On 9 March 2013 03:47, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Salil, can you run fslregister with --debug as the first option, capture
the terminal output, and send it to me?
thanks
doug

On 03/07/2013 09:02 PM, Anastasia Yendiki wrote:
>
> Hi Salil - I'm cc-ing Doug who may be able to help. The error happens
> when bbregister invokes fslregister, in this particular line of
> fslregister:
> set refvol = `stem2fname $SUBJECTS_DIR/$subjid/mri/$fsvol`
>
> When run on brainmask.mgz, it returns "ERROR: could not determine file".
>
> a.y
>
> On Wed, 6 Mar 2013, Salil Soman wrote:
>
>>
>> Thank you for your email. Changing the mask option got me past the
>> error I
>> was having initially, but now I get these new errors:
>>
>> mri_convert ERROR: could not determine file for
>> /mnt/glusterfs/salsoman/output/FS/WCA_0226_T1_FS/mri/ERROR:/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregis
>>
>> ter.30396/fslregister/refvol.fslregister.nii
>> mri_convert ERROR: could not determine file for
>> /mnt/glusterfs/salsoman/output/FS/WCA_0226_T1_FS/mri/ERROR:/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregis
>>
>> ter.30396/fslregister/refvol.fslregister.nii
>>
>> Thank you for your consideration.
>>
>> Best wishes,
>>
>> -S
>>
>> On Wed, Mar 6, 2013 at 1:15 PM, Anastasia Yendiki
>> <ayendiki@nmr.mgh.harvard.edu> wrote:
>>
>> Hi Salil - The problem is that you've set dob0 = 1 but you haven't set
>> b0mlist and b0plist, so it doesn't know where to find your field maps
>> to do
>> the B0 unwarping.
>>
>> a.y
>>
>>
>>
>
>

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