[Freesurfer] Error running recon from command line

[Harshad Shanbhag]

Hello,

I installed FreeSurfer according to instructions on the website. To
overlay FSL data, I used the following instructions from the FMRIB
website.

avwswapdim TEST x -z y TEST_reorient
slices TEST_reorient
bet TEST_reorient TEST_brain -f 0.4
mri_convert /home/bbernal/freesurfer/subjects/TEST/mri/orig/001/TEST_brain.img .
recon-all -stage1 -subjid TEST

However, the program gives me errors at this stage. I saved the error
messages to the file that I have attached. Could you please have a
look at it and help me with this.

Thank you.

Sincerely,
Harshad.


error log
Description: Binary data
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[Freesurfer] Tksurfer Error

[Harshad Shanbhag]

Hello,

I am facing a problem in running tkmedit or tksurfer. So I looked up
the posts and
found a thread which explained using tkmedit.static instead of
tkmedit. I did that and I could run tkmedit. However, I can't find the
tksurfer.static file in that same directory. Please let me know how I
could run tksurfer.

I get this error message when i run tksurfer from the command line.

tksurfer: error while loading shared libraries: libglut.so.3: cannot
open shared object file: No such file or directory.

Thank You.

Sincerely,
Harshad.
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[Freesurfer] Error: Nu Correct

[Harshad Shanbhag]

Hi all,

I am trying to use FreeSurfer to overlay FSL data. 

On running the command
$ recon-all -stage1 -subjid TEST

I get the following error,

Nu Intensity Correction Tue Mar  1 14:54:08 EST 2005
mri_convert orig nu/nu0.mnc
mri_convert orig nu/nu0.mnc
reading from orig...
TR=1.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to nu/nu0.mnc...
nu_correct -clobber nu/nu0.mnc nu/nu1.mnc
nu_correct: Command not found.
ERROR: nu_correct

I do have MNI Tools installed, in the freesurfer folder.

Please let me know what I should do.

Thank you.
Harshad.
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[Freesurfer] (no subject)

[Harshad Shanbhag]

Hi all,

My earlier error was due to perl not properly configured. Thank you
all for the help. However, on running

recon-all -stage1 -subjid TEST, I am now getting the error message
mri_fill: could not find corpus callosum
No such file or directory
INFO: Modifying dst c_(r,a,s), using the transform dst
ERROR: mri_fill exited with non-zero status

Please help me out.

Thank you,
Harshad.
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