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<div>Hi Zhen,</div>
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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.
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<div>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’)</div>
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<div>Good luck,</div>
<div>Jan-Mathijs</div>
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<div>On 20 Feb 2025, at 00:31, 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: 12pt; font-family: Aptos, sans-serif;">Hi Jan-Mathijs,<o:p></o:p></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">I followed the instruction but still cannot run the script correctly.<o:p></o:p></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">For $1 <DIRNAME>, I input the directory containing the freesurfer results (>>7.4.1/subjects in my computer).<o:p></o:p></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">For $2 <SUBJECTNAME>, I input the subject (>>sub-001 in my computer).<o:p></o:p></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">These were defined in the /.bashrc file. I think they are likely correct.<o:p></o:p></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><o:p> </o:p></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">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></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><o:p> </o:p></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">I also tried some other options for the third step ($3) but always got the same error message:<o:p></o:p></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><o:p> </o:p></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">While running >>>>/workbench/subject-001.L.sulc.native.shape.gii CORTEX_LEFT<o:p></o:p></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><o:p> </o:p></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">ERROR: NAME OF FILE: subject-001.L.sulc.native.shape.gii<o:p></o:p></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">PATH TO FILE: >>>>/sub-001/workbench File does not exist<o:p></o:p></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><o:p> </o:p></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><o:p> </o:p></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">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></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><o:p> </o:p></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">I wonder if you have any ideas.<o:p></o:p></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">Thanks<o:p></o:p></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><o:p> </o:p></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">Zhen<o:p></o:p></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><o:p> </o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><b><span style="font-size: 11pt; font-family: Calibri, sans-serif;">From:</span></b><span style="font-size: 11pt; font-family: Calibri, sans-serif;"><span class="Apple-converted-space"> </span>fieldtrip
<fieldtrip-bounces@science.ru.nl><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, February 6, 2025 2:39 AM<br>
<b>To:</b><span class="Apple-converted-space"> </span>FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Cc:</b><span class="Apple-converted-space"> </span>Schoffelen, J.M. (Jan Mathijs) <janmathijs.schoffelen@donders.ru.nl><br>
<b>Subject:</b><span class="Apple-converted-space"> </span>[EXTERNAL] Re: [FieldTrip] Source analysis web_command<o:p></o:p></span></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><o:p> </o:p></div>
<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">Hi Zhen,<span class="Apple-converted-space"> </span><o:p></o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><o:p> </o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">Can you please consult the docstring of the ft_postfreesurferscript.sh?<o:p></o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><o:p> </o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">Among others, it mentions: <o:p></o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><o:p> </o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"># This script is adjusted from HCP's FS2CaretConvertRegisterNonlinear<o:p></o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"># script, and creates sets of cortical meshes at various resolutions,<o:p></o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"># which are surface-registered to a template, and which can be directly<o:p></o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"># used for group-level averaging. The results will be stored in the <o:p></o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"># directory 'workbench', in the subject-specific freesurfer folder.<o:p></o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"># <o:p></o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"># Use as:<o:p></o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">#<o:p></o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"># ft_postfreesurferscript.sh <DIRNAME> <SUBJECTNAME> <TEMPLATEDIRNAME><o:p></o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">#<o:p></o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"># 1. <DIRNAME> points to the directory which contains the subject specific<o:p></o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"># directory that contains the freesurfer results.<o:p></o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"># 2. <SUBJECTNAME> is the name of the subject specific directory.<o:p></o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"># 3. <TEMPLATEDIRNAME> is the directory that contains the required template<o:p></o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"># meshes.<o:p></o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><o:p> </o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">This is indicating that you need to specify the location of the template meshes as an argument to the script. <o:p></o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><o:p> </o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">Good luck,<o:p></o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">Jan-Mathijs<o:p></o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><o:p> </o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><o:p> </o:p></div>
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<br>
<o:p></o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;">On 4 Feb 2025, at 18:42, Ni, Zhen (NIH/NINDS) [C] <<a href="mailto:zhen.ni@nih.gov" style="color: blue; text-decoration: underline;">zhen.ni@nih.gov</a>> wrote:<o:p></o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><o:p> </o:p></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 9pt; font-family: "Segoe UI", sans-serif; color: rgb(33, 33, 33);">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: blue; text-decoration: underline;">Learn
why this is important</a><o:p></o:p></span></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif;">Thank you, Jan-Mathijs,<o:p></o:p></span></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="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></span></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif;"> <o:p></o:p></span></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="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></span></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif;"> <o:p></o:p></span></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif;">Zhen<o:p></o:p></span></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif;"> <o:p></o:p></span></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><b><span style="font-size: 11pt; font-family: Calibri, sans-serif;">From:</span></b><span class="apple-converted-space"><span style="font-size: 11pt; font-family: Calibri, sans-serif;"> </span></span><span style="font-size: 11pt; font-family: Calibri, sans-serif;">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></span></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif;"> <o:p></o:p></span></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="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></span></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif;"> <o:p></o:p></span></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif;">Good luck,<o:p></o:p></span></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif;">Jan-Mathijs<o:p></o:p></span></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif;"> <o:p></o:p></span></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif;"> <o:p></o:p></span></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="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></span></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif;"> <o:p></o:p></span></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="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></span></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif;"> <o:p></o:p></span></div>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 10.5pt; font-family: Helvetica, sans-serif;">_______________________________________________<br>
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<div style="margin: 0in; font-size: 12pt; font-family: Aptos, sans-serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif;"> <o:p></o:p></span></div>
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<span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(156, 101, 0);">CAUTION:</span><span class="apple-converted-space"><span style="font-size: 10pt; font-family: Calibri, sans-serif;"> </span></span><span style="font-size: 10pt; font-family: Calibri, sans-serif;">This
email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.</span><span style="font-size: 11pt; font-family: Calibri, sans-serif;"><o:p></o:p></span></div>
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<span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(156, 101, 0);">CAUTION:</span><span style="font-size: 10pt; font-family: Calibri, sans-serif;"><span class="Apple-converted-space"> </span>This email originated from outside of the organization.
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