Hi Mahmoud,
Sorry for the delay in answering your question below. I was away for the
holidays for a while.
Have you already resolved the issue you describe (the "no output
filename specified" error in the FreeSurferPipeline)? I noticed a
subsequent message from you to the hcp-users list in which you state:
I've applied HCP pipeline scripts to our structural data and it looks
like everything goes well to the end of PostFreeSurferPipelline.
That being the case, does that mean that you've already resolved the
problem with the "Error: no output filename specified!" in the
FreeSurferPipeline?
If you have, you can likely ignore the remainder of this message.
-------------------------
I have taken a look at the log files that you sent, and it appears to me
that the FreeSurferHiresPial.sh script (which is invoked as part of the
FreeSurferPipeline) is successfully running through line 52 in the
current latest version of the FreeSurferHiresPial.sh script. That line
looks like:
52: mri_surf2surf --s $SubjectID --sval-xyz pial.T2 --reg $regII
$mridir/orig.mgz --tval-xyz --tval pial --hemi rh
After that line, there are statements that extract some information from
the brain.finalsurfs.mgz file and create the
<studydir>/<subjectid>/T1w/<subjectid>/mri/c_ras.mat matrix file.
54: MatrixX=`mri_info $mridir/brain.finalsurfs.mgz | grep "c_r" | cut -d
"=" -f 5 | sed s/" "/""/g`
55: MatrixY=`mri_info $mridir/brain.finalsurfs.mgz | grep "c_a" | cut -d
"=" -f 5 | sed s/" "/""/g`
56: MatrixZ=`mri_info $mridir/brain.finalsurfs.mgz | grep "c_s" | cut -d
"=" -f 5 | sed s/" "/""/g`
57: echo "1 0 0 ""$MatrixX" > $mridir/c_ras.mat
58: echo "0 1 0 ""$MatrixY" >> $mridir/c_ras.mat
59: echo "0 0 1 ""$MatrixZ" >> $mridir/c_ras.mat
60: echo "0 0 0 1" >> $mridir/c_ras.mat
Next is a call to mris_convert on line 62 of the
FreeSurferHiresPial.sh script.
62: mris_convert "$surfdir"/lh.white "$surfdir"/lh.white.surf.gii
I don't seem to find any evidence in your log files that the call to
mris_convert is succeeding. So your run seems to be ending with the
"Error: no output filename specified!" message somewhere between lines
54 and 62.
It seems a bit unlikely that the problem is in lines 54 through 60, but
just to check, can you confirm for me that the file
<studydir>/<subjectid>/T1w/<subjectid>/mri/c_ras.mat exists? In the case
shown in your logs, I believe this file should actually be named:
/home/mydata/HCPReady/111_Sigma7/T1w/111_Sigma7/mir/c_ras.mat. If it
exists, is it a 4 line text file that looks something like the
following?
1 0 0 -1.0000
1 0 -17.5000
0 1 19.0000
0 0 1
The last numeric values on each of the first three lines will probably
differ from the above.
Assuming that the c_ras.mat file is successfully created, then I would
note that line 62 is the first use of the $surfdir variable in the
FreeSurferHiresPial.sh script (after setting its value). In the case
shown in your log files, the $surfdir variable should have a value of
/home/mydata/HCPReady/111_Signma7/T1w/111_Sigma7/surf.
Could you please verify that such a directory exists and is writable?
Thanks,
Tim
On Tue, Dec 22, 2015, at 07:06, Mahmoud wrote:
> Hello Tim and others,
>
> Following the previous posts, I renamed my dataset directory and ran
> the PreFreeSurferPipeline on it and it looks like finished
> successfully. After running the FreeSurferPipeline I got the same
> error "Error: no output filename specified!" . I've attached the
> FreeSurferPipeline output and error log here for you reference.
>
> I appreciate your help and time.
>
> Thank you, Mahmoud
>
> On Fri, Dec 18, 2015 at 11:39 AM, Mahmoud <[email protected]> wrote:
>> Dear Tim,
>>
>> I got it. Thank you for detailed explanation.
>>
>> Best, Mahmoud
>>
>> On Fri, Dec 18, 2015 at 11:29 AM, Timothy B. Brown
>> <[email protected]> wrote:
>>> Hi Mahmoud,
>>>
>>> Short answer:
>>>
>>> Because of directory structure conventions and file naming
>>> conventions used in the pipeline scripts, you cannot rename the
>>> subject directory and expect that the pipelines will run without (at
>>> least) also renaming a number of other files in the subject
>>> directory. So renaming the subject directory will break quite a
>>> number of things.
>>>
>>> Long answer:
>>>
>>> The FreeSurferPipeline in particular and the other pipeline scripts
>>> in general depend upon a directory structure for the data that has a
>>> root *study* folder in which each subdirectory of that *study*
>>> folder is named for the subject id. So if the data you are
>>> processing are in a directory named my_study, and you had only two
>>> subjects with subject ids xyz and abc, then you would need to have
>>> xyz and abc subdirectories in your my_study directory.
>>>
>>> Seems like you've got that all set up correctly initially.
>>>
>>> But...the pipeline scripts also depend upon file naming conventions
>>> that use the subject id in the file names. For example, if the
>>> subject subdirectory is named xyz, then a number of files in that
>>> directory tree will be expected to be named starting with xyz. For
>>> example, there is an expectation that there will be a file named
>>> my_study/xyz/unprocessed/3T/T1_MPR1/xyz_3T_T1w_MPR1.nii.gz. Notice
>>> that the two places the subject id is used have to match. Similarly,
>>> many of the pipelines will generate output files that are used by
>>> subsequent pipelines using a naming convention in which the names of
>>> the generated files will start with the subject id.
>>>
>>> So, I suspect that this is the problem you are encountering. When
>>> you run FreeSurferPipeLineBatch and tell it to process subject
>>> xyz_1, the FreeSurferPipeline script is expecting to find a number
>>> of input files with names that start with xyz_1. But they're not
>>> there because your xyz_1 directory is just a copy of the original
>>> xyz directory. So many of the files in it start with simply xyz.
>>>
>>> Hope that helps,
>>>
>>> Tim
>>>
>>> On Fri, Dec 18, 2015, at 07:55, Mahmoud wrote:
>>>> Dear experts,
>>>>
>>>> After running the PreFreeSurferPipelineBatch for subjectID = xyz I
>>>> changed the ID (i.e. renamed the subject directory name) to xyz_1
>>>> and ran the FreeSurferPipeLineBatch which ended up with this error
>>>> in the error log file (I just copied the few last lines):
>>>>
>>>> measuring cortical thickness... writing cortical thickness estimate
>>>> to 'thickness' file. positioning took 5.6 minutes Error: no output
>>>> filename specified!
>>>>
>>>> Is this because of that name change? if so, is there any solution
>>>> to it ?
>>>>
>>>> Thank you! Mahmoud
>>>> _______________________________________________
>>>>
HCP-Users mailing list
>>>> [email protected]
>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>> --
>>> Timothy B. Brown Business & Technology Application Analyst III
>>> Pipeline Developer (Human Connectome Project) tbbrown(at)wustl.edu
>>> ________________________________________
>>> The material in this message is private and may contain Protected
>>> Healthcare Information (PHI). If you are not the intended recipient,
>>> be advised that any unauthorized use, disclosure, copying or the
>>> taking of any action in reliance on the contents of this information
>>> is strictly prohibited. If you have received this email in error,
>>> please immediately notify the sender via telephone or return mail.
> Email had 2 attachments:
> * FreeSurferPipeline.sh.e1326051
>
25k (application/octet-stream)
> * FreeSurferPipeline.sh.o1326051
>
465k (application/octet-stream)
--
Timothy B. Brown
Business & Technology Application Analyst III
Pipeline Developer (Human Connectome Project)
tbbrown(at)wustl.edu
________________________________________
The material in this message is private and may contain Protected Healthcare
Information (PHI).
If you are not the intended recipient, be advised that any unauthorized use,
disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited.
If you have received this email in error, please immediately notify the sender
via telephone or
return mail.
_______________________________________________
HCP-Users mailing list
[email protected]
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
