Re: [Freesurfer] error in analyze command failed: mri_concat - Freesurfer

20 Nov 2012

      I don't think it should be as long as you are consistent. It might be 
worth trying to track down this problem just so that you don't have to 
mix versions.
doug
On 11/20/2012 03:37 PM, Berg, S.F. van den wrote:
...
Hi Doug,
Thanks for respons. We also install the dev version of freesurfer. We do the recon-all with the stable version. But smoothing with the dev version. Qdec is till now on correctly running with the dev version.
Running qDEC with the dev version. Is that a problem?
Thanks,
Stan
________________________________________
From: Douglas N Greve [greve@nmr.mgh.harvard.edu]
Sent: 20 November 2012 21:04
To: Berg, S.F. van den
Subject: Re: [Freesurfer] error in analyze command failed: mri_concat
If you change the order or leave one out, does it still crash?
On 11/19/2012 11:21 AM, Berg, S.F. van den wrote:
...
Hi Doug,
I try the mri_concat command with the --debug flag. Output is also in the text file
Thanks.
Stan
-------- freesurfer-Linux-centos5_x86_64-dev-20110315 --------
SUBJECTS_DIR      /data1/projects/ysbrand-vumc/pddatabase-freesurfer
guest@somerenserver:~$ mri_concat --debug /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.volume.fwhm10.fsaverage.mgh --o /data1/projects/ysbrand-vumc/pddatabase-freesurfer/qdec/hippocampus/y.mgh11 /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh
10 /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.volume.fwhm10.fsaverage.mgh
9 /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.volume.fwhm10.fsaverage.mgh
8 /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.volume.fwhm10.fsaverage.mgh
7 /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.volume.fwhm10.fsaverage.mgh
6 /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.volume.fwhm10.fsaverage.mgh
5 /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.volume.fwhm10.fsaverage.mgh
4 /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.volume.fwhm10.fsaverage.mgh
3 /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.volume.fwhm10.fsaverage.mgh
2 --o
ninputs = 9
Checking inputs
Checking  0 /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh
reading MRI_FRAME structure from file...
Segmentation fault

From: Douglas N Greve [greve@nmr.mgh.harvard.edu]
Sent: 19 November 2012 16:50
To: Berg, S.F. van den
Subject: Re: [Freesurfer] error in analyze command failed: mri_concat
Hi Stan, can you run it again this time with --debug as the first
argument and send me the result?
thanks
doug
On 11/19/2012 08:00 AM, Berg, S.F. van den wrote:
...
Hi Doug,
Like you said. I run the command in the terminal.
I run the mri_concat command with 9 subjects in the command line. for the LH thickness and volume. A segmentation fault is the problem.
What do i have to do in this case?
Many thanks,
Stan
-------- freesurfer-Linux-centos5_x86_64-dev-20110315 --------
SUBJECTS_DIR      /data1/projects/ysbrand-vumc/pddatabase-freesurfer
guest@somerenserver:~$ mri_concat /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.volume.fwhm10.fsaverage.mgh --o /data1/projects/ysbrand-vumc/pddatabase-freesurfer/qdec/hippocampus/y.mgh
ninputs = 9
Checking inputs
reading MRI_FRAME structure from file...
Segmentation fault
guest@somerenserver:~$ mri_concat /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.thickness.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.thickness.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.thickness.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.thickness.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.thickness.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.thickness.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.thickness.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.thickness.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.thickness.fwhm10.fsaverage.mgh --o /data1/projects/ysbrand-vumc/pddatabase-freesurfer/qdec/caudalmiddlefrontal_curv/y.mgh
ninputs = 9
Checking inputs
reading MRI_FRAME structure from file...
Segmentation fault
guest@somerenserver:~$

From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu]
Sent: 13 November 2012 17:32
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] error in analyze command failed: mri_concat
Hi Stan, can you run that mri_concat command from the terminal command line and send me the resulting terminal output? I've put the command below
doug
mri_concat /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.volume.fwhm10.fsaverage.mgh --o /data1/projects/ysbrand-vumc/pddatabase-freesurfer/qdec/hippocampus/y.mgh
On 11/13/2012 06:53 AM, Berg, S.F. van den wrote:
...
mri_concat /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.volume.fwhm10.fsaverage.mgh --o /data1/projects/ysbrand-vumc/pddatabase-freesurfer/qdec/hippocampus/y.mgh
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Mail 13 november 2012:
Hello Freesurfer experts,
I have got some problems with qdec. For testing my data i make an design with age, sexe and right and left hippocampus. The same design as the tutorial on the freesurfer wiki. When starting analyze i get an  Error in Analyze: command failed: mri_concat /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh.
surf is the map with the smoothings. The correct smoothings file. In this design is 10 is correctly presented in the map surf.
Thanks,
Stan
lh-Avg-Intercept-volume -----------------------
Does the average volume differ from zero?
    1.000   1.000   0.000   0.000;
lh-Avg-volume-Left-Hippocampus-Cor -----------------------
Does the correlation between volume and Left-Hippocampus, accounting for gender, differ from zero?
    0.000   0.000   1.000   1.000;
lh-Diff-male-female-Intercept-volume -----------------------
Does the average volume differ between male and female?
    1.000  -1.000   0.000   0.000;
lh-Diff-male-female-Cor-volume-Left-Hippocampus -----------------------
Does the volume--Left-Hippocampus correlation differ between male and female?
    0.000   0.000   1.000  -1.000;
ninputs = 9
Checking inputs
reading MRI_FRAME structure from file...
Error in Analyze: command failed: mri_concat /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.volume.fwhm10.fsaverage.mgh --o /data1/projects/ysbrand-vumc/pddatabase-freesurfer/qdec/hippocampus/y.mgh
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/