Hi XJ - In your configuration file, you've set both doregflt and doregbbr
to 0. You have to set one of them to 1, otherwise no intra-subject
registration will be done and every step that relies on it will fail.
a.y
On Fri, 15 Jun 2012, XJ Kang wrote:
> 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
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>
>>>>>
>>>>>
>>>>
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>>> it is
>>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
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