Following Chris’s advice I have looked into this a little more. If I have a T2w image in my fmriprep anat folder then fmriprep detects the T2w image and processes it along with the T1w image in the freesurfer mri directory.
Here is the contents of my anat folder for a single subject containing a T2w image.
aging1a âžś anat llr
total 29822
-rw-rw-r-- 1 bkraft infinite 1312 Feb 19 2018 sub-imove1011_ses-1_T1w.json
-rw-rw-r-- 1 bkraft infinite 1351 Feb 19 2018 sub-imove1011_ses-1_T2w.json
-rw-rw---- 1 bkraft infinite 10956897 Feb 19 2018 sub-imove1011_ses-1_T1w.nii.gz
-rw-rw---- 1 bkraft infinite 9050621 Feb 19 2018 sub-imove1011_ses-1_T2w.nii.gz
Here is the corresponding freesurfer/mri directory
aging1a âžś mri ls
aparc.a2009s+aseg.mgz brainmask.auto.mgz orig T2.prenorm.mgz
aparc+aseg.mgz brainmask.mgz orig.mgz talairach.label_intensities.txt
aparc.DKTatlas+aseg.mgz brain.mgz orig_nu.mgz talairach.log
aseg.auto.mgz ctrl_pts.mgz rawavg.mgz transforms
aseg.auto_noCCseg.label_intensities.txt filled.mgz rh.ribbon.mgz wm.asegedit.mgz
aseg.auto_noCCseg.mgz lh.ribbon.mgz ribbon.mgz wm.mgz
aseg.mgz mri_nu_correct.mni.log segment.dat wmparc.mgz
aseg.presurf.hypos.mgz mri_nu_correct.mni.log.bak T1.mgz wm.seg.mgz
aseg.presurf.mgz norm.mgz T2.mgz
brain.finalsurfs.mgz nu.mgz T2.norm.mgz
You can see the T2 images in the mri directory.
If I do the same thing with FLAIR images.
aging1a âžś anat llr
total 27982
-rw-rw---- 1 bkraft infinite 1351 Aug 29 11:54 sub-imove9011_ses-1_FLAIR.json
-rw-rw---- 1 bkraft infinite 10956897 Aug 29 11:54 sub-imove9011_ses-1_T1w.nii.gz
-rw-rw---- 1 bkraft infinite 9050621 Aug 29 11:54 sub-imove9011_ses-1_FLAIR.nii.gz
-rw-rw---- 1 bkraft infinite 1312 Aug 29 11:54 sub-imove9011_ses-1_T1w.json
Here is the corresponding freesurfer/mri directory
aging1a âžś mri ls
aparc.a2009s+aseg.mgz brain.finalsurfs.mgz norm.mgz T1.mgz
aparc+aseg.mgz brainmask.auto.mgz nu.mgz talairach.label_intensities.txt
aparc.DKTatlas+aseg.mgz brainmask.mgz orig talairach.log
aseg.auto.mgz brain.mgz orig.mgz transforms
aseg.auto_noCCseg.label_intensities.txt ctrl_pts.mgz orig_nu.mgz wm.asegedit.mgz
aseg.auto_noCCseg.mgz filled.mgz rawavg.mgz wm.mgz
aseg.mgz lh.ribbon.mgz rh.ribbon.mgz wmparc.mgz
aseg.presurf.hypos.mgz mri_nu_correct.mni.log ribbon.mgz wm.seg.mgz
aseg.presurf.mgz mri_nu_correct.mni.log.bak segment.dat
There is no corresponding FLAIR images. I have processed other data sets with FLAIR images directly with FreeSurfer’s recon-all scripts. Here is a snippet of that output.
aging1a âžś mri ls
aparc.a2009s+aseg.mgz mri_nu_correct.mni.log.bak
aparc+aseg.mgz norm.mgz
aseg.auto.mgz nu.mgz
aseg.auto_noCCseg.label_intensities.txt nu_noneck.mgz
aseg.auto_noCCseg.mgz orig
aseg.mgz orig.mgz
brain.finalsurfs.manedit.mgz orig_nu.log
brain.finalsurfs.mgz orig_nu.mgz
brain.finalsurfs.mgz.qm_edit_pial.bkraft.d20161215_110456 overlay_ortho.png
brain.finalsurfs.mgz.qm_edit_pial.clinvill.d20161214_134308 rawavg.mgz
brain.finalsurfs.mgz.qm_edit_pial.clinvill.d20161214_135103 rh.ribbon.mgz
brainmask.auto.mgz ribbon.mgz
brainmask.mgz segment.dat
T1.mgz
talairach.label_intensities.txt
talairach.log
brain.mgz transforms
ctrl_pts.mgz wm.asegedit.mgz
filled.mgz wm.mgz
FLAIR.mgz wmparc.mgz
lh.ribbon.mgz wm.seg.mgz
mri_nu_correct.mni.log
The FLAIR images are clearly present in the standard FreeSurfer recon-all processing.
I checked the logs of the fmriprep processing the FLAIR images and I didn’t see any errors or anything out of the ordinary.
Any suggestions on what is the next step to track down this problem, which could be human error on my part, would be greatly appreciated.
Thanks.
Bob