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Hi Zhen,
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<div>Can you please consult the docstring of the ft_postfreesurferscript.sh?</div>
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<div>Among others, it mentions: </div>
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<div># This script is adjusted from HCP's FS2CaretConvertRegisterNonlinear</div>
<div># script, and creates sets of cortical meshes at various resolutions,</div>
<div># which are surface-registered to a template, and which can be directly</div>
<div># used for group-level averaging. The results will be stored in the </div>
<div># directory 'workbench', in the subject-specific freesurfer folder.</div>
<div># </div>
<div># Use as:</div>
<div>#</div>
<div># ft_postfreesurferscript.sh <DIRNAME> <SUBJECTNAME> <TEMPLATEDIRNAME></div>
<div>#</div>
<div># 1. <DIRNAME> points to the directory which contains the subject specific</div>
<div># directory that contains the freesurfer results.</div>
<div># 2. <SUBJECTNAME> is the name of the subject specific directory.</div>
<div># 3. <TEMPLATEDIRNAME> is the directory that contains the required template</div>
<div># meshes.</div>
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<div>This is indicating that you need to specify the location of the template meshes as an argument to the script. </div>
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<div>Good luck,</div>
<div>Jan-Mathijs</div>
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<div>On 4 Feb 2025, at 18:42, Ni, Zhen (NIH/NINDS) [C] <zhen.ni@nih.gov> wrote:</div>
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You don't often get email from<span class="Apple-converted-space"> </span><a href="mailto:zhen.ni@nih.gov" style="color: blue; text-decoration: underline;">zhen.ni@nih.gov</a>.<span class="Apple-converted-space"> </span><a href="https://aka.ms/LearnAboutSenderIdentification" style="color: revert !important; text-decoration: underline; background: revert !important; direction: revert !important; display: revert !important; font-size: revert !important; opacity: revert !important; rotate: revert !important; scale: revert !important; visibility: revert !important;">Learn
why this is important</a></div>
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<div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">Thank you, Jan-Mathijs,<o:p></o:p></div>
<div style="margin: 0in; font-size: 11pt; 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></div>
<div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div>
<div style="margin: 0in; font-size: 11pt; 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></div>
<div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div>
<div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">Zhen<o:p></o:p></div>
<div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div>
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<div style="border-width: 1pt medium medium; border-style: solid none none; border-color: rgb(225, 225, 225) currentcolor currentcolor; border-image: none; padding: 3pt 0in 0in;">
<div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><b>From:</b><span class="Apple-converted-space"> </span>fieldtrip <<a href="mailto:fieldtrip-bounces@science.ru.nl" style="color: blue; text-decoration: underline;">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" style="color: blue; text-decoration: underline;">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" style="color: blue; text-decoration: underline;">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></div>
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<div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div>
<div style="margin: 0in; font-size: 11pt; 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></div>
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<div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div>
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<div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">Good luck,<o:p></o:p></div>
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<div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">Jan-Mathijs<o:p></o:p></div>
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<div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div>
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<o:p></o:p></div>
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<div style="margin: 0in; font-size: 11pt; 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" style="color: blue; text-decoration: underline;">fieldtrip@science.ru.nl</a>>
wrote:<o:p></o:p></div>
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<div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p> </o:p></div>
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<div style="margin: 0in; font-size: 11pt; 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></div>
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<div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"> <o:p></o:p></div>
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<span style="font-size: 10pt; color: rgb(156, 101, 0);">CAUTION:</span><span style="font-size: 10pt;"><span class="Apple-converted-space"> </span>This email originated from outside of the organization. Do not click links or open attachments unless you recognize
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