Hi, I am also getting the error where the txt files cannot be opened because they were not created beforehand. Where does the trac-all -prior step take place? Does it appear within the trac-all -prep script?
Thank you,
Ammar Moiyadi, BS Professional Research Assistant Department of Psychiatry University of Colorado Anschutz Medical Campus 303-724-5490 ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of freesurfer-request@nmr.mgh.harvard.edu [freesurfer-request@nmr.mgh.harvard.edu] Sent: Friday, July 29, 2011 10:00 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 89, Issue 99
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Today's Topics:
1. trac-all -path errors (Ping-Hong Yeh) 2. Re: trac-all -path errors (Priti Srinivasan)
----------------------------------------------------------------------
Message: 1 Date: Fri, 29 Jul 2011 11:09:28 -0400 From: Ping-Hong Yeh pinghongyeh@gmail.com Subject: [Freesurfer] trac-all -path errors To: freesurfer@nmr.mgh.harvard.edu Message-ID: CAL1NnmP2+KdE5cNMVH4-qhnvSeMeQA7AjQ+cp-qPFtmGv3A+0Q@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1
Hi,
I got the error running "trac-all -path -c configure.txt"
ERROR: Could not open ${SUBJECTS_DIR}/$Subject/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt
I can only find only image files in the "dlabel/diff" directory, but not text files.
Which step(s) create the lh.cst_AS_avg33_mni_flt_cpts_5.txt file?
Thanks,
Ping
------------------------------
Message: 2 Date: Fri, 29 Jul 2011 11:26:13 -0400 (EDT) From: "Priti Srinivasan" rspriti@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] trac-all -path errors To: "Ping-Hong Yeh" pinghongyeh@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: 42727.132.183.139.239.1311953173.squirrel@mail.nmr.mgh.harvard.edu Content-Type: text/plain;charset=iso-8859-1
Hi Ping,
The text files get created in the trac-all -prior stage. Maybe something went wrong in that step. Is this the case for all the tracts or just for this tract? If you can send us the trac-all.log file under the scripts directory it'll be easier to troubleshoot as to what went wrong.
-Priti
Hi,
I got the error running "trac-all -path -c configure.txt"
ERROR: Could not open ${SUBJECTS_DIR}/$Subject/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt
I can only find only image files in the "dlabel/diff" directory, but not text files.
Which step(s) create the lh.cst_AS_avg33_mni_flt_cpts_5.txt file?
Thanks,
Ping _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
End of Freesurfer Digest, Vol 89, Issue 99 ******************************************
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Hi Ammar - Yes, -prior is the last step included in -prep. Are the text files missing for all tracts, or specifically for lh.cst?
Thanks, a.y
On Mon, 1 Aug 2011, Moiyadi, Ammar wrote:
Hi, I am also getting the error where the txt files cannot be opened because they were not created beforehand. Where does the trac-all -prior step take place? Does it appear within the trac-all -prep script?
Thank you,
Ammar Moiyadi, BS Professional Research Assistant Department of Psychiatry University of Colorado Anschutz Medical Campus 303-724-5490 ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of freesurfer-request@nmr.mgh.harvard.edu [freesurfer-request@nmr.mgh.harvard.edu] Sent: Friday, July 29, 2011 10:00 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 89, Issue 99
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
- trac-all -path errors (Ping-Hong Yeh)
- Re: trac-all -path errors (Priti Srinivasan)
Message: 1 Date: Fri, 29 Jul 2011 11:09:28 -0400 From: Ping-Hong Yeh pinghongyeh@gmail.com Subject: [Freesurfer] trac-all -path errors To: freesurfer@nmr.mgh.harvard.edu Message-ID: CAL1NnmP2+KdE5cNMVH4-qhnvSeMeQA7AjQ+cp-qPFtmGv3A+0Q@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1
Hi,
I got the error running "trac-all -path -c configure.txt"
ERROR: Could not open ${SUBJECTS_DIR}/$Subject/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt
I can only find only image files in the "dlabel/diff" directory, but not text files.
Which step(s) create the lh.cst_AS_avg33_mni_flt_cpts_5.txt file?
Thanks,
Ping
Message: 2 Date: Fri, 29 Jul 2011 11:26:13 -0400 (EDT) From: "Priti Srinivasan" rspriti@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] trac-all -path errors To: "Ping-Hong Yeh" pinghongyeh@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: 42727.132.183.139.239.1311953173.squirrel@mail.nmr.mgh.harvard.edu Content-Type: text/plain;charset=iso-8859-1
Hi Ping,
The text files get created in the trac-all -prior stage. Maybe something went wrong in that step. Is this the case for all the tracts or just for this tract? If you can send us the trac-all.log file under the scripts directory it'll be easier to troubleshoot as to what went wrong.
-Priti
Hi,
I got the error running "trac-all -path -c configure.txt"
ERROR: Could not open ${SUBJECTS_DIR}/$Subject/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt
I can only find only image files in the "dlabel/diff" directory, but not text files.
Which step(s) create the lh.cst_AS_avg33_mni_flt_cpts_5.txt file?
Thanks,
Ping _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
End of Freesurfer Digest, Vol 89, Issue 99
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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Anastasia Yendiki -
Moiyadi, Ammar