># This script is adjusted from HCP's FS2CaretConvertRegisterNonlinear<o:p></o:p></p>
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<p class="MsoNormal"># script, and creates sets of cortical meshes at various resolutions,<o:p></o:p></p>
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<p class="MsoNormal"># which are surface-registered to a template, and which can be directly<o:p></o:p></p>
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<p class="MsoNormal"># used for group-level averaging. The results will be stored in the <o:p></o:p></p>
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<p class="MsoNormal"># directory 'workbench', in the subject-specific freesurfer folder.<o:p></o:p></p>
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<p class="MsoNormal"># <o:p></o:p></p>
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<p class="MsoNormal"># Use as:<o:p></o:p></p>
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<p class="MsoNormal">#<o:p></o:p></p>
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<p class="MsoNormal"># ft_postfreesurferscript.sh <DIRNAME> <SUBJECTNAME> <TEMPLATEDIRNAME><o:p></o:p></p>
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<p class="MsoNormal">#<o:p></o:p></p>
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<p class="MsoNormal"># 1. <DIRNAME> points to the directory which contains the subject specific<o:p></o:p></p>
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<p class="MsoNormal"># directory that contains the freesurfer results.<o:p></o:p></p>
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<p class="MsoNormal"># 2. <SUBJECTNAME> is the name of the subject specific directory.<o:p></o:p></p>
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<p class="MsoNormal"># 3. <TEMPLATEDIRNAME> is the directory that contains the required template<o:p></o:p></p>
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<p class="MsoNormal"># meshes.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">This is indicating that you need to specify the location of the template meshes as an argument to the script. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Good luck,<o:p></o:p></p>
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<p class="MsoNormal">Jan-Mathijs<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
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<p class="MsoNormal">On 4 Feb 2025, at 18:42, Ni, Zhen (NIH/NINDS) [C] <<a href="mailto:zhen.ni@nih.gov">zhen.ni@nih.gov</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<span style="font-size:9.0pt;font-family:"Segoe UI",sans-serif;color:#212121">You don't often get email from<span class="apple-converted-space"> </span><a href="mailto:zhen.ni@nih.gov">zhen.ni@nih.gov</a>.<span class="apple-converted-space"> </span><a href="https://aka.ms/LearnAboutSenderIdentification">Learn
why this is important</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Thank you, Jan-Mathijs,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">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”<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">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”.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Zhen<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span class="apple-converted-space"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span></span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">fieldtrip
<<a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a>><span class="apple-converted-space"> </span><b>On Behalf Of<span class="apple-converted-space"> </span></b>Schoffelen, J.M. (Jan Mathijs) via fieldtrip<br>
<b>Sent:</b><span class="apple-converted-space"> </span>Thursday, January 30, 2025 3:19 AM<br>
<b>To:</b><span class="apple-converted-space"> </span>FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>
<b>Cc:</b><span class="apple-converted-space"> </span>Schoffelen, J.M. (Jan Mathijs) <<a href="mailto:janmathijs.schoffelen@donders.ru.nl">janmathijs.schoffelen@donders.ru.nl</a>><br>
<b>Subject:</b><span class="apple-converted-space"> </span>[EXTERNAL] Re: [FieldTrip] Source analysis web_command<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">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.<span class="apple-converted-space"> </span><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Good luck,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Jan-Mathijs<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><br>
<br>
<br>
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">On 29 Jan 2025, at 21:07, Ni, Zhen (NIH/NINDS) [C] via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>> wrote:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">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.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><a href="https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202&data=05%7C02%7Cfieldtrip%40science.ru.nl%7Cabac4922c9714aedfb8308dd513da5db%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638756047409138926%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=0VW%2FXh1g03eIkzBAYY68dYpRtwpguMv5rntHiGBKzVI%3D&reserved=0" originalSrc="https://doi.org/10.1371/journal.pcbi.1002202" shash="VrJT/joj7tz7/dMfHYTCPbsVEW7Sb7P8YniVdTsgoP7H1Mt+Y5MVAMqk7j2lARt/ZCuqdvPrtRbUBDFgWdiZHs00V4nqAuwD71mUAhFdPSPdjkHvStm+HaQH7J2KBXkQsaeJXq9wsQL3W2s75VG7f6JfJCllBTtGELIyAazUGb4="><span style="font-size:10.5pt;font-family:"Helvetica",sans-serif">https://doi.org/10.1371/journal.pcbi.1002202</span></a><o:p></o:p></span></p>
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