Hi Chris,
this is a good question for the list (cc'ed), others may or will have the same problem.
The problem is with your table file, specifically the new line character. DOS uses \r\n , Mac \r and Linux \n. Your text file uses \r, so it probably was created on a mac.
The problem is that the "cat" command (at least in linux) does not work on your file: cat long.qdec.table.dat is empty
You can convert the \r to \n (linux format): tr '\r' '\n' < long.qdec.table.dat > long2.qdec.table.dat
and then should be able to run the preproc command.
People with DOS formats should not run the above "tr' command as they will end up with 2 newlines instead of 1. Maybe DOS txt files work with 'cat' directly (so there is no need)? If anyone on the list knows a good way of cat and awk a file independently of the new line (and working on all OS), let me know. This is the command I use:
cat $fsgdf | awk '{if ($1 != "fsid" && substr($1,0,1) != "#") printf("%s.long.%s\n", $1, $2)}'
to generate the subjects id's from the table's first two columns.
Best, Martin
On 06/03/2013 03:45 PM, Christopher McCarthy wrote:
Dr. Reuter,
We corresponded in the past about QDEC, and you gave me great help. The lab I work for is now moving towards using the Longitudinal Mixed Effects Model. When I go to run the command:
mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target study_average --hemi lh --meas thickness --out lh.thickness.mgh
I get the error: 'ERROR: no subjects specified.' I am attaching my long.qdec.table.dat, which works fine when loaded by QDEC. Do you have any idea of why I am getting this error?
Thanks,
Chris McCarthy
Dr. Reuter,
Thanks for your help, it got me through the error I was having. On to the next one:
When I enter the command:
mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target fsaverage --hemi lh --meas thickness --out lh.thickness.mgh
it spits out the following two lines before quitting:
nsubjects = 45 ERROR: cannot find /media/freesurfer/.long.
Any idea what I'm missing?
Thanks for your help and patience,
Chris
On Mon, Jun 3, 2013 at 5:08 PM, Martin Reuter mreuter@nmr.mgh.harvard.eduwrote:
Hi Chris,
this is a good question for the list (cc'ed), others may or will have the same problem.
The problem is with your table file, specifically the new line character. DOS uses \r\n , Mac \r and Linux \n. Your text file uses \r, so it probably was created on a mac.
The problem is that the "cat" command (at least in linux) does not work on your file: cat long.qdec.table.dat is empty
You can convert the \r to \n (linux format): tr '\r' '\n' < long.qdec.table.dat > long2.qdec.table.dat
and then should be able to run the preproc command.
People with DOS formats should not run the above "tr' command as they will end up with 2 newlines instead of 1. Maybe DOS txt files work with 'cat' directly (so there is no need)? If anyone on the list knows a good way of cat and awk a file independently of the new line (and working on all OS), let me know. This is the command I use:
cat $fsgdf | awk '{if ($1 != "fsid" && substr($1,0,1) != "#") printf("%s.long.%s\n", $1, $2)}'
to generate the subjects id's from the table's first two columns.
Best, Martin
On 06/03/2013 03:45 PM, Christopher McCarthy wrote:
Dr. Reuter,
We corresponded in the past about QDEC, and you gave me great help. The lab I work for is now moving towards using the Longitudinal Mixed Effects Model. When I go to run the command:
mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target study_average --hemi lh --meas thickness --out lh.thickness.mgh
I get the error: 'ERROR: no subjects specified.' I am attaching my long.qdec.table.dat, which works fine when loaded by QDEC. Do you have any idea of why I am getting this error?
Thanks,
Chris McCarthy
-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu
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/**compliancelinehttp://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.
Is that all the output to the terminal? If so, add --debug as the first argument and send us the resulting terminal output doug On 06/04/2013 01:41 PM, Christopher McCarthy wrote:
Dr. Reuter,
Thanks for your help, it got me through the error I was having. On to the next one:
When I enter the command:
mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target fsaverage --hemi lh --meas thickness --out lh.thickness.mgh
it spits out the following two lines before quitting:
nsubjects = 45 ERROR: cannot find /media/freesurfer/.long.
Any idea what I'm missing?
Thanks for your help and patience,
Chris
On Mon, Jun 3, 2013 at 5:08 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu mailto:mreuter@nmr.mgh.harvard.edu> wrote:
Hi Chris, this is a good question for the list (cc'ed), others may or will have the same problem. The problem is with your table file, specifically the new line character. DOS uses \r\n , Mac \r and Linux \n. Your text file uses \r, so it probably was created on a mac. The problem is that the "cat" command (at least in linux) does not work on your file: cat long.qdec.table.dat is empty You can convert the \r to \n (linux format): tr '\r' '\n' < long.qdec.table.dat > long2.qdec.table.dat and then should be able to run the preproc command. People with DOS formats should not run the above "tr' command as they will end up with 2 newlines instead of 1. Maybe DOS txt files work with 'cat' directly (so there is no need)? If anyone on the list knows a good way of cat and awk a file independently of the new line (and working on all OS), let me know. This is the command I use: cat $fsgdf | awk '{if ($1 != "fsid" && substr($1,0,1) != "#") printf("%s.long.%s\n", $1, $2)}' to generate the subjects id's from the table's first two columns. Best, Martin On 06/03/2013 03:45 PM, Christopher McCarthy wrote: Dr. Reuter, We corresponded in the past about QDEC, and you gave me great help. The lab I work for is now moving towards using the Longitudinal Mixed Effects Model. When I go to run the command: mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target study_average --hemi lh --meas thickness --out lh.thickness.mgh I get the error: 'ERROR: no subjects specified.' I am attaching my long.qdec.table.dat, which works fine when loaded by QDEC. Do you have any idea of why I am getting this error? Thanks, Chris McCarthy -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 <tel:%2B1-617-724-5652> Email: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> reuter@mit.edu <mailto:reuter@mit.edu> Web : http://reuter.mit.edu 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 Chris,
still the same (kind of) problem. For some reason you are getting an empty line in the qdec table so it expands the name to ".long." . Open your long.qdec.table.dat in an editor (e.g. nedit or gedit), maybe try to copy it into a new editor window, safe it and hope the editor fixes the problem. Also try cat ./qdec/long.qdec.table.dat to see what it prints, there should be no empty lines.
You can also use hexdump -cb ./qdec/long.qdec.table.dat to take a look at the files content, there should be single \n at the end of each line.
Best, Martin
On 06/04/2013 01:41 PM, Christopher McCarthy wrote:
Dr. Reuter,
Thanks for your help, it got me through the error I was having. On to the next one:
When I enter the command:
mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target fsaverage --hemi lh --meas thickness --out lh.thickness.mgh
it spits out the following two lines before quitting:
nsubjects = 45 ERROR: cannot find /media/freesurfer/.long.
Any idea what I'm missing?
Thanks for your help and patience,
Chris
On Mon, Jun 3, 2013 at 5:08 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu mailto:mreuter@nmr.mgh.harvard.edu> wrote:
Hi Chris, this is a good question for the list (cc'ed), others may or will have the same problem. The problem is with your table file, specifically the new line character. DOS uses \r\n , Mac \r and Linux \n. Your text file uses \r, so it probably was created on a mac. The problem is that the "cat" command (at least in linux) does not work on your file: cat long.qdec.table.dat is empty You can convert the \r to \n (linux format): tr '\r' '\n' < long.qdec.table.dat > long2.qdec.table.dat and then should be able to run the preproc command. People with DOS formats should not run the above "tr' command as they will end up with 2 newlines instead of 1. Maybe DOS txt files work with 'cat' directly (so there is no need)? If anyone on the list knows a good way of cat and awk a file independently of the new line (and working on all OS), let me know. This is the command I use: cat $fsgdf | awk '{if ($1 != "fsid" && substr($1,0,1) != "#") printf("%s.long.%s\n", $1, $2)}' to generate the subjects id's from the table's first two columns. Best, Martin On 06/03/2013 03:45 PM, Christopher McCarthy wrote: Dr. Reuter, We corresponded in the past about QDEC, and you gave me great help. The lab I work for is now moving towards using the Longitudinal Mixed Effects Model. When I go to run the command: mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target study_average --hemi lh --meas thickness --out lh.thickness.mgh I get the error: 'ERROR: no subjects specified.' I am attaching my long.qdec.table.dat, which works fine when loaded by QDEC. Do you have any idea of why I am getting this error? Thanks, Chris McCarthy -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 <tel:%2B1-617-724-5652> Email: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> reuter@mit.edu <mailto:reuter@mit.edu> Web : http://reuter.mit.edu 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.
Hi
I updated mris_preproc (for both the --qdec and --qdec-long flags) and now it can also read \r (old mac) files. It can also deal with empty lines in the files. This will be in the next release, if anyone else gets stuck, request an updated version of mris_preproc from us.
thanks, Martin
On 06/04/2013 03:05 PM, Martin Reuter wrote:
Hi Chris,
still the same (kind of) problem. For some reason you are getting an empty line in the qdec table so it expands the name to ".long." . Open your long.qdec.table.dat in an editor (e.g. nedit or gedit), maybe try to copy it into a new editor window, safe it and hope the editor fixes the problem. Also try cat ./qdec/long.qdec.table.dat to see what it prints, there should be no empty lines.
You can also use hexdump -cb ./qdec/long.qdec.table.dat to take a look at the files content, there should be single \n at the end of each line.
Best, Martin
On 06/04/2013 01:41 PM, Christopher McCarthy wrote:
Dr. Reuter,
Thanks for your help, it got me through the error I was having. On to the next one:
When I enter the command:
mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target fsaverage --hemi lh --meas thickness --out lh.thickness.mgh
it spits out the following two lines before quitting:
nsubjects = 45 ERROR: cannot find /media/freesurfer/.long.
Any idea what I'm missing?
Thanks for your help and patience,
Chris
On Mon, Jun 3, 2013 at 5:08 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu mailto:mreuter@nmr.mgh.harvard.edu> wrote:
Hi Chris, this is a good question for the list (cc'ed), others may or will have the same problem. The problem is with your table file, specifically the new line character. DOS uses \r\n , Mac \r and Linux \n. Your text file uses \r, so it probably was created on a mac. The problem is that the "cat" command (at least in linux) does not work on your file: cat long.qdec.table.dat is empty You can convert the \r to \n (linux format): tr '\r' '\n' < long.qdec.table.dat > long2.qdec.table.dat and then should be able to run the preproc command. People with DOS formats should not run the above "tr' command as they will end up with 2 newlines instead of 1. Maybe DOS txt files work with 'cat' directly (so there is no need)? If anyone on the list knows a good way of cat and awk a file independently of the new line (and working on all OS), let me know. This is the command I use: cat $fsgdf | awk '{if ($1 != "fsid" && substr($1,0,1) != "#") printf("%s.long.%s\n", $1, $2)}' to generate the subjects id's from the table's first two columns. Best, Martin On 06/03/2013 03:45 PM, Christopher McCarthy wrote: Dr. Reuter, We corresponded in the past about QDEC, and you gave me great help. The lab I work for is now moving towards using the Longitudinal Mixed Effects Model. When I go to run the command: mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target study_average --hemi lh --meas thickness --out lh.thickness.mgh I get the error: 'ERROR: no subjects specified.' I am attaching my long.qdec.table.dat, which works fine when loaded by QDEC. Do you have any idea of why I am getting this error? Thanks, Chris McCarthy -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 <tel:%2B1-617-724-5652> Email: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> reuter@mit.edu <mailto:reuter@mit.edu> Web : http://reuter.mit.edu 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.-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web :http://reuter.mit.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Christopher McCarthy -
Douglas N Greve -
Martin Reuter