Dear Freesurfer team,
I am trying to perform qdec longitudinal analysis.
I have ran produced the template and long files, as well as the longitudinal table.
I am currently trying to perform the long_mis_slopes command however I keep getting:
ERROR: qdec table /qdec/long.qdec.respsex.table.dat not found or empty?
I am using
Freesurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0
Platform: OS X El Capitan
The table does exist, however, I keep getting the same error. The table has the columns that are specified as being necessary (fsid, fsid-base, and an age column - "days" in my case). Currently it also has a response and sex column. I have changed the age column to "years", changed the location in/out of my subjects folder into a 'qdec' folder within /subjects. I removed the fsid column and received an error output of
ERROR: qdec table missing correct column headers?
Make sure first column is labeled 'fsid' for the time point and
second column is 'fsid-base' to specify the subject tempate (base), e.g.:
fsid fsid-base age
me1 me 22.3
me2 me 23.2
you1 you 21.6
you2 you 22.5
suggesting that it can see the .dat table. Additionally, from the terminal I can open the table in microsoft excel, pico etc. However, it fails when it tries to parse the table.
I have attached a log of the varying attempts I have made to use the long_mris_slopes command. I have also attached what is essentially the .dat table I have been trying to use for your viewing as well. I've searched the list and can't seem to find discussion of this error with regards to the long_mis_slopes command. Am I missing something? Does anyone have any thoughts on how to trouble shoot this?
Thank you.
Quinn
Quinn,
Could be that the table has any strange character in it (e.g. strange white space etc. )
Try to create a table in a simple text editor by typing the header line and the first 1 or two rows (space separated). If it can read that, then it is probably the format of your table.
Best, Martin
On Oct 21, 2016, at 9:24 PM, Quinn McLellan quinn.mclellan@ucalgary.ca wrote:
Dear Freesurfer team,
I am trying to perform qdec longitudinal analysis. I have ran produced the template and long files, as well as the longitudinal table.
I am currently trying to perform the long_mis_slopes command however I keep getting: ERROR: qdec table /qdec/long.qdec.respsex.table.dat not found or empty?
I am using Freesurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0 Platform: OS X El Capitan
The table does exist, however, I keep getting the same error. The table has the columns that are specified as being necessary (fsid, fsid-base, and an age column - "days" in my case). Currently it also has a response and sex column. I have changed the age column to "years", changed the location in/out of my subjects folder into a 'qdec' folder within /subjects. I removed the fsid column and received an error output of ERROR: qdec table missing correct column headers? Make sure first column is labeled 'fsid' for the time point and second column is 'fsid-base' to specify the subject tempate (base), e.g.:
fsid fsid-base age me1 me 22.3 me2 me 23.2 you1 you 21.6 you2 you 22.5
suggesting that it can see the .dat table. Additionally, from the terminal I can open the table in microsoft excel, pico etc. However, it fails when it tries to parse the table.
I have attached a log of the varying attempts I have made to use the long_mris_slopes command. I have also attached what is essentially the .dat table I have been trying to use for your viewing as well. I've searched the list and can't seem to find discussion of this error with regards to the long_mis_slopes command. Am I missing something? Does anyone have any thoughts on how to trouble shoot this?
Thank you.
Quinn <long.qdec.respsex.table.dat><qdec.long.log.txt>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hey Martin,
Thank you for the reply.
Yes, I ended up recreating the table solely within a text editor and it worked so it was some sort of formatting issue.
Thank you for your time.
Quinn
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Martin Reuter mreuter@nmr.mgh.harvard.edu Sent: October 29, 2016 3:38:34 PM To: Freesurfer support list Subject: Re: [Freesurfer] Bug Reporting: mris_long_slopes qdec table not found
Quinn,
Could be that the table has any strange character in it (e.g. strange white space etc. )
Try to create a table in a simple text editor by typing the header line and the first 1 or two rows (space separated). If it can read that, then it is probably the format of your table.
Best, Martin
On Oct 21, 2016, at 9:24 PM, Quinn McLellan <quinn.mclellan@ucalgary.camailto:quinn.mclellan@ucalgary.ca> wrote:
Dear Freesurfer team,
I am trying to perform qdec longitudinal analysis. I have ran produced the template and long files, as well as the longitudinal table.
I am currently trying to perform the long_mis_slopes command however I keep getting: ERROR: qdec table /qdec/long.qdec.respsex.table.dat not found or empty?
I am using Freesurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0 Platform: OS X El Capitan
The table does exist, however, I keep getting the same error. The table has the columns that are specified as being necessary (fsid, fsid-base, and an age column - "days" in my case). Currently it also has a response and sex column. I have changed the age column to "years", changed the location in/out of my subjects folder into a 'qdec' folder within /subjects. I removed the fsid column and received an error output of ERROR: qdec table missing correct column headers? Make sure first column is labeled 'fsid' for the time point and second column is 'fsid-base' to specify the subject tempate (base), e.g.:
fsid fsid-base age me1 me 22.3 me2 me 23.2 you1 you 21.6 you2 you 22.5
suggesting that it can see the .dat table. Additionally, from the terminal I can open the table in microsoft excel, pico etc. However, it fails when it tries to parse the table.
I have attached a log of the varying attempts I have made to use the long_mris_slopes command. I have also attached what is essentially the .dat table I have been trying to use for your viewing as well. I've searched the list and can't seem to find discussion of this error with regards to the long_mis_slopes command. Am I missing something? Does anyone have any thoughts on how to trouble shoot this?
Thank you.
Quinn <long.qdec.respsex.table.dat><qdec.long.log.txt>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Martin Reuter -
Quinn McLellan