Hi Ye
you need to give recon-all a T1-weighted anatomical (e.g. mprage,
SPGR/FLASH, etc...), not the fMRI data.
cheers
Bruce
On Wed, 26 Jun 2013, ye tian wrote:
Dear Bruce,
Recon-all exits with the following error
ERROR: input(s) cannot have multiple frames!
$SUBJECTS_DIR/Barba50527_2/mri/orig/001.mgz has 439 frames
If I open 001.mgz using freeview, I obtain the image in the attachment saved
as freeview 001.mgz.png.
In order to make sure that my problem does not come from further upstream, I
am including the major steps that I took to get to this error.
MAJOR STEPS
STEP0:
My inherited data has names
BARBA50527.MR.MEDITATE_MEDITATION.#.#.year.month.day.#.#.#.#.#.IMA
where each # is a string of numbers.
STEP1:
The images can be grouped into five categories, according to the numbers in
the names that occupy the positions of the red #: 1.1-1.3, 2.1,
3.1-3.160, 4.1-4.439, 5.1-5.439
[1] Note: Images from groups 4 & 5 are very different from the images of
groups 1, 2 and 3. A link to a youtube video of all the images can be seen
in note[1].
STEP2:
recon-all -s Barba50527_2
-i
/Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.4.1.2010.07.27.10.52.51
.437500.56148038.IMA
-i
/Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.5.1.2010.07.27.10.52.51
.437500.56148502.IMA
recon-all completes without error.
[2] Note: other attempts leads to different errors. See note [2] for
details.
STEP3:
recon-all -s Barba50527_2 -autorecon1
Exits with the error message at the beginning of the email. The number 439
seems to come from the number of files in each group.
USEFUL COMMENTS
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23764.html
I will do it for 001.mgz and 002.mgz and will let you know how it goes.
QUESTIONS
1. Do I really need to manually parse the sequence of images? If so, how?
2. I don't really need to mri_convert my files into other formats, e.g.,
.dcm, do I?
3. Each file from groups 4 and 5 have multiple images. Do I need to cut them
into sub-images, each with one brain?
Thank you very much!
Sincerely,
Ye
NOTES:
Note [1]
A video of the data can be found at
http://www.youtube.com/watch?v=W8ZFGvGvHVc&list=UUfGdQq3j1gqPAc4z6Spmu2g
On the top left corner:
the white text is: current frame number / total frame number
the yellow text is: the name of the frame
Note[2]
recon-all -s Barba50527_2
-i
/Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.1.1.2010.07.27.10.52.51
.437500.56141898.IMA
Completes without error
recon-all -s Barba50527_2 -autorecon1
Warning: only one run found
Error: MRIsample(): source matrix has zero determinant; matrix is: EOF
econ-all -s Barba50527_2
-i
/Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.1.1.2010.07.27.10.52.51
.437500.56141898.IMA
-i
/Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.2.1.2010.07.27.10.52.51
.437500.56148502.IMA
-i
/Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.3.1.2010.07.27.10.52.51
.437500.56148502.IMA
-i
/Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.4.1.2010.07.27.10.52.51
.437500.56148038.IMA
-i
/Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.5.1.2010.07.27.10.52.51
.437500.56148502.IMA
error.log: matrix dimensionality
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