Error: Folder does not exist error: recon-all-t1.sh

[teffalump]

When I try to run the recon-all-t1.sh shell script it has an error for the line below as that folder that does not exist. I believe I have tracked it to these lines

At the end of the shell script

raveio/inst/shell-templates/recon-all-t1.sh

Lines 126 to 130 in e3c52d6

	# Removing temporary fs root
	rm -r "$wdir_fs"
	# Copy raw MRI to FreeSurfer folder so 3D viewer can recognize it
	cp -f "$mri_path" "$SUBJECTS_DIR/fs/mri/rave_slices$mri_ext"

SUBJECTS_DIR is

raveio/inst/shell-templates/recon-all-t1.sh

Line 95 in e3c52d6

SUBJECTS_DIR="$wdir_fs/rave-imaging"

wdir_fs is in the .cache path, on my computer is expanded to ~/.cache/R/raveio/FreeSurfer/<subject id> and it is deleted by the rm command preceding cp and consequently SUBJECTS_DIR (~/.cache/R/raveio/FreeSurfer/<subject id>/rave-imaging) does not exist which caused the No such file or directory

I believe SUBJECTS_DIR should be exchanged for $wdir_actual/rave-imaging or equivalent, similar to:

raveio/inst/shell-templates/yael-preprocess.sh

Line 159 in e3c52d6

cp -f "$wdir_actual/rave-imaging/ants/mri/brain.finalsurfs.nii.gz" "$wdir_actual/rave-imaging/fs/mri/rave_slices.nii.gz"

[dipterix]

Yes, this is a typo+bug that existed for a while. Basically RAVE uses the brain.finalsurfs.mgz as underlay by default. RAVE allows you to set custom underlay by putting rave_slices.??? under the mri folder, provided that this file sits under the same coordinates as the T1 image.

I was trying to copy the raw T1 here and name it rave_slices. This operation is optional (part of reasons why I didn't fix it). Also, the T1 images are sometime too dark, or the contrast is too low. I'm currently working on the 3D viewer so you can adjust the brightness and contrast on the fly. Also I have recently release a new pipeline (with non-linear normalization to template MNI152) that does the brain masking and intensity correction without FreeSurfer.

Maybe it would be a good chance for me to come back and fix this after the dynamical contrast & brightness adjustment. Please let me know if this is urgent to you and I can prioritize.

[dipterix]

Also we have a slack channel for RAVE and YAEL for more interactive Q&A. Please let me know if you would like to join or send your edu email to slack at rave.wiki. Thanks for reporting this issue : )

[dipterix]

I fixed this problem. Could you update RAVE and retry? @teffalump

[teffalump]

Hi, sorry for delay. I'll try the updated code soon.

[dipterix]

Not a hurry at all. Thanks for posting this issue : )

[teffalump]

Just ran it on a new sEEG patient and works. Thanks.