Hi Again,
I now think I understand what you meant.
You are not trying to run registration and segmentation
separate from FIRST, but instead running them as
separate steps as part of FIRST - right?
However, I still need to know the exact command
you are running and what is failing (in the previous
email I meant to say that *without* this info we
cannot diagnose the problem). In your original
email sounded like run_first or run_first_all was
failing, as you got the *.com* files. But from this email
it looks like first_flirt is failing. Can you just confirm
the exact command you are running and all the
files and errors it produces. From this we should
be able to sort it out.
All the best,
Mark
On 12 Nov 2010, at 01:45, Mark Jenkinson wrote:
> Hi,
>
> I'm still not clear on what you are doing.
> Can you send the exact first_flirt and run_first command lines?
> With that it is too difficult to diagnose the problem.
>
> Also, what do you mean by saying that you run the "segmentation"
> separately?!? That is what FIRST is intended to do - segmentation.
> How can you run this separately??
>
> All the best,
> Mark
>
>
> On 11 Nov 2010, at 22:42, Michael Bonares wrote:
>
>> Thanks Mark. I should have elaborated. "This problem" refers to the inability of the run_first_all command to be executed properly, resulting in the previously mentioned outputs (.com files and .logs folder), but not the expected .nii.gz, .vtk, and .bvars files.
>>
>> I decided to run the registration and the segmentation separately. After running first_flirt output_name output_name_to_std_sub -b, the following error message appears:
>>
>> STOPPING PROGRAM
>> Stage 2: use subcortical mask
>> ** ERROR (nifti_image_read): failed to find header file for 'Feb01_2008_T1_nu_final_masked_to_std_sub_tmp_stage1'
>> ** ERROR: nifti_image_open(Feb01_2008_T1_nu_final_masked_to_std_sub_tmp_stage1): bad header info
>> Error: failed to open file Feb01_2008_T1_nu_final_masked_to_std_sub_tmp_stage1
>> ERROR: Could not open image Feb01_2008_T1_nu_final_masked_to_std_sub_tmp_stage1
>> Image Exception : #22 :: Failed to read volume Feb01_2008_T1_nu_final_masked_to_std_sub_tmp_stage1
>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>> /usr/local/fsl//bin/first_flirt: line 116: 2137 Aborted ${FSLDIR}/bin/flirt -in ${B}_tmp_stage1 -out ${B}_tmp_stage2 -ref ${FSLDIR}/data/standard/${refim} -omat ${B}_tmp_stage2.mat -nosearch -refweight ${FSLDIR}/data/standard/MNI152lin_T1_1mm_subbr_mask
>> Could not open matrix file Feb01_2008_T1_nu_final_masked_to_std_sub_tmp_stage1.mat
>> Cannot read input-matrix
>>
>> Any advice?
>>
>> Michael
>>
>> On Wed, Nov 10, 2010 at 7:24 PM, Mark Jenkinson <[log in to unmask]> wrote:
>> Hi,
>>
>> I'm not sure what "this problem" is.
>> The files you mention are simply initial files giving
>> commands and log files. Check the output_name.logs
>> directory and see if there are any error messages in
>> the *.e* files, as it says in the documentation.
>> Hopefully this will shed some light on the problem.
>>
>> All the best,
>> Mark
>>
>>
>> On 10 Nov 2010, at 18:13, Michael B wrote:
>>
>>> I also have this problem and have not yet figured out how to solve it.
>>>
>>> Again, the output is as follows:
>>> output_name.com
>>> output_name.com2
>>> output_name.com3
>>> output_name.logs
>>>
>>> This is in addition to the appearance of a random 5-digit number on the bash terminal, after the run_first_all command has been executed.
>>>
>>> Michael
>>>
>>
>
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