Re: [Freesurfer] problem fast_selxavg3b

[Douglas N Greve]

I don't think they are using the compiled version of selxavg. Rather, 
the matlab script makes a unix call to run an FS binary. I think this 
would happen for any binary. Desiree, can you run that command 
(mris_fwhm) outside of matlab to see if it runs?

On 10/06/2015 10:21 AM, Z K wrote:
> Hello,
>
> I have seen errors that look like the error below (i.e. 
> GLIBCXX_3.4.15) when their is an incompatibility between the OS, 
> matlab, and the compiled binary. Looking at your path to matlab I see 
> "/opt/matlab/R2010b". Thats pretty old.
>
> Doug,
> I recall you telling me these binaries are compiled against matlab 8.3 
> (R2014a)? Perhaps Desiree should use that version.
>
> -Zeke
>
>
> On 10/05/2015 07:32 PM, Douglas Greve wrote:
>> I don't think it is a matlab problem. We call some binaries from inside
>> matlab, and the problem is with those. It looks like the version of FS
>> does not match your operating system or that you are missing a library.
>> Maybe Zeke can help sort it out.
>> doug
>>
>> On 10/5/15 2:31 AM, Desiree Thielemann wrote:
>>>
>>> Dear freesurfer experts,
>>>
>>> I included the new function fast_selxavg3b but I got another problem:
>>>
>>> First error:
>>>
>>> /opt/freesurfer/bin/mris_fwhm --mask
>>> /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/mask.nii.gz
>>>  
>>>
>>> --i
>>> /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.nii.gz
>>>  
>>>
>>> --o
>>> /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.sm.nii.gz
>>>  
>>>
>>> --fwhm 20.00 --smooth-only --s fsaverage --hemi lh --sd
>>> /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann
>>> /opt/freesurfer/bin/mris_fwhm: symbol lookup error:
>>> /opt/freesurfer/bin/mris_fwhm: undefined symbol: ncerr
>>>
>>> ERROR: /opt/freesurfer/bin/mris_fwhm --mask
>>> /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/mask.nii.gz
>>>  
>>>
>>> --i
>>> /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.nii.gz
>>>  
>>>
>>> --o
>>> /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.sm.nii.gz
>>>  
>>>
>>> --fwhm 20.00 --smooth-only --s fsaverage --hemi lh --sd
>>> /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann
>>>
>>> ans =
>>>
>>>   127
>>>
>>> Second error with another server running the analyses:
>>>
>>> /opt/freesurfer/bin/mris_fwhm:
>>> /opt/matlab/R2010b/sys/os/glnxa64/libstdc++.so.6: version
>>> `GLIBCXX_3.4.11' not found (required by /opt/freesurfer/bin/mris_fwhm)
>>> /opt/freesurfer/bin/mris_fwhm:
>>> /opt/matlab/R2010b/sys/os/glnxa64/libstdc++.so.6: version
>>> `GLIBCXX_3.4.15' not found (required by /opt/freesurfer/bin/mris_fwhm)
>>>
>>>
>>> The problem seems to be the version of matlab. Which version would you
>>> suggest to use while using the function fast_selxavg3b? And why is
>>> there an undefined symbol?
>>>
>>> Do you have any suggestions how to solve the problem?
>>>
>>> Best regard,
>>> Desiree
>>>
>>>
> --
>>> ERROR: fast_selxavg3() failed\n
>>>
>>> Zitat von Douglas Greve :
>>>
 oops, sorry, that did not make it into the distribution. You can get
 it here

 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_selxavg3b.m
  



 thanks
 doug


 On 9/29/15 9:15 AM, Silvia Désirée Thielemann wrote:
> Dear members of the freesurfer mailing list,
>
> I'm using freesurfer-Linux-centos7_x86_64-dev-20150728. I started to
> analyse mri data with fs-fast. I did the preprocessing and used the
> function mkanalysis-sess and mkcontrast-sess without any problems. I
> tried to run the function selxavg3-sess next and it stopped with the
> error message:
>
> /opt/freesurfer/fsfast/toolbox/fast_selxavg3.m
>>> /opt/freesurfer/fsfast/toolbox/fast_ldanaflac.m
>>> /opt/freesurfer/matlab/MRIread.m
>>> ??? Undefined function or method 'fast_selxavg3b' for input
>>> arguments of type
> 'char'.
>
>>> --
> ERROR: fast_selxavg3() failed\n
>
> I looked for the function fast_selxavg3b in matlab. Unfortunatly only
> the function fast_selxavg3 is included in the fsfast/toolbox. By
> trying to use the function fast_selxavg3, it recommand me to use
> fast_selxavg3b. I could not find the function in the internet.
>
> Do you have any suggestions what to do?
>
> Best regards,
> Desiree
>
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Re: [Freesurfer] Error Messages for Accessing Bin

[dgw]

what operating system are you running? 64 bit or 32 bit?
Why did you decide to install version 5.0 instead of the current stable 5.3?

hth
d

On Mon, Oct 5, 2015 at 5:41 PM, Timothy Le  wrote:
> Hi,
> From the following output, how should I proceed?
> Thank you very much
> Timothy Le
>
> On Oct 2, 2015, at 11:55 AM, Timothy Quang-Tin Le  wrote:
>
> Hi,
> Thank you very much for your response. The output of that command was:
>
> tle7@sni-vcs-gotlib:~$ ls -l /home/tle7/freesurfer/bin/mri_convert
> -rwxrwx--x 1 tle7 stanford 1672136 Aug 15  2010
> /home/tle7/freesurfer/bin/mri_convert
> tle7@sni-vcs-gotlib:~$
>
>
> On Fri, Oct 2, 2015 at 10:39 AM, dgw  wrote:
>>
>> Timothy,
>>
>> What is the output of this command:
>>
>> ls -l /home/tle7/freesurfer/bin/mri_convert
>>
>> ?
>>
>> hth
>> d
>>
>> On Fri, Oct 2, 2015 at 1:36 PM, Timothy Quang-Tin Le 
>> wrote:
>> > Hi,
>> > I tried the chmod command, but it did not work. How I check that I've
>> > downloaded the correct version?
>> > Thank you very much
>> > Timothy
>> >
>> > On Thu, Oct 1, 2015 at 8:10 AM, Bruce Fischl
>> > 
>> > wrote:
>> >>
>> >> can you try chmod a+x on one of them and see if it can then be
>> >> executed?
>> >> e.g.:
>> >>
>> >> chmod a+x  /home/tle7/freesurfer/bin/mri_convert
>> >>  /home/tle7/freesurfer/bin/mri_convert
>> >>
>> >> and see if you get an error. If not, you probably downloaded the wrong
>> >> hardware version
>> >> cheers
>> >> Bruce
>> >>
>> >>
>> >>
>> >> On Tue, 29 Sep 2015, Timothy Quang-Tin Le wrote:
>> >>
>> >>>
>> >>>   Hello,
>> >>> When I run the command "sFSstart" on version 5.0.0, I am receiving the
>> >>> messages below. Would you please explain to me what the problem is? It
>> >>> seems like there is trouble accessing the bin.
>> >>> Thank you
>> >>>
>> >>>  freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 
>> >>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>> >>> FREESURFER_HOME   /home/tle7/freesurfer
>> >>> FSFAST_HOME   /home/tle7/freesurfer/fsfast
>> >>> FSF_OUTPUT_FORMAT nii
>> >>> SUBJECTS_DIR  /home/tle7/freesurfer/subjects
>> >>> MNI_DIR   /home/tle7/freesurfer/mni
>> >>> tle7@sni-vcs-gotlib:~$ sFSstart practicemotherdaughter 00152-DT2
>> >>> studyPath /home/tle7/freesurfer/subjects/practicemotherdaughter
>> >>> H 0
>> >>> checking sid number 00152-DT2
>> >>> 1
>> >>>
>> >>> 00152-DT2/MR.1.2.840.113619.2.283.4120.7575399.15360.1319907833.100.dcm
>> >>> Subject Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0
>> >>> Current Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0
>> >>> INFO: SUBJECTS_DIR is /home/tle7/freesurfer/subjects
>> >>> Actual FREESURFER_HOME /home/tle7/freesurfer
>> >>> Linux sni-vcs-gotlib.stanford.edu 3.13.0-61-generic #100-Ubuntu SMP
>> >>> Wed Jul 29 11:21:34 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
>> >>> /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file
>> >>> not executable.
>> >>> /home/tle7/freesurfer/bin/flirt.fsl: Exec format error. Binary file
>> >>> not executable.
>> >>> /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file
>> >>> not executable.
>> >>> /home/tle7/freesurfer/bin/tkregister2_cmdl: Exec format error. Binary
>> >>> file not executable.
>> >>> /home/tle7/freesurfer/bin/mri_normalize: Exec format error. Binary
>> >>> file not executable.
>> >>> /home/tle7/freesurfer/bin/mri_watershed: Exec format error. Binary
>> >>> file not executable.
>> >>> /home/tle7/freesurfer/bin/mri_gcut: Exec format error. Binary file not
>> >>> executable.
>> >>> /home/tle7/freesurfer/bin/mri_segment: Exec format error. Binary file
>> >>> not executable.
>> >>> /home/tle7/freesurfer/bin/mri_label2label: Exec format error. Binary
>> >>> file not executable.
>> >>> /home/tle7/freesurfer/bin/mri_em_register: Exec format error. Binary
>> >>> file not executable.
>> >>> /home/tle7/freesurfer/bin/mri_ca_normalize: Exec format error. Binary
>> >>> file not executable.
>> >>> /home/tle7/freesurfer/bin/mri_ca_register: Exec format error. Binary
>> >>> file not executable.
>> >>> /home/tle7/freesurfer/bin/mri_ca_label: Exec format error. Binary file
>> >>> not executable.
>> >>> /home/tle7/freesurfer/bin/mri_pretess: Exec format error. Binary file
>> >>> not executable.
>> >>> /home/tle7/freesurfer/bin/mri_fill: Exec format error. Binary file not
>> >>> executable.
>> >>> /home/tle7/freesurfer/bin/mri_tessellate: Exec format error. Binary
>> >>> file not executable.
>> >>> /home/tle7/freesurfer/bin/mri_concatenate_lta: Exec format error.
>> >>> Binary file not executable.
>> >>> /home/tle7/freesurfer/bin/mri_normalize_tp2: Exec format error. Binary
>> >>> file not executable.
>>
>> >>> /home/tle7/freesurfer/bin/mris_smooth: Exec format error. Binary file
>> >>> not executable.
>> >>> /home/tle7/freesurfer/bin/mris_inflate: Exec format error. Binary file
>> >>> not executable.
>> >>> 

Re: [Freesurfer] Questions about the correction methods in Surfstat

[MCLAREN, Donald]

>The output figure is attached. In the colorbar of the figure, left
represents cluster corrected p value and right one represents the vertex
>corrected p value, right?
Right.

>So, the warm color region in the figure can be survived by the RFT vertex
correction, and the cool color region in the figure can be >survived by the
RFT cluster correction, right?
Right. RFT vertex correction is not a correct definition, it is a RFT
correction based on the maximum peak in contrast with the larger cluster
extent approach.

>If so, the regions with either warm or cool color region that can be
survived after correction. When I report the results, I can report the
>regions with warm color (vertex level correction) or report the regions
with cool color (cluster level correction), right?
Both thresholdings can be reported but I prefer peak thresholds (warm
colors) due to the lack of spatial specificity with clustering thresholds.

>In addtion, how can I understand the region overlapped by the warm and
cool color (like he postier cingulate cortex), can >simultaneously pass
double correction of vertex level and cluster level?
It is not a double corrections. The figure simply shows two different RFT
thresholding approaches.

The final question is about the RFT cluster correction method, in the SPM
or other software (like REST). Generally, on the cluster level correction,
you should be based on a voxel (vertex) uncorrected height threshold of
e.g. p<0.001 combined with a RFT-correlated cluster threshould of e.g.,
p<0.05, right? What is the detailed correction procedure in the Surfstat
software?
Exactly the same, p=0.001 for defining supra-threshold clusters and p=0.05
for RFT correction.

Regards, Felix.

Best Regards,
Donald McLaren, PhD


On Sun, Sep 13, 2015 at 9:36 AM, chenhf_uestc  wrote:

> Dear Surfstat Users,
>
> I have a question about the RFT correction method in the Surfstat(
> http://www.math.mcgill.ca/keith/surfstat/).
> In the online manual, the command to perform RFT correction is as follows:
> [ pval, peak, clus ] = SurfStatP( slm, mask );
>
> pval.P contains P-values for peaks, and pval.C contains P-values for
> clusters. This special structure is recognised by SurfStatView which draws
> the figure in a special way:
>
> SurfStatView( pval, avsurf, 'Males-females removing age' );
>
> The output figure is attached. In the colorbar of the figure, left
> represents cluster corrected p value and right one represents the vertex
> corrected p value, right? So, the warm color region in the figure can be
> survived by the RFT vertex correction, and the cool color region in the
> figure can be survived by the RFT cluster correction, right? If so, the
> regions with either warm or cool color region that can be survived after
> correction. When I report the results, I can report the regions with warm
> color (vertex level correction) or report the regions with cool color
> (cluster level correction), right?
>
> In addtion, how can I understand the region overlapped by the warm and
> cool color (like he postier cingulate cortex), can simultaneously pass
> double correction of vertex level and cluster level?
>
> The final question is about the RFT cluster correction method, in the SPM
> or other software (like REST). Generally, on the cluster level correction,
> you should be based on a voxel (vertex) uncorrected height threshold of
> e.g. p<0.001 combined with a RFT-correlated cluster threshould of e.g.,
> p<0.05, right? What is the detailed correction procedure in the Surfstat
> software?
>
> Any help would be greatly appreciate.
>
> Best,
> Feng
>
>
>
>
>
>
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>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
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> properly
> dispose of the e-mail.
>
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Re: [Freesurfer] Questions about the correction methods in Surfstat

[chenhf_uestc]

I see.
Thanks a lot, Donald

Best,
Feng



发件人："MCLAREN, Donald" 
发送时间：2015-10-07 11:01
主题：Re: [Freesurfer] Questions about the correction methods in Surfstat
收件人："Freesurfer support list"
抄送：

>The output figure is attached. In the colorbar of the figure, left represents 
>cluster corrected p value and right one represents the vertex >corrected p 
>value, right? 

Right.


>So, the warm color region in the figure can be survived by the RFT vertex 
>correction, and the cool color region in the figure can be >survived by the 
>RFT cluster correction, right? 
Right. RFT vertex correction is not a correct definition, it is a RFT 
correction based on the maximum peak in contrast with the larger cluster extent 
approach.  

>If so, the regions with either warm or cool color region that can be survived 
>after correction. When I report the results, I can report the >regions with 
>warm color (vertex level correction) or report the regions with cool color 
>(cluster level correction), right?

Both thresholdings can be reported but I prefer peak thresholds (warm colors) 
due to the lack of spatial specificity with clustering thresholds.


>In addtion, how can I understand the region overlapped by the warm and cool 
>color (like he postier cingulate cortex), can >simultaneously pass double 
>correction of vertex level and cluster level?

It is not a double corrections. The figure simply shows two different RFT 
thresholding approaches.


The final question is about the RFT cluster correction method, in the SPM or 
other software (like REST). Generally, on the cluster level correction, you 
should be based on a voxel (vertex) uncorrected height threshold of e.g. 
p<0.001 combined with a RFT-correlated cluster threshould of e.g., p<0.05, 
right? What is the detailed correction procedure in the Surfstat software?

Exactly the same, p=0.001 for defining supra-threshold clusters and p=0.05 for 
RFT correction.



Regards, Felix.


Best Regards, 
Donald McLaren, PhD




On Sun, Sep 13, 2015 at 9:36 AM, chenhf_uestc  wrote:

Dear Surfstat Users,

I have a question about the RFT correction method in the 
Surfstat(http://www.math.mcgill.ca/keith/surfstat/).
In the online manual, the command to perform RFT correction is as follows:
[ pval, peak, clus ] = SurfStatP( slm, mask ); 

pval.P contains P-values for peaks, and pval.C contains P-values for clusters. 
This special structure is recognised by SurfStatView which draws the figure in 
a special way:

SurfStatView( pval, avsurf, 'Males-females removing age' ); 

The output figure is attached. In the colorbar of the figure, left represents 
cluster corrected p value and right one represents the vertex corrected p 
value, right? So, the warm color region in the figure can be survived by the 
RFT vertex correction, and the cool color region in the figure can be survived 
by the RFT cluster correction, right? If so, the regions with either warm or 
cool color region that can be survived after correction. When I report the 
results, I can report the regions with warm color (vertex level correction) or 
report the regions with cool color (cluster level correction), right?

In addtion, how can I understand the region overlapped by the warm and cool 
color (like he postier cingulate cortex), can simultaneously pass double 
correction of vertex level and cluster level? 

The final question is about the RFT cluster correction method, in the SPM or 
other software (like REST). Generally, on the cluster level correction, you 
should be based on a voxel (vertex) uncorrected height threshold of e.g. 
p<0.001 combined with a RFT-correlated cluster threshould of e.g., p<0.05, 
right? What is the detailed correction procedure in the Surfstat software?

Any help would be greatly appreciate.

Best,
Feng







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Re: [Freesurfer] freeview and ?h.cortex.patch.flat

[Lee Tirrell]

Hi Xiaomin,

At this time, viewing the ?h.cortex.patch.flat isn't possible in freeview.  You 
can load it using tksurfer by loading your subject's inflated surface, then 
going to File -> Patch -> LoadPatch and choosing the correct patch.flat file. 
These instructions are detailed here:


https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#Flattening

Best,
Lee

On Thu, 1 Oct 2015, Xiaomin Yue wrote:


Hi,
Can the developmental freeview display ?h.cortex.patch.flat?  I can't find 
answers in the mail list.  If not, is there any way to convert the patch.flat 
to a format freeview can display?

Thanks,
Xiaomin

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[Freesurfer] Postdoctoral Positions - Headache & Orofacial Pain Effort Lab, University of Michigan: Migraine and TMD Neuroimaging and Neuromodulation Research

[adasilva]

The Headache and Orofacial Pain Effort (H.O.P.E.) Lab at the University of Michigan requests applications for two postdoctoral positions to work on migraine and TMD research programs funded by the National Institute of Health. The programs use novel methodologies in neuroimaging and neuromodulation to investigate and target central mechanisms of chronic pain in vivo. Extensive knowledge of neuromoimaging analysis software systems as well as programming experience is required, as is some level of comfort with novel neuromodulatory protocols. Previous research experience and publications with positron emission tomography (PET) and/or MRI-based neuroimaging methods and analyses are also needed. We are seeking applicants with advanced degrees and strong self-motivation to work in a highly creative, altruistic, and mentoring environment with students and residents from different departments across campus. The applicant will be exposed to several tech-innovations, many developed in house, for clinical translational pain research (e.g., migraine, TMD, dental and cancer pain), such as mobile technology, multimodal neuroimaging (PET, MRI, fNIRS, EEG) and neuromodulation montages (TMS and [HD]-tDCS). Initially, a curriculum vitae, letter of intent, and contact information for three professional references should be emailed to: adasi...@umich.eduAlexandre F. DaSilva, DDS, DMedScDirector, Headache and Orofacial Pain Effort (H.O.P.E.) LabTechno-Innovations in Pain Research, Therapeutics and Educationhttp://media.dent.umich.edu/labs/hope/ Biologic & Material Sciences, School of DentistryThe Molecular & Behavioral Neuroscience Institute (MBNI)University of Michigan The University of Michigan is an equal opportunity affirmative action employer.

DaSilva Letterhead.PosdocFellow.docx
Description: MS-Word 2007 document
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[Freesurfer] Individual regions of CorticalParcellation_Yeo2011

[Yi-Chia Erica Kung]

Dear Prof. Yeo,

I would like to extract the brain regions of the functional canonical
network, such as DMN, SAL, or CEN, withFreesurfer. And I found that you
have provided the split regions of 7&17 Network in previous discussion
string. (https://www.mail-archive.com/freesurfer
%40nmr.mgh.harvard.edu/msg41288.html
 )

However, the dropbox download link you offered has expired.
Would you mind uploading it again?

Thank you very much.

Erica
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Re: [Freesurfer] 7T thalamic segmentation inconsistencies.

[Benjamin Peterson]

Bruce,
Thank you for such a quick response. I have attached a link to the T1
dicom files. The T1 was acquired using an MP rage sequence.
​
 Thalamic T1 Files

​
Thanks,
Ben (University of Minnesota, Noam Harel's Lab)

On Tue, Oct 6, 2015 at 11:45 AM, Bruce Fischl 
wrote:

> Hi Ben
>
> if you upload the datasets we will take a look. I imagine this is due to
> dielectric resonance effects. What sequence did you use?
>
> Bruce
> On Tue, 6 Oct 2015,
> Benjamin Peterson wrote:
>
> > We have three 7T scans of the same person done on separate days. After
> > running all three T1 images using the "recon-all" function, we obtain
> > thalamic volumes. The volumes varied by up to 25% which seems quite
> drastic
> > for the same person. Is there a way to decrease this variability? Are
> there
> > some parameters to change for 7T? Would the subcortical segmentation work
> > better with a T2 or DTI image?
> > Thanks in advance,
> > Ben
> >
> >
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Re: [Freesurfer] Calculate the cortical thickness in patients with brain tumor

[chenhf_uestc]

Hi, Bruce

Do you mean that if the tumor located in the subcortical area, there is not 
large impact to reconstruction; if the tumor located in the cortical regions, 
there will affect the cortex reconstruction?

Another question is that I have MRI data from stroke patients. However, there 
are different lesions in the brain across the patients, including cerebral 
cortex and subcortical area. How could I perform reconstruction analysis?

Best,
Feng





发件人：Bruce Fischl 
发送时间：2015-10-01 23:11
主题：Re: [Freesurfer] Calculate the cortical thickness in patients with brain 
tumor
收件人："Freesurfer support list"
抄送：

Hi Feng 

it depends on where the tumor is 

cheers 
Bruce 
On Wed, 30 Sep 2015, chenhf_uestc wrote: 

> Hi, freesurfer experts, 
>   
> If my data came from the patients with brain tumors, could I perform 
> recon-all analyses to calculate cortical thickness, surface area and so on. 
> If not, could I mask the brain region with tumor and then conduct such 
> analyses? I think the tumor might lead to the inaccuracy of cortical 
> reconstruction 
>   
> Best, 
> Feng 
>  
> 
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Re: [Freesurfer] freeview and ?h.cortex.patch.flat

[Xiaomin Yue]

Thanks

Xiaomin




On Tue, Oct 6, 2015 at 11:35 AM -0700, "Lee Tirrell" 
 wrote:
Hi Xiaomin,

At this time, viewing the ?h.cortex.patch.flat isn't possible in freeview.  You
can load it using tksurfer by loading your subject's inflated surface, then
going to File -> Patch -> LoadPatch and choosing the correct patch.flat file.
These instructions are detailed here:

https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#Flattening

Best,
Lee

On Thu, 1 Oct 2015, Xiaomin Yue wrote:

> Hi,
> Can the developmental freeview display ?h.cortex.patch.flat?  I can't find 
> answers in the mail list.  If not, is there any way to convert the patch.flat 
> to a format freeview can display?
>
> Thanks,
> Xiaomin
>
>
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Re: [Freesurfer] Query about the calculation of surface area

[chenhf_uestc]

Thanks a lot, Bruce

If I want to compare the surface area between the patients and healthy control 
groups, which area file should I use? The area or the area.pial? Or I should 
compare both of them? If I should use both, is there any possibility that I 
would obtain different results from area and area.pial? I mean, in this case, a 
brain region has significantly different area but same (not significant) 
area.pial. How can I explain them in my research paper?

BTW, just out of curiosity, in the stats file such as lh.aparc.stats, why just 
thickness has the mean and std value, but other measures do not have the std 
value? 
SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd

Best,
Feng



发件人：Bruce Fischl 
发送时间：2015-10-06 20:45
主题：Re: [Freesurfer] Query about the calculation of surface area
收件人："Freesurfer support list"
抄送：

yes, that is correct 
Bruce 


On Tue, 6 Oct 2015, chenhf_uestc wrote: 

> Thanks, Bruce   So, in the stats folder of each subject, the  
> lh.aparc.a2009s.stats file provides surfarea of each region. This value  
> is the area for the white surface, right?
> Is the area of each vertex obtained by the average the area of triangles su  
> rrounding the vertex?Best, Feng 
>  
>  
>   发件人：Bruce Fischl  
> 发送时间：2015-10-06 20:25 
> 主题：Re: [Freesurfer] Query about the calculation of surface area 
> 收件人："Freesurfer support list" 
> 抄送： 
>   
> Hi Feng  
>   
> we compute the surface area of each surface and store it separately. The   
> ?h.area files are for the white surface and the ?h.area.pial for the pial  
>   
> cheers  
> Bruce  
> On   
> Tue, 6 Oct 2015, chenhf_uestc wrote:  
>   
> > Dear Freesurfer experts,  
> >
> > I have a question about the calculation of surface area. The cortical  
> > thickness is the distance between the pial and white matter. But, what ab 
> out  
> > the surface area? Calculation based on pial or white matter? Or average t 
> he  
> > area of both of them.  
> >
> > Is the area of each vertex obtained by the average the area of triangles 
?? ?> surrounding the vertex?  
> > In addition, where can I find the definition of meancurv, gauscurv, foldi 
> nd,  
> > curvind? I do not find it in the fswiki.  
> >
> > Best,  
> > Feng  
> >
> >   
> >  
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[Freesurfer] Query about the calculation of surface area

[chenhf_uestc]

Dear Freesurfer experts,

I have a question about the calculation of surface area. The cortical thickness 
is the distance between the pial and white matter. But, what about the surface 
area? Calculation based on pial or white matter? Or average the area of both of 
them. 

Is the area of each vertex obtained by the average the area of triangles 
surrounding the vertex? 
In addition, where can I find the definition of meancurv, gauscurv, foldind, 
curvind? I do not find it in the fswiki.

Best,
Feng___
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Re: [Freesurfer] mris_surf2vol

[Kevin Aquino]

Hi Doug,

sorry to be a bother, this doesn't work on my machine,
running:
file mri_surf2vol.mac64

gets me:

mri_surf2vol.mac64: ELF 64-bit LSB executable, x86-64, version 1 (SYSV),
dynamically linked (uses shared libs), for GNU/Linux 2.4.0, not stripped



Cheers,


*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham.

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney

*E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
www.physics.usyd.edu.au/~aquino/

--

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On Tue, Oct 6, 2015 at 12:35 AM, Douglas Greve 
wrote:

> here you go
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2vol.mac64
>
>
> On 10/5/15 11:24 AM, Kevin Aquino wrote:
>
> Hi Doug,
>
> Thanks for the file, do you happen to have one that is compiled for a
> 64bit mac installation of freesurfer?
>
> Cheers!
>
> Cheers,
>
>
> *Dr Kevin Aquino*
> Research fellow,
> Sir Peter Mansfield Magnetic Resonance Center, The University of
> Nottingham.
>
> Honorary Research Fellow
> School of Physics, Faculty of Science, University of Sydney
>
> *E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
> www.physics.usyd.edu.au/~aquino/
> 
>
> --
>
> The brain is a wonderful organ. It starts working the moment you get up
> and does not stop until you get into the office.
> -
> Robert Frost
>
> CRICOS 00026A
> This email plus any attachments to it are confidential. Any unauthorised
> use is strictly prohibited. If you receive this email in error, please
> delete it and any attachments.
>
> Please think of our environment and only print this e-mail if necessary.
>
>
> On Fri, Oct 2, 2015 at 6:26 PM, Douglas Greve 
> wrote:
>
>>
>> Try using Method 1 from this version of mri_surf2vol
>>
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2vol
>>
>>
>> On 10/2/15 11:38 AM, Kevin Aquino wrote:
>>
>> Ah sorry for not being clear,
>>
>> Basically I would like the output from mris_surf2vol with the mask option
>> to be less speckled.
>>
>> For example, in the image attached:
>> http://www.physics.usyd.edu.au/~aquino/example_mri_surf2vol.png
>>
>> there are some voxels missing. Is there an option to fill these voxels?
>>
>>
>> Cheers,
>>
>>
>> *Dr Kevin Aquino*
>> Research fellow,
>> Sir Peter Mansfield Magnetic Resonance Center, The University of
>> Nottingham.
>>
>> Honorary Research Fellow
>> School of Physics, Faculty of Science, University of Sydney
>>
>> *E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
>> www.physics.usyd.edu.au/~aquino/
>> 
>>
>> --
>>
>> The brain is a wonderful organ. It starts working the moment you get up
>> and does not stop until you get into the office.
>> -
>> Robert Frost
>>
>> CRICOS 00026A
>> This email plus any attachments to it are confidential. Any unauthorised
>> use is strictly prohibited. If you receive this email in error, please
>> delete it and any attachments.
>>
>> Please think of our environment and only print this e-mail if necessary.
>>
>>
>> On Fri, Oct 2, 2015 at 1:42 PM, Bruce Fischl 
>> wrote:
>>
>>> Hi Kevin
>>>
>>> I'm not clear on what you need. Would mri_surf2vol --fillribbon do what
>>> you want? I don't really know what else "voxelize" means
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Fri, 2 Oct 2015, Kevin Aquino wrote:
>>>
>>> Hi all,
 I am trying to "voxelize" the cortical surfaces generated in freesurfer
 and
 I am a little stuck.

 I have been using mris_surf2vol with the --mask option however this
 generates a very speckled representation of the cortical surface on the
 voxels. What I would prefer would be the level sets of the cortical
 surface
 interpolated onto voxels, even if they are at a different resolution
 that
 could be enough. Is this possible with any of the available commands?

 I also went down the route of mris_volmask however, this generates the
 cortical ribbon, which is something that I don't need.

 Cheers,


 Dr Kevin Aquino
 Research fellow,
 Sir Peter Mansfield Magnetic Imaging Center,
 School of Physics & astronomy, The University of Nottingham.

 Honorary Research Fellow
 School of Physics, Faculty of Science, 

Re: [Freesurfer] Lost toolbar in freeview

[Antonin Skoch]

Dear Ruopeng,

I am using Ubuntu 12.04. LTS 32bits.

There is no directory


~/Library/Preferences

in my home directory. There is only "GNUstep" directory containing 
subdirectories "Defaults" and "Library". "Library" dir is empty and "Defaults" 
contains .GNUstepDefaults file, which is very short file containing only 
NSGlobalDomain entry.

Regards,

Antonin___
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Re: [Freesurfer] high area.pial values

[Andrews, Derek]

Dear Bruce,

Thank you for your response regarding high area values.

I have indeed observed high values (I.e. >20) in both the white and pial
surfaces of my subjects, albeit only at a few vertices. The vertices
indices that contain the highest values in these surface appear around
~258,000-324,000. Would you consider this the end of the array? And if
not, what could cause a value of ~80 in the ~258,000 vertex of a pial
surface reconstruction?

As a background to what I¹m hoping to accomplish: I am using Freesurfer
features (arrays) as inputs for pattern classification, therefore I am
interested in potential impact on my models due to these outliers.
Smoothing reduces the effect of these outliers, however also raises the
values of surrounding vertices. I am thinking of replacing these high
values with an average area measure taken across all participants prior to
smoothing. 

Again, thank you for your insights in this topic.

Best, Derek 




Derek Sayre Andrews, MSc
PhD Candidate & IoPPN Student Forum Chair

Department of Forensic and Neurodevelopmental Sciences &
The Sackler Institute for Translational Neurodevelopment
Institute of Psychiatry, Psychology & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: derek.andr...@kcl.ac.uk





On 25/09/2015 17:00, "Bruce Fischl"  wrote:

>are they only high on the pial and not on the white? I would have guessed
>that they would be high on both, and further that it is due to the
>topology 
>correction and the quirks of the way we retesselate. One easy way to find
>out if this is true is if the vertex index is near the end of the list
>(i.e. close to the total number of vertices, since the vertices added
>during the correction are at the end of the array)
>
>cheers
>Bruce
>
>On Fri, 25 Sep 2015, Andrews, Derek wrote:
>
>> Dear FreeSurfer Support Team
>> 
>> First of all, I must thank you for your excellent software!
>> 
>> I have been looking at distributions of various free surfer features
>> (histograms of the vertex wise measures).  I have noticed some high
>>values
>> among the pial and white matter surfaces, these values range from 20-85.
>>  Again, this in only in a handful of vertices (out of millions of
>>measures).
>> I am wondering what could account for such a high value?
>> 
>> Thank you for your help in clarifying this.
>> 
>> Best, Derek 
>> 
>> 
>> 
>>_
>>___
>> 
>> Derek Sayre Andrews, MSc
>> PhD Candidate
>> 
>> Department of Forensic and Neurodevelopmental Sciences &
>> 
>> The Sackler Institute for Translational Neurodevelopment
>> Institute of Psychiatry, Psychology & Neuroscience, King's College
>>London
>> 
>> Telephone: +44 (0)20 7848 5701
>> Email: derek.andr...@kcl.ac.uk
>> 
>> 
>> 
>>___
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Re: [Freesurfer] Query about the calculation of surface area

[chenhf_uestc]

Thanks, Bruce

So, in the stats folder of each subject, the lh.aparc.a2009s.stats file 
provides surfarea of each region. This value is the area for the white surface, 
right?

Is the area of each vertex obtained by the average the area of triangles 
surrounding the vertex? 

Best,
Feng



发件人：Bruce Fischl 
发送时间：2015-10-06 20:25
主题：Re: [Freesurfer] Query about the calculation of surface area
收件人："Freesurfer support list"
抄送：

Hi Feng 

we compute the surface area of each surface and store it separately. The  
?h.area files are for the white surface and the ?h.area.pial for the pial 

cheers 
Bruce 
On  
Tue, 6 Oct 2015, chenhf_uestc wrote: 

> Dear Freesurfer experts, 
>   
> I have a question about the calculation of surface area. The cortical 
> thickness is the distance between the pial and white matter. But, what about 
> the surface area? Calculation based on pial or white matter? Or average the 
> area of both of them. 
>   
> Is the area of each vertex obtained by the average the area of triangles 
> surrounding the vertex? 
> In addition, where can I find the definition of meancurv, gauscurv, foldind, 
> curvind? I do not find it in the fswiki. 
>   
> Best, 
> Feng 
>   
>  
> 
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Re: [Freesurfer] Query about the calculation of surface area

[Bruce Fischl]

yes, that is correct
Bruce


On Tue, 6 Oct 2015, chenhf_uestc wrote:

Thanks, Bruce   So, in the stats folder of each subject, the 
lh.aparc.a2009s.stats file provides surfarea of each region. This value 
is the area for the white surface, right?   
Is the area of each vertex obtained by the average the area of triangles su 
rrounding the vertex?    Best, Feng



  发件人：Bruce Fischl 
发送时间：2015-10-06 20:25
主题：Re: [Freesurfer] Query about the calculation of surface area
收件人："Freesurfer support list"
抄送：
 
Hi Feng 
 
we compute the surface area of each surface and store it separately. The  
?h.area files are for the white surface and the ?h.area.pial for the pial 
 
cheers 
Bruce 
On  
Tue, 6 Oct 2015, chenhf_uestc wrote: 
 
> Dear Freesurfer experts, 
>   
> I have a question about the calculation of surface area. The cortical 
> thickness is the distance between the pial and white matter. But, what ab
out 
> the surface area? Calculation based on pial or white matter? Or average t
he 
> area of both of them. 
>   
> Is the area of each vertex obtained by the average the area of triangles

?? ?> surrounding the vertex? 

> In addition, where can I find the definition of meancurv, gauscurv, foldi
nd, 
> curvind? I do not find it in the fswiki. 
>   
> Best, 
> Feng 
>   
>  
> 
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Re: [Freesurfer] Query about the calculation of surface area

[Bruce Fischl]

Hi Feng

we compute the surface area of each surface and store it separately. The 
?h.area files are for the white surface and the ?h.area.pial for the pial


cheers
Bruce
On 
Tue, 6 Oct 2015, chenhf_uestc wrote:



Dear Freesurfer experts,
 
I have a question about the calculation of surface area. The cortical
thickness is the distance between the pial and white matter. But, what about
the surface area? Calculation based on pial or white matter? Or average the
area of both of them.
 
Is the area of each vertex obtained by the average the area of triangles
surrounding the vertex?
In addition, where can I find the definition of meancurv, gauscurv, foldind,
curvind? I do not find it in the fswiki.
 
Best,
Feng
 

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Re: [Freesurfer] Calculate the cortical thickness in patients with brain tumor

[Bruce Fischl]

Hi Feng

it's impossible to give a comprehensive answer to this type of question 
other than try it and see if it works. Too much depends on the exact 
placement and contrast properties of the lesions

Bruce
On Tue, 6 Oct 2015, 
chenhf_uestc wrote:



Hi, Bruce
 
Do you mean that if the tumor located in the subcortical area, there is not
large impact to reconstruction; if the tumor located in the cortical
regions, there will affect the cortex reconstruction?
 
Another question is that I have MRI data from stroke patients. However,
there are different lesions in the brain across the patients, including
cerebral cortex and subcortical area. How could I perform reconstruction
analysis?
 
Best,
Feng
 
 


  发件人：Bruce Fischl 
发送时间：2015-10-01 23:11
主题：Re: [Freesurfer] Calculate the cortical thickness in patients
with brain tumor
收件人："Freesurfer support list"
抄送：
 
Hi Feng 
 
it depends on where the tumor is 
 
cheers 
Bruce 
On Wed, 30 Sep 2015, chenhf_uestc wrote: 
 
> Hi, freesurfer experts, 
>   
> If my data came from the patients with brain tumors, could I perform 
> recon-all analyses to calculate cortical thickness, surface area and so o
n. 
> If not, could I mask the brain region with tumor and then conduct such 
> analyses? I think the tumor might lead to the inaccuracy of cortical 
> reconstruction 
>   
> Best, 
> Feng 
>  
> 
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Re: [Freesurfer] high area.pial values

[Bruce Fischl]

Hi Derek

if you run mris_info or mris_euler_number it will tell you how many 
vertices/faces are in the array.  I'm not sure what would cause such a high 
value, but you should be able to visualize it and see (once you have the 
vertex numbers that are in the face you can use freeview to goto them by 
typing the number into the "cursor" info panel at the bottom.


cheers
Bruce



On Tue, 6 Oct 2015, Andrews, Derek wrote:


Dear Bruce,

Thank you for your response regarding high area values.

I have indeed observed high values (I.e. >20) in both the white and pial
surfaces of my subjects, albeit only at a few vertices. The vertices
indices that contain the highest values in these surface appear around
~258,000-324,000. Would you consider this the end of the array? And if
not, what could cause a value of ~80 in the ~258,000 vertex of a pial
surface reconstruction?

As a background to what I¹m hoping to accomplish: I am using Freesurfer
features (arrays) as inputs for pattern classification, therefore I am
interested in potential impact on my models due to these outliers.
Smoothing reduces the effect of these outliers, however also raises the
values of surrounding vertices. I am thinking of replacing these high
values with an average area measure taken across all participants prior to
smoothing.

Again, thank you for your insights in this topic.

Best, Derek




Derek Sayre Andrews, MSc
PhD Candidate & IoPPN Student Forum Chair

Department of Forensic and Neurodevelopmental Sciences &
The Sackler Institute for Translational Neurodevelopment
Institute of Psychiatry, Psychology & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: derek.andr...@kcl.ac.uk





On 25/09/2015 17:00, "Bruce Fischl"  wrote:


are they only high on the pial and not on the white? I would have guessed
that they would be high on both, and further that it is due to the
topology
correction and the quirks of the way we retesselate. One easy way to find
out if this is true is if the vertex index is near the end of the list
(i.e. close to the total number of vertices, since the vertices added
during the correction are at the end of the array)

cheers
Bruce

On Fri, 25 Sep 2015, Andrews, Derek wrote:


Dear FreeSurfer Support Team

First of all, I must thank you for your excellent software!

I have been looking at distributions of various free surfer features
(histograms of the vertex wise measures).  I have noticed some high
values
among the pial and white matter surfaces, these values range from 20-85.
 Again, this in only in a handful of vertices (out of millions of
measures).
I am wondering what could account for such a high value?

Thank you for your help in clarifying this.

Best, Derek



_
___

Derek Sayre Andrews, MSc
PhD Candidate

Department of Forensic and Neurodevelopmental Sciences &

The Sackler Institute for Translational Neurodevelopment
Institute of Psychiatry, Psychology & Neuroscience, King's College
London

Telephone: +44 (0)20 7848 5701
Email: derek.andr...@kcl.ac.uk



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Re: [Freesurfer] Lost toolbar in freeview

[Antonin Skoch]

Dear Ruopeng,

thank you, it worked! Only, just to let you know, this tiny popup menu item was 
completely blank in my case, without any inscription. When I left-clicked at 
it, the menu bar appeared, and on this popup menu item only checkmark newly 
appeared.

Regards,

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[Freesurfer] repeated measures ANOVA using the FSGD file

[pablo najt]

Dear FS expertsTrying to set up a Linear Mixed Effects, which I understand 
would basically be a repeated measures design. My design has 3 groups (HC, PT 
relatives and PT).Instead of time points  of the same subject my design matrix 
uses each family member within a family. So I will have many subjects within 
family_1, same for family_2 and so on...I also want to include gender as a 
covariate. In short my question is:For my design in repeated measures do I need 
to define all my groups for each discrete variable as how we do it for glm?For 
example if I want to have variables GROUP + GENDER + FAMILY.Should i do it as 
follows?class HC_Female_Family1class PT_Female_Family1class 
HC_Male_Family2class HC_Female_Family2..
Many thanks,Pablo
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Re: [Freesurfer] Lost toolbar in freeview

[Ruopeng Wang]

In that case, simply click right-mouse button on the empty space on the menu 
bar. There should be a tiny menu item says “tool bar”. Check it and you should 
see tool bar again.

Best,
Ruopeng

> On Oct 6, 2015, at 6:32 AM, Antonin Skoch  wrote:
> 
> Dear Ruopeng,
> 
> I am using Ubuntu 12.04. LTS 32bits.
> 
> There is no directory
> ~/Library/Preferences
> 
> in my home directory. There is only "GNUstep" directory containing 
> subdirectories "Defaults" and "Library". "Library" dir is empty and 
> "Defaults" contains .GNUstepDefaults file, which is very short file 
> containing only NSGlobalDomain entry.
> 
> Regards,
> 
> Antonin
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Re: [Freesurfer] 7T thalamic segmentation inconsistencies.

[Bruce Fischl]

Hi Ben

if you upload the datasets we will take a look. I imagine this is due to 
dielectric resonance effects. What sequence did you use?

Bruce
On Tue, 6 Oct 2015, 
Benjamin Peterson wrote:

> We have three 7T scans of the same person done on separate days. After
> running all three T1 images using the "recon-all" function, we obtain
> thalamic volumes. The volumes varied by up to 25% which seems quite drastic
> for the same person. Is there a way to decrease this variability? Are there
> some parameters to change for 7T? Would the subcortical segmentation work
> better with a T2 or DTI image?
> Thanks in advance,
> Ben
> 
>
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[Freesurfer] Tracula Tracts density

[John Anderson]

Hi Anastasia,

How can I calculate the tract density from the output of tracula.

For example in the final stats file for the cortico spinal tract I can see the number of sample paths in the WM tract. Is this number refer to the tract density ( number of DTI fibers comprising the tract - in other words the number of distinct tracts that pass through the manually constructed sets of ROIs) ?

 

 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
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[Freesurfer] 7T thalamic segmentation inconsistencies.

[Benjamin Peterson]

We have three 7T scans of the same person done on separate days. After
running all three T1 images using the "recon-all" function, we obtain
thalamic volumes. The volumes varied by up to 25% which seems quite drastic
for the same person. Is there a way to decrease this variability? Are there
some parameters to change for 7T? Would the subcortical segmentation work
better with a T2 or DTI image?

Thanks in advance,
Ben
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Re: [Freesurfer] Error Messages for Accessing Bin

[Timothy Le]

Hi,
We have a 64 bit system. We chose to install 5.0 because we already have data 
processed in 5.0 and want to keep the data consistent.
What would you advise us to do?
Thank you 
Timothy

> On Oct 6, 2015, at 7:47 AM, dgw  wrote:
> 
> what operating system are you running? 64 bit or 32 bit?
> Why did you decide to install version 5.0 instead of the current stable 5.3?
> 
> hth
> d
> 
>> On Mon, Oct 5, 2015 at 5:41 PM, Timothy Le  wrote:
>> Hi,
>> From the following output, how should I proceed?
>> Thank you very much
>> Timothy Le
>> 
>> On Oct 2, 2015, at 11:55 AM, Timothy Quang-Tin Le  wrote:
>> 
>> Hi,
>> Thank you very much for your response. The output of that command was:
>> 
>> tle7@sni-vcs-gotlib:~$ ls -l /home/tle7/freesurfer/bin/mri_convert
>> -rwxrwx--x 1 tle7 stanford 1672136 Aug 15  2010
>> /home/tle7/freesurfer/bin/mri_convert
>> tle7@sni-vcs-gotlib:~$
>> 
>> 
>>> On Fri, Oct 2, 2015 at 10:39 AM, dgw  wrote:
>>> 
>>> Timothy,
>>> 
>>> What is the output of this command:
>>> 
>>> ls -l /home/tle7/freesurfer/bin/mri_convert
>>> 
>>> ?
>>> 
>>> hth
>>> d
>>> 
>>> On Fri, Oct 2, 2015 at 1:36 PM, Timothy Quang-Tin Le 
>>> wrote:
 Hi,
 I tried the chmod command, but it did not work. How I check that I've
 downloaded the correct version?
 Thank you very much
 Timothy
 
 On Thu, Oct 1, 2015 at 8:10 AM, Bruce Fischl
 
 wrote:
> 
> can you try chmod a+x on one of them and see if it can then be
> executed?
> e.g.:
> 
> chmod a+x  /home/tle7/freesurfer/bin/mri_convert
> /home/tle7/freesurfer/bin/mri_convert
> 
> and see if you get an error. If not, you probably downloaded the wrong
> hardware version
> cheers
> Bruce
> 
> 
> 
>> On Tue, 29 Sep 2015, Timothy Quang-Tin Le wrote:
>> 
>> 
>>  Hello,
>> When I run the command "sFSstart" on version 5.0.0, I am receiving the
>> messages below. Would you please explain to me what the problem is? It
>> seems like there is trouble accessing the bin.
>> Thank you
>> 
>>  freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 
>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>> FREESURFER_HOME   /home/tle7/freesurfer
>> FSFAST_HOME   /home/tle7/freesurfer/fsfast
>> FSF_OUTPUT_FORMAT nii
>> SUBJECTS_DIR  /home/tle7/freesurfer/subjects
>> MNI_DIR   /home/tle7/freesurfer/mni
>> tle7@sni-vcs-gotlib:~$ sFSstart practicemotherdaughter 00152-DT2
>> studyPath /home/tle7/freesurfer/subjects/practicemotherdaughter
>> H 0
>> checking sid number 00152-DT2
>> 1
>> 
>> 00152-DT2/MR.1.2.840.113619.2.283.4120.7575399.15360.1319907833.100.dcm
>> Subject Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0
>> Current Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0
>> INFO: SUBJECTS_DIR is /home/tle7/freesurfer/subjects
>> Actual FREESURFER_HOME /home/tle7/freesurfer
>> Linux sni-vcs-gotlib.stanford.edu 3.13.0-61-generic #100-Ubuntu SMP
>> Wed Jul 29 11:21:34 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
>> /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/flirt.fsl: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/tkregister2_cmdl: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mri_normalize: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mri_watershed: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mri_gcut: Exec format error. Binary file not
>> executable.
>> /home/tle7/freesurfer/bin/mri_segment: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/mri_label2label: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mri_em_register: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mri_ca_normalize: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mri_ca_register: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mri_ca_label: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/mri_pretess: Exec format error. Binary file
>> not executable.
>> /home/tle7/freesurfer/bin/mri_fill: Exec format error. Binary file not
>> executable.
>> /home/tle7/freesurfer/bin/mri_tessellate: Exec format error. Binary
>> file not executable.
>> /home/tle7/freesurfer/bin/mri_concatenate_lta: Exec format error.
>> Binary file not executable.

[Freesurfer] Postdoc position at Martinos Center for Biomedical Imaging

[Allison Stevens]

Postdoc position at Martinos Center for Biomedical Imaging - Massachusetts 
General Hospital / Harvard Medical School


The Laboratory for Computational Neuroimaging at the Martinos Center for 
Biomedical Imaging has a job opening for a post-doctoral fellow to work on 
modeling cortical layers and boundaries using Magnetic Resonance Imaging 
(MRI) and Optical Coherence Tomography (OCT).


The project will take place at the Martinos Center 
(http://www.nmr.mgh.harvard.edu/) and will involve developing 
computational methods with the goal of extracting quantitative information 
from OCT images and leveraging the information for MRI analysis. 
Cutting-edge imaging infrastructure for both these modalities is available 
at the center and will be used for the project. The methods developed will 
have be to distributed to the research community through widely used 
Freesurfer software suite.


Applicants are expected to have finished their PhD in medical image 
analysis, computer vision or a related field with a track record of 
relevant publications. The project requires experience with mathematical 
modeling and good programming skills in C/C++ and Matlab/Python. 
Experience with image registration, deformable surfaces/contours, machine 
vision techniques and neuroimaging are welcome.


The postdoctoral fellow will work closely with Bruce Fischl and Ender 
Konukoglu.


Applications must be sent by email to Ender Konukoglu 
(end...@nmr.mgh.harvard.edu) and contain a CV, list of publications and 
names of three references. The intended start date for the position is 
December 2015 however, the exact date is negotiable. 
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Re: [Freesurfer] problem fast_selxavg3b

[Z K]

Hello,

I have seen errors that look like the error below (i.e. GLIBCXX_3.4.15) 
when their is an incompatibility between the OS, matlab, and the 
compiled binary. Looking at your path to matlab I see 
"/opt/matlab/R2010b". Thats pretty old.

Doug,
I recall you telling me these binaries are compiled against matlab 8.3 
(R2014a)? Perhaps Desiree should use that version.

-Zeke


On 10/05/2015 07:32 PM, Douglas Greve wrote:
> I don't think it is a matlab problem. We call some binaries from inside
> matlab, and the problem is with those. It looks like the version of FS
> does not match your operating system or that you are missing a library.
> Maybe Zeke can help sort it out.
> doug
>
> On 10/5/15 2:31 AM, Desiree Thielemann wrote:
>>
>> Dear freesurfer experts,
>>
>> I included the new function fast_selxavg3b but I got another problem:
>>
>> First error:
>>
>> /opt/freesurfer/bin/mris_fwhm --mask
>> /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/mask.nii.gz
>> --i
>> /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.nii.gz
>> --o
>> /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.sm.nii.gz
>> --fwhm 20.00 --smooth-only --s fsaverage --hemi lh --sd
>> /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann
>> /opt/freesurfer/bin/mris_fwhm: symbol lookup error:
>> /opt/freesurfer/bin/mris_fwhm: undefined symbol: ncerr
>>
>> ERROR: /opt/freesurfer/bin/mris_fwhm --mask
>> /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/mask.nii.gz
>> --i
>> /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.nii.gz
>> --o
>> /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann/PT_2prae_VP01_2_f/bold/firstlevel.sm06.stc.lh/rho1mn.sm.nii.gz
>> --fwhm 20.00 --smooth-only --s fsaverage --hemi lh --sd
>> /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/fsfast/Thielemann
>>
>> ans =
>>
>>   127
>>
>> Second error with another server running the analyses:
>>
>> /opt/freesurfer/bin/mris_fwhm:
>> /opt/matlab/R2010b/sys/os/glnxa64/libstdc++.so.6: version
>> `GLIBCXX_3.4.11' not found (required by /opt/freesurfer/bin/mris_fwhm)
>> /opt/freesurfer/bin/mris_fwhm:
>> /opt/matlab/R2010b/sys/os/glnxa64/libstdc++.so.6: version
>> `GLIBCXX_3.4.15' not found (required by /opt/freesurfer/bin/mris_fwhm)
>>
>>
>> The problem seems to be the version of matlab. Which version would you
>> suggest to use while using the function fast_selxavg3b? And why is
>> there an undefined symbol?
>>
>> Do you have any suggestions how to solve the problem?
>>
>> Best regard,
>> Desiree
>>
>>
 --
>> ERROR: fast_selxavg3() failed\n
>>
>> Zitat von Douglas Greve :
>>
>>> oops, sorry, that did not make it into the distribution. You can get
>>> it here
>>>
>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_selxavg3b.m
>>>
>>>
>>> thanks
>>> doug
>>>
>>>
>>> On 9/29/15 9:15 AM, Silvia Désirée Thielemann wrote:
 Dear members of the freesurfer mailing list,

 I'm using freesurfer-Linux-centos7_x86_64-dev-20150728. I started to
 analyse mri data with fs-fast. I did the preprocessing and used the
 function mkanalysis-sess and mkcontrast-sess without any problems. I
 tried to run the function selxavg3-sess next and it stopped with the
 error message:

 /opt/freesurfer/fsfast/toolbox/fast_selxavg3.m
>> /opt/freesurfer/fsfast/toolbox/fast_ldanaflac.m
>> /opt/freesurfer/matlab/MRIread.m
>> ??? Undefined function or method 'fast_selxavg3b' for input
>> arguments of type
 'char'.

>> --
 ERROR: fast_selxavg3() failed\n

 I looked for the function fast_selxavg3b in matlab. Unfortunatly only
 the function fast_selxavg3 is included in the fsfast/toolbox. By
 trying to use the function fast_selxavg3, it recommand me to use
 fast_selxavg3b. I could not find the function in the internet.

 Do you have any suggestions what to do?

 Best regards,
 Desiree

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