[Freesurfer] qcache for qdec longitudinal analysis

2016-08-22 Thread Nick Corriveau Lecavalier 
Hi Freesurfer team,


I am planning on following this page for my longitudinal group analysis using 
QDEC: http://www.freesurfer.net/fswiki/FsTutorial/QdecGroupAnalysis_freeview. 
However, it tells me to run -qcache for all of my subjects. Since I already ran 
the -long stream for all my subjects, do I need to rerun them all adding the 
-qcache command?


Also, I have also run the long_mris_slopes on all of my subjects, which 
produced smoothed thickness files for all of my subjects (which are all in the 
''base'' files). Does these files are okay for my QDEC analysis, or I really 
need to run all of my subjects all over again adding -qcache?


Thank you very much,


Nick Corriveau-Lecavalier, B.Sc. (Hons.)
Étudiant au Ph.D. recherche/intervention, option neuropsychologie clinique
Coordonateur à la recherche, Association étudiante des cycles supérieurs en 
psychologie de l'Université de Montréal (AÉCSPUM)
Université de Montréal
Centre de recherche de l'Institut universitaire de gériatrie de Montréal, 
bureau M7819
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Re: [Freesurfer] Support for surface data on NeuroVault.org

2016-08-22 Thread Chris Filo Gorgolewski 
Thank you for your comments. Some more questions below:

On Mon, Aug 22, 2016 at 1:09 PM, Douglas N Greve 
wrote:
>
> > 1. In NeuroVault users are asked to upload their statistical maps in
> > form of files. I'm planning to target outputs of mri_glmfit:
> > preferably Z.mgh but also sig.mgh. Is this the most sensible thing to do?
> Yes. You may also want the gamma.mgh file as that is the size of the
> effect (eg, thickness change in mm )
>
This would be very useful - an effect size in meaningful units is a rarity
in neuroimaging!


> > 7. Finally NeuroVault gives users ability to compare maps and even
> > search through the whole repository to find statistical maps with
> > similar patterns. This is currently implemented for volumetric data,
> > but could be extended to surface data. The problem arises when one
> > wants to compare MNI volumetric data with fsaverage surface data. So
> > far I have been using mri_vol2surf with target subject being fsaverage
> > (with a supplied affine correction matrix), but this solution is far
> > from optimal since fsaverage folding patterns are quite different from
> > MNI. I was thinking that maybe a more accurate way of dealing with
> > this would be to reconstruct MNI152 cortical surface model, do surface
> > registration of it to fsaverage, and use that to sample statistical
> > maps in MNI space. What do you think?
> I would probably go the other direction, ie, sample the MNI152 maps into
> surface space.
>
This is exactly what I want to do. The question is what is the most
accurate way of sampling MNI152 maps to fsaverage?

Best,
Chris



> >
> > Thank you for any help feedback you can provide!
> >
> > Best,
> > Chris Gorgolewski
> >
> >
> > ___
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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Re: [Freesurfer] Recon-all error using Freesurfer 6.0

2016-08-22 Thread Douglas N Greve 
Nothing looks suspicious. Try setting


setenv SUBJECTS_DIR /usr/local/DTI_processed_data/freesurfer_data_dir

ie, removing the trailing "/"

On 08/22/2016 02:12 AM, Elpiniki Andrew wrote:
> Hello Freesurfer experts,
>
> I'm having a bit of difficulty running the recon-all command. I 
> recently downloaded Freesurfer version 6.0.
>
> The command that I'm running is:
>
>  recon-all -all -s $name -hippocampal-subfields-T1
>
> However I keep receiving this error:
>
> If: Expression Syntax
>
> I've attached the output using the -debug flag.
>
> I'm using Linux ( centos6.3). Not sure if this is related but I 
> initially had an issue with recon-all stopped with an error when I 
> first ran the same dataset. There was an error in the log file " too 
> many levels of symbolic links".
> So, I created a new subjects directory and created a symlink to the 
> fsaverage dir as per the instructions on the freesurfer wiki page.
>
>
> Thankyou very much in advance for your time and efforts!
>
> Kind regards,
> Elpiniki
>
>
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Fax: 617-726-7422

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Re: [Freesurfer] Support for surface data on NeuroVault.org

2016-08-22 Thread Douglas N Greve 


On 08/20/2016 01:21 PM, Chris Filo Gorgolewski wrote:
> Dear FreeSurfer community,
> I am one of the developers of NeuroVault.org  - 
> an open repository for vizualizing, analyzing, and sharing of 
> statistical and parcellation maps of the human brain. So far 
> NeuroVault was limited only to volumetric data in the MNI space since 
> this is the most common way of reporting MRI results. Now I would like 
> to start working on adding support for surface data beginning with 
> outputs of FreeSurfer. Since I'm not a FreeSurfer expert I would like 
> to ask the community a few questions:
>
> 1. In NeuroVault users are asked to upload their statistical maps in 
> form of files. I'm planning to target outputs of mri_glmfit: 
> preferably Z.mgh but also sig.mgh. Is this the most sensible thing to do?
Yes. You may also want the gamma.mgh file as that is the size of the 
effect (eg, thickness change in mm )
>
> 2. I want to be able to tell if a given map is in fsaverage space. Is 
> there any place in the .mgh header that specifies which space the map 
> is in?
No.
>
> 3. fsaverage has different subsampling flavours - how often are they 
> used? Is support for them an important feature?
Not very often. I would probably not worry about it.
>
> 4. Results come in two files - one per each hemisphere. Is there any 
> way (from the headers) to check if two files provided by a user match?
match in what way? There is nothing in the mgh file to indicate laterality.
>
> 5. As with the volumetric data I want to provide a 3D interactive 
> viewer. I had some initial success with Brain Browser. Are you aware 
> of any other javascript based viewers that work well with FreeSurfer data?
I'm not, but I'm not the best person to ask.
>
> 6. Which surface should be the default view: inflated, pial, or white?
I always to with pial with the aparc outlines. Others may feel differently.
>
> 7. Finally NeuroVault gives users ability to compare maps and even 
> search through the whole repository to find statistical maps with 
> similar patterns. This is currently implemented for volumetric data, 
> but could be extended to surface data. The problem arises when one 
> wants to compare MNI volumetric data with fsaverage surface data. So 
> far I have been using mri_vol2surf with target subject being fsaverage 
> (with a supplied affine correction matrix), but this solution is far 
> from optimal since fsaverage folding patterns are quite different from 
> MNI. I was thinking that maybe a more accurate way of dealing with 
> this would be to reconstruct MNI152 cortical surface model, do surface 
> registration of it to fsaverage, and use that to sample statistical 
> maps in MNI space. What do you think?
I would probably go the other direction, ie, sample the MNI152 maps into 
surface space.
>
> Thank you for any help feedback you can provide!
>
> Best,
> Chris Gorgolewski
>
>
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-- 
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
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Re: [Freesurfer] Recon-all Correcting Defect 0

2016-08-22 Thread Douglas N Greve 
It looks like there is a very large defect. Check the wm.mgz file to see 
if the cerebellum has been removed.


On 08/21/2016 08:46 AM, Heidi Foo wrote:
> Dear FreeSurfer team,
>
> I apologize for sending this email again. I am currently running 
> recon-all for my subjects but for 2 of them, it stops at XL correcting 
> defect. Do you have any ideas how I can deal with this problem? 
> Attached the log file for your reference.
>
> Thanks.
>
> Regards,
> Heidi
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] $SUBJECTS_DIR

2016-08-22 Thread Douglas N Greve 
There is already a label called ?h.cortex.label for all of cortex. For 
lobes, you can use mris_annotation2label to break up the annotation into 
its constituent labels, then use mri_mergelabels to combine subsets into 
a lobe, then use mris_label2annot to combine the lobes into a new 
annotation. Search through the mail archives because this has been 
asked/answered before


On 08/21/2016 01:43 PM, Adil Javed wrote:
> Thanks,
>
> any thoughts about Q#2:
> 2-Also, Is there a way to segment the cortices as a whole, like left 
> and right frontal cx, parietal cx, temporal cx, occipital cx?
>
> Thanks
>
> aj
>
>
> On Saturday, August 20, 2016 9:21 PM, "sha...@nmr.mgh.harvard.edu" 
>  wrote:
>
>
> Hi Adil,
>   My understanding is that, you can always change the location of
> SUBJECTS_DIR. Just use this command:
>   setenv SUBJECTS_DIR 
>
> You do not need to mention this new address in your recon-all command.
>
> Good luck
>
>
>
> > HI,1-I'm working with FreeSurfer that is on a server.  I don't have
> > permission to create files under the $SUBJECTS_DIR.  Is there any 
> way I
>
> > can specify -subject to be in a directory for which I do have 
> permission?
> > for example: recon-all -subject /location of the file or my own
> > subject_dir location -all
> > 2-Also, Is there a way to segment the cortices as a whole, like left and
> > right frontal cx, parietal cx, temporal cx, occipital cx?
> >
> >
> > Thanks,
> > AJ___
>
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Fax: 617-726-7422

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Re: [Freesurfer] Structural group analysis

2016-08-22 Thread Douglas N Greve 
Not sure what you are trying to do. Are you comparing the average 
thickness in premotor to that in primary motor? What would it mean to 
visualize that?


On 08/22/2016 09:52 AM, Silas wrote:
>
> Dear FreeSurfer team,
>
>
> I'm doing a structural analysis with around 20 subjects and I'm 
> specifically interested in the areas premotor cortex and primary motor 
> cortex. By matlab analysis I've found a very strong statistical 
> significant difference in the cortical thickness when comparing these 
> two areas with all subjects (data extracted from FreeSurfer recon-all 
> pipeline). I would like to visualize these results on the surface of 
> fsaverage, and I'm familiar with the FreeSurfer group analysis 
> pipeline. So far I've simply made a OSGM group analysis and visualized 
> these results on the fsaverage in a premade label of premotor cortex 
> and primary motor cortex and correlated for multiple comparisons using 
> your precomputed monte carlo simulation - but this doesn't make it.
>
>
> Do you guys have a clever way to visualize these results in 
> FreeSurfer? I have one group and would like to visualize the 
> difference between two areas. I've thought about presenting each 
> subject two times in the FSGD-file (primary motor cortex and premotor 
> cortex), but this isn't possible and seems as a clumsy way to solve 
> this problem.
>
>
> Please let me know if my problem is incomprehensible!
>
>
> Best, Silas
>
>
>
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-- 
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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
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[Freesurfer] Structural group analysis

2016-08-22 Thread Silas 
Dear FreeSurfer team,


I'm doing a structural analysis with around 20 subjects and I'm specifically 
interested in the areas premotor cortex and primary motor cortex. By matlab 
analysis I've found a very strong statistical significant difference in the 
cortical thickness when comparing these two areas with all subjects (data 
extracted from FreeSurfer recon-all pipeline). I would like to visualize these 
results on the surface of fsaverage, and I'm familiar with the FreeSurfer group 
analysis pipeline. So far I've simply made a OSGM group analysis and visualized 
these results on the fsaverage in a premade label of premotor cortex and 
primary motor cortex and correlated for multiple comparisons using your 
precomputed monte carlo simulation - but this doesn't make it.


Do you guys have a clever way to visualize these results in FreeSurfer? I have 
one group and would like to visualize the difference between two areas. I've 
thought about presenting each subject two times in the FSGD-file (primary motor 
cortex and premotor cortex), but this isn't possible and seems as a clumsy way 
to solve this problem.


Please let me know if my problem is incomprehensible!


Best, Silas
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