Re: [Freesurfer] longitudinal processing

[Martin Reuter]

Hi Catherine,

with edits I think it is best to re-use the 5.0 cross data for the
longitudinal processing.

Also conceptually there is a difference between longitudinal processing
and longitudinal statistical analysis. 
The image processing will reduce variability of your measures and even
if you are interested in cross sectional differences between groups
(e.g. thickness differences at baseline), it would be a good idea to run
everything through the longitudinal stream. If there is longitudinal
image data, I think it will always be advantageous to process it with
the longitudinal stream as opposed to the cross sectional. 

Different scanners are usually not problematic if each subject stays on
their scanner and scanners are randomly assigned across groups. If
scanners get switched in a longitudinal study, many bad things can
happen:
- one group switches on average earlier than the other -> bias
- only a single or very few time points are on one side of the switch ->
cannot model the scanner effect well, as there is no reliable slope on
that side of the switch.
Anyway it may be a good idea to model the scanner as a covariate and
test for a scanner effect. We have seen effects even in software updates
on the scanner (e.g. growing brains) and certainly a hardware switch
will drastically change the images.

Linear mixed effects models are the right mechanism to analyze
longitudinal data.

Best, Martin



On Wed, 2013-01-09 at 19:22 +, Catherine Bois wrote:
> Thank you for your reply. I am currently trying to decide which method  
> would be the best to analyze the data we have...We have ca 500 scans  
> of individuals with differing number of time points for different  
> individuals and certain clinical measures we wish to relate to  
> particularly cortical thickness and different cortical regions.  
> However, the problem is that the scans were not all collected with the  
> same scanner; would longitudinal still prove to be advantageous over  
> cross-sectional analysis. As all the manual edits have been conducted  
> in version 5.0 it would be preferable to keep these and use version  
> 5.1 for -base -long (unless of course this could be done with better  
> consistency if using version 5.1?). I was also planning to analyze the  
> data with linear mixed effect models, does this sound reasonable?
> 
> Thanks very much for your help
> 
> 
> 
> 
> Quoting Martin Reuter  on Wed, 09 Jan  
> 2013 13:46:35 -0500:
> 
> > Hi Catherine,
> >
> > yes, the first step is independent (cross sectional) processing of all
> > time points (normal recon-all).
> >
> > We usually do not recommend to mix versions. But the 5.1 longitudinal
> > stream has been designed in a way that it can take the cross sectional
> > data from 5.0. So it is possible. Just make sure that if you add time
> > points and subjects you still use 5.0 for the cross sectional recons and
> > 5.1 for base and long to be consistent.
> >
> > Alternatively wait a little longer and re-run everything from scratch
> > with the new 5.2 version that will come out hopefully this month.
> >
> > Best, Martin
> >
> > On Wed, 2013-01-09 at 14:22 +, Catherine Bois wrote:
> >> Sorry, another question about longitudinal processing; just realized
> >> that my institution has been using version 5.0, so all the cross
> >> sectional processing has been done with this version, is it ok to go
> >> ahead and do base and long with version 5.1 once I have managed to get
> >> this installed?
> >>
> >> Thanks,
> >>
> >> - Forwarded message from c.b...@sms.ed.ac.uk -
> >> Date: Wed, 09 Jan 2013 13:35:12 +
> >> From: Catherine Bois 
> >>  Subject: longitudinal processing
> >>   To: freesurfer@nmr.mgh.harvard.edu
> >>
> >> Hi, just to clarify,
> >>
> >> When beginning longitudinal analysis, the first step is the same as
> >> cross-sectional processing, eg just the "normal" recon-all command,
> >> for each subject, and each individual time point? Then the norm.mgz
> >> files are used?
> >>
> >> Thanks
> >>
> >> --
> >> The University of Edinburgh is a charitable body, registered in
> >> Scotland, with registration number SC005336.
> >>
> >>
> >>
> >> - End forwarded message -
> >>
> >>
> >
> >
> >
> >
> > The information in this e-mail is intended only for the person to whom it 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 in error
> > but does not contain patient information, please contact the sender  
> > and properly
> > dispose of the e-mail.
> >
> 
> 
> 
> 


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Re: [Freesurfer] problem with preprocessing

[Douglas N Greve]

Hi Maryam, can you verify that the rh surfaces for that subject are ok? 
Load rh.white with rh.thickness as an overlay
doug


On 01/09/2013 05:31 PM, Maryam Vaziri Pashkam wrote:
> Hi Doug,
>
> I am running preprocessing on freesurfer 5.1 using this line:
>
> preproc-sess -s 121210_xu_Object4catmod_10 -df sessdir -per-run 
> -sliceorder siemens -fsd bold  -fwhm 0 -mni305-2mm -surface self lhrh  
> -force
>
> and I get a "Segmentation fault " error. Here is part of the output 
> with the error:
>
> 
> mri_segreg --mov bold/007/tmp.bbregister.28256/template.nii --init-reg 
> bold/007/tmp.bbregister.28256/reg.init.dat --out-reg 
> bold/007/tmp.bbregister.28256/bbr.pass1.dat --subsamp-brute 100 
> --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white 
> --gm-proj-frac 0.5 --gm-gt-wm 0.5
> $Id: mri_segreg.c,v 1.103 2011/03/02 00:04:24 nicks Exp $
> setenv SUBJECTS_DIR /ncf/vcn/Maryam/mri-space/subjects
> cd 
> /ncf/vcn/Maryam/mri-space/studies/Obj4cat_mod/unpackdata/121210_xu_Object4catmod_10
> mri_segreg --mov bold/007/tmp.bbregister.28256/template.nii --init-reg 
> bold/007/tmp.bbregister.28256/reg.init.dat --out-reg 
> bold/007/tmp.bbregister.28256/bbr.pass1.dat --subsamp-brute 100 
> --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white 
> --gm-proj-frac 0.5 --gm-gt-wm 0.5
> sysname  Linux
> hostname ncfws09.rc.fas.harvard.edu 
> machine  x86_64
> user mvpashkam
> movvol bold/007/tmp.bbregister.28256/template.nii
> regfile bold/007/tmp.bbregister.28256/reg.init.dat
> subject green_alligator_kcb
> dof 6
> outregfile bold/007/tmp.bbregister.28256/bbr.pass1.dat
> UseMask 0
> UseLH 1
> UseRH 1
> nsubsamp 100
> PenaltySign  -1
> PenaltySlope 0.50
> PenaltyCenter 0.00
> surfname white
> GMProjFrac 0.50
> WMProjAbs 2.00
> lhcostfile (null)
> rhcostfile (null)
> interp  trilinear (1)
> frame  0
> TolPowell 0.000100
> nMaxItersPowell 36
> n1dmin  3
> Profile   0
> Gdiag_no  -1
> AddNoise  0 (0)
> SynthSeed 1358526945
> TransRandMax 0.00
> RotRandMax 0.00
> Translations 0.00 0.00 0.00
> Rotations   0.00 0.00 0.00
> Input reg
>  1.000  -0.007   0.027  -1.374;
> -0.026   0.032   0.999  -28.956;
>  0.008   0.999  -0.032   7.006;
>  0.000   0.000   0.000   1.000;
>
> Loading mov
> Projecting LH Surfs
> Loading lh.white surf
> Loading lh.thickness for GM
> GM Proj: 1 0.50 2.00
> WM Proj: 0 0.50 2.00
> Projecting RH Surfs
> Loading rh.white surf
> Loading rh.thickness
> Segmentation fault
>
>
> I have attached the full log file. I am not sure where the problem is. 
> The anatomical data of the subject has been analyzed using recon all 
> on freesurfer 4.5. I have used similar method for 9 other subjects and 
> there was no error on any of them before. Any idea why am I getting a 
> segmentation error?
>
> Thanks,
> Maryam

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] FreeSurfer problem on VirtualBox Linux

[Nick Schmansky]

Carissa,

Unfortunately I dont think we can help with this problem, as we
currently do not have the resources to support the Windows VM instance.
However, an alternative that has worked for others is to do the
following: install the FSL Windows VM, described here:

http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Windows

once that is up-and-running, then within that linux instance, just
download and install our linux centos 4 freesurfer build.  this also
means you can update to v5.2 when that is released in a couple weeks.

Nick


On Wed, 2013-01-09 at 08:34 +, Carissa Nadia Kuswanto (IMH) wrote:
> Hi there,
> 
>  
> 
> My operating system is Windows XP SP3 and it has been loaded with
> VirtualBox 4.2.6 for Windows hosts and we would like to run
> freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full.vdi. But when
> we attempt to launch FreeSurfer, the terminal seems to hang with the
> following message: 
> 
>  
> 
> GRUB loading stage 1.5 
> 
> GRUB loading, please wait...
> 
>  
> 
> Would you kindly help us on how to overcome this problem? I thank you
> in advance for your kind attention.
> 
>  
> 
> Best regards,
> 
> Carissa
> 
> 
> 
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Re: [Freesurfer] Tracula preprocessing step error

[Anastasia Yendiki]

Hi Allison - Instead of using excel, I would use a unix-based text editor, 
whichever is available on the system where you are running the analyses. 
This way you can ensure that unix commands read your text files properly.

The 3 values for each diffusion gradient vector are its x, y, z 
components, so I wouldn't change their order, unless you have reason to 
believe that the order is not correct the way it was given to you.

Hope this helps,
a.y

On Wed, 9 Jan 2013, Allison Gruber wrote:

> Hi Anastasia,
>
> Thanks so much for your help. I was able to correct this problem in my
> configuration file. I have now run into another error- "bvecs and
> bvals don't have the same number of entries." I have read other
> postings about this error and can see that my bvec file is not
> formatted correctly when I import into Excel. However, I am not sure
> how to correctly fix this formatting. I know that I have 28 bval entries and 
> 84 bvec entries, so the overall number is correct. I am just unclear on how 
> to fix the formatting of the bvec file so that it corresponds correctly to 
> the ordering in the bval file (which order the bvec entries should appear in 
> within the three columns). Do you have any resources on this?
>
> Thank you again for your help,
> Allison
>
> Quoting Anastasia Yendiki :
>
>> 
>> Hi Allison - The mri_convert command at the top of your log file is
>> trying to convert the directory /Users/Desktop/Tracula/diffusion_DTI to
>> a nifti file. From the name of that nifti file, it looks like it's
>> expecting to find a field map and not finding it.
>> 
>> Hope this helps,
>> a.y
>> 
>> On Tue, 8 Jan 2013, Allison Gruber wrote:
>> 
>> > Dear Freesurfer experts,
>> > 
>> > I have encountered the following error while running the tracula
>> > pre-processing command and was hoping you could help me understand how
>> > to correct this.
>> > 
>> > Selection from log:
>> > 
>> > mri_convert /Users/Desktop/Tracula/diffusion_DTI/
>> > /Users/Desktop/Tracula/diffusion_DTI/SubjectX/dmri/b0mag.nii.gz
>> > mri_convert /Users/Desktop/Tracula/diffusion_DTI/
>> > /Users/Desktop/Tracula/diffusion_DTI/SubjectX/dmri/b0mag.nii.gz
>> > corRead(): can't open file /Users/Desktop/Tracula/diffusion_DTI/COR-.info
>> > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
>> > reading from /Users/Desktop/Tracula/diffusion_DTI/...
>> > Darwin MacBook-Pro.local 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr
>> > 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64
>> > 
>> > trac-preproc exited with ERRORS at Tue Jan  8 14:34:39 EST 2013
>> > 
>> > Please let me know if this is not enough information. Thank you for 
>> > your help.
>> > 
>> > Allison
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> > 
>> > 
>> > 
>> 
>> 
>> The information in this e-mail is intended only for the person to whom it 
>> 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
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>
>
>
>
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Re: [Freesurfer] Problems in testing out newly installed Freesurfer with autorecon-1 option

[Nick Schmansky]

Susan,

there appear to be two problems here.  the first and main problem is the
one:

nu_correct: Command not found.

nu_correct is a script which has as its first line:

#!/usr/bin/perl -w

so can you check that you have perl installed at /usr/bin/perl?

better yet, run this script:

fixup_mni_paths

which does the checking for you and attempts to fix the scripts.

the other problem appears to be the fact that mri_nu_correct.mni doesnt
exit upon finding the error that the files are missing.  this is bad,
although in looking at the script, it ought to.   the next release will
contain a double check.  from the looks of your script, it appears that
you are running recon-all with a subject that had its data already
processed, so nu.mgz existed already, so it just used that and continued
on.  so the results are correct (assuming nu.mgz was decent to begin
with), but resolving the nu_correct issue is the important thing to do.

Nick


On Wed, 2013-01-09 at 11:00 -0500, Susan Kuo wrote:
> Hi, 
>   I'm currently in the process of verifying that my install of
> Freesurfer works. I have an Ubuntu 12.04.1 LTS box. I encountered what
> appeared to be 4 errors after running  recon-all -s bert -autorecon1.
> The last line I included here states that the command completed
> without error, so I'm not sure if I should be concerned
> thatnu_correct wasn't found, or that there were loading errors, and
> a mincREAD() error. Could you help me identify what I need to do to
> correct these issues? I've included the standard output for this
> command as a text file here. There appear to be 4 issues: 
> 
> 
> 
> 
> ***ISSUE 1: cannot find nu_correct *
> nu_correct: Command not found.
> INFO: current FREESURFER_HOME does not match that of previous
> processing.
> 
> 
> ***ISSUE 2: No such file or directory error
> cp: cannot stat `./tmp.mri_nu_correct.mni.25253/nu2.mnc': No such file
> or directory
> mri_binarize --i ./tmp.mri_nu_correct.mni.25253/nu2.mnc --min -1
> --o ./tmp.mri_nu_correct.mni.25253/ones.mgz
> mincRead(): can't find file ./tmp.mri_nu_correct.mni.25253/nu2.mnc
> 
> 
> ***ISSUE 3: Loading error**
> Loading ./tmp.mri_nu_correct.mni.25253/ones.mgz
> ERROR: loading ./tmp.mri_nu_correct.mni.25253/ones.mgz
> mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.25253/ones.mgz
> --i ./tmp.mri_nu_correct.mni.25253/nu2.mnc
> --sum ./tmp.mri_nu_correct.mni.25253/sum.junk
> --avgwf ./tmp.mri_nu_correct.mni.25253/output.mean.dat
> mghRead(./tmp.mri_nu_correct.mni.25253/ones.mgz, -1): could not open
> file
> 
> 
> ***ISSUE 4: Loading error**
> Loading ./tmp.mri_nu_correct.mni.25253/ones.mgz
> ERROR: loading ./tmp.mri_nu_correct.mni.25253/ones.mgz
> (standard_in) 1: syntax error
> mris_calc
> -o ./tmp.mri_nu_correct.mni.25253/nu2.mnc 
> ./tmp.mri_nu_correct.mni.25253/nu2.mnc mul
> mincRead(): can't find file ./tmp.mri_nu_correct.mni.25253/nu2.mnc
> 
> 
> This is the last line to standard output, and it seems
> reassuring**
> recon-all -s bert finished without error at Tue Jan  8 17:49:19 EST
> 2013
> 
> 
> 
> 
> I appreciate whatever help you can give me, and thank you very much
> for your time! The attached is a text file. 
> 
> 
> 
> 
> Best, 
> S Kuo 
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Re: [Freesurfer] Tracula preprocessing step error

[Allison Gruber]

Hi Anastasia,

Thanks so much for your help. I was able to correct this problem in my
configuration file. I have now run into another error- "bvecs and
bvals don't have the same number of entries." I have read other
postings about this error and can see that my bvec file is not
formatted correctly when I import into Excel. However, I am not sure
how to correctly fix this formatting. I know that I have 28 bval  
entries and 84 bvec entries, so the overall number is correct. I am  
just unclear on how to fix the formatting of the bvec file so that it  
corresponds correctly to the ordering in the bval file (which order  
the bvec entries should appear in within the three columns). Do you  
have any resources on this?

Thank you again for your help,
Allison

Quoting Anastasia Yendiki :

>
> Hi Allison - The mri_convert command at the top of your log file is
> trying to convert the directory /Users/Desktop/Tracula/diffusion_DTI to
> a nifti file. From the name of that nifti file, it looks like it's
> expecting to find a field map and not finding it.
>
> Hope this helps,
> a.y
>
> On Tue, 8 Jan 2013, Allison Gruber wrote:
>
>> Dear Freesurfer experts,
>>
>> I have encountered the following error while running the tracula
>> pre-processing command and was hoping you could help me understand how
>> to correct this.
>>
>> Selection from log:
>>
>> mri_convert /Users/Desktop/Tracula/diffusion_DTI/
>> /Users/Desktop/Tracula/diffusion_DTI/SubjectX/dmri/b0mag.nii.gz
>> mri_convert /Users/Desktop/Tracula/diffusion_DTI/
>> /Users/Desktop/Tracula/diffusion_DTI/SubjectX/dmri/b0mag.nii.gz
>> corRead(): can't open file /Users/Desktop/Tracula/diffusion_DTI/COR-.info
>> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
>> reading from /Users/Desktop/Tracula/diffusion_DTI/...
>> Darwin MacBook-Pro.local 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr
>> 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64
>>
>> trac-preproc exited with ERRORS at Tue Jan  8 14:34:39 EST 2013
>>
>> Please let me know if this is not enough information. Thank you for  
>>   your help.
>>
>> Allison
>> ___
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>>
>>
>>
>
>
> The information in this e-mail is intended only for the person to whom it 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
> in error
> but does not contain patient information, please contact the sender and
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Re: [Freesurfer] longitudinal processing

[Martin Reuter]

Hi Catherine, 

yes, the first step is independent (cross sectional) processing of all
time points (normal recon-all).

We usually do not recommend to mix versions. But the 5.1 longitudinal
stream has been designed in a way that it can take the cross sectional
data from 5.0. So it is possible. Just make sure that if you add time
points and subjects you still use 5.0 for the cross sectional recons and
5.1 for base and long to be consistent.

Alternatively wait a little longer and re-run everything from scratch
with the new 5.2 version that will come out hopefully this month.

Best, Martin

On Wed, 2013-01-09 at 14:22 +, Catherine Bois wrote:
> Sorry, another question about longitudinal processing; just realized  
> that my institution has been using version 5.0, so all the cross  
> sectional processing has been done with this version, is it ok to go  
> ahead and do base and long with version 5.1 once I have managed to get  
> this installed?
> 
> Thanks,
> 
> - Forwarded message from c.b...@sms.ed.ac.uk -
>  Date: Wed, 09 Jan 2013 13:35:12 +
>  From: Catherine Bois 
>   Subject: longitudinal processing
>To: freesurfer@nmr.mgh.harvard.edu
> 
> Hi, just to clarify,
> 
> When beginning longitudinal analysis, the first step is the same as  
> cross-sectional processing, eg just the "normal" recon-all command,  
> for each subject, and each individual time point? Then the norm.mgz  
> files are used?
> 
> Thanks
> 
> -- 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> 
> 
> 
> - End forwarded message -
> 
> 


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[Freesurfer] Postdoctoral Position at Harvard Medical School/Boston Children's Hospital

[Gaab, Nadine]

The Gaab Labhttp://www.childrenshospital.org/research/gaablab and 
(www.babymri.org)) at the Laboratories of Cognitive 
Neuroscience at Children's Hospital Boston (Developmental Medicine Center) 
invites applications for a NIH funded post-doctoral associate in the area of 
developmental cognitive neuroscience/pediatric fMRI. Available resources 
include a 3.0T MRI scanner, a child-friendly Mock scanner and analysis 
platforms based in MATLAB/UNIX. The candidate will be expected to design, 
organize and conduct pediatric and infant (f)MRI experiments, analyze 
behavioral and fMRI data, prepare manuscripts for publication, and participate 
in conferences.

The NIH and foundation funded projects will focus on neural and behavioral 
pre-markers of developmental dyslexia in infants and pre-reading children as 
well as typical reading and language development. The successful applicant 
should have a doctoral degree in a field related to developmental cognitive 
neuroscience (e.g., cognitive neuroscience, neuroscience, developmental 
psychology, medicine or psychology). Individuals with a background in 
electrical engineering, biomedical engineering or computer science will also be 
considered, as appropriate. The successful applicant must possess excellent 
English verbal and written communication skills. Applicants are expected to 
have a very strong research background in the design and statistical analysis 
of functional brain-imaging experiments. Experience with SPM, FSL, Freesurfer, 
UNIX/LINUX/ and/or programming skills (MATLAB, C++; Python) are desirable and 
experience with MVPA or connectivity analyses a plus. Experience with pediatric 
functional neuroimaging and language and reading research are useful. 
Approximate start date is Spring/Summer 2013 (the earlier the better). 
Successful applicants will be appointed at Children's Hospital Boston and 
Harvard Medical School. For consideration please send a statement of interest, 
a CV and a list of three potential referees via email to Nadine Gaab, PhD

(nadine.g...@childrens.harvard.edu). 
The search will continue until the position is filled.


--
"If we knew what it was we were doing, it would not be called research, would 
it?" A. Einstein (1879-1955)

Nadine Gaab, PhD
Assistant Professor of Pediatrics
Harvard Medical School

Faculty Affiliate
Program in Neuroscience, Harvard Medical School

Member of the Faculty of Education
Harvard Graduate School of Education

Children's Hospital Boston
Department of Medicine/Division of Developmental Medicine
Laboratories of Cognitive Neuroscience
1 Autumn Street (Office 643)
Boston, MA 02115
nadine.g...@childrens.harvard.edu
phone: (857)-218-3021
Main Lab: 617-355-0400
fax: 617-730-0518
http://www.childrenshospital.org/research/gaablab
 www.babymri.org

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Re: [Freesurfer] freesurfer question

[Louis Nicholas Vinke]

Hi Catherine,
If it's the mtl pial surface around the hippocampus then the pial surface 
is not expected to be accurate in that region.  See FAQ question at link 
below.

http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Thesurfacesnearthemedialwall.2Chippocampus.2Candamygdalaaren.27taccuratelyfollowingthestructuresthere.HowcanIfixthis.3F

-Louis

On Wed, 9 Jan 2013, Catherine Bois wrote:

> Hi,
>
> I am currently editing some scans (ie adding control points etc),
> however I keep finding that after the editing often the brains look
> "worse" than they did before; especially the medial temporal lobe
> area. I have taken care not to put too many control points in/made
> sure not to place them in partial volume areas, and only in areas that
> are clearly excluded white matter. This problem has happened
> repeatedly, yet looking at scans that my colleagues have edited (some
> with up to 2000 control points) this problem does not occur. Has this
> happened before, is it the software "malfunctioning" in some way?
>
> Thank you very much for your reply,
>
>
>
>
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Re: [Freesurfer] error: could not read 65536 bytes at slice 76 in skull stripping process

[Sandra Preissler]

Hi Bruce,

Thanks for your fast reply.
I checked it again and there is 131 GB disk space free on the device.

Best regards
Sandra

Zitat von Bruce Fischl :

> Hi Sandra
>
> can you check to make sure that you have enough disk space and that  
> that partition isn't full?
>
> cheers
> Bruce
> On Wed, 9 Jan 2013, Sandra Preissler wrote:
>
>> Dear freesurfer users,
>>
>> I have an unexpected error using autorecon1.
>> The error occurred during the skull stripping process of a person  
>> called ?PTpost_P04?.
>>
>> First I tried: recon-all ?autorecon1 ?s PTpost_P04
>> After the first error (recon-all -s PTpost_P04 exited with ERRORS)  
>> I checked the logfile and tried the following:
>> cd  
>> /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri
>>
>> followed directly by:
>> mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz  
>> -T1 -brain_atlas  
>> /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca  
>> transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
>>
>> I became the error message:
>> ?could not read 65536 bytes at slice 76?
>>
>> The information about the freesurfer version and linux version used are:
>> FREESURFER_HOME: /opt/freesurfer
>> Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
>> Kernel info: Linux 2.6.34.10-0.6-default x86_64
>>
>> It would be great if anybody could help me in solving this.
>>
>> Best regards
>> Sandra
>>
>>
>> 
>> This message was sent through https://webmail.uni-jena.de
>
>
> The information in this e-mail is intended only for the person to whom it 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 in error
> but does not contain patient information, please contact the sender  
> and properly
> dispose of the e-mail.
>
>




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Re: [Freesurfer] unable to download updated mri_segstats

[Douglas N Greve]

Try now. I've also put a .mac version there.
doug


On 01/09/2013 01:04 AM, Salil Soman wrote:
> Hi,
>
> The link 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux
>  from 
> the release notes for freesurfer 5.1 
> (http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes) appears 
> broken. I also checked the anonymous ftp site and found only the 
> directories bbr-papers and growth-curves within the 
> /transfer/outgoing/flat/greve directory. Could someone please direct 
> me to the correct download link for the updated file?
>
> Also, is there an updated version of mri_segstats for mac?
>
> Thank you.
>
> Salil Soman, MD, MS
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] Problems in testing out newly installed Freesurfer with autorecon-1 option

[Susan Kuo]

Hi,
  I'm currently in the process of verifying that my install of Freesurfer
works. I have an Ubuntu 12.04.1 LTS box. I encountered what appeared to be
4 errors after running  *recon-all -s bert -autorecon1.*
The last line I included here states that the command completed without
error, so I'm not sure if I should be concerned that*nu_correct* wasn't
found, or that there were loading errors, and a *mincREAD()* error. Could
you help me identify what I need to do to correct these issues? I've
included the standard output for this command as a text file here. There
appear to be 4 issues:


***ISSUE 1: cannot find *nu_correct* *
nu_correct: Command not found.
INFO: current FREESURFER_HOME does not match that of previous processing.

***ISSUE 2: No such file or directory error
cp: cannot stat `./tmp.mri_nu_correct.mni.25253/nu2.mnc': No such file or
directory
mri_binarize --i ./tmp.mri_nu_correct.mni.25253/nu2.mnc --min -1 --o
./tmp.mri_nu_correct.mni.25253/ones.mgz
mincRead(): can't find file ./tmp.mri_nu_correct.mni.25253/nu2.mnc

***ISSUE 3: Loading error**
Loading ./tmp.mri_nu_correct.mni.25253/ones.mgz
ERROR: loading ./tmp.mri_nu_correct.mni.25253/ones.mgz
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.25253/ones.mgz --i
./tmp.mri_nu_correct.mni.25253/nu2.mnc --sum
./tmp.mri_nu_correct.mni.25253/sum.junk --avgwf
./tmp.mri_nu_correct.mni.25253/output.mean.dat
mghRead(./tmp.mri_nu_correct.mni.25253/ones.mgz, -1): could not open file

***ISSUE 4: Loading error**
Loading ./tmp.mri_nu_correct.mni.25253/ones.mgz
ERROR: loading ./tmp.mri_nu_correct.mni.25253/ones.mgz
(standard_in) 1: syntax error
mris_calc -o ./tmp.mri_nu_correct.mni.25253/nu2.mnc
./tmp.mri_nu_correct.mni.25253/nu2.mnc mul
mincRead(): can't find file ./tmp.mri_nu_correct.mni.25253/nu2.mnc

This is the last line to standard output, and it seems
reassuring**
recon-all -s bert finished without error at Tue Jan  8 17:49:19 EST 2013


I appreciate whatever help you can give me, and thank you very much for
your time! The attached is a text file.


Best,
S Kuo


freesurfer
Description: Binary data
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[Freesurfer] longitudinal processing

[Catherine Bois]

Sorry, another question about longitudinal processing; just realized  
that my institution has been using version 5.0, so all the cross  
sectional processing has been done with this version, is it ok to go  
ahead and do base and long with version 5.1 once I have managed to get  
this installed?

Thanks,

- Forwarded message from c.b...@sms.ed.ac.uk -
 Date: Wed, 09 Jan 2013 13:35:12 +
 From: Catherine Bois 
  Subject: longitudinal processing
   To: freesurfer@nmr.mgh.harvard.edu

Hi, just to clarify,

When beginning longitudinal analysis, the first step is the same as  
cross-sectional processing, eg just the "normal" recon-all command,  
for each subject, and each individual time point? Then the norm.mgz  
files are used?

Thanks

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



- End forwarded message -


-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.


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Re: [Freesurfer] QA Tools Snaps Scrambled - Clairification

[Irwin, William]

Hi Louis-

I was speaking cryptically and/or imprecisely. Of course there are dependencies 
for IM-- in fact about 8 libraries which are uniquely required by IM. I was 
thinking about a higher (or lower) level of dependency. This would suggest a 
more system-level problem, but I'm not having problems with any of the other 
apps running on my system. Obviously I'm not asking you to help diagnose the 
health of my system, but though you might have some thoughts/suggestions.

Regards,
Wil

-Original Message-
From: Irwin, William 
Sent: Wednesday, January 09, 2013 5:37 AM
To: Louis Nicholas Vinke
Cc: freesurfer@nmr.mgh.harvard.edu; Irwin, William
Subject: RE: [Freesurfer] QA Tools Snaps Scrambled

Hi Louis-

No problem doing command line conversion of an rgb to either jpg or gif in 
terms of error messages. However, the converted files are scrambled. Might 
there be a dependency on which ImageMagick relies which still in place, but 
corrupted? I was under the impression ImageMagick was self-contained.

This is a real mystery

-Wil

-Original Message-
From: Louis Nicholas Vinke [mailto:vi...@nmr.mgh.harvard.edu]
Sent: Tuesday, January 08, 2013 6:29 PM
To: Irwin, William
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] QA Tools Snaps Scrambled

Hi Irwin,
It sounds like the snapshots from tksurfer are fine, but the ones from tkmedit 
are not being generated properly.  It may be this peculiar bug where 
ImageMagick has trouble reading rgb files. Try converting an rgb file to a jpg 
'convert file.rgb file.jpg'.  You may get the error 'Improper image header'.  
The tksurfer tcl script saves tiff files, the tkmedit tcl script saves rgbs, 
which may explain why some images are fine.
-Louis

On Tue, 8 Jan 2013, Irwin, William wrote:

> 
> Hi-
> 
>  
> 
> I’ve come across a peculiar behavior with recon_checker, and am hoping 
> someone can shed some light on this.
> 
>  
> 
> I have used it 100’s of times in the past, but not for about 2 months. 
> I recently processed a large set of cases I wanted to QC. When I ran 
> it, some, but not all, of the snaps were corrupted. Specifically the 
> talairach, aseg, surfs, and all the ‘detailed snaps’, which are 
> basically additional instances of the aforementioned types. The 
> inflated, curv, and parc are all just fine. As the process runs, all 
> images are being displayed in the pop-up windows, and the html page is 
> created.
> 
>  
> 
> While there have been no system changes which should affect this, I 
> upgraded from ImageMagick 6.5.4 to 6.8.1 to see if this would fix the 
> problem. The problem remains. And the problem remains w/ or w/o the 
> flag for detailed snaps.
> 
>  
> 
> If all of the images were corrupted, I would have certainly concluded 
> something has gone awry with my system. The fact that only some of the 
> images are corrupted makes me scratch my head.
> 
>  
> 
> Thoughts? Suggestions?
> 
>  
> 
> Thanks,
> 
> Wil
> 
> 
>


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[Freesurfer] creating picture using 3D slicer

[L. Koenders]

Dear FreeSurfer people,

I have a problem creating a picture with my FreeSurfer volumetric data, for 
which I have been using 3D Slicer.
First, let me explain what I am trying to do. We have a list with cortical and 
subcortical grey matter areas that were significantly different between our 
patient and control group. I want to make one picture showing all these areas, 
and the 3D model as can be made with 3D Slicer with a part of the surface 
'clipped out' would be perfect.

I tried to do this by loading the surfaces and parcellation map in Slicer. I 
could successfully load the volumes (mri.mgz, aseg.mgz) and the surfaces 
(lh.pial and rh.pial). But when I load the parcellation map (aparc.annot) as a 
scalar overlay for the already loaded model, slicer crashes.

I emailed the 3D slicer helpdesk with this problem, but I hope you might have 
some ideas as well. My question is if there  is a way to fix this problem, and 
if not; if there's another way to get the type of picture I want?

I really hope you can help me, thanks in advance!

Kind regards,
Laura


AMC Disclaimer : http://www.amc.nl/disclaimer



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Re: [Freesurfer] freesurfer question

[Bruce Fischl]

Hi Catherine

what version are you running? We have a fix in 5.2 that helps this 
problem. It's not quite out yet, but you could download a beta if you want

cheers
Bruce

On Wed, 9 Jan 2013, Catherine Bois wrote:

> Hi,
>
> I am currently editing some scans (ie adding control points etc),
> however I keep finding that after the editing often the brains look
> "worse" than they did before; especially the medial temporal lobe
> area. I have taken care not to put too many control points in/made
> sure not to place them in partial volume areas, and only in areas that
> are clearly excluded white matter. This problem has happened
> repeatedly, yet looking at scans that my colleagues have edited (some
> with up to 2000 control points) this problem does not occur. Has this
> happened before, is it the software "malfunctioning" in some way?
>
> Thank you very much for your reply,
>
>
>
>
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Re: [Freesurfer] error: could not read 65536 bytes at slice 76 in skull stripping process

[Bruce Fischl]

Hi Sandra

can you check to make sure that you have enough disk space and that that 
partition isn't full?

cheers
Bruce
On Wed, 9 Jan 2013, Sandra Preissler wrote:

> Dear freesurfer users,
>
> I have an unexpected error using autorecon1.
> The error occurred during the skull stripping process of a person called 
> ?PTpost_P04?.
>
> First I tried: recon-all ?autorecon1 ?s PTpost_P04
> After the first error (recon-all -s PTpost_P04 exited with ERRORS) I checked 
> the logfile and tried the following:
> cd 
> /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri
>
> followed directly by:
> mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 
> -brain_atlas /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca 
> transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
>
> I became the error message:
> ?could not read 65536 bytes at slice 76?
>
> The information about the freesurfer version and linux version used are:
> FREESURFER_HOME: /opt/freesurfer
> Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
> Kernel info: Linux 2.6.34.10-0.6-default x86_64
>
> It would be great if anybody could help me in solving this.
>
> Best regards
> Sandra
>
>
> 
> This message was sent through https://webmail.uni-jena.de
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Re: [Freesurfer] QA Tools Snaps Scrambled

[Irwin, William]

Hi Louis-

No problem doing command line conversion of an rgb to either jpg or gif in 
terms of error messages. However, the converted files are scrambled. Might 
there be a dependency on which ImageMagick relies which still in place, but 
corrupted? I was under the impression ImageMagick was self-contained.

This is a real mystery

-Wil

-Original Message-
From: Louis Nicholas Vinke [mailto:vi...@nmr.mgh.harvard.edu] 
Sent: Tuesday, January 08, 2013 6:29 PM
To: Irwin, William
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] QA Tools Snaps Scrambled

Hi Irwin,
It sounds like the snapshots from tksurfer are fine, but the ones from tkmedit 
are not being generated properly.  It may be this peculiar bug where 
ImageMagick has trouble reading rgb files. Try converting an rgb file to a jpg 
'convert file.rgb file.jpg'.  You may get the error 'Improper image header'.  
The tksurfer tcl script saves tiff files, the tkmedit tcl script saves rgbs, 
which may explain why some images are fine.
-Louis

On Tue, 8 Jan 2013, Irwin, William wrote:

> 
> Hi-
> 
>  
> 
> I’ve come across a peculiar behavior with recon_checker, and am hoping 
> someone can shed some light on this.
> 
>  
> 
> I have used it 100’s of times in the past, but not for about 2 months. 
> I recently processed a large set of cases I wanted to QC. When I ran 
> it, some, but not all, of the snaps were corrupted. Specifically the 
> talairach, aseg, surfs, and all the ‘detailed snaps’, which are 
> basically additional instances of the aforementioned types. The  
> inflated, curv, and parc are all just fine. As the process runs, all 
> images are being displayed in the pop-up windows, and the html page is 
> created.
> 
>  
> 
> While there have been no system changes which should affect this, I 
> upgraded from ImageMagick 6.5.4 to 6.8.1 to see if this would fix the 
> problem. The problem remains. And the problem remains w/ or w/o the 
> flag for detailed snaps.
> 
>  
> 
> If all of the images were corrupted, I would have certainly concluded 
> something has gone awry with my system. The fact that only some of the 
> images are corrupted makes me scratch my head.
> 
>  
> 
> Thoughts? Suggestions?
> 
>  
> 
> Thanks,
> 
> Wil
> 
> 
>


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[Freesurfer] longitudinal processing

[Catherine Bois]

Hi, just to clarify,

When beginning longitudinal analysis, the first step is the same as  
cross-sectional processing, eg just the "normal" recon-all command,  
for each subject, and each individual time point? Then the norm.mgz  
files are used?

Thanks

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.


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[Freesurfer] freesurfer question

[Catherine Bois]

Hi,

I am currently editing some scans (ie adding control points etc),  
however I keep finding that after the editing often the brains look  
"worse" than they did before; especially the medial temporal lobe  
area. I have taken care not to put too many control points in/made  
sure not to place them in partial volume areas, and only in areas that  
are clearly excluded white matter. This problem has happened  
repeatedly, yet looking at scans that my colleagues have edited (some  
with up to 2000 control points) this problem does not occur. Has this  
happened before, is it the software "malfunctioning" in some way?

Thank you very much for your reply,



-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.


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[Freesurfer] FreeSurfer problem on VirtualBox Linux

[Carissa Nadia Kuswanto (IMH)]

Hi there,

My operating system is Windows XP SP3 and it has been loaded with VirtualBox 
4.2.6 for Windows hosts and we would like to run 
freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full.vdi. But when we attempt 
to launch FreeSurfer, the terminal seems to hang with the following message:


GRUB loading stage 1.5

GRUB loading, please wait...

Would you kindly help us on how to overcome this problem? I thank you in 
advance for your kind attention.

Best regards,
Carissa


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[Freesurfer] ask about demean in GLM model setup

[chenchunhuichina]

Dear experts,

I am confused by demean during GLM model setup and would like someone here can 
help me. Thanks!

Suppose I have a continuous behavior data and I want to find out which brain 
region(s) correlated with it. The simple way is to calculate correltation 
between brain data and behavior data, or in GLM to set up a model Y=AX+B+e, A 
is slope, B is constent and e is error, Y is brain data and X is beahvior data. 
So this design matrix have two collumns: behavior data and ones.
or we can think of demean that dX=X-mean(X), dY=Y-mean(Y)
Y=A'dX+B'+e', A' should be the same a A and B' differed from B, and B' maybe 
more interpretatable. 

I was told that -D opion in FSL randomise will demean X and Y at the same time. 
one can set up models like dY=A1dX+B1+e1, or dY=A2dX+e2. I simulated a data in 
SPSS and confirmed that A1,A2 is the same as A, B1 is 0. but t test for A1 A2 
differed a little, A1 is the same as above models.

So it seems to me that include a constent in the model is always right, right?
My confusion is why Y also need to demean and how was it done in randomise? 
when one says "demean" or "mean centering", he/she means demean X only or 
demean X and Y both?

Thanks for any clarification!

2013-01-09 



Chunhui Chen
_

State Key Laboratory of Cognitive Neuroscience and Learning
Beijing Normal University
Beijing, China 100875
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