Hi - The txt files are missing for all the tracts as it turns out trac-all -prep exited with errors before getting to -prior. It appears there is a problem with my bvec file since the dmri/bvec is reading all 0's. As a result, i get this error "Error: bvecs and bvals don't have the same number of entries". I have attached my bvec.txt file and trac-all log - any ideas to where the problem may lie?
Thank You,
Ammar Moiyadi, BS Professional Research Assistant Department of Psychiatry University of Colorado Anschutz Medical Campus 303-724-5490 ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, August 01, 2011 12:32 PM To: Moiyadi, Ammar Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] trac-all -path errors
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
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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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Ammar - It looks like it's the same text file formatting issue that someone else had recently. Did you create this file in excel by any chance? It can't be read properly under unix.
a.y
On Wed, 3 Aug 2011, Moiyadi, Ammar wrote:
Hi - The txt files are missing for all the tracts as it turns out trac-all -prep exited with errors before getting to -prior. It appears there is a problem with my bvec file since the dmri/bvec is reading all 0's. As a result, i get this error "Error: bvecs and bvals don't have the same number of entries". I have attached my bvec.txt file and trac-all log - any ideas to where the problem may lie?
Thank You,
Ammar Moiyadi, BS Professional Research Assistant Department of Psychiatry University of Colorado Anschutz Medical Campus 303-724-5490 ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, August 01, 2011 12:32 PM To: Moiyadi, Ammar Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] trac-all -path errors
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
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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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi - I created the text file with gedit in Lucid Ubuntu. I checked my locale and my lang reads en_US.UTF-8, is this the same for you?
Thank you,
Ammar Moiyadi, BS Professional Research Assistant Department of Psychiatry University of Colorado Anschutz Medical Campus 303-724-5490 ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Wednesday, August 03, 2011 10:25 AM To: Moiyadi, Ammar Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] trac-all -path errors
Hi Ammar - It looks like it's the same text file formatting issue that someone else had recently. Did you create this file in excel by any chance? It can't be read properly under unix.
a.y
On Wed, 3 Aug 2011, Moiyadi, Ammar wrote:
Hi - The txt files are missing for all the tracts as it turns out trac-all -prep exited with errors before getting to -prior. It appears there is a problem with my bvec file since the dmri/bvec is reading all 0's. As a result, i get this error "Error: bvecs and bvals don't have the same number of entries". I have attached my bvec.txt file and trac-all log - any ideas to where the problem may lie?
Thank You,
Ammar Moiyadi, BS Professional Research Assistant Department of Psychiatry University of Colorado Anschutz Medical Campus 303-724-5490 ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, August 01, 2011 12:32 PM To: Moiyadi, Ammar Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] trac-all -path errors
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
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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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Yes, that's the lang that I got, too. But the text file shows up with ^M's where the ends of lines should be on darwin and on centos only the first 2 lines show up.
On Wed, 3 Aug 2011, Moiyadi, Ammar wrote:
Hi - I created the text file with gedit in Lucid Ubuntu. I checked my locale and my lang reads en_US.UTF-8, is this the same for you?
Thank you,
Ammar Moiyadi, BS Professional Research Assistant Department of Psychiatry University of Colorado Anschutz Medical Campus 303-724-5490 ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Wednesday, August 03, 2011 10:25 AM To: Moiyadi, Ammar Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] trac-all -path errors
Hi Ammar - It looks like it's the same text file formatting issue that someone else had recently. Did you create this file in excel by any chance? It can't be read properly under unix.
a.y
On Wed, 3 Aug 2011, Moiyadi, Ammar wrote:
Hi - The txt files are missing for all the tracts as it turns out trac-all -prep exited with errors before getting to -prior. It appears there is a problem with my bvec file since the dmri/bvec is reading all 0's. As a result, i get this error "Error: bvecs and bvals don't have the same number of entries". I have attached my bvec.txt file and trac-all log - any ideas to where the problem may lie?
Thank You,
Ammar Moiyadi, BS Professional Research Assistant Department of Psychiatry University of Colorado Anschutz Medical Campus 303-724-5490 ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, August 01, 2011 12:32 PM To: Moiyadi, Ammar Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] trac-all -path errors
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Anastasia - I decided to made an entirely new txt file and the proper dmri/bvec file is now being created. Unfortunately now I'm running into a memory allocation problem. Since I'm running on ubuntu I'm not sure its the same problem that mac users are facing. Any suggestions for how to proceed?
Ammar Moiyadi, BS Professional Research Assistant Department of Psychiatry University of Colorado Anschutz Medical Campus 303-724-5490 ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Wednesday, August 03, 2011 10:37 AM To: Moiyadi, Ammar Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] trac-all -path errors
Yes, that's the lang that I got, too. But the text file shows up with ^M's where the ends of lines should be on darwin and on centos only the first 2 lines show up.
On Wed, 3 Aug 2011, Moiyadi, Ammar wrote:
Hi - I created the text file with gedit in Lucid Ubuntu. I checked my locale and my lang reads en_US.UTF-8, is this the same for you?
Thank you,
Ammar Moiyadi, BS Professional Research Assistant Department of Psychiatry University of Colorado Anschutz Medical Campus 303-724-5490 ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Wednesday, August 03, 2011 10:25 AM To: Moiyadi, Ammar Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] trac-all -path errors
Hi Ammar - It looks like it's the same text file formatting issue that someone else had recently. Did you create this file in excel by any chance? It can't be read properly under unix.
a.y
On Wed, 3 Aug 2011, Moiyadi, Ammar wrote:
Hi - The txt files are missing for all the tracts as it turns out trac-all -prep exited with errors before getting to -prior. It appears there is a problem with my bvec file since the dmri/bvec is reading all 0's. As a result, i get this error "Error: bvecs and bvals don't have the same number of entries". I have attached my bvec.txt file and trac-all log - any ideas to where the problem may lie?
Thank You,
Ammar Moiyadi, BS Professional Research Assistant Department of Psychiatry University of Colorado Anschutz Medical Campus 303-724-5490 ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, August 01, 2011 12:32 PM To: Moiyadi, Ammar Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] trac-all -path errors
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
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Hi Ammar - At which point does the allocation error occur? It'd help to see your trac-all.log.
Thanks, a.y
On Thu, 4 Aug 2011, Moiyadi, Ammar wrote:
Thanks Anastasia - I decided to made an entirely new txt file and the proper dmri/bvec file is now being created. Unfortunately now I'm running into a memory allocation problem. Since I'm running on ubuntu I'm not sure its the same problem that mac users are facing. Any suggestions for how to proceed?
Ammar Moiyadi, BS Professional Research Assistant Department of Psychiatry University of Colorado Anschutz Medical Campus 303-724-5490 ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Wednesday, August 03, 2011 10:37 AM To: Moiyadi, Ammar Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] trac-all -path errors
Yes, that's the lang that I got, too. But the text file shows up with ^M's where the ends of lines should be on darwin and on centos only the first 2 lines show up.
On Wed, 3 Aug 2011, Moiyadi, Ammar wrote:
Hi - I created the text file with gedit in Lucid Ubuntu. I checked my locale and my lang reads en_US.UTF-8, is this the same for you?
Thank you,
Ammar Moiyadi, BS Professional Research Assistant Department of Psychiatry University of Colorado Anschutz Medical Campus 303-724-5490 ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Wednesday, August 03, 2011 10:25 AM To: Moiyadi, Ammar Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] trac-all -path errors
Hi Ammar - It looks like it's the same text file formatting issue that someone else had recently. Did you create this file in excel by any chance? It can't be read properly under unix.
a.y
On Wed, 3 Aug 2011, Moiyadi, Ammar wrote:
Hi - The txt files are missing for all the tracts as it turns out trac-all -prep exited with errors before getting to -prior. It appears there is a problem with my bvec file since the dmri/bvec is reading all 0's. As a result, i get this error "Error: bvecs and bvals don't have the same number of entries". I have attached my bvec.txt file and trac-all log - any ideas to where the problem may lie?
Thank You,
Ammar Moiyadi, BS Professional Research Assistant Department of Psychiatry University of Colorado Anschutz Medical Campus 303-724-5490 ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, August 01, 2011 12:32 PM To: Moiyadi, Ammar Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] trac-all -path errors
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
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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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freesurfer@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
Moiyadi, Ammar