External Email - Use Caution
Thank you Doug.
The preproc-sess command line runs fine.
An error occurs on:
fcseed-sess -s ID -cfg wm.config -overwrite
ERROR: could not determine file for rs-fMRI_AROMA/ID/rest/001/fmcpr
Best regards
Stefano
> Il giorno 19 mar 2024, alle ore 15:54, Douglas N. Greve
> <dgr...@mgh.harvard.edu> ha scritto:
>
> Hi Stefano, I think I found and fixed the problem. Can you try these?
>
> On 3/19/2024 7:30 AM, Stefano Delli Pizzi wrote:
>> External Email - Use Caution
>>
>> Hi Doug,
>>
>> The raw functional file is firstly passed with motion correction (i.e.,
>> mc-sess -s ID -fsd rest -per-run) and AROMA filtering.
>> Next, I have renamed the ICA filtered file as f.nii.gz.
>> Then, I run:
>>
>> preproc-sess -s ${1} -surface fsaverage lhrh -nomc -fwhm 0 -mni305 -fsd rest
>> -per-run -sliceorder even -force
>>
>> There are issues with labels since excluding motion correction doesn't
>> produce key files necessary for concatenating the files.
>> The preprocessing script is searching for the fmcpr.nii.gz file, which
>> cannot be found because it is not created using the -nomc option.
>>
>> When I duplicate and rename the file f.nii.gz as fmcpr.nii.gz and rerun
>> preproc, the operation is done and the fmcpr.odd.sm0.fsaverage.lh is
>> created.
>>
>> However, when I run the next steps (fcseed-sess -s ID -cfg wm.config
>> -overwrite), a second error occurs (reported below) because the script
>> searches for fmcpr, which cannot be produced since I used -mc.
>>
>> ERROR: could not determine file for
>> /Volumes/mnu/MRI/PPMI/NIFTI/FreeSurfer/rs-fMRI_AROMA/ID/rest/001/fmcpr This
>> error seems to be related to the script searching for the fmcpr file, which
>> isn't available due to the use of -mc.
>>
>> Thank you.
>>
>> Best regards,
>>
>>
>> Stefano
>>
>>
>>
>>
>>> Il giorno 18 mar 2024, alle ore 17:16, Stefano Delli Pizzi
>>> <sdellipi...@gmail.com <mailto:sdellipi...@gmail.com>> ha scritto:
>>>
>>> Hi Doug have you any news
>>> Thank you very much!
>>> Stefano
>>>
>>>> Il giorno 12 mar 2024, alle ore 10:26, Stefano Delli Pizzi
>>>> <sdellipi...@gmail.com <mailto:sdellipi...@gmail.com>> ha scritto:
>>>>
>>>> Thank you.
>>>> I’m attaching the file.
>>>> Stefano
>>>> <preproc-sess>
>>>>
>>>>> Il giorno 11 mar 2024, alle ore 22:20, Douglas N. Greve
>>>>> <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> ha scritto:
>>>>>
>>>>> can you send me this file
>>>>> /Applications/freesurfer/7.4.1/fsfast/bin/preproc-sess
>>>>>
>>>>>
>>>>> On 3/11/2024 3:58 AM, Stefano Delli Pizzi wrote:
>>>>>> External Email - Use Caution
>>>>>>
>>>>>> It seems to me that I've done what you suggest.
>>>>>> Attached is a new outputs.
>>>>>> Thanks
>>>>>> Stefano
>>>>>>
>>>>>>
>>>>>>
>>>>>>> Il giorno 10 mar 2024, alle ore 23:44, Douglas N. Greve
>>>>>>> <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> ha scritto:
>>>>>>>
>>>>>>> Are you sure that you are using the new version that I gave you? It
>>>>>>> looks like the previous version. Also, it does not look like the entire
>>>>>>> terminal output.
>>>>>>>
>>>>>>> On 3/8/2024 12:11 PM, Stefano Delli Pizzi wrote:
>>>>>>>> External Email - Use Caution
>>>>>>>>
>>>>>>>> The entire terminal output is attached.
>>>>>>>> Thanks!
>>>>>>>>
>>>>>>>>> Il giorno 8 mar 2024, alle ore 15:56, Douglas N. Greve
>>>>>>>>> <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> ha scritto:
>>>>>>>>>
>>>>>>>>> entire terminal output
>>>>>>>>
>>>>>>>
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>>>>>>>
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>>>>>>> .
>>>>>>
>>>>>
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>>>>> <https://secure-web.cisco.com/1jYq_7i1WV2KuJNwpF_8LuUmEt1uXm4GShRtNXC1xe4Y_Bcgi7ubGv5tYLWaiMMMvai3kMGIy815rdOHCuxa26TgzCG7N39_7gO7R1qweyEpbyWhg2jPzT7Jn6y5R9IDYEnulWkwidyb-Qib5lu4h6a_s5YcAdb0N9IiBeDpqWrbBe0hv15Vk8W8n6xL2cuFQJvTXex04uH4CPIgZEpJ6hpPWv7aOcOY-RxxGp_lf2-1SdLn_S3KEKrLQ68nS_U4WOd-L3Q1TxZnV8azAM2dMdrMpcc6aFGCMa7ROC27axgF_fs3uFwdABdIGbgPRYiaC/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
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>>>>
>>
>
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> .
>
> <preproc-sess.txt><rawfunc2surf-sess.txt><rawfunc2tal-sess.txt>
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