You only need to specify path names if you don't want to reconstruct all 42
paths. But from the list, it looks like you want all 42 paths, so you don't
need to specify anything. Skip all of those lines and you'll get the default
behavior.
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of King-Wai Chu
<kingwai....@gmail.com>
Sent: Friday, August 5, 2022 5:03 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Tracula Config file.
External Email - Use Caution
Hi Alan,
In your pathlist, the 1st path is acomm. You have "ac" in your file.
Change ac to acomm and you should be good to go.
Best,
King-Wai
On Fri, Aug 5, 2022 at 4:23 PM Alan Francis
<alandarkene...@gmail.com<mailto:alandarkene...@gmail.com>> wrote:
External Email - Use Caution
Hi King-Wai -
First of all, thank you so much for taking the time to investigate my RC file.
I made the changes that you suggested, but the error keeps coming up.
I have attached the file.
Thanks again,
Alan
On Fri, Aug 5, 2022 at 2:03 PM King-Wai Chu
<kingwai....@gmail.com<mailto:kingwai....@gmail.com>> wrote:
External Email - Use Caution
Hi Alan,
They still don't match.
See attached excel file.
Best,
King-Wai
On Fri, Aug 5, 2022 at 2:35 PM Alan Francis
<alandarkene...@gmail.com<mailto:alandarkene...@gmail.com>> wrote:
External Email - Use Caution
Hello King-Wai -
I made the change to the ncpts. But still an error message persists.
ERROR: length of pathway list (ac cc.bodyc cc.bodyp cc.bodypf cc.bodypm
cc.bodyt cc.genu cc.rostrum cc.splenium mcp
lh.af<http://secure-web.cisco.com/176zMSj3UUw45_cb2va9_7R3HkQuwfRe5m-Jin3wUtPQzI7d7v-4q3wsR4r7d9QwcivOKE9o_ck5a8bD31V8Alz3RMRAqwD40qDD6beX-PR54tGixx6CoFmVQnysbHjU1XbkibncfdFfAspteTiir7dInIx1CMDoCbTjgCo1yWpKeaYT_T_CwT_XaD2dhaKQtPEa3KtAp-rYguCD_hTzKhR9hOuHYaNzEswTUZkNeOT6WzmTfrpOzlpTz3Y-88kcq_Fp7P_6-b3XlHLU8qaVysYr0v9wgIs1cVAsFXW650tR8lYMjuEtTabKSUDfuIt1w/http%3A%2F%2Flh.af>
rh.af<http://secure-web.cisco.com/1VDPO3flA2xT8Xe4QNyDHk8mB-iJPBmqbzJh8Ak3H7m3aboNxipSP5XdnS6-BRf6dVaBZVL3J4xJQDCFC-OzwOleYSxZlP6umvRawDz1ssWH6sSZSyeW5sMIcd5xrkcDEp9S8xKKx8mMBqIw5wf15JXFCl5KdUJYU3FQnMgGlE8YKWJJSYYH4xlAsRr-XQmDZjKEDqgo-iTzJLYKCYkdg2MiNllERsTkN8cgQOj10x__sATAtZ8mttvg5jsnIdxmz1aw-IoSssPLVmzOR9ZH68zXb7GlLFW1_mQnWQlikbNpk8pZ6NDKJ1KGEqbgP5WAR/http%3A%2F%2Frh.af>
lh.ar<http://secure-web.cisco.com/10AwBuDvjtYPMWc5I6IFFbSdkEzmH7lfcINs51mwMkqD-v7R2ogbxacwoENokJedngVSa3zH1HprCx9ofYjv7pPe6IFzmie_eYY1ufkHFk46-wqcAPThSeTQVbxpDurdQIa2d2m0PXOi6M7IArX374zjsRg-W0FfD71Pi2TMH9W7xIg6-J2Mb2zugeJe7xFeKkOtTSmfIgXsudarxOVjVqRwAMza06IVZWA9J2wQJp-DA0XA4NO9kG8rtcJFoKsv0oGekPWJP68PbAA5km1er-o4uv3KmV7o69WsDlPPXpUncByNoHjOXoKKQwb3A7xZp/http%3A%2F%2Flh.ar>
rh.ar<http://secure-web.cisco.com/1jrRoArncaOHPIoRxxz497IFzd9_Rhwadrox-w1yLdBEVwxfLgNkksVeNV0gZM-TEkFC1KyN1OnqGgMDR8Y2ecOy24HiNpROCvNgXGQ-rDBTaoxLzPL5iOOmlv962OLCwMPn9MB75unkA88cuu-Qzp-F0ZBAvSWGMj7Or79Kf0imRH28p9oQthbeOC_ClugWmVx2zAmHf79bQJfDeryRAzGMWNKnc3sKj-osDqEw-XcK0vCGocui3-i2TbiumRxbhFc31CmeOrLUIlYMyv6z_QXryv5UO08LW8pJ7ZgEudTy9GtTkoewa8dGkt57s496S/http%3A%2F%2Frh.ar>
lh.atr rh.atr lh.cbd rh.cbd lh.cbv rh.cbv lh.cst rh.cst lh.emc rh.emc lh.fat
rh.fat lh.fx rh.fx lh.ilf rh.ilf lh.mlf rh.mlf lh.or rh.or lh.slf1 rh.slf1
lh.slf2 rh.slf2 lh.slf3 rh.slf3 lh.uf rh.uf) and endpoint label ID list
ERROR: (0 0 0 0 0 0 0 0 0 0 0 10 49 10 49 0 0 0 0 16 16 0 0 0 0 28 60 0 0 0 0
10 49 0 0 0 0 0 0 0 0) do not match
I have attached the RC file. Could you please shed some light on this?
Thank you
Alan
On Fri, Aug 5, 2022 at 11:29 AM King-Wai Chu
<kingwai....@gmail.com<mailto:kingwai....@gmail.com>> wrote:
External Email - Use Caution
Hi Alan,
Your pathlist and "Number of path control points"(ncpts) don't match.
You have more than 3 paths in the pathlist and only 3 numbers in ncpts.
Best,
King-Wai
On Fri, Aug 5, 2022 at 10:53 AM Alan Francis
<alandarkene...@gmail.com<mailto:alandarkene...@gmail.com>> wrote:
External Email - Use Caution
Good morning Anastasia -
I made the changes you suggested and removed "extraneous" commands. But the
error message still persists. Could you please shed some light on this?
Attached - latest RC file.
The error message is : unmatched ' " '
Thank you
Alan
On Thu, Aug 4, 2022 at 12:04 PM Yendiki, Anastasia
<ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Alan - dcmroot is the root directory under which the dicom files are saved.
It's actually optional. In your case, either of the following will have the
same, correct effect:
set dcmroot = /home/afrancis/Imaging
set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
OR
set dcmlist =
(/home/afrancis/Imaging/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz)
In addition, there are a lot of things that you left in there from the example
RC file. You should delete them entirely, unless you specifically want to set
one of those things to something other than the default. These are examples
that may not give you the default behavior. Also the field mapping files -
delete those lines because you're just using the example names and they're not
going to work. You want your RC file to have the minimum necessary for your
analysis.
Best,
Anastasia.
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Alan Francis
<alandarkene...@gmail.com<mailto:alandarkene...@gmail.com>>
Sent: Thursday, August 4, 2022 12:23 PM
To: Freesurfer
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Tracula Config file.
External Email - Use Caution
Hi Anastasia -
Hope you are well. I am running tracula on FS 7.2. I created the RC file based
on your recommendations. However it is giving me an error message when I run
it. The error is : Unmatched ' " "
I have attached the RC file. Could you please see where I have made an error.
Thanks so much,
Best regards,
Alan
--
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
Alan N. Francis PhD
Assistant Professor of Neuroscience
Institute of Neuroscience
University of Texas, School of Medicine
Rio Grande Valley
Texas.
_______________________________________________
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--
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
Alan N. Francis PhD
Assistant Professor of Neuroscience
Institute of Neuroscience
University of Texas, School of Medicine
Rio Grande Valley
Texas.
_______________________________________________
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.
--
King-Wai Chu, Ph.D.
Program Analyst
Mental Illness Research, Education and Clinical Center (MIRECC, VISN3)
James J. Peters Dept. of Veterans Administration Medical Center (OOMH)
130 W. Kingsbridge Road
Bronx, NY 10468
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--
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
Alan N. Francis PhD
Assistant Professor of Neuroscience
Institute of Neuroscience
University of Texas, School of Medicine
Rio Grande Valley
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.
--
King-Wai Chu, Ph.D.
Program Analyst
Mental Illness Research, Education and Clinical Center (MIRECC, VISN3)
James J. Peters Dept. of Veterans Administration Medical Center (OOMH)
130 W. Kingsbridge Road
Bronx, NY 10468
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Alan N. Francis PhD
Assistant Professor of Neuroscience
Institute of Neuroscience
University of Texas, School of Medicine
Rio Grande Valley
Texas.
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King-Wai Chu, Ph.D.
Program Analyst
Mental Illness Research, Education and Clinical Center (MIRECC, VISN3)
James J. Peters Dept. of Veterans Administration Medical Center (OOMH)
130 W. Kingsbridge Road
Bronx, NY 10468
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