[MINC-users] mritotal models (OS X)

[Vladimir S. FONOV]

mritotal is a perl script that uses minctracc, bestlinreg_s is also perl 
script that uses minctracc, minctracc is not depricated.

If you want to do non-linear registration there are several options - 
nlfit_s (uses minctracc), elastix, ANTs - all included in minc-toolkit.

I didn't maintain mritotal because I switched to bestlinreg_s in my 
scripts.

On 15-11-12 02:54 PM, Pedro Telles Cougo Pinto wrote:
> Thanks for the quick response, Vladimir. I see elastix is also part of the minc-toolkit; should we prefer it for nonlinear registration? Is mritotal deprecated in general?
>
> Best regards,
> Pedro
>
>> On Nov 11, 2015, at 18:10, Vladimir S. FONOV <vladimir.fonov at gmail.com> wrote:
>>
>> Hello Pedro,
>>
>> these files are meant to work with newer version of the script - called bestlinreg_s  , you can replace the call to mritotal to
>>
>> bestlinreg_s -lsq7 -nmi <input_t1.mnc> /opt/minc/share/average305_t1_tal_lin.mnc <output.xfm>
>>
>>
>>
>>
>> On 15-11-11 02:48 PM, Pedro Telles Cougo Pinto wrote:
>>> Hi,
>>>
>>> I installed minc-toolkit for OS X (minc-toolkit-1.9.10-20150710-Darwin-10.9-x86_64.dmg <http://packages.bic.mni.mcgill.ca/minc-toolkit/MacOSX/minc-toolkit-1.9.10-20150710-Darwin-10.9-x86_64.dmg>) and I’m having some issues with models for mritotal. I would appreciate any help.
>>>
>>> First, the installation puts mritotal.cfg (and other mritotal .cfg files) at /opt/minc-itk4/etc, however mritotal still tries to find the .cfg files at /opt/minc-itk4/etc/mni_autoreg/ . I simply moved the .cfg files to a newly created /opt/minc-itk4/etc/mni_autoreg directory, but I’m not sure about the best definitive fix for this (changing the package file architecture?).
>>>
>>> I used the most recent model files from http://packages.bic.mni.mcgill.ca: bic-mni-models-0.1.1-20120421.dmg <http://packages.bic.mni.mcgill.ca/minc-toolkit/MacOSX/bic-mni-models-0.1.1-20120421.dmg> to get ICBM152 files and mni305_lin_minc2.zip <http://packages.bic.mni.mcgill.ca/mni-models/mni305/mni305_lin_minc2.zip> (README gives compiling instructions, but the zip comes only with the .mnc files) for the 305 model, all located to /opt/minc/share (mritotal.cfg was edited to reflect this). Running mritotal gives the following message:
>>>
>>> Loading configuration file /opt/minc-itk4/bin/../etc/mni_autoreg/mritotal.cfg
>>> Loading protocol default (protocol file = /opt/minc-itk4/bin/../etc/mni_autoreg/mritotal.default.cfg)
>>> /opt/minc/share/average305_t1_tal_lin_16_blur.mnc does not exist
>>> /opt/minc/share/average305_t1_tal_lin_8_blur.mnc does not exist
>>> /opt/minc/share/average305_t1_tal_lin_8_dxyz.mnc does not exist
>>> /opt/minc/share/average305_t1_tal_lin_16_mask.mnc does not exist
>>> /opt/minc/share/average305_t1_tal_lin_8_mask.mnc does not exist
>>> Died at /opt/minc-itk4/bin/mritotal line 728.
>>>
>>> Were these 305 files supposed to be built as part of compiling? Both bic-mni-models-0.1.1-20120421.dmg <http://packages.bic.mni.mcgill.ca/minc-toolkit/MacOSX/bic-mni-models-0.1.1-20120421.dmg> and mni305_lin_minc2.zip <http://packages.bic.mni.mcgill.ca/mni-models/mni305/mni305_lin_minc2.zip> were from 2012; am I trying to get the models from wrong sources?
>>>

-- 
Best regards,

  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com