You have to have the directory structure set up properly. You can put task and rest in the same session or in different sessions

On 10/24/19 9:43 AM, Renew Andrade wrote:

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Dear FreeSurfer experts: I am trying to use my own data so I don’t have the same tutorial structure. I do keep the folder structure as similar as possible in order for FreeSurfer to run but I cannot have different sessions for example I just have resting or bold but not both. Is it a problem when running this analysis?

This is my directory structure

*➜ **~*cd /Users/andraderenew/Downloads/2 *➜ **2**git:(**master**) **✗*ls *rest* *➜ **2**git:(**master**) **✗*cd rest *➜ **rest**git:(**master**) **✗*ls dti_FA.nii.gz dti_L2.nii.gz dti_MD.nii.gz dti_S0.nii.gz dti_V2.nii.gz dti_L1.nii.gz dti_L3.nii.gz dti_MO.nii.gz dti_V1.nii.gz dti_V3.nii.gz *➜ **rest**git:(**master**) **✗*

Sincerely,  Andrade.

look in sess01/bold, you should see 001 and 002. Do you?

On 10/22/2019 9:40 AM, Renew Andrade wrote: External Email - Use Caution

Dear experts: I am trying to run preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run But the outcome is ERROR: no run directories found.

What could be wrong? If you need more information let me know!

Sincerely, Andrade.

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