Re: [Freesurfer] long_mris_slopes/cross.qdec.table.dat
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-pe...@gmx.de To: mreu...@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: mreu...@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 06:57:16 -0700 To: bohn-pe...@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-pe...@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: mreu...@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 02:46:05 -0700 To: bohn-pe...@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-pe...@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: mreu...@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 05:21:39 -0400 To: bohn-pe...@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-pe...@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 listfreesur...@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:mreu...@nmr.mgh.harvard.edu reuter@mit.eduWeb : http://reuter.mit.edu
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-pe...@gmx.de To: mreu...@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: mreu...@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 06:57:16 -0700 To: bohn-pe...@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-pe...@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: mreu...@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 02:46:05 -0700 To: bohn-pe...@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-pe...@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: mreu...@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 05:21:39 -0400 To: bohn-pe...@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-pe...@gmx.de mailto:bohn-pe...@gmx.de wrote: Dear Freesurfer experts, I was trying to run some longitudinal analysis but whenever I want to
Re: [Freesurfer] long_mris_slopes/cross.qdec.table.dat
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: mreu...@nmr.mgh.harvard.edu To: bohn-pe...@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-pe...@gmx.de To: mreu...@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: mreu...@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 06:57:16 -0700 To: bohn-pe...@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
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: mreu...@nmr.mgh.harvard.edu To: bohn-pe...@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-pe...@gmx.de mailto:bohn-pe...@gmx.de To: mreu...@nmr.mgh.harvard.edu mailto:mreu...@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: mreu...@nmr.mgh.harvard.edu mailto:mreu...@nmr.mgh.harvard.edu Date: Thu, 20 Jun 2013 06:57:16 -0700 To: bohn-pe...@gmx.de mailto:bohn-pe...@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-pe...@gmx.de mailto:bohn-pe...@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
