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This is typically done *before* running FreeSurfer, and to the best of my knowledge, there is no FreeSurfer tool that does it. Also I think there is no one way to do it in generak. The names produced depend on your DICOM to NIFTI conversion software and can typically be influenced by many different command line arguments/settings passed to the software.
We use a bash shell script to run the conversion from DICOM to Nifti (using the dcm2niix Software) and then rename the files accordingly, but the script needs to be adapted slightly for each new data set.
Tim
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
On 02/14/2022 7:53 AM krystaly krystaly@hku.hk wrote:
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Dear Freesurfer experts,
There are a bunch of RAW DICOM files in my dataset. I recognize that the name of the images begins with Z, i.e. “Z01”, “Z02”… “Z8568”. After converting them into NIfTI format with mricron, it yields the name in this format: myFolder_MPRAGE_19770703150928_1.nii
It’s rather inconvenient to have those names and have been stuck on organizing the images in different categories, i.e. T1, T2, M0, FLAIR and PCASL. I would like to have them named by subject numbers rather than a series of name and digits. For example, T2 DICOM images of a Subject 101 are named 101.nii under a folder called “T2”.
Could you please advise if there is anyway categorizing the patients’ data into aforementioned categories automatically with Freesurfer?
You help will be highly appreciated! Thanks.
Best regards, Krystal
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