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 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
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---------------------------------
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:
mreu...@nmr.mgh.harvard.edu <mailto:mreu...@nmr.mgh.harvard.edu>
reu...@mit.edu <mailto:reu...@mit.edu>
Web : http://reuter.mit.edu <http://reuter.mit.edu/>
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information in this e-mail is intended only for the person to whom it
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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
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_______________________________________________ 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:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
Web : http://reuter.mit.edu
_______________________________________________
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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
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but does not contain patient information, please contact the sender and properly
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