Not totally sure with 5.0, but I don't think it requires same voxel space for all time points (since 5.1), so it should work to run the analysis with 5.3 on that data. Cheers Martin
Peter Bohn bohn-peter@gmx.de wrote:
Thanks a lot! Do I have to repeat creating the base and the longitudinal runs once I use the new version or are they compatible concerning this aspect?
Thank you very much!
Best regards
Peter
From: mreuter@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 02:46:05 -0700 To: bohn-peter@gmx.de; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Yes, those scripts are available since 5.2. You need to update to a newer version.
Best Martin
Peter Bohn bohn-peter@gmx.de wrote:
Hi Martin,
thanks a lot fort he quick reply! When I type freesurfer into the window it shows me v5.0.0 as the version. Sorry for my prior mistake concerning the version’s name. All other commands I use run perfectly fine.
Thanks once again!
Best regards
Peter
From: mreuter@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 05:21:39 -0400 To: bohn-peter@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Hi Peter, can you run any free surfer command at all? Looks to me that you did not source free surfer. What happens if you typefreesurferinto the terminal window? It should print the version. Best, Martin On Jun 20, 2013, at 5:17 AM, Peter Bohn bohn-peter@gmx.de wrote:
Dear Freesurfer experts,
I was trying to run some longitudinal analysis but whenever I want to use the commands “long_mris_slopes” or “long_qdec_table” I just get “command not found” as an answer. When I try to look up a package that might include the command, by typing “cnf long_mris_slopes”, I also just get “command not found” as an answer. We are currently using version v 1.313.2.6.
Does anyone of you know if the two commands that I would like to run, are included in this version? Where would I have to look for the additional package if it exists? Or am I by any chance just typing the commands incorrect?
Many thanks for the help!
Sincerely yours
Peter_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
---------------------------------Dr. Martin ReuterAssistant 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.eduWeb : http://reuter.mit.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
--
Sent from my phone, please excuse brevity. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Dear Freesurfer experts,
thanks to your help I was able to install the new version and run the „long_mris_slopes“ command. In the next step I shrank the longitudinal QDEC table into the cross sectional form by using “long_qdec_table” which also worked so far. Loading that table into QDEC and generating stats data table is no problem but afterwards, when I try to analyze the data in the “Design” section, I received an error message. It always says “couldn’t open…/1CAGB/surf/lh.thikness.fwhm10/fsaverage.mgz or .mgh file”.
As an additional explanation for this example:
1CAGB is the base for the first time point CA and the second time point GB. Files with the wanted name exist in the surf directories of the two time points but not in the surf directory of the base. The closest thing in the base surf directory is called “lh.long.thikness.avg.fwhm10.mgh”.
Could it be that there is a mistake in the “cross.qdec.table.dat”? Just like in the manual for creating the “long.qdec.table.dat”, I listed all the single time points under fsid and the base under fsid-base.and created the cross table afterwards. But when I open the “cross.qdec.table.dat”, the base names (1CAGB etc. in this example) are listed under “fsid”.
Did I do something wrong during the creation of the long.qdec.table.dat or the cross.qdec.table.dat? Do you have any other explanation otherwise?
Thank you very much for your help!
Best regards
Peter Bohn
From: mreuter@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 06:57:16 -0700 To: bohn-peter@gmx.de; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Not totally sure with 5.0, but I don't think it requires same voxel space for all time points (since 5.1), so it should work to run the analysis with 5.3 on that data.
Cheers Martin
Peter Bohn bohn-peter@gmx.de wrote:
Thanks a lot! Do I have to repeat creating the base and the longitudinal runs once I use the new version or are they compatible concerning this aspect?
Thank you very much!
Best regards
Peter
From: mreuter@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 02:46:05 -0700 To: bohn-peter@gmx.de; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Yes, those scripts are available since 5.2. You need to update to a newer version.
Best Martin
Peter Bohn bohn-peter@gmx.de wrote:
Hi Martin,
thanks a lot fort he quick reply! When I type freesurfer into the window it shows me v5.0.0 as the version. Sorry for my prior mistake concerning the version’s name. All other commands I use run perfectly fine.
Thanks once again!
Best regards
Peter
From: mreuter@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 05:21:39 -0400 To: bohn-peter@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Hi Peter, can you run any free surfer command at all? Looks to me that you did not source free surfer. What happens if you typefreesurferinto the terminal window? It should print the version. Best, Martin On Jun 20, 2013, at 5:17 AM, Peter Bohn bohn-peter@gmx.de wrote:
Dear Freesurfer experts,
I was trying to run some longitudinal analysis but whenever I want to use the commands “long_mris_slopes” or “long_qdec_table” I just get “command not found” as an answer. When I try to look up a package that might include the command, by typing “cnf long_mris_slopes”, I also just get “command not found” as an answer. We are currently using version v 1.313.2.6.
Does anyone of you know if the two commands that I would like to run, are included in this version? Where would I have to look for the additional package if it exists? Or am I by any chance just typing the commands incorrect?
Many thanks for the help!
Sincerely yours
Peter_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
---------------------------------Dr. Martin ReuterAssistant 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.eduWeb : http://reuter.mit.edu
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Dear Freesurfer experts,
Or could it be that I made a mistake creating the “Qdecrc” file?
I simply created a text file in the qdec directory and named it “$SUBJECTS_DIR/qdec/.Qdecrc” and put the four lines in it as advised. Should it just be named “.Qdecr” or is there supposed to be an empty line somewhere in the file?
Thanks a lot!
Best regards
Peter
From: bohn-peter@gmx.de To: mreuter@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Date: Mon, 1 Jul 2013 15:32:04 +0200 Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Dear Freesurfer experts,
thanks to your help I was able to install the new version and run the „long_mris_slopes“ command. In the next step I shrank the longitudinal QDEC table into the cross sectional form by using “long_qdec_table” which also worked so far. Loading that table into QDEC and generating stats data table is no problem but afterwards, when I try to analyze the data in the “Design” section, I received an error message. It always says “couldn’t open…/1CAGB/surf/lh.thikness.fwhm10/fsaverage.mgz or .mgh file”.
As an additional explanation for this example:
1CAGB is the base for the first time point CA and the second time point GB. Files with the wanted name exist in the surf directories of the two time points but not in the surf directory of the base. The closest thing in the base surf directory is called “lh.long.thikness.avg.fwhm10.mgh”.
Could it be that there is a mistake in the “cross.qdec.table.dat”? Just like in the manual for creating the “long.qdec.table.dat”, I listed all the single time points under fsid and the base under fsid-base.and created the cross table afterwards. But when I open the “cross.qdec.table.dat”, the base names (1CAGB etc. in this example) are listed under “fsid”.
Did I do something wrong during the creation of the long.qdec.table.dat or the cross.qdec.table.dat? Do you have any other explanation otherwise?
Thank you very much for your help!
Best regards
Peter Bohn
From: mreuter@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 06:57:16 -0700 To: bohn-peter@gmx.de; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Not totally sure with 5.0, but I don't think it requires same voxel space for all time points (since 5.1), so it should work to run the analysis with 5.3 on that data.
Cheers Martin
Peter Bohn bohn-peter@gmx.de wrote:
Thanks a lot! Do I have to repeat creating the base and the longitudinal runs once I use the new version or are they compatible concerning this aspect?
Thank you very much!
Best regards
Peter
From: mreuter@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 02:46:05 -0700 To: bohn-peter@gmx.de; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Yes, those scripts are available since 5.2. You need to update to a newer version.
Best Martin
Peter Bohn bohn-peter@gmx.de wrote:
Hi Martin,
thanks a lot fort he quick reply! When I type freesurfer into the window it shows me v5.0.0 as the version. Sorry for my prior mistake concerning the version’s name. All other commands I use run perfectly fine.
Thanks once again!
Best regards
Peter
From: mreuter@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 05:21:39 -0400 To: bohn-peter@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Hi Peter, can you run any free surfer command at all? Looks to me that you did not source free surfer. What happens if you typefreesurferinto the terminal window? It should print the version. Best, Martin On Jun 20, 2013, at 5:17 AM, Peter Bohn bohn-peter@gmx.de wrote:
Dear Freesurfer experts,
I was trying to run some longitudinal analysis but whenever I want to use the commands “long_mris_slopes” or “long_qdec_table” I just get “command not found” as an answer. When I try to look up a package that might include the command, by typing “cnf long_mris_slopes”, I also just get “command not found” as an answer. We are currently using version v 1.313.2.6.
Does anyone of you know if the two commands that I would like to run, are included in this version? Where would I have to look for the additional package if it exists? Or am I by any chance just typing the commands incorrect?
Many thanks for the help!
Sincerely yours
Peter_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
---------------------------------Dr. Martin ReuterAssistant 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.eduWeb : http://reuter.mit.edu
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Peter,
it needs to be .Qdecrc and have these lines:
MEASURE1 = long.thickness-avg MEASURE2 = long.thickness-rate MEASURE3 = long.thickness-pc1 MEASURE4 = long.thickness-spc
You will then see in the /Design/ tab in Qdec, that you can now select e.g. long.thickness-rate under /Measure/ as the dependent variable.
You wrote below that you get this error: "couldn’t open…/1CAGB/surf/lh.thikness.fwhm10/fsaverage.mgz or .mgh file" note that thickness is spelled with 'ck'. Check your .Qdecrc if there's a typo.
Best, Martin
On 07/01/2013 09:45 AM, Peter Bohn wrote:
Dear Freesurfer experts,
Or could it be that I made a mistake creating the “Qdecrc” file? I simply created a text file in the qdec directory and named it “$SUBJECTS_DIR/qdec/.Qdecrc” and put the four lines in it as advised. Should it just be named “.Qdecr” or is there supposed to be an empty line somewhere in the file?
Thanks a lot!
Best regards
Peter
From: bohn-peter@gmx.de To: mreuter@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Date: Mon, 1 Jul 2013 15:32:04 +0200 Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Dear Freesurfer experts,
thanks to your help I was able to install the new version and run the „long_mris_slopes“ command. In the next step I shrank the longitudinal QDEC table into the cross sectional form by using “long_qdec_table” which also worked so far. Loading that table into QDEC and generating stats data table is no problem but afterwards, when I try to analyze the data in the “Design” section, I received an error message. It always says “couldn’t open…/1CAGB/surf/lh.thikness.fwhm10/fsaverage.mgz or .mgh file”.
As an additional explanation for this example:
1CAGB is the base for the first time point CA and the second time point GB. Files with the wanted name exist in the surf directories of the two time points but not in the surf directory of the base. The closest thing in the base surf directory is called “lh.long.thikness.avg.fwhm10.mgh”.
Could it be that there is a mistake in the “cross.qdec.table.dat”? Just like in the manual for creating the “long.qdec.table.dat”, I listed all the single time points under fsid and the base under fsid-base.and created the cross table afterwards. But when I open the “cross.qdec.table.dat”, the base names (1CAGB etc. in this example) are listed under “fsid”.
Did I do something wrong during the creation of the long.qdec.table.dat or the cross.qdec.table.dat? Do you have any other explanation otherwise?
Thank you very much for your help!
Best regards
Peter Bohn
From: mreuter@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 06:57:16 -0700 To: bohn-peter@gmx.de; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Not totally sure with 5.0, but I don't think it requires same voxel space for all time points (since 5.1), so it should work to run the analysis with 5.3 on that data. Cheers Martin
Peter Bohn bohn-peter@gmx.de wrote:
Thanks a lot! Do I have to repeat creating the base and the longitudinal runs once I use the new version or are they compatible concerning this aspect? Thank you very much! Best regards Peter ------------------------------------------------------------------------ From: mreuter@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 02:46:05 -0700 To: bohn-peter@gmx.de; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Yes, those scripts are available since 5.2. You need to update to a newer version. Best Martin Peter Bohn <bohn-peter@gmx.de> wrote: Hi Martin, thanks a lot fort he quick reply! When I type freesurfer into the window it shows me v5.0.0 as the version. Sorry for my prior mistake concerning the version’s name. All other commands I use run perfectly fine. Thanks once again! Best regards Peter ------------------------------------------------------------------------ From: mreuter@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 05:21:39 -0400 To: bohn-peter@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Hi Peter, can you run any free surfer command at all? Looks to me that you did not source free surfer. What happens if you type freesurfer into the terminal window? It should print the version. Best, Martin On Jun 20, 2013, at 5:17 AM, Peter Bohn <bohn-peter@gmx.de <mailto:bohn-peter@gmx.de>> wrote: Dear Freesurfer experts, I was trying to run some longitudinal analysis but whenever I want to use the commands “long_mris_slopes” or “long_qdec_table” I just get “command not found” as an answer. When I try to look up a package that might include the command, by typing “cnf long_mris_slopes”, I also just get “command not found” as an answer. We are currently using version v 1.313.2.6. Does anyone of you know if the two commands that I would like to run, are included in this version? Where would I have to look for the additional package if it exists? Or am I by any chance just typing the commands incorrect? Many thanks for the help! Sincerely yours Peter _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --------------------------------- Dr. Martin Reuter 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 <mailto:mreuter@nmr.mgh.harvard.edu> reuter@mit.edu <mailto:reuter@mit.edu> Web : http://reuter.mit.edu <http://reuter.mit.edu/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.-- Sent from my phone, please excuse brevity. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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.
Dear Martin,
”thickness” was a typo. Can you maybe check my attached file? I suppose that I put the four lines in it correctly. I only named it “.Qdecrc”. When I save the file in the qdec folder of my Subject directory, the file isn´t visible anymore. Is it supposed to be like that? It is there but not visible. Furthermore I can´t chose e.g. long.thickness-rate in the Design Tab.
Thank you very much and I am sorry for bothering you so much.
Best regards
Peter
Date: Mon, 1 Jul 2013 11:33:39 -0400 From: mreuter@nmr.mgh.harvard.edu To: bohn-peter@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/cross.qdec.table.dat
Hi Peter,
it needs to be .Qdecrc and have these lines:
MEASURE1 = long.thickness-avg MEASURE2 = long.thickness-rate MEASURE3 = long.thickness-pc1 MEASURE4 = long.thickness-spc You will then see in the Design tab in Qdec, that you can now select e.g. long.thickness-rate under Measure as the dependent variable.
You wrote below that you get this error:
"couldn’t open…/1CAGB/surf/lh.thikness.fwhm10/fsaverage.mgz or .mgh file"
note that thickness is spelled with 'ck'. Check your .Qdecrc if there's a typo.
Best, Martin
On 07/01/2013 09:45 AM, Peter Bohn wrote:
Dear Freesurfer experts,
Or could it be that I made a mistake creating the “Qdecrc” file?
I simply created a text file in the qdec directory and named it “$SUBJECTS_DIR/qdec/.Qdecrc” and put the four lines in it as advised. Should it just be named “.Qdecr” or is there supposed to be an empty line somewhere in the file?
Thanks a lot!
Best regards
Peter
From: bohn-peter@gmx.de
To: mreuter@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
Date: Mon, 1 Jul 2013 15:32:04 +0200
Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Dear Freesurfer experts,
thanks to your help I was able to install the new version and run the „long_mris_slopes“ command. In the next step I shrank the longitudinal QDEC table into the cross sectional form by using “long_qdec_table” which also worked so far. Loading that table into QDEC and generating stats data table is no problem but afterwards, when I try to analyze the data in the “Design” section, I received an error message. It always says “couldn’t open…/1CAGB/surf/lh.thikness.fwhm10/fsaverage.mgz or .mgh file”.
As an additional explanation for this example:
1CAGB is the base for the first time point CA and the second time point GB. Files with the wanted name exist in the surf directories of the two time points but not in the surf directory of the base. The closest thing in the base surf directory is called “lh.long.thikness.avg.fwhm10.mgh”.
Could it be that there is a mistake in the “cross.qdec.table.dat”? Just like in the manual for creating the “long.qdec.table.dat”, I listed all the single time points under fsid and the base under fsid-base.and created the cross table afterwards. But when I open the “cross.qdec.table.dat”, the base names (1CAGB etc. in this example) are listed under “fsid”.
Did I do something wrong during the creation of the long.qdec.table.dat or the cross.qdec.table.dat? Do you have any other explanation otherwise?
Thank you very much for your help!
Best regards
Peter Bohn
From: mreuter@nmr.mgh.harvard.edu
Date: Thu, 20 Jun 2013 06:57:16 -0700
To: bohn-peter@gmx.de; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Not totally sure with 5.0, but I don't think it requires same voxel space for all time points (since 5.1), so it should work to run the analysis with 5.3 on that data.
Cheers Martin
Peter Bohn bohn-peter@gmx.de wrote:
Thanks a lot! Do I have to repeat creating the base and the longitudinal runs once I use the new version or are they compatible concerning this aspect?
Thank you very much!
Best regards
Peter
From: mreuter@nmr.mgh.harvard.edu
Date: Thu, 20 Jun 2013 02:46:05 -0700
To: bohn-peter@gmx.de; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Yes, those scripts are available since 5.2. You need to update to a newer version.
Best Martin
Peter Bohn bohn-peter@gmx.de wrote:
Hi Martin,
thanks a lot fort he quick reply! When I type freesurfer into the window it shows me v5.0.0 as the version. Sorry for my prior mistake concerning the version’s name. All other commands I use run perfectly fine.
Thanks once again!
Best regards
Peter
From: mreuter@nmr.mgh.harvard.edu
Date: Thu, 20 Jun 2013 05:21:39 -0400
To: bohn-peter@gmx.de
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Hi Peter,
can you run any free surfer command at all? Looks to me that you did not source free surfer. What happens if you type freesurfer into the terminal window? It should print the version.
Best, Martin
On Jun 20, 2013, at 5:17 AM, Peter Bohn bohn-peter@gmx.de wrote:
Dear Freesurfer experts,
I was trying to run some longitudinal analysis but whenever I want to use the commands “long_mris_slopes” or “long_qdec_table” I just get “command not found” as an answer. When I try to look up a package that might include the command, by typing “cnf long_mris_slopes”, I also just get “command not found” as an answer. We are currently using version v 1.313.2.6.
Does anyone of you know if the two commands that I would like to run, are included in this version? Where would I have to look for the additional package if it exists? Or am I by any chance just typing the commands incorrect?
Many thanks for the help!
Sincerely yours
Peter
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--------------------------------- Dr. Martin Reuter 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
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.
--
Sent from my phone, please excuse brevity.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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
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 Peter,
file looks good, you could try adding a newline at the end. The file should be hidden (all files starting with a . are hidden). Not sure why you cannot select the rate as the measure. Is your environment variable ($SUBJECTS_DIR) setup correctly?
Best, Martin
On 07/01/2013 12:00 PM, Peter Bohn wrote:
Dear Martin,
”thickness” was a typo. Can you maybe check my attached file? I suppose that I put the four lines in it correctly. I only named it “.Qdecrc”. When I save the file in the qdec folder of my Subject directory, the file isn´t visible anymore. Is it supposed to be like that? It is there but not visible. Furthermore I can´t chose e.g. long.thickness-rate in the Design Tab.
Thank you very much and I am sorry for bothering you so much.
Best regards
Peter
Date: Mon, 1 Jul 2013 11:33:39 -0400 From: mreuter@nmr.mgh.harvard.edu To: bohn-peter@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/cross.qdec.table.dat
Hi Peter,
it needs to be .Qdecrc and have these lines: MEASURE1 = long.thickness-avg MEASURE2 = long.thickness-rate MEASURE3 = long.thickness-pc1 MEASURE4 = long.thickness-spc You will then see in the /Design/ tab in Qdec, that you can now select e.g. long.thickness-rate under /Measure/ as the dependent variable.
You wrote below that you get this error: "couldn’t open…/1CAGB/surf/lh.thikness.fwhm10/fsaverage.mgz or .mgh file" note that thickness is spelled with 'ck'. Check your .Qdecrc if there's a typo.
Best, Martin
On 07/01/2013 09:45 AM, Peter Bohn wrote:
Dear Freesurfer experts, Or could it be that I made a mistake creating the “Qdecrc” file? I simply created a text file in the qdec directory and named it “$SUBJECTS_DIR/qdec/.Qdecrc” and put the four lines in it as advised. Should it just be named “.Qdecr” or is there supposed to be an empty line somewhere in the file? Thanks a lot! Best regards Peter ------------------------------------------------------------------------ From: bohn-peter@gmx.de <mailto:bohn-peter@gmx.de> To: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>; freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Date: Mon, 1 Jul 2013 15:32:04 +0200 Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Dear Freesurfer experts, thanks to your help I was able to install the new version and run the „long_mris_slopes“ command. In the next step I shrank the longitudinal QDEC table into the cross sectional form by using “long_qdec_table” which also worked so far. Loading that table into QDEC and generating stats data table is no problem but afterwards, when I try to analyze the data in the “Design” section, I received an error message. It always says “couldn’t open…/1CAGB/surf/lh.thikness.fwhm10/fsaverage.mgz or .mgh file”. As an additional explanation for this example: 1CAGB is the base for the first time point CA and the second time point GB. Files with the wanted name exist in the surf directories of the two time points but not in the surf directory of the base. The closest thing in the base surf directory is called “lh.long.thikness.avg.fwhm10.mgh”. Could it be that there is a mistake in the “cross.qdec.table.dat”? Just like in the manual for creating the “long.qdec.table.dat”, I listed all the single time points under fsid and the base under fsid-base.and created the cross table afterwards. But when I open the “cross.qdec.table.dat”, the base names (1CAGB etc. in this example) are listed under “fsid”. Did I do something wrong during the creation of the long.qdec.table.dat or the cross.qdec.table.dat? Do you have any other explanation otherwise? Thank you very much for your help! Best regards Peter Bohn ------------------------------------------------------------------------ From: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> Date: Thu, 20 Jun 2013 06:57:16 -0700 To: bohn-peter@gmx.de <mailto:bohn-peter@gmx.de>; freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Not totally sure with 5.0, but I don't think it requires same voxel space for all time points (since 5.1), so it should work to run the analysis with 5.3 on that data. Cheers Martin Peter Bohn <bohn-peter@gmx.de> <mailto:bohn-peter@gmx.de> wrote: Thanks a lot! Do I have to repeat creating the base and the longitudinal runs once I use the new version or are they compatible concerning this aspect? Thank you very much! Best regards Peter ------------------------------------------------------------------------ From: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> Date: Thu, 20 Jun 2013 02:46:05 -0700 To: bohn-peter@gmx.de <mailto:bohn-peter@gmx.de>; freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Yes, those scripts are available since 5.2. You need to update to a newer version. Best Martin Peter Bohn <bohn-peter@gmx.de> <mailto:bohn-peter@gmx.de> wrote: Hi Martin, thanks a lot fort he quick reply! When I type freesurfer into the window it shows me v5.0.0 as the version. Sorry for my prior mistake concerning the version’s name. All other commands I use run perfectly fine. Thanks once again! Best regards Peter ------------------------------------------------------------------------ From: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> Date: Thu, 20 Jun 2013 05:21:39 -0400 To: bohn-peter@gmx.de <mailto:bohn-peter@gmx.de> CC: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Hi Peter, can you run any free surfer command at all? Looks to me that you did not source free surfer. What happens if you type freesurfer into the terminal window? It should print the version. Best, Martin On Jun 20, 2013, at 5:17 AM, Peter Bohn <bohn-peter@gmx.de <mailto:bohn-peter@gmx.de>> wrote: Dear Freesurfer experts, I was trying to run some longitudinal analysis but whenever I want to use the commands “long_mris_slopes” or “long_qdec_table” I just get “command not found” as an answer. When I try to look up a package that might include the command, by typing “cnf long_mris_slopes”, I also just get “command not found” as an answer. We are currently using version v 1.313.2.6. Does anyone of you know if the two commands that I would like to run, are included in this version? Where would I have to look for the additional package if it exists? Or am I by any chance just typing the commands incorrect? Many thanks for the help! Sincerely yours Peter _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --------------------------------- Dr. Martin Reuter 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 <mailto:mreuter@nmr.mgh.harvard.edu> reuter@mit.edu <mailto:reuter@mit.edu> Web : http://reuter.mit.edu <http://reuter.mit.edu/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. -- Sent from my phone, please excuse brevity. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 mailto:mreuter@nmr.mgh.harvard.edu reuter@mit.edu mailto: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 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.
Dear Martin,
I tried adding another line in the file which didn´t change anything. My subject directory is called “QDEC_Final” and in that directory I created the “qdec” folder which includes the tables and also the”.Qdecrc” file. The file is definitely there and can be listed by using “ls -a”.
So I suppose there shouldn´t be any mistakes so far. I created the .Qdecrc file by opening a new text file, writing down the four lines and saving it under the name “.Qdecrc” afterwards. While saving it I used the default UTF-8 encoding in Kwrite.
Still there seems to be the Problem that qdec can´t find the .Qdecrc file.
Do you still have any other idea as for what to try? Would renaming the files in the base directory be an solution or would that lead to many other problems?
Thanks a lot!
Best regards
Peter
Date: Mon, 1 Jul 2013 14:04:24 -0400 From: mreuter@nmr.mgh.harvard.edu To: bohn-peter@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/cross.qdec.table.dat
Hi Peter,
file looks good, you could try adding a newline at the end. The file should be hidden (all files starting with a . are hidden). Not sure why you cannot select the rate as the measure. Is your environment variable ($SUBJECTS_DIR) setup correctly?
Best, Martin
On 07/01/2013 12:00 PM, Peter Bohn wrote:
Dear Martin,
”thickness” was a typo. Can you maybe check my attached file? I suppose that I put the four lines in it correctly. I only named it “.Qdecrc”. When I save the file in the qdec folder of my Subject directory, the file isn´t visible anymore. Is it supposed to be like that? It is there but not visible. Furthermore I can´t chose e.g. long.thickness-rate in the Design Tab.
Thank you very much and I am sorry for bothering you so much.
Best regards
Peter
Date: Mon, 1 Jul 2013 11:33:39 -0400
From: mreuter@nmr.mgh.harvard.edu
To: bohn-peter@gmx.de
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] long_mris_slopes/cross.qdec.table.dat
Hi Peter,
it needs to be .Qdecrc and have these lines:
MEASURE1 = long.thickness-avg MEASURE2 = long.thickness-rate MEASURE3 = long.thickness-pc1 MEASURE4 = long.thickness-spc You will then see in the Design tab in Qdec, that you can now select e.g. long.thickness-rate under Measure as the dependent variable.
You wrote below that you get this error:
"couldn’t open…/1CAGB/surf/lh.thikness.fwhm10/fsaverage.mgz or .mgh file"
note that thickness is spelled with 'ck'. Check your .Qdecrc if there's a typo.
Best, Martin
On 07/01/2013 09:45 AM, Peter Bohn wrote:
Dear Freesurfer experts,
Or could it be that I made a mistake creating the “Qdecrc” file?
I simply created a text file in the qdec directory and named it “$SUBJECTS_DIR/qdec/.Qdecrc” and put the four lines in it as advised. Should it just be named “.Qdecr” or is there supposed to be an empty line somewhere in the file?
Thanks a lot!
Best regards
Peter
From: bohn-peter@gmx.de
To: mreuter@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
Date: Mon, 1 Jul 2013 15:32:04 +0200
Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Dear
Freesurfer experts,
thanks to your help I was able to install the new version and run the „long_mris_slopes“ command. In the next step I shrank the longitudinal QDEC table into the cross sectional form by using “long_qdec_table” which also worked so far. Loading that table into QDEC and generating stats data table is no problem but afterwards, when I try to analyze the data in the “Design” section, I received an error message. It always says “couldn’t open…/1CAGB/surf/lh.thikness.fwhm10/fsaverage.mgz or .mgh file”.
As an additional explanation for this example:
1CAGB is the base for the first time point CA and the second time point GB. Files with the wanted name exist in the surf directories of the two time points but not in the surf directory of the base. The closest thing in the base surf directory is called “lh.long.thikness.avg.fwhm10.mgh”.
Could it be that there is a mistake in the “cross.qdec.table.dat”? Just like in the manual for creating the “long.qdec.table.dat”, I listed all the single time points under fsid and the base under fsid-base.and created the cross table afterwards. But when I open the “cross.qdec.table.dat”, the base names (1CAGB etc. in this example) are listed under “fsid”.
Did I do something wrong during the creation of the long.qdec.table.dat or the cross.qdec.table.dat? Do you have any other explanation otherwise?
Thank you very much for your help!
Best regards
Peter Bohn
From: mreuter@nmr.mgh.harvard.edu
Date: Thu, 20 Jun 2013 06:57:16 -0700
To: bohn-peter@gmx.de; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Not totally sure with 5.0, but I don't think it requires same voxel space for all time points (since 5.1), so it should work to run the analysis with 5.3 on that data.
Cheers Martin
Peter Bohn bohn-peter@gmx.de wrote:
Thanks a lot! Do I have to repeat creating the base and the longitudinal runs once I use the new version or are they compatible concerning this aspect?
Thank you very much!
Best regards
Peter
From: mreuter@nmr.mgh.harvard.edu
Date: Thu, 20 Jun 2013 02:46:05 -0700
To: bohn-peter@gmx.de; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Yes, those scripts are available since 5.2. You need to update to a newer version.
Best Martin
Peter Bohn bohn-peter@gmx.de wrote:
Hi Martin,
thanks a lot fort he quick reply! When I type freesurfer into the window it shows me v5.0.0 as the version. Sorry for my prior mistake concerning the version’s name. All other commands I use run perfectly fine.
Thanks once again!
Best regards
Peter
From: mreuter@nmr.mgh.harvard.edu
Date: Thu, 20 Jun 2013 05:21:39 -0400
To: bohn-peter@gmx.de
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Hi Peter,
can you run any free surfer command at all? Looks to me that you did not source free surfer. What happens if you type freesurfer into the terminal window? It should print the version.
Best, Martin
On Jun 20, 2013, at 5:17 AM, Peter Bohn bohn-peter@gmx.de
wrote:
Dear Freesurfer experts,
I was trying to run some longitudinal analysis but whenever I want to use the commands “long_mris_slopes” or “long_qdec_table” I just get “command not found” as an answer. When I try to look up a package that might include the command, by typing “cnf long_mris_slopes”, I also just get “command not found” as an answer. We are currently using version v 1.313.2.6.
Does anyone of you know if the two commands that I would like to run, are included in this version? Where would I have to look for the additional package if it exists? Or am I by any chance just typing the commands incorrect?
Many thanks for the help!
Sincerely yours
Peter
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--------------------------------- Dr. Martin Reuter 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 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.
--
Sent from my phone, please excuse brevity.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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 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
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.
Is your environment variable ($SUBJECTS_DIR) setup correctly? It needs to point to where the subjects and the qdec directory are.
so you should have a dir structure like this inside your subjects dir (QDEC_Final):
subject1_tp1 subject1_tp2 ... qdec/.Qdecrc that is the same as: $SUBJECTS_DIR/qdec/.Qdecrc if your environment variable is set correctly
On 07/02/2013 12:10 PM, Peter Bohn wrote:
Dear Martin,
I tried adding another line in the file which didn´t change anything. My subject directory is called “QDEC_Final” and in that directory I created the “qdec” folder which includes the tables and also the”.Qdecrc” file. The file is definitely there and can be listed by using “ls -a”. So I suppose there shouldn´t be any mistakes so far. I created the .Qdecrc file by opening a new text file, writing down the four lines and saving it under the name “.Qdecrc” afterwards. While saving it I used the default UTF-8 encoding in Kwrite.
Still there seems to be the Problem that qdec can´t find the .Qdecrc file. Do you still have any other idea as for what to try? Would renaming the files in the base directory be an solution or would that lead to many other problems?
Thanks a lot!
Best regards
Peter
Date: Mon, 1 Jul 2013 14:04:24 -0400 From: mreuter@nmr.mgh.harvard.edu To: bohn-peter@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/cross.qdec.table.dat
Hi Peter,
file looks good, you could try adding a newline at the end. The file should be hidden (all files starting with a . are hidden). Not sure why you cannot select the rate as the measure. Is your environment variable ($SUBJECTS_DIR) setup correctly?
Best, Martin
On 07/01/2013 12:00 PM, Peter Bohn wrote:
Dear Martin, ”thickness” was a typo. Can you maybe check my attached file? I suppose that I put the four lines in it correctly. I only named it “.Qdecrc”. When I save the file in the qdec folder of my Subject directory, the file isn´t visible anymore. Is it supposed to be like that? It is there but not visible. Furthermore I can´t chose e.g. long.thickness-rate in the Design Tab. Thank you very much and I am sorry for bothering you so much. Best regards Peter ------------------------------------------------------------------------ Date: Mon, 1 Jul 2013 11:33:39 -0400 From: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> To: bohn-peter@gmx.de <mailto:bohn-peter@gmx.de> CC: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] long_mris_slopes/cross.qdec.table.dat Hi Peter, it needs to be .Qdecrc and have these lines: MEASURE1 = long.thickness-avg MEASURE2 = long.thickness-rate MEASURE3 = long.thickness-pc1 MEASURE4 = long.thickness-spc You will then see in the /Design/ tab in Qdec, that you can now select e.g. long.thickness-rate under /Measure/ as the dependent variable. You wrote below that you get this error: "couldn’t open…/1CAGB/surf/lh.thikness.fwhm10/fsaverage.mgz or .mgh file" note that thickness is spelled with 'ck'. Check your .Qdecrc if there's a typo. Best, Martin On 07/01/2013 09:45 AM, Peter Bohn wrote: Dear Freesurfer experts, Or could it be that I made a mistake creating the “Qdecrc” file? I simply created a text file in the qdec directory and named it “$SUBJECTS_DIR/qdec/.Qdecrc” and put the four lines in it as advised. Should it just be named “.Qdecr” or is there supposed to be an empty line somewhere in the file? Thanks a lot! Best regards Peter ------------------------------------------------------------------------ From: bohn-peter@gmx.de <mailto:bohn-peter@gmx.de> To: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>; freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Date: Mon, 1 Jul 2013 15:32:04 +0200 Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Dear Freesurfer experts, thanks to your help I was able to install the new version and run the „long_mris_slopes“ command. In the next step I shrank the longitudinal QDEC table into the cross sectional form by using “long_qdec_table” which also worked so far. Loading that table into QDEC and generating stats data table is no problem but afterwards, when I try to analyze the data in the “Design” section, I received an error message. It always says “couldn’t open…/1CAGB/surf/lh.thikness.fwhm10/fsaverage.mgz or .mgh file”. As an additional explanation for this example: 1CAGB is the base for the first time point CA and the second time point GB. Files with the wanted name exist in the surf directories of the two time points but not in the surf directory of the base. The closest thing in the base surf directory is called “lh.long.thikness.avg.fwhm10.mgh”. Could it be that there is a mistake in the “cross.qdec.table.dat”? Just like in the manual for creating the “long.qdec.table.dat”, I listed all the single time points under fsid and the base under fsid-base.and created the cross table afterwards. But when I open the “cross.qdec.table.dat”, the base names (1CAGB etc. in this example) are listed under “fsid”. Did I do something wrong during the creation of the long.qdec.table.dat or the cross.qdec.table.dat? Do you have any other explanation otherwise? Thank you very much for your help! Best regards Peter Bohn ------------------------------------------------------------------------ From: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> Date: Thu, 20 Jun 2013 06:57:16 -0700 To: bohn-peter@gmx.de <mailto:bohn-peter@gmx.de>; freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Not totally sure with 5.0, but I don't think it requires same voxel space for all time points (since 5.1), so it should work to run the analysis with 5.3 on that data. Cheers Martin Peter Bohn <bohn-peter@gmx.de> <mailto:bohn-peter@gmx.de> wrote: Thanks a lot! Do I have to repeat creating the base and the longitudinal runs once I use the new version or are they compatible concerning this aspect? Thank you very much! Best regards Peter ------------------------------------------------------------------------ From: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> Date: Thu, 20 Jun 2013 02:46:05 -0700 To: bohn-peter@gmx.de <mailto:bohn-peter@gmx.de>; freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Yes, those scripts are available since 5.2. You need to update to a newer version. Best Martin Peter Bohn <bohn-peter@gmx.de> <mailto:bohn-peter@gmx.de> wrote: Hi Martin, thanks a lot fort he quick reply! When I type freesurfer into the window it shows me v5.0.0 as the version. Sorry for my prior mistake concerning the version’s name. All other commands I use run perfectly fine. Thanks once again! Best regards Peter ------------------------------------------------------------------------ From: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> Date: Thu, 20 Jun 2013 05:21:39 -0400 To: bohn-peter@gmx.de <mailto:bohn-peter@gmx.de> CC: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Hi Peter, can you run any free surfer command at all? Looks to me that you did not source free surfer. What happens if you type freesurfer into the terminal window? It should print the version. Best, Martin On Jun 20, 2013, at 5:17 AM, Peter Bohn <bohn-peter@gmx.de <mailto:bohn-peter@gmx.de>> wrote: Dear Freesurfer experts, I was trying to run some longitudinal analysis but whenever I want to use the commands “long_mris_slopes” or “long_qdec_table” I just get “command not found” as an answer. When I try to look up a package that might include the command, by typing “cnf long_mris_slopes”, I also just get “command not found” as an answer. We are currently using version v 1.313.2.6. Does anyone of you know if the two commands that I would like to run, are included in this version? Where would I have to look for the additional package if it exists? Or am I by any chance just typing the commands incorrect? Many thanks for the help! Sincerely yours Peter _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --------------------------------- Dr. Martin Reuter 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 <mailto:mreuter@nmr.mgh.harvard.edu> reuter@mit.edu <mailto:reuter@mit.edu> Web : http://reuter.mit.edu <http://reuter.mit.edu/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. -- Sent from my phone, please excuse brevity. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 <mailto:mreuter@nmr.mgh.harvard.edu> reuter@mit.edu <mailto:reuter@mit.edu> Web :http://reuter.mit.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 mailto:mreuter@nmr.mgh.harvard.edu reuter@mit.edu mailto: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 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.
Dear Martin,
yes the subject directory setup is correct. I suppose that otherwise “generate stats data tables” in qdec also wouldn’t work which isn’t the case. The QDEC_Final directory includes two time points for each patient, the patients base, the “long” folders that were created for each patient’s time points and the “qdec” folder. The “.Qdecrc” file is inside of the qdec folder. Should there also be a folder named “Qdecrc” in the qdec folder or really just the “.Qdecrc” file? Or do I have to create a folder named “qdec/.Qdecrc” in my “QDEC_Final” folder?
I suppose I don´t have to type “$SUBJECTS_DIR/qdec/.Qdecrc” in the shell I am working in before starting qdec.
I am awfully sorry for asking so many stupid questions but I ran out of things I could try.
Thanks a lot once again!
Best regards
Peter
Date: Tue, 2 Jul 2013 12:15:09 -0400 From: mreuter@nmr.mgh.harvard.edu To: bohn-peter@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/cross.qdec.table.dat
Is your environment variable ($SUBJECTS_DIR) setup correctly? It needs to point to where the subjects and the qdec directory are.
so you should have a dir structure like this inside your subjects dir (QDEC_Final):
subject1_tp1
subject1_tp2
...
qdec/.Qdecrc
that is the same as:
$SUBJECTS_DIR/qdec/.Qdecrc
if your environment variable is set correctly
On 07/02/2013 12:10 PM, Peter Bohn wrote:
Dear Martin,
I tried adding another line in the file which didn´t change anything. My subject directory is called “QDEC_Final” and in that directory I created the “qdec” folder which includes the tables and also the”.Qdecrc” file. The file is definitely there and can be listed by using “ls -a”.
So I suppose there shouldn´t be any mistakes so far. I created the .Qdecrc file by opening a new text file, writing down the four lines and saving it under the name “.Qdecrc” afterwards. While saving it I used the default UTF-8 encoding in Kwrite.
Still there seems to be the Problem that qdec can´t find the .Qdecrc file.
Do you still have any other idea as for what to try? Would renaming the files in the base directory be an solution or would that lead to many other problems?
Thanks a lot!
Best regards
Peter
Date: Mon, 1 Jul 2013 14:04:24 -0400
From: mreuter@nmr.mgh.harvard.edu
To: bohn-peter@gmx.de
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] long_mris_slopes/cross.qdec.table.dat
Hi Peter,
file looks good, you could try adding a newline at the end. The file should be hidden (all files starting with a . are hidden). Not sure why you cannot select the rate as the measure. Is your environment variable ($SUBJECTS_DIR) setup correctly?
Best, Martin
On 07/01/2013 12:00 PM, Peter Bohn wrote:
Dear Martin,
”thickness” was a typo. Can you maybe check my attached file? I suppose that I put the four lines in it correctly. I only named it “.Qdecrc”. When I save the file in the qdec folder of my Subject directory, the file isn´t visible anymore. Is it supposed to be like that? It is there but not visible. Furthermore I can´t chose e.g. long.thickness-rate in the Design Tab.
Thank you very much and I am sorry for bothering you so much.
Best regards
Peter
Date: Mon, 1 Jul 2013 11:33:39 -0400
From: mreuter@nmr.mgh.harvard.edu
To: bohn-peter@gmx.de
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] long_mris_slopes/cross.qdec.table.dat
Hi Peter,
it needs to be .Qdecrc and have these lines:
MEASURE1 = long.thickness-avg MEASURE2 = long.thickness-rate MEASURE3 = long.thickness-pc1 MEASURE4 = long.thickness-spc You will then see in the Design tab in Qdec, that you can now select e.g. long.thickness-rate under Measure as the dependent variable.
You wrote below that you get this error:
"couldn’t open…/1CAGB/surf/lh.thikness.fwhm10/fsaverage.mgz or .mgh file"
note that thickness is spelled with 'ck'. Check your .Qdecrc if there's a typo.
Best, Martin
On 07/01/2013 09:45 AM, Peter Bohn wrote:
Dear
Freesurfer experts,
Or
could it be that I made a mistake creating the “Qdecrc” file?
I simply created a text file in the qdec directory and named it “$SUBJECTS_DIR/qdec/.Qdecrc” and put the four lines in it as advised. Should it just be named “.Qdecr” or is there supposed to be an empty line somewhere in the file?
Thanks a lot!
Best regards
Peter
From: bohn-peter@gmx.de
To: mreuter@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
Date: Mon, 1 Jul 2013 15:32:04 +0200
Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Dear Freesurfer experts,
thanks to your help I was able to install the new version and run the „long_mris_slopes“ command. In the next step I shrank the longitudinal QDEC table into the cross sectional form by using “long_qdec_table” which also worked so far. Loading that table into QDEC and generating stats data table is no problem but afterwards, when I try to analyze the data in the “Design” section, I received an error message. It always says “couldn’t open…/1CAGB/surf/lh.thikness.fwhm10/fsaverage.mgz or .mgh file”.
As an additional explanation for this example:
1CAGB is the base for the first time point CA and the second time point GB. Files with the wanted name exist in the surf directories of the two time points but not in the surf directory of the base. The closest thing in the base surf directory is called “lh.long.thikness.avg.fwhm10.mgh”.
Could it be that there is a mistake in the “cross.qdec.table.dat”? Just like in the manual for creating the “long.qdec.table.dat”, I listed all the single time points under fsid and the base under fsid-base.and created the cross table afterwards. But when I open the “cross.qdec.table.dat”, the base names (1CAGB etc. in this example) are listed under “fsid”.
Did I do something wrong during the creation of the long.qdec.table.dat or the cross.qdec.table.dat? Do you have any other explanation otherwise?
Thank you very much for your help!
Best regards
Peter Bohn
From: mreuter@nmr.mgh.harvard.edu
Date: Thu, 20 Jun 2013 06:57:16 -0700
To: bohn-peter@gmx.de; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Not totally sure with 5.0, but I don't think it requires same voxel space for all time points (since 5.1), so it should work to run the analysis with 5.3 on that data.
Cheers Martin
Peter Bohn bohn-peter@gmx.de wrote:
Thanks a lot! Do I have to repeat creating the base and the longitudinal runs once I use the new version or are they compatible concerning this aspect?
Thank you very much!
Best regards
Peter
From: mreuter@nmr.mgh.harvard.edu
Date: Thu, 20 Jun 2013 02:46:05 -0700
To: bohn-peter@gmx.de; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Yes, those scripts are available since 5.2. You need to update to a newer version.
Best Martin
Peter Bohn bohn-peter@gmx.de wrote:
Hi Martin,
thanks a lot fort he quick reply! When I type freesurfer into the window it shows me v5.0.0 as the version. Sorry for my prior mistake concerning the version’s name. All other commands I use run perfectly fine.
Thanks once again!
Best regards
Peter
From: mreuter@nmr.mgh.harvard.edu
Date: Thu, 20 Jun 2013 05:21:39 -0400
To: bohn-peter@gmx.de
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Hi Peter,
can you run any free surfer command at all? Looks to me that you did not source free surfer. What happens if you type freesurfer into the terminal window? It should print the version.
Best, Martin
On Jun 20, 2013, at 5:17 AM, Peter Bohn bohn-peter@gmx.de wrote:
Dear Freesurfer experts,
I was trying to run some longitudinal analysis but whenever I want to use the commands “long_mris_slopes” or “long_qdec_table” I just get “command not found” as an answer. When I try to look up a package that might include the command, by typing “cnf long_mris_slopes”, I also just get “command not found” as an answer. We are currently using version v 1.313.2.6.
Does anyone of you know if the two commands that I would like to run, are included in this version? Where would I have to look for the additional package if it exists? Or am I by any chance just typing the commands incorrect?
Many thanks for the help!
Sincerely yours
Peter
_______________________________________________ Freesurfer
mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--------------------------------- Dr. Martin Reuter 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 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.
--
Sent from my phone, please excuse brevity.
_______________________________________________
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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 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 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
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.
OK your structure is correct, there are a few things to test next. Let's take this offline until we know what's going on and then post the result to the list to avoid spamming everyone.
Best, Martin
On 07/02/2013 12:38 PM, Peter Bohn wrote:
Dear Martin,
yes the subject directory setup is correct. I suppose that otherwise “generate stats data tables” in qdec also wouldn’t work which isn’t the case. The QDEC_Final directory includes two time points for each patient, the patients base, the “long” folders that were created for each patient’s time points and the “qdec” folder. The “.Qdecrc” file is inside of the qdec folder. Should there also be a folder named “Qdecrc” in the qdec folder or really just the “.Qdecrc” file? Or do I have to create a folder named “qdec/.Qdecrc” in my “QDEC_Final” folder?
I suppose I don´t have to type “$SUBJECTS_DIR/qdec/.Qdecrc” in the shell I am working in before starting qdec.
I am awfully sorry for asking so many stupid questions but I ran out of things I could try.
Thanks a lot once again!
Best regards
Peter
Date: Tue, 2 Jul 2013 12:15:09 -0400 From: mreuter@nmr.mgh.harvard.edu To: bohn-peter@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] long_mris_slopes/cross.qdec.table.dat
Is your environment variable ($SUBJECTS_DIR) setup correctly? It needs to point to where the subjects and the qdec directory are.
so you should have a dir structure like this inside your subjects dir (QDEC_Final):
subject1_tp1 subject1_tp2 ... qdec/.Qdecrc that is the same as: $SUBJECTS_DIR/qdec/.Qdecrc if your environment variable is set correctly
On 07/02/2013 12:10 PM, Peter Bohn wrote:
Dear Martin, I tried adding another line in the file which didn´t change anything. My subject directory is called “QDEC_Final” and in that directory I created the “qdec” folder which includes the tables and also the”.Qdecrc” file. The file is definitely there and can be listed by using “ls -a”. So I suppose there shouldn´t be any mistakes so far. I created the .Qdecrc file by opening a new text file, writing down the four lines and saving it under the name “.Qdecrc” afterwards. While saving it I used the default UTF-8 encoding in Kwrite. Still there seems to be the Problem that qdec can´t find the .Qdecrc file. Do you still have any other idea as for what to try? Would renaming the files in the base directory be an solution or would that lead to many other problems? Thanks a lot! Best regards Peter ------------------------------------------------------------------------ Date: Mon, 1 Jul 2013 14:04:24 -0400 From: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> To: bohn-peter@gmx.de <mailto:bohn-peter@gmx.de> CC: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] long_mris_slopes/cross.qdec.table.dat Hi Peter, file looks good, you could try adding a newline at the end. The file should be hidden (all files starting with a . are hidden). Not sure why you cannot select the rate as the measure. Is your environment variable ($SUBJECTS_DIR) setup correctly? Best, Martin On 07/01/2013 12:00 PM, Peter Bohn wrote: Dear Martin, ”thickness” was a typo. Can you maybe check my attached file? I suppose that I put the four lines in it correctly. I only named it “.Qdecrc”. When I save the file in the qdec folder of my Subject directory, the file isn´t visible anymore. Is it supposed to be like that? It is there but not visible. Furthermore I can´t chose e.g. long.thickness-rate in the Design Tab. Thank you very much and I am sorry for bothering you so much. Best regards Peter ------------------------------------------------------------------------ Date: Mon, 1 Jul 2013 11:33:39 -0400 From: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> To: bohn-peter@gmx.de <mailto:bohn-peter@gmx.de> CC: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] long_mris_slopes/cross.qdec.table.dat Hi Peter, it needs to be .Qdecrc and have these lines: MEASURE1 = long.thickness-avg MEASURE2 = long.thickness-rate MEASURE3 = long.thickness-pc1 MEASURE4 = long.thickness-spc You will then see in the /Design/ tab in Qdec, that you can now select e.g. long.thickness-rate under /Measure/ as the dependent variable. You wrote below that you get this error: "couldn’t open…/1CAGB/surf/lh.thikness.fwhm10/fsaverage.mgz or .mgh file" note that thickness is spelled with 'ck'. Check your .Qdecrc if there's a typo. Best, Martin On 07/01/2013 09:45 AM, Peter Bohn wrote: Dear Freesurfer experts, Or could it be that I made a mistake creating the “Qdecrc” file? I simply created a text file in the qdec directory and named it “$SUBJECTS_DIR/qdec/.Qdecrc” and put the four lines in it as advised. Should it just be named “.Qdecr” or is there supposed to be an empty line somewhere in the file? Thanks a lot! Best regards Peter ------------------------------------------------------------------------ From: bohn-peter@gmx.de <mailto:bohn-peter@gmx.de> To: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>; freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Date: Mon, 1 Jul 2013 15:32:04 +0200 Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Dear Freesurfer experts, thanks to your help I was able to install the new version and run the „long_mris_slopes“ command. In the next step I shrank the longitudinal QDEC table into the cross sectional form by using “long_qdec_table” which also worked so far. Loading that table into QDEC and generating stats data table is no problem but afterwards, when I try to analyze the data in the “Design” section, I received an error message. It always says “couldn’t open…/1CAGB/surf/lh.thikness.fwhm10/fsaverage.mgz or .mgh file”. As an additional explanation for this example: 1CAGB is the base for the first time point CA and the second time point GB. Files with the wanted name exist in the surf directories of the two time points but not in the surf directory of the base. The closest thing in the base surf directory is called “lh.long.thikness.avg.fwhm10.mgh”. Could it be that there is a mistake in the “cross.qdec.table.dat”? Just like in the manual for creating the “long.qdec.table.dat”, I listed all the single time points under fsid and the base under fsid-base.and created the cross table afterwards. But when I open the “cross.qdec.table.dat”, the base names (1CAGB etc. in this example) are listed under “fsid”. Did I do something wrong during the creation of the long.qdec.table.dat or the cross.qdec.table.dat? Do you have any other explanation otherwise? Thank you very much for your help! Best regards Peter Bohn ------------------------------------------------------------------------ From: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> Date: Thu, 20 Jun 2013 06:57:16 -0700 To: bohn-peter@gmx.de <mailto:bohn-peter@gmx.de>; freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Not totally sure with 5.0, but I don't think it requires same voxel space for all time points (since 5.1), so it should work to run the analysis with 5.3 on that data. Cheers Martin Peter Bohn <bohn-peter@gmx.de> <mailto:bohn-peter@gmx.de> wrote: Thanks a lot! Do I have to repeat creating the base and the longitudinal runs once I use the new version or are they compatible concerning this aspect? Thank you very much! Best regards Peter ------------------------------------------------------------------------ From: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> Date: Thu, 20 Jun 2013 02:46:05 -0700 To: bohn-peter@gmx.de <mailto:bohn-peter@gmx.de>; freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Yes, those scripts are available since 5.2. You need to update to a newer version. Best Martin Peter Bohn <bohn-peter@gmx.de> <mailto:bohn-peter@gmx.de> wrote: Hi Martin, thanks a lot fort he quick reply! When I type freesurfer into the window it shows me v5.0.0 as the version. Sorry for my prior mistake concerning the version’s name. All other commands I use run perfectly fine. Thanks once again! Best regards Peter ------------------------------------------------------------------------ From: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> Date: Thu, 20 Jun 2013 05:21:39 -0400 To: bohn-peter@gmx.de <mailto:bohn-peter@gmx.de> CC: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found Hi Peter, can you run any free surfer command at all? Looks to me that you did not source free surfer. What happens if you type freesurfer into the terminal window? It should print the version. Best, Martin On Jun 20, 2013, at 5:17 AM, Peter Bohn <bohn-peter@gmx.de <mailto:bohn-peter@gmx.de>> wrote: Dear Freesurfer experts, I was trying to run some longitudinal analysis but whenever I want to use the commands “long_mris_slopes” or “long_qdec_table” I just get “command not found” as an answer. When I try to look up a package that might include the command, by typing “cnf long_mris_slopes”, I also just get “command not found” as an answer. We are currently using version v 1.313.2.6. Does anyone of you know if the two commands that I would like to run, are included in this version? Where would I have to look for the additional package if it exists? Or am I by any chance just typing the commands incorrect? Many thanks for the help! Sincerely yours Peter _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --------------------------------- Dr. Martin Reuter 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 <mailto:mreuter@nmr.mgh.harvard.edu> reuter@mit.edu <mailto:reuter@mit.edu> Web : http://reuter.mit.edu <http://reuter.mit.edu/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. -- Sent from my phone, please excuse brevity. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 <mailto:mreuter@nmr.mgh.harvard.edu> reuter@mit.edu <mailto:reuter@mit.edu> Web :http://reuter.mit.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 <mailto:mreuter@nmr.mgh.harvard.edu> reuter@mit.edu <mailto:reuter@mit.edu> Web :http://reuter.mit.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 mailto:mreuter@nmr.mgh.harvard.edu reuter@mit.edu mailto:reuter@mit.edu Web :http://reuter.mit.edu
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Peter Bohn