Hi Rujing
what directory did you run the chmod from? You are probably better off
running:
chmod a+rx $FREESURFER_HOME/bin/*
see if that works. If not check yout path to make sure it includes that dir
cheers
Bruce
On Fri, 27 Dec 2013, Rujing Zha wrote:
Dear Bruce and others,
As my server has a bad graphic card, so I want to install freesurfer in my
computer. My computer can support OpenGL, and I installed ubuntu as I didnot
know how to setup the graphic card driver in CentOS(I didnot know whether it
was needed to setup). I completed the freeesurfer license and configured the
bashrc. Then I ran the freesurfer command, such as freeview, but it told me
that permission denied. So I "chmod 777 -R freesurfer", but it still told me
"permission denied". My system is "ubuntu1310desktopamd64".
Bruce, or others, would you please help me?
All what I have done is to visualize the overlay,underlay and annotation in
freeview but my server cannot do that.
Thanks.
All the best.
2013-12-27
____________________________________________________________________________
Rujing Zha
____________________________________________________________________________
发件人：Bruce Fischl <fis...@nmr.mgh.harvard.edu>
发送时间：2013-10-31 03:58
主题：Re: [Freesurfer] reconall error
收件人："Rashmi Singh"<rsi...@laureateinstitute.org>
抄送："freesurfer@nmr.mgh.harvard.edu"<freesurfer@nmr.mgh.harvard.edu>
Hi Rashmi
can you try 5.3 and see if it works? Alternatively you can email me the
orig.mgz and I can try it
Bruce
On Wed, 30 Oct 2013, Rashmi Singh wrote:
> Hey Bruce,
> I ran FreeSurfer recon -all (with flags -use-mritotal and -notal-check
> flags) with a data set that failed showing the same error that I had
> received earlier.
> I am sure have the correct data set.
> I am attaching the recon-all.log and the data.
> We have FreeSurfer Version 5.1.0
> Please advice.
> Thanks,
> Rashmi
>
> On 10/23/13 9:06 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
>
>> Hi Rashmi
>>
>> what version are you running? If 5.3, upload the subject and I'll take a
>> look
>> Bruce
>> On Tue, 22 Oct 2013, Rashmi Singh wrote:
>>
>>> Hello FreeSurfer experts,
>>> I am trying to run recon all on my data set, but I got following error
?? ?>>> message.
>>> Please help me understand the message and suggest solution.
>>> Thanks,
>>> Rashmi
>>>
>>> #@# Skull Stripping Tue Oct 22 13:57:00 CDT 2013
>>>
>>> /home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/ANAL2013/CombT
1T
>>> 2Practice/FreeSurfer/AA470-2prac/
>>> mri
>>>
>>> mri_em_register -skull nu.mgz
>>> /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca
>>> transforms/talairach_with_skull.lta
>>>
>>> aligning to atlas containing skull, setting unknown_nbr_spacing = 5
>>> reading 1 input volumes...
>>> logging results to talairach_with_skull.log
>>> reading '/opt/freesurfer/average/RB_all_withskull_2008-03-26.gca'...
>>> gcaAllocMax: node dims 64 64 64
>>> gcaAllocMax: prior dims 128 128 128
>>> gcaAllocMax: max_labels 0
>>> average std = 23.1 using min determinant for regularization = 53.4
>>> 0 singular and 5702 ill-conditioned covariance matrices regularized
>>> reading 'nu.mgz'...
>>> freeing gibbs priors...done.
>>> bounding unknown intensity as < 20.2 or > 943.7
>>> total sample mean = 92.0 (1443 zeros)
>>> ************************************************
>>> spacing=8, using 3481 sample points, tol=1.00e-05...
>>> ************************************************
>>> register_mri: find_optimal_transform
>>> find_optimal_transform: nsamples 3481, passno 0, spacing 8
>>> GCAhistoScaleImageIntensities: could not find wm peak
>>> resetting wm mean[0]: 117 --> 126
>>> resetting gm mean[0]: 74 --> 74
>>> input volume #1 is the most T1-like
>>> using real data threshold=6.0
>>> skull bounding box = (130, 148, 130) --> (130, 148, 130)
>>> using (130, 148, 130) as brain centroid...
>>> mean wm in atlas = 126, using box (130,148,130) --> (129, 147,129) to
>>> find MRI wm
>>> WARNING: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=255,
>>> mri_peak=-1
>>> before smoothing, mri peak at 0
>>> WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=255,
>>> mri_peak=-1
>>> after smoothing, mri peak at 0, scaling input intensities by inf
>>> Linux enders 2.6.32-52-server #114-Ubuntu SMP Wed Sep 11 19:06:34 UTC
>>> 2013 x86_64 GNU/Linux
>>>
>>> recon-all -s AA470-2prac exited with ERRORS at Tue Oct 22 13:57:26 CDT
?? ?>>> 2013
>>>
>>> To report a problem, see
>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>>
>>>
>>>
>>
>>
>> The information in this e-mail is intended only for the person to whom i
t
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you i
n
>> error
>> but does not contain patient information, please contact the sender and
?? ?>> properly
>> dispose of the e-mail.
>
>
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contains patient information, please contact the Partners Compliance HelpLine at
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