[Freesurfer] MCSRCH ERROR

[Kenichiro Tanaka]

Hello All,

While processing a brain image data(.mgz) through ver5.0.0, I got the
following errors.
I have no idea how to resolve them.
I need outputs in stats directory, there are only lh.aparc.a2009s.stats,
lh.aparc.stats, and lh.curv.stats.
What caused them?
How should I resolve them?

IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR
RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE
INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 005: -log(p) =
10318.1 tol 0.10
.
.
.
inflating to sphere (rms error  2.00)
000: dt: 0., rms radial error=175.699, avgs=0
005/300: dt: 0.9000, rms radial error=175.446, avgs=0
010/300: dt: 0.9000, rms radial error=174.904, avgs=0
015/300: dt: 0.9000, rms radial error=174.193, avgs=0
020/300: dt: 0.9000, rms radial error=173.383, avgs=0
025/300: dt: 0.9000, rms radial error=172.518, avgs=0
030/300: dt: 0.9000, rms radial error=171.620, avgs=0
035/300: dt: 0.9000, rms radial error=170.706, avgs=0
040/300: dt: 0.9000, rms radial error=169.784, avgs=0
045/300: dt: 0.9000, rms radial error=168.860, avgs=0
050/300: dt: 0.9000, rms radial error=167.935, avgs=0
055/300: dt: 0.9000, rms radial error=167.012, avgs=0
060/300: dt: 0.9000, rms radial error=166.092, avgs=0
065/300: dt: 0.9000, rms radial error=165.175, avgs=0
070/300: dt: 0.9000, rms radial error=164.262, avgs=0
075/300: dt: 0.9000, rms radial error=163.352, avgs=0
080/300: dt: 0.9000, rms radial error=162.447, avgs=0
085/300: dt: 0.9000, rms radial error=161.547, avgs=0
090/300: dt: 0.9000, rms radial error=160.651, avgs=0
095/300: dt: 0.9000, rms radial error=159.759, avgs=0
100/300: dt: 0.9000, rms radial error=158.871, avgs=0
105/300: dt: 0.9000, rms radial error=157.989, avgs=0
110/300: dt: 0.9000, rms radial error=157.110, avgs=0
115/300: dt: 0.9000, rms radial error=156.236, avgs=0
120/300: dt: 0.9000, rms radial error=155.367, avgs=0
125/300: dt: 0.9000, rms radial error=154.502, avgs=0
130/300: dt: 0.9000, rms radial error=153.642, avgs=0
135/300: dt: 0.9000, rms radial error=152.786, avgs=0
140/300: dt: 0.9000, rms radial error=151.934, avgs=0
145/300: dt: 0.9000, rms radial error=151.087, avgs=0
150/300: dt: 0.9000, rms radial error=150.245, avgs=0
155/300: dt: 0.9000, rms radial error=149.407, avgs=0
160/300: dt: 0.9000, rms radial error=148.573, avgs=0
165/300: dt: 0.9000, rms radial error=147.744, avgs=0
170/300: dt: 0.9000, rms radial error=146.919, avgs=0
175/300: dt: 0.9000, rms radial error=146.098, avgs=0
180/300: dt: 0.9000, rms radial error=145.282, avgs=0
185/300: dt: 0.9000, rms radial error=144.470, avgs=0
190/300: dt: 0.9000, rms radial error=143.663, avgs=0
195/300: dt: 0.9000, rms radial error=142.860, avgs=0
200/300: dt: 0.9000, rms radial error=142.061, avgs=0
205/300: dt: 0.9000, rms radial error=141.266, avgs=0
210/300: dt: 0.9000, rms radial error=140.476, avgs=0
215/300: dt: 0.9000, rms radial error=139.693, avgs=0
220/300: dt: 0.9000, rms radial error=138.914, avgs=0
225/300: dt: 0.9000, rms radial error=138.140, avgs=0
230/300: dt: 0.9000, rms radial error=137.370, avgs=0
235/300: dt: 0.9000, rms radial error=136.604, avgs=0
240/300: dt: 0.9000, rms radial error=135.842, avgs=0
245/300: dt: 0.9000, rms radial error=135.085, avgs=0
250/300: dt: 0.9000, rms radial error=134.332, avgs=0
255/300: dt: 0.9000, rms radial error=133.583, avgs=0
260/300: dt: 0.9000, rms radial error=132.838, avgs=0
265/300: dt: 0.9000, rms radial error=132.098, avgs=0
270/300: dt: 0.9000, rms radial error=131.362, avgs=0
275/300: dt: 0.9000, rms radial error=130.629, avgs=0
280/300: dt: 0.9000, rms radial error=129.901, avgs=0
285/300: dt: 0.9000, rms radial error=129.177, avgs=0
290/300: dt: 0.9000, rms radial error=128.456, avgs=0
295/300: dt: 0.9000, rms radial error=127.740, avgs=0
300/300: dt: 0.9000, rms radial error=127.028, avgs=0

spherical inflation complete.
.
.
.
epoch 4 (K=1280.0), pass 1, starting sse = 541.21
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.32/19 = 0.01710
finalwriting spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.10 hours
distance error %10.00
.
.
.
pass 1: epoch 1 of 3 starting distance error %21.36
pass 1: epoch 2 of 3 starting distance error %21.04
unfolding complete - removing small folds...
starting distance error %20.80
removing remaining folds...
final distance error %20.81
364: 0 negative triangles
.
.
.


Thanks,

Kenichiro Tanaka.

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[Freesurfer] the Subcortical Segmentation and the Cortical Parcellation

[Kenichiro Tanaka]

Hello All,

I have a question about segmentation and parcellation.

What is the difference between the subcortical segmentation and the
cortical parcellation?
Especially I do not understand the difference between subcortical and
cortical and between segmentation and parcellation.
I tried to read FreeSurfer Wiki, but I did not understand it well.
Could you tell me it?

Thanks.

Kenichiro Tanaka.

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[Freesurfer] about recon-all command

[Kenichiro Tanaka]

Hello All,

I have a question about recon-all command with -cw256 option.
What is the difference between recon-all and recon-all with -cw256?
What is -cw256 option?

When I tried executing recon-all command, I had an error message:

/
// ERROR! FOV=320.000  256
// Include the flag -cw256 with recon-all!
//
/

I did the following using another 001.mgz file:

I compared aseg.stats file after recon-all execution with aseg.stats
file after
recon-all -cw256 execution using diff command.
aseg.stats file after recon-all  execution was much different from
aseg.stats file after
recon-all -cw256 execution.
What's wrong with it?

I tried to search information about -cw256on internet, but I could not
find out.
Please tell me -cw256.

Thanks.

Kenichiro Tanaka
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[Freesurfer] mri_convert question: converting dicom to mgz

[Kenichiro Tanaka]

Hello, all.
I have not been able to convert dicom files to a mgz file using mri_convert.
Could you tell me how to use mri_convert to do that and the example?
I typed the following command and run:

mri_convert -it dicom -ot mgz 001/ 001.mgz

Then I got the following message:
mri_convert -it dicom -ot mgz 001/ 001.mgz
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from 001/...
Starting DICOMRead2()
dcmfile = 001
dcmdir = .
ERROR: 001 is not a dicom file

There are 126 dicom files in the directory 001/.
OS is CentOS 4.8(64bit), and the version of the Freesurfer I am using is 4.5. 
Thank you for all your help.

Kenichiro Tanaka.

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dispose of the e-mail.