Hi Priti,
I removed the NaNs in the 4D images and re-ran trac-all -prep. The
warning message is gone (of course) but the error message of
dlable/diff/White-Matter++.flt.nii.gz is still there since no
"White-Matter++.flt.nii.gz" in the diff directory. Only one image in
dlabel/diff/: lowb_brain_mask.nii.gz.
fslstats -t /home/xkang/DTI//S0001/dmri/dwi.nii.gz -k
/home/xkang/DTI//S0001/dlabel/diff/White-Matter++.flt.nii.gz -m -s |
awk '{print $1/$2}' > /home/xkang/DTI//S0001/dmri/dwi_snr.txt
** ERROR (nifti_image_read): failed to find header file for
'/home/xkang/DTI//S0001/dlabel/diff/White-Matter++.flt'
** ERROR:
nifti_image_open(/home/xkang/DTI//S0001/dlabel/diff/White-Matter++.flt):
bad header info
ERROR: failed to open file
/home/xkang/DTI//S0001/dlabel/diff/White-Matter++.flt
ERROR: Could not open image
/home/xkang/DTI//S0001/dlabel/diff/White-Matter++.flt
Image Exception : #22 :: Failed to read volume
/home/xkang/DTI//S0001/dlabel/diff/White-Matter++.flt.nii.gz
I am not sure if the error will affect the next steps of -bedp and
-path. I want to make sure before run -bedp since that will take several
hours.
Also there is no dpath directory yet. Probably it will be created during
the -path processing?
Thanks.
XJ
On 6/15/2012 12:15 PM, Priti Srinivasan wrote:
> Hi XJ,
>
> I'm just starting to look at your log files. Just curious, did you decide
> to not do eddy current correction and b0 inhomogenity correction or
> accidentally left it out?
>
> When I look at the configuration file, you've given all the parameters for
> b0 inhomogenity correction, but it is set to '0' (set dob0 = 0) and the
> same is the case for eddy current correction too (set doeddy = 0). Just
> wanted to make sure you did not set that '0' accidentally. Eddy current
> correction is definitely one of the recommended preprocessing steps, so
> you might want to consider doing that.
>
> Also looks like your original input dwi file (with NaNs) may be the root
> cause of the problem. If you do have the original dicoms, you can give
> that as an input. I'm not sure if you can give a series of 3D Nifti DWI
> files as an input in the configurations file...Anastasia (cc'd) might be
> able to answer that question.
>
> Hope that helps,
> Priti
>> ---------------------------- Original Message ----------------------------
>> Subject: Re: [Freesurfer] TRACULA dpath problem
>> From: "XJ Kang"<xk...@ucdavis.edu>
>> Date: Fri, June 15, 2012 2:22 pm
>> To: "Priti Srinivasan"<rspr...@nmr.mgh.harvard.edu>
>> --------------------------------------------------------------------------
>>
>> Hi Priti,
>>
>> Attached are the tracula conf file and log files from two subjects.
>>
>> I ran the two subjects. The results are almost the same. Here are what I
>> found so far:
>>
>> 1. There are NaN values in the 4D image. I created it from 3D images
>> using "fslmerge -a", and the 3G images have no NaNs.
>> 2. The image "dlabel/diff/White-Matter++.flt" was not found. Probably
>> this is the origin of all the problems?
>>
>> Do you want me to send the email to you or to the mailing list? Probably
>> many people are not interested in my email if I post on the whole list.
>>
>> Thank you.
>>
>> XJ
>>
>> On 6/15/2012 11:02 AM, Priti Srinivasan wrote:
>>> Can you send us your configuration file (mytracula.conf) and log file
>>> (it
>>> should be under scripts/trac-all.log). I can take a look.
>>>
>>> Priti
>>>
>>>> Hi,
>>>>
>>>> I am trying to run the last step of TRACULA. I used the command line:
>>>>
>>>> % trac-all -path -c mytracula.conf
>>>>
>>>> Here is all the info I got on the screen:
>>>>
>>>> INFO: SUBJECTS_DIR is /home/sata2/FreeSurfer/Subjects.Verio
>>>> INFO: Diffusion root is /home/xkang/DTI/
>>>> Actual FREESURFER_HOME /home/local/freesurfer-v510
>>>> trac-paths -c /home/xkang/DTI//S0006/scripts/dmrirc.local -log
>>>> /home/xkang/DTI//S0006/scripts/trac-all.log -cmd
>>>> /home/xkang/DTI//S0006/scripts/trac-all.cmd
>>>> #-------------------------------------
>>>> /usr/local/freesurfer/bin/trac-paths
>>>> #-------------------------------------
>>>> #@# Path reconstruction Fri Jun 15 10:47:44 PDT 2012
>>>> #-------------------------------------
>>>> trac-paths finished without error at Fri Jun 15 10:47:44 PDT 2012
>>>>
>>>>
>>>>
>>>> I didn't see "dpath" under the subject's directory. Seems nothing has
>>>> been done. I already ran the "trac-all -prep" and "trac-all -bedp". I
>>>> have the directories dlable, dmri and dmir.bedpostX, but not dpath. Can
>>>> any body help where the problems are?
>>>>
>>>> I use DTI images in NIFTI format and the resolution is 2x2x2, which is
>>>> not the same as that of the FreeSurfer orig.mgz. Probably this is fine.
>>>>
>>>> Thanks.
>>>>
>>>> XJ Kang
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>>>>
>>>>
>>>>
>>>
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