[Freesurfer] local gyrification index (lGI) Error in Design

[Katherine Damme]

Hello FreeSurfer Group

I would like to make a two group comparison controlling for both gender and
medication status. The only way that I have sorted out doing this is to
make eight groups (ClinicalGroup x Sex x Meds) but I get an error that my
design is poorly scaled:

 

ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08



Possible problem with experimental design:

Check for duplicate entries and/or lack of range of

continuous variables within a class.

If you seek help with this problem, make sure to send:

  1. Your command line:

mri_glmfit --y lh.lgi.mgh --fsgd FSGD_GroupSexTP_AntiPsych.txt --glmdir
lh.lgi.glmdir --surf average lh --C contrast.txt

  2. The FSGD file (if using one)

  3. And the design matrix above
GroupDescriptorFile 1
Title GroupGenderAntipsychotic
Class UHR_F_1
Class UHR_F_2
Class UHR_M_1
Class UHR_M_2
Class HC_F_1
Class HC_F_2
Class HC_M_1
Class HC_M_2
Variables Antipsychotic
Input 1001_MR1 UHR_F_1 0
Input 1001_MR2 UHR_F_2 0
Input 1004_MR1 UHR_F_1 0
Input 1004_MR3 UHR_F_2 0
Input 1005_MR1 UHR_M_1 1
Input 1005_MR2 UHR_M_2 1
Input 1006_MR1 UHR_F_1 1
Input 1006_MR2 UHR_F_2 1
Input 1007_MR1 UHR_M_1 0
Input 1007_MR3 UHR_M_2 0
Input 1008_MR1 UHR_F_1 0
Input 1008_MR2 UHR_F_2 0
Input 1009_MR1 UHR_M_1 0
Input 1009_MR2 UHR_M_2 0
Input 1010_MR1 UHR_M_1 0
Input 1010_MR2 UHR_M_2 0
Input 1011_MR1 UHR_M_1 0
Input 1011_MR2 UHR_M_2 0
Input 1012_MR1 UHR_M_1 1
Input 1012_MR2 UHR_M_2 1
Input 1014_MR1 UHR_F_1 0
Input 1014_MR2 UHR_F_2 0
Input 1016_MR1 UHR_M_1 0
Input 1016_MR2 UHR_M_2 0
Input 1017_MR1 UHR_F_1 0
Input 1017_MR2 UHR_F_2 0
Input 1018_MR1 UHR_M_1 0
Input 1018_MR2 UHR_M_2 0
Input 1020_MR1 UHR_F_1 0
Input 1020_MR2 UHR_F_2 0
Input 1021_MR1 UHR_F_1 0
Input 1021_MR2 UHR_F_2 0
Input 1023_MR1 UHR_M_1 0
Input 1023_MR2 UHR_M_2 0
Input 1024_MR1 UHR_M_1 1
Input 1024_MR2 UHR_M_2 1
Input 1025_MR1 UHR_M_1 0
Input 1025_MR2 UHR_M_2 0
Input 1027_MR1 UHR_M_1 0
Input 1027_MR2 UHR_M_2 0
Input 1029_MR1 UHR_M_1 0
Input 1029_MR2 UHR_M_2 0
Input 1031_MR1 UHR_M_1 0
Input 1031_MR2 UHR_M_2 0
Input 1032_MR1 UHR_M_1 0
Input 1032_MR2 UHR_M_2 0
Input 1033_MR1 UHR_M_1 0
Input 1033_MR2 UHR_M_2 0
Input 1034_MR1 UHR_F_1 0
Input 1034_MR2 UHR_F_2 0
Input 1035_MR1 UHR_M_1 0
Input 1035_MR2 UHR_M_2 0
Input 1036_MR1 UHR_F_1 0
Input 1036_MR2 UHR_F_2 0
Input 1037_MR1 UHR_M_1 0
Input 1037_MR2 UHR_M_2 0
Input 1039_MR1 UHR_M_1 0
Input 1039_MR2 UHR_M_2 0
Input 1040_MR1 UHR_F_1 0
Input 1040_MR2 UHR_F_2 0
Input 1043_MR1 UHR_M_1 1
Input 1043_MR2 UHR_M_2 1
Input 1046_MR1 UHR_F_1 0
Input 1046_MR2 UHR_F_2 0
Input 1050_MR1 UHR_F_1 0
Input 1050_MR2 UHR_F_2 0
Input 1053_MR1 UHR_M_1 0
Input 1053_MR2 UHR_M_2 0
Input 1054_MR1 UHR_F_1 0
Input 1054_MR2 UHR_F_2 0
Input 1058_MR1 UHR_M_1 0
Input 1058_MR2 UHR_M_2 0
Input 2001_MR1 HC_M_1 0
Input 2001_MR2 HC_M_2 0
Input 2004_MR1 HC_F_1 0
Input 2004_MR2 HC_F_2 0
Input 2007_MR1 HC_M_1 0
Input 2007_MR2 HC_M_2 0
Input 2010_MR1 HC_M_1 0
Input 2010_MR2 HC_M_2 0
Input 2011_MR1 HC_F_1 0
Input 2011_MR2 HC_F_2 0
Input 2012_MR1 HC_F_1 0
Input 2012_MR2 HC_F_2 0
Input 2013_MR1 HC_F_1 0
Input 2013_MR2 HC_F_2 0
Input 2015_MR1 HC_F_1 0
Input 2015_MR2 HC_F_2 0
Input 2016_MR1 HC_F_1 0
Input 2016_MR2 HC_F_2 0
Input 2017_MR1 HC_F_1 0
Input 2017_MR2 HC_F_2 0
Input 2018_MR1 HC_F_1 0
Input 2018_MR2 HC_F_2 0
Input 2019_MR1 HC_M_1 0
Input 2019_MR2 HC_M_2 0
Input 2024_MR1 HC_F_1 0
Input 2024_MR2 HC_F_2 0
Input 2025_MR1 HC_M_1 0
Input 2025_MR2 HC_M_2 0
Input 2027_MR1 HC_F_1 0
Input 2027_MR2 HC_F_2 0
Input 2029_MR1 HC_M_1 0
Input 2029_MR2 HC_M_2 0
Input 2030_MR1 HC_F_1 0
Input 2030_MR2 HC_F_2 0
Input 2031_MR1 HC_F_1 0
Input 2031_MR2 HC_F_2 0
Input 2032_MR1 HC_M_1 0
Input 2032_MR2 HC_M_2 0
Input 2033_MR1 HC_F_1 0
Input 2033_MR2 HC_F_2 0
Input 2034_MR1 HC_F_1 0
Input 2034_MR2 HC_F_2 0
Input 2038_MR1 HC_F_1 0
Input 2038_MR2 HC_F_2 0
Input 2041_MR1 HC_F_1 0
Input 2041_MR2 HC_F_2 0
Input 2042_MR1 HC_M_1 0
Input 2042_MR2 HC_M_2 0
Input 2043_MR1 HC_F_1 0
Input 2043_MR2 HC_F_2 0
Input 2050_MR1 HC_F_1 0
Input 2050_MR2 HC_F_2 0
Input 2053_MR1 HC_M_1 0
Input 2053_MR2 HC_M_2 0
Input 2057_MR1 HC_F_1 0
Input 2057_MR2 HC_F_2 0
Input 2058_MR1 HC_M_1 0
Input 2058_MR2 HC_M_2 0
Input 2059_MR1 HC_M_1 0
Input 2059_MR2 HC_M_2 0
Input 2061_MR1 HC_F_1 0
Input 2061_MR2 HC_F_2 0
Input 1048_MR1 UHR_M_1 1
Input 1048_MR2 UHR_M_2 1
Input 1061_MR1 UHR_M_1 1
Input 1061_MR2 UHR_M_2 1
Input 1062_MR1 UHR_M_1 0
Input 1062_MR2 UHR_M_2 0
Input 1067_MR1 UHR_M_1 0
Input 1067_MR2 UHR_M_2 0
Input 1074_MR1 UHR_F_1 0
Input 1074_MR2 UHR_F_2 0
Input 1075_MR1 UHR_F_1 0
Input 1075_MR2 UHR_F_2 0
Input 2062_MR1 HC_M_1 0
Input 2062_MR2 HC_M_2 0
Input 2065_MR1 HC_F_1 0
Input 2065_MR2 HC_F_2 0
Input 2067_MR1 HC_F_1 0
Input 2067_MR2 HC_F_2 0
Input 2070_MR1 HC_F_1 0
Input 2070_MR2 HC_F_2 0
Input 2071_MR1 HC_M_1 0
Input 2071_MR2 HC_M_2 0
Input 2076_MR1 HC_F_1 0
Input 2076_MR2 HC_F_2 0
Input 2078_MR1 HC_F_1 0
Input 2078_MR2 HC_F_2 0


command_matrix
Description: Binary data

Re: [Freesurfer] Installing and enabling cuda

[R Edgar]

On 16 May 2017 at 23:10, Ramesh Babu  wrote:

> I have come across that I have freesurfer support cuda version 5, but I have
> already installed latest version.
> Can I use latest version for freeesurfer or should I install version 5?
> Since I am not expert in this field I need guidance to remove latest version
> of cuda and installing and enabling version 5.
>
> Your help will be appreciated.
>
> PC details:
> I am using Intel® Core™ i7-4790 CPU @ 3.60GHz × 8 processor with 15.6 GiB
> ram, GeForce GT 610/PCIe/SSE2 graphic card.

I have CUDA 8 on my machine, and it seems to run quite happily
(although I do compile myself). I don't believe that NVIDIA have made
any breaking changes in the CUDA SDK, although looking at things
recently, some might be coming.

HTH,

Richard

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Re: [Freesurfer] -usegpu vs -parallel in recon-all

[R Edgar]

On 17 May 2017 at 18:40, Octavian Lie  wrote:

> With FS6, -parallel -openmp x can really speed things up. I inherited code
> from prior versions using -usegpu flag for GPU/CUDA (not supported more
> recently). Is the latter redundant or affecting in any way the -parallel
> -openmp x performance, should we take it out, please advise.

I'm not aware of any specific problems - I compile with both CUDA and
OpenMP enabled - but I am not an expert in bits of neuroanatomy which
might be going awry. I can say that results obtained with the GPU will
not be bit-for-bit identical to those using just the CPU. This is not
unexpected, but might affect your decision on how to analyse your
data.

Richard
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Re: [Freesurfer] cuda-gpu problem

[R Edgar]

On 20 May 2017 at 00:56, Ramesh Babu  wrote:

> I am using Intel® Core™ i7-4790 CPU @ 3.60GHz × 8 processor with 15.6 GiB
> ram, GeForce GT 610/PCIe/SSE2 graphic card.
>
> I have successfully installed cuda runtime version 5.0. After that I
> performed cuda detect and output result is pasted below.
>
> $ cudadetect
> Detecting CUDA... There is 1 device supporting CUDA:
>
> Device 0: "GeForce GT 610"
>   CUDA Driver Version:   8.0
>   CUDA Runtime Version:  5.0
>   CUDA Capability Major revision number: 2
>   CUDA Capability Minor revision number: 1
>   Total amount of global memory: 2080440320 bytes
>   Number of multiprocessors: 1
>   Number of cores:   32
>   Total amount of constant memory:   65536 bytes
>   Total amount of shared memory per block:   49152 bytes
>   Total number of registers available per block: 32768
>   Warp size: 32
>   Maximum number of threads per block:   1024
>   Maximum sizes of each dimension of a block:1024 x 1024 x 64
>   Maximum sizes of each dimension of a grid: 65535 x 65535 x 65535
>   Maximum memory pitch:  2147483647 bytes
>   Texture alignment: 512 bytes
>   Clock rate:1.62 GHz
>   Concurrent copy and execution: Yes
>   Run time limit on kernels: Yes
>   Integrated:No
>   Support host page-locked memory mapping:   Yes
>   Compute mode:  Default (multiple host
> threads can use this device simultaneously)
>
> Then statrted recon-all with use-gpu flag.
> $ recon-all -all -i grp229_t1.nii -s grp229 -sd grp229 -use-gpu
>
> But it was giving some error report continuously and I interrupted the
> process. Please see the attached log report and help me to use gpu
> effectively.

Sorry, can you highlight the error message in the log? I did a quick
scan and it looked like normal output to me.

Having said that, I see that you've got a display hooked up to this
card, and that it's only 2 GiB of RAM. Both of those *might* give
problems.

Richard

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Re: [Freesurfer] Cuda 8, Centos 7, FreeSurfer 6

[R Edgar]

On 19 May 2017 at 00:37, neuroimage analyst
 wrote:

> We recently installed Centos 7 with cuda 8 and tried to build the FreeSurfer
> 6.0 using the wiki instructions but were unsuccessful to do so. Has anyone
> successfully built FreeSurfer 6 on Cuda 8 (Centos 7) and willing to share
> the binaries with us or share their steps with us? We will greatly
> appreciate that.

Can you give me some more information about the problems you are
seeing? I'm not sure which version of CentOS I have installed
(whatever the latest was about a year ago), but I do have CUDA 8 and I
can compile the CUDA version of both em and ca register (I which  I
have a certain proprietary interest).

Regards,

Richard
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Re: [Freesurfer] ERROR: nu_correct

[X K]

I had the same problem with one server. The freesurfer version
is freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c.
The system is openSUSE13.2 for both servers. But one works well (A), while
another one showed this problem (B). I found the kernel is somehow
different, though I am not sure whether this is the point. kernel for A is
3.16.7-35-desktop, while kernel for B is 3.16.6-2-desktop.
They have the same verion of perl, v5.20.1.

Hope this case would be helpful for fixing the issue.

Best,
Xiangzhen


On Tue, Apr 11, 2017 at 8:12 PM, Z K  wrote:

> What version of freesurfer are you using? My guess is 5.3 or earlier?
>
> With pre v6.0 versions of freesurfer, the Talairach transform step will
> fail at the mri_nu_correct.mni command on newer Linux distributions that
> come with perl version 5.22 (and higher) due to an incompatibility with
> the mni tools shipped with FreeSurfer and newer versions of perl. The
> issue has been fixed in version 6.0.
>
> On 04/05/2017 05:12 PM, Das S. wrote:
> > Dear Freesurfer  Developers,
> > I was trying to use the recon-all -autorecon1 -subjid bert and got an
> error. When I checked I found the error was coming while executing the
> below command:
> > nu_correct -clobber ./tmp.mri_nu_correct.mni.7555/nu0.mnc
> ./tmp.mri_nu_correct.mni.7555/nu1.mnc -tmpdir
> ./tmp.mri_nu_correct.mni.7555/0/ -iterations 1000 -distance 50
> >
> > When I executed the command separately I got below error message:
> >
> > Can't use 'defined(@array)' (Maybe you should just omit the defined()?)
> at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165.
> > nu_correct: crashed while running nu_estimate_np_and_em (termination
> status=65280)
> > ERROR: nu_correct
> >
> >
> > Can you please suggest why the error is coming and how to remove it.
> > Many thanks
> > Sarbani
> >
> > ___
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> >
> >
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>
> 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.
>
>


-- 
-
Kong Xiangzhen
State Key Laboratory of Cognitive Neuroscience and Learning,
Beijing Normal University,
Beijing, China, 100875.
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