Hi,
Just to comment on this thread (as I'm not sure if it is successfully resolved or not):
1) if you just want to apply a single matrix to a 4D timeseries then you do not need applyxfm4d, as flirt with -applyxfm will work fine too, although you can use applyxfm4d if you wish
2) ApplyXFM with the identity option (as suggested by one responder) is not what you want, so ignore that
3) In one of your commands you have: /Users/yaelgrossman/Desktop/CYT20110701C.8P1//Users/yaelgrossman/Desktop/CYT20110701C.8P1/CYT20110701C_5_regdefault_bptfpixo_gauss1_flirt_braintest1.mat
which looks like you've incorrectly copied the start of the path in twice. This is why it says it cannot find this file.
4) Wolf is also right that you seem to change the filename of the matrix between the flirt and applyxfm4d calls, which you shouldn't.
All the best,
Mark
On 21 Jul 2013, at 20:48, wolf zinke <[log in to unmask]> wrote:
> Hi
>
> Puh, long pathnames in command line calls are awkward to read ;-) you could put them in a variable, or if this anyway is your working directory, ommit them.
>
> Besides that you seem to use for bot calls different matrix files:
>
> for flirt: -omat CYT20110701C_5_regdefault_bptfpixo_gauss1_flirt.mat
>
> for applyxfm4d: CYT20110701C_5_regdefault_bptfpixo_gauss1_flirt_braintest1.mat
>
> And the one you use for applyxfm4d seems not to exist, thus the error message.
>
> hope this helps,
> wolf
>
> On 21/07/13 21:18, Yael Grossman wrote:
>> Hi,
>> So I've aligned my two images (input and reference) and used flirt to generate a matrix, but when I try to use that matrix in applyxfm4d, it says it cannot read the mat file. (I'm aligning CYT20110701C_5_regdefault_bptfpixo_gauss1_braintest1 to CYT20110627D_default_bptfpixo_gauss1_braintest1, both of which are 4D fMRI images).
>>
>> Here's the command line I use for flirt:
>> flirt -in /Users/yaelgrossman/Desktop/CYT20110701C.8P1/CYT20110701C_5_regdefault_bptfpixo_gauss1.nii.gz -ref /Users/yaelgrossman/Desktop/CYT20110627D.8L1/CYT20110627D_default_bptfpixo_gauss1.nii.gz -out /Users/yaelgrossman/Desktop/CYT20110701C.8P1/CYT20110701C_5_regdefault_bptfpixo_gauss1_flirt.nii.gz -omat /Users/yaelgrossman/Desktop/CYT20110701C.8P1/CYT20110701C_5_regdefault_bptfpixo_gauss1_flirt.mat
>>
>> Then the applyxfm4d:
>> applyxfm4d /Users/yaelgrossman/Desktop/CYT20110701C.8P1/CYT20110701C_5_regdefault_bptfpixo_gauss1_braintest1.nii.gz /Users/yaelgrossman/Desktop/CYT20110627D.8L1/CYT20110627D_default_bptfpixo_gauss1_braintest1.nii.gz /Users/yaelgrossman/Desktop/CYT20110701C.8P1/CYT20110701C_5_regdefault_bptfpixo_gauss1_flirt4D_braintest1_4D.nii.gz /Users/yaelgrossman/Desktop/CYT20110701C.8P1//Users/yaelgrossman/Desktop/CYT20110701C.8P1/CYT20110701C_5_regdefault_bptfpixo_gauss1_flirt_braintest1.mat -singlematrix
>>
>> This is the error:
>> Could not open matrix file /Users/yaelgrossman/Desktop/CYT20110701C.8P1//Users/yaelgrossman/Desktop/CYT20110701C.8P1/CYT20110701C_5_regdefault_bptfpixo_gauss1_flirt_braintest1.mat
>> Segmentation fault: 11
>>
>> I just don't know what applyxfm4d wants from my matrix, so if anyone can help, I would be extremely grateful!
>>
>> Thank you,
>> Yael
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