[MINC-users] mincaverage error

[Lisa F. Akiyama]

Hi again,

Some update:

I was just able to add each file one by one to create a sum image, and was
able to divide this by the total #N value (constant) using mincmath.
Then, I ran mincnorm.
Is this equivalent/close enough to what mincaverage -normalize does?

Thanks.


Best,
Lisa
 ______________________________




On Mon, Mar 7, 2011 at 11:04 AM, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:

> Alex Z.,
>
> Here's a list of pre-processing I performed on each site S and site I files
> before putting them through mincaverage:
> 1) N3 intensity nonuniformity correction
> 2) mincnorm so that the range would be 0-100
> 3) Linear registration of subject images to standard template: bestlinreg
> using Vladimir Fonov's NIHPD-BIC model for 00-02 year age range (range
> 0-100) as the target. I also created a brain mask image and specified as the
> target_mask that in the command. Used -lsq9.
>     When I look at the header of the files, they all have a stamp
> mentioning that the files went through mincresample with -like NIHPD-BIC
> template.
>     I've check each individual's resampled image and they all seem fairly
> well registered. (There were a few images that didn't do so well, but after
> creating the subject specific brainmask and re-running bestlinreg on these
> individuals, the outcomes were good)
>
> I just ran mincinfo on all files: They all have the same dimension lengths,
> steps and start values.
>
> I'm not sure whether I should run the following as you suggested earlier
> since I've registered them to a standard template already and also because
> they have the same dimensions.
>
>  If you do want to register them without prior registration, you could
>> still get this to work by simply resampling all volumes to one of
>> them, e.g.,
>> mincresample -like <file1.mnc> <file2.mnc> <file2_resampled.mnc>
>
>
> Claude,
>
> mincinfo and mincheader will give you information about the orientation
>
> of the images. Watch for +ve vs -ve steps, voxel sizes, start coords,
>
> direction cosines, storage format.
>
>
> It seems like all files have very similar headers. Regardless of which site
> the scan came from, they had the same dimension length, step, start,
> direction cosine, and units (mm) for x, y, and z.
> I've attached mincinfo and mincheader outputs for S1 and I1 to this email
> for your reference.
>
>  For example, S1+S2+...+SN+S1+S2+... Does adding more images make
>
> it blow up? I want you to repeat images of the same site, not mixed
>
> sites.
>
>
> I ran the following trials:
>
> 1) mincaverage -normalize -filelist all-S-site-files.txt Savg.mnc  ===> OK;
> looks fine
>
> 2) mincaverage -normalize -filelist all-I-site-files.txt Iavg.mnc  ===> OK;
> looks fine
>
> 3) mincaverage -normalize -filelist Savg.mnc-and-all-S-site-files.txt ===>
> ERROR; miicv_attach: MINC package entry point
>  ncvarid: ncid -1: NetCDF: Not a valid ID
>
> 3a) mincaverage -normalize -filelist Savg.mnc-and-one-S-site-file.txt ===>
> OK.
>
> 3b) mincaverage -normalize -filelist Savg.mnc-and-27(out of 28
> total)-S-site_files.txt ===> OK. Same size, looks identical to original
> Savg.mnc
>       However, when I ran Savg.mnc-and-27-S-site-files (removed a different
> subject image than previously), error message "
>       ncvarid: ncid -1: NetCDF: Not a valid ID" appeared.  Haven't tested
> for all possible pairings.
>
>
> 4) mincaverage -normalize -filelist Iavg.mnc-and-all-I-site-files.txt ===>
> OK; looks fine, same size and looks identical to original Iavg.mnc
>
>
> 4a) mincaverage -normalize -filelist Iavg.mnc-and-14(out of 15
> total)-I-site-files.txt (tried this with removing different subjects each
> time although I haven't tested all possible pairings) ===> OK; looks good,
> same size, and looks identical to original Iavg.mnc
>
>
>
> It appears that there is something sketchy with the site S files rather
> than the site I files.
>
> Thank you.
>
>
> Best,
> Lisa
>
>
> On Sat, Mar 5, 2011 at 8:45 PM, Claude LEPAGE <claude at bic.mni.mcgill.ca>wrote:
>
>> Hi,
>>
>> I thought about the resampling issue too, as suggested by Alex,
>> but after doing a mincaverage -help:
>>
>>  -check_dimensions:      Check that dimension info matches across files
>> (default).
>>  -nocheck_dimensions:    Do not check dimension info.
>>
>> It seems that the default is to check dimensions! Maybe the check
>> is wrong...
>>
>> Lisa, since you don't get an error when averaging images from the
>> same site, can you keep adding more images from the same site?
>> For example, S1+S2+...+SN+S1+S2+... Does adding more images make
>> it blow up? I want you to repeat images of the same site, not mixed
>> sites.
>>
>> mincinfo and mincheader will give you information about the orientation
>> of the images. Watch for +ve vs -ve steps, voxel sizes, start coords,
>> direction cosines, storage format. Alex's suggestion to resample
>> like a template file makes a lot of sense.
>>
>> When you manage to obtain an output, does it make sense when you
>> look at it in register/Display?
>>
>> Claude
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
>