Hi,
well, if it works on another machine then you know it's not a problem of
your data, or of SPM per se. This is very high resolution data, and my
first guess would be you need more RAM to process it. However, your
first error message line could also indicate a problem with disk space,
or permissions. I would recommend checking these, and perhaps trying to
run one image dataset at a time.
Cheers,
Marko
Necip Çapraz wrote:
> Dear SPMers,
>
> Thank you for your help. I tried to run the same steps in another
> Windows machine (with larger RAM memory and 64bit one), it worked.
> While I am using my own Mac (64 bit) for processing (I have to use it),
> it seems something is going wrong:
>
> Error using nifti/create>create_each (line 29)
> Unable to write header for
> "/Volumes/Untitled/tezdata/niftis/AD001/BULUNUR_SERDAL/16757_005_Ax_3D_BRAVO_(1mm3)_20150427/20150427_16757_005_VBM+TBSS_Ax_3D_BRAVO_(1mm3).nii".
> In file "[log in to unmask]" (v1143), function
> "create_each" at line 29.
> In file "[log in to unmask]" (v1143), function
> "create" at line 15.
> In file "/Users/necip/Documents/spm8/spm_get_space.m" (v4208), function
> "spm_get_space" at line 49.
> In file "/Users/necip/Documents/spm8/config/spm_run_coreg_estimate.m"
> (v4380), function "spm_run_coreg_estimate" at line 28.
>
> @John: vox sizes: 0.5x0.5x0.5
> dimensions: 512x512x312
>
> What is the problem now?
>
> Thank you,
>
> Best regards,
> Necip
>
> 2015-12-03 12:43 GMT+02:00 John Ashburner <[log in to unmask]
> <mailto:[log in to unmask]>>:
>
> This time, the out of memory error is coming from somewhere
> different. I'm not sure what the cause is, but my guess is that the
> conversion from DICOM to NIfTI may be going slightly wrong.
>
> What happens if you display one of the images? This will also show
> voxel sizes in the z direction, as well as the image dimensions.
> Maybe the images are ridiculously large.
>
> Best regards,
> -John
>
>
> On 3 December 2015 at 09:29, Necip Çapraz <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Hi,
> Thank you for your interest. I am writing more clearly what I did.
>
> @Marko: Steps: Normalization (Est&Write)
> Segmentation
> Smoothing
> (no more realignment)
>
> I am using SPM8 and MATLAB 2013a with a 32bit Windows machine.
>
> @John: from .info file
> Voxel size x (mm): 0.5
> Voxel size y (mm): 0.5
>
> Error:
>
> Error using spm_bsplinc
> Out of memory. Type HELP MEMORY for your options.
> In file "G:\spm\spm8\spm_write_sn.m" (v4201), function
> "nonlin_transform" at line 205.
> In file "G:\spm\spm8\spm_write_sn.m" (v4201), function
> "spm_write_sn" at line 120.
> In file "G:\spm\spm8\config\spm_run_normalise_estwrite.m"
> (v4152), function "spm_run_normalise_estwrite" at line 25.
>
> Best,
> Necip
>
>
>
> 2015-12-02 13:09 GMT+02:00 Necip Çapraz <[log in to unmask]
> <mailto:[log in to unmask]>>:
>
> Dear SPMers,
>
> I need some help about preprocessing my structural data.
> I convert the data from dicom to .nii format, then while
> running the preprocessing steps, I got this error.
>
> "Error using spm_bsplinc
> Out of memory. Type HELP MEMORY for your options.
> In file "G:\spm\spm8\spm_realign.m" (v6071), function
> "smooth_vol" at line 405.
> In file "G:\spm\spm8\spm_realign.m" (v6071), function
> "realign_series" at line 265.
> In file "G:\spm\spm8\spm_realign.m" (v6071), function
> "spm_realign" at line 118.
> In file "G:\spm\spm8\config\spm_run_realign_estwrite.m"
> (v4152), function "spm_run_realign_estwrite" at line 26."
>
> What should I do?
>
> Thanks for your help,
>
>
> Necip Capraz, MD
>
> Katip Celebi University Medical School
> Dept of Psychiatry
> Izmir, Turkey
>
>
>
>
--
____________________________________________________
PD Dr. med. Marko Wilke
Facharzt für Kinder- und Jugendmedizin
Leiter, Experimentelle Pädiatrische Neurobildgebung
Universitäts-Kinderklinik
Abt. III (Neuropädiatrie)
Marko Wilke, MD, PhD
Pediatrician
Head, Experimental Pediatric Neuroimaging
University Children's Hospital
Dept. III (Pediatric Neurology)
Hoppe-Seyler-Str. 1
D - 72076 Tübingen, Germany
Tel. +49 7071 29-83416
Fax +49 7071 29-5473
[log in to unmask]
http://www.medizin.uni-tuebingen.de/kinder/epn/
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