Re: [Freesurfer] mri_mcsim for individual subjects and references {Disarmed}

[Kevin Aquino]

Actually,

would would be preferable would be running a permutations test something
that you describe in:

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg49846.html

is there an easy to run mri_glmfit-sim's permutation simulations on a
single subject?
I've run through the FS-FAST pipeline

mkanalysis-sess -fsd bold -surface self rh -fwhm 4.5 -event-related
-paradigm attn.par -nconditions 4 -spmhrf 0 -TR 1.9 -analysis
myanalysis -per-session
-refeventdur 450 -force -nuisreg moco.txt -1 -polyfit 0
mkcontrast-sess -analysis myanalysis -contrast attn -c 1 -a 2 -a 3 -c 4
selxavg3-sess -s SESSION -analysis self_attn_sm_reg.rh -no-preproc -fwhm

But mri_glmfit-sim is expecting the output from mri_glmfit

mri_glmfit-sim --glmdir . --perm 1000 3 pos --log ./selxavg3.log
>> ERROR: cannot find ./mri_glmfit.log

should I just run mri_glmfit with the appropriate flags, or is there a
mri_glmfit-sim version for data that has passed through selxavg3 ?


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*
https://kevinaquino.github.io 

--

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On Tue, May 16, 2017 at 12:34 PM, Kevin Aquino 
wrote:

> Hi all,
>
> First of all, Freesurfer V6 is working like a dream, my 0.7 mm
> segmentations are running really well and in comparisons to hi-resrecon in
> 5.3 and early beta, I'm having to do fewer manual corrections!
>
>
> Now for my questions,
>
> 1. I'm running mri_mcsim in order to correct for multiple comparisons via
> the FS-FAST stream. I'm wondering how many iterations are advised, and how
> can one check for convergence in an automatic fashion.
>
> I've run the simulations with 1000 and 10,000 iterations on a 1mm
> segmentation with the FWHM simulations at 8mm. (i.e. using mri_mcsim --o .
> --base mc-z --save-iter  --surf subject lh/rh --nreps 1 --fwhm 8) and I
> can't see many differences between the two when correcting for multiple
> comparisons (i.e. using cluster-sess -analysis  myanalysis -thresh 3 -cwp
> .05 -s SESSION -sign pos).
>
> 2. I'm trying to find some references that detail the simulations and form
> the corrections, does anyone have advice which list I can read/start off
> with, as well as some key papers that use it (esp on a single subject
> level). I really like this approach and It does look to circumvent (I
> think...) a lot of the problems of cluster-wise corrections described with
> Eklund et al. (Cluster failure paper).
>
> 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* 
> *MailScanner
> has detected a possible fraud attempt from "www.physics.usyd.edu.au"
> claiming to be* https://kevinaquino.github.io
> 
>
> --
>
> 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
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[Freesurfer] mri_mcsim for individual subjects and references {Disarmed}

[Kevin Aquino]

Hi all,

First of all, Freesurfer V6 is working like a dream, my 0.7 mm
segmentations are running really well and in comparisons to hi-resrecon in
5.3 and early beta, I'm having to do fewer manual corrections!


Now for my questions,

1. I'm running mri_mcsim in order to correct for multiple comparisons via
the FS-FAST stream. I'm wondering how many iterations are advised, and how
can one check for convergence in an automatic fashion.

I've run the simulations with 1000 and 10,000 iterations on a 1mm
segmentation with the FWHM simulations at 8mm. (i.e. using mri_mcsim --o .
--base mc-z --save-iter  --surf subject lh/rh --nreps 1 --fwhm 8) and I
can't see many differences between the two when correcting for multiple
comparisons (i.e. using cluster-sess -analysis  myanalysis -thresh 3 -cwp
.05 -s SESSION -sign pos).

2. I'm trying to find some references that detail the simulations and form
the corrections, does anyone have advice which list I can read/start off
with, as well as some key papers that use it (esp on a single subject
level). I really like this approach and It does look to circumvent (I
think...) a lot of the problems of cluster-wise corrections described with
Eklund et al. (Cluster failure paper).

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*
https://kevinaquino.github.io 

--

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

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Re: [Freesurfer] Freesurfer white matter outer edge to volume

[Gamaliz]

My idea is to convert the registered white surface into a volume, so
it can be shown in a volume viewer (not a surface viewer). I need to
display a DTI image and mark the edges of the white matter as a line
on top if it.


This is not the exact command, I am not sitting in front of my
station, but it goes something like it. I tried many combinations, the
general error was related to the template files not on the correct
format (it could have been they couldn't be found to be opened too,
the error seemed generic).


mri_surf2vol --surfval white --hemi lh --outvol test.mgz  --template
T1.mgz --volreg T1.mgz --sd /home/user/Desktop/sf/sub1


I am at a loss for the --volreg flag.


The sd seems to indicate the directory of freesurfer (but then how is
the command aware of the specficic subject I am trying to process? I
tried using: --identity subject no luck.


'sub1' us my subject, located not in the default freesurfer directory.

There are no examples or a lot of help using it

https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol


If this is not enough I can get back to you with the specific error tomorrow.


On Mon, May 15, 2017 at 10:02 PM, Douglas Greve 
wrote:

> what was your mri_surf2vol cmd line? And what was the terminal output?
>
> On 5/15/17 9:59 PM, Gamaliz wrote:
>
> I looked at the ribbon.mgz, but it is a pial surface, not really
> delineated white matter the way I need it. There is a command called
> mri_sur2vol, I have tried to use it, but unsuccessfully, no idea if that is
> the solution to my problem.
>
> On Mon, May 15, 2017 at 9:57 PM, Douglas Greve 
> wrote:
>
>> not sure what you mean. Have you looked at the ribbon.mgz file?
>>
>> On 5/15/17 5:20 PM, Gamaliz wrote:
>>
>> I need to create an image which overlaps the T1/mgz and the outer surface
>> of the white matter. How do I convert the surface into a mgz volume?
>>
>>
>> --
>> gAbE
>>
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>> du/mailman/listinfo/freesurfer The information in this e-mail is
>> intended only for the person to whom it is addressed. If you believe this
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>> 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.
>
> --
> gAbE
>
> ___
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> 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
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> properly
> dispose of the e-mail.
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-- 
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Re: [Freesurfer] mri_convert

[John Anderson]

Hi Doug thank you for the quick response!

The source is a Siemens scanner. Data derived from the Spine. I don't know what 
is the optimal way to convert these ima images to nifti

what is the source of the ima file? was it anonymized? You can try something 
like adding

-iid -1 0 0 -ijd 0 1 0 -ikd 0 0 1

but this is just guessing at the orientation

 Original Message 
Subject: mri_convert
Local Time: May 15, 2017 9:58 PM
UTC Time: May 16, 2017 1:58 AM
From: john.ande...@protonmail.com
To: Freesurfer support list 

Dear Freessurfer experts,
i want to convert IMA files to nifti using mri_convert I did the following:

mri_convert 54365413.ima output.nii

I got this error
WARNING: bad orientation matrix (determinant = 0) in nifti1 file ...
... continuing.

if I run mri_info on output.nii I see

voxel-to-ras determinant 0

ras to voxel transform:
mat = NULL!
MatrixFree: NULL mat POINTER!

How can I correctly convert IMA to nifti
Thank you for any suggestion
John___
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Re: [Freesurfer] mri_convert

[Douglas Greve]

what is the source of the ima file? was it anonymized? You can try 
something like adding


-iid -1 0 0 -ijd 0 1 0 -ikd 0 0 1

but this is just guessing at the orientation


On 5/15/17 9:58 PM, John Anderson wrote:

Dear Freessurfer experts,
i want to convert IMA files to nifti using mri_convert I did the 
following:


mri_convert 54365413.ima output.nii

I got this error
WARNING: bad orientation matrix (determinant = 0) in nifti1 file ...
... continuing.

if I run mri_info on output.nii I see

voxel-to-ras determinant 0

ras to voxel transform:
mat = NULL!
MatrixFree: NULL mat POINTER!


How can I correctly convert IMA to nifti
Thank you for any suggestion
John



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Re: [Freesurfer] Freesurfer white matter outer edge to volume

[Douglas Greve]

what was your mri_surf2vol cmd line? And what was the terminal output?


On 5/15/17 9:59 PM, Gamaliz wrote:
I looked at the ribbon.mgz, but it is a pial surface, not really 
delineated white matter the way I need it. There is a command called 
mri_sur2vol, I have tried to use it, but unsuccessfully, no idea if 
that is the solution to my problem.


On Mon, May 15, 2017 at 9:57 PM, Douglas Greve 
> wrote:


not sure what you mean. Have you looked at the ribbon.mgz file?


On 5/15/17 5:20 PM, Gamaliz wrote:

I need to create an image which overlaps the T1/mgz and the outer
surface of the white matter. How do I convert the surface into a
mgz volume?


-- 
gAbE



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 . If the e-mail was sent
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gAbE

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Re: [Freesurfer] Freesurfer white matter outer edge to volume

[Gamaliz]

I looked at the ribbon.mgz, but it is a pial surface, not really delineated
white matter the way I need it. There is a command called mri_sur2vol, I
have tried to use it, but unsuccessfully, no idea if that is the solution
to my problem.

On Mon, May 15, 2017 at 9:57 PM, Douglas Greve 
wrote:

> not sure what you mean. Have you looked at the ribbon.mgz file?
>
> On 5/15/17 5:20 PM, Gamaliz wrote:
>
> I need to create an image which overlaps the T1/mgz and the outer surface
> of the white matter. How do I convert the surface into a mgz volume?
>
>
> --
> gAbE
>
>
> ___
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>
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>
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> 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
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> but does not contain patient information, please contact the sender and
> properly
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-- 
gAbE
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[Freesurfer] mri_convert

[John Anderson]

Dear Freessurfer experts,
i want to convert IMA files to nifti using mri_convert I did the following:

mri_convert 54365413.ima output.nii

I got this error
WARNING: bad orientation matrix (determinant = 0) in nifti1 file ...
... continuing.

if I run mri_info on output.nii I see

voxel-to-ras determinant 0

ras to voxel transform:
mat = NULL!
MatrixFree: NULL mat POINTER!

How can I correctly convert IMA to nifti
Thank you for any suggestion
John___
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Re: [Freesurfer] Freesurfer white matter outer edge to volume

[Douglas Greve]

not sure what you mean. Have you looked at the ribbon.mgz file?


On 5/15/17 5:20 PM, Gamaliz wrote:
I need to create an image which overlaps the T1/mgz and the outer 
surface of the white matter. How do I convert the surface into a mgz 
volume?



--
gAbE


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Re: [Freesurfer] probability maps

[Douglas Greve]

you can do something like

a = MRIread('map1.mgz');

b = MRIread('map2.mgz');

c = MRIread('map3.mgz');

d = (a.vol > thresh + b.vol > thresh + d.vol> thresh)/3;

[mm ii] = max(d);

Then the vertex number will be ii-1 (need to convert from 1-based to 
0-based)





On 5/15/17 3:34 PM, Trisanna Sprung-Much wrote:

Hi Bruce

The maps are .mgz format and are % overlap (across 40 subjects). They 
were generated using


-labels turned into surface overlay using mri_vol2surf
-then registered to fsaverage using mri_surf2surf
-then averaged within fsaverage space using mri_concat and then 
mris_fwhm to smooth.


Best
Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Mon, May 15, 2017 at 2:53 PM, Bruce Fischl 
> wrote:


what format is your map of p-values in?
On Mon, 15 May 2017, Trisanna
Sprung-Much wrote:

> Hi Bruce
> I would not know where to start (not an avid matlab user) - what
input would
> be needed to be fed into matlab?
>
> Trisanna
>
> --
> Ph.D. CandidateMcGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Mon, May 15, 2017 at 12:52 PM, Bruce Fischl
>
> wrote:
>   hmmm, should be pretty easy in matlab, no?
>   On Mon, 15 May 2017, Trisanna
>   Sprung-Much wrote:
>
>   > Hi there
>   > I have generated some anatomical probabilistic maps as
>   overlays on the
>   > fsaverage pial surface. Is there a way to automatically find
>   the vertex
>   > coordinates of the vertex with the highest probability of
>   overlap? Or does
>   > this have to be done manually in Freeview?
>   >
>   > Many thanks
>   >
>   > Trisanna
>   > --
>   > Ph.D. CandidateMcGill University
>   > Integrated Program in Neuroscience
>   > Psychology
>   >
>   >
>   >
>   >
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Re: [Freesurfer] Cortical Thickness

[Douglas Greve]

it depends on how you entered them into the qdec levels files. It will 
be level1-level2



On 5/15/17 6:04 PM, Limachia, Gaurang (NIH/NINDS) [F] wrote:


Hello Freesurfer Experts,


I finished running the qdec analysis on our patient and healthy 
control populations. While looking at the clusters I am having a hard 
time telling which group -controls or patients have a larger cortical 
thickness?  Additionally, I wanted to know if it would be possible to 
save the images created by qdec as a jpeg or png file. I would greatly 
appreciate your help.


Thanks,


Gaurang



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Re: [Freesurfer] decimate overlay

[Douglas Greve]

I don't understand what you are trying to do. Can you elaborate? Sending 
command lines is always helpful



On 5/15/17 6:50 PM, Dorothy Sincasto wrote:

Hi freesurfers,

I have an overlay with 4k vertices and I want to decimate it to 1k. 
This overlay is actually an atlas with a label value for each vertex. 
My surfaces will have 1k vertices and I need the overlay to 1k so I 
know which areas each vertex belong to.


I tried to decimate the atlas.mgh but it gives me this error:

ERROR: MRISread: file 
'/Users/dsinc35/Desktop/projects/parcellation/MMP_atlas_L.mgh' has 0 
vertices! Probably trying to use a scalar data file as a surface!


Maybe there is a way to project it?

Any thoughts?

Thanks,

Dorothy



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Re: [Freesurfer] Error reading FSGD file

[Douglas Greve]

Do you have unix permissions to the file? Can you send the file?


On 5/15/17 6:25 PM, Laura Ferrero Montes wrote:
>Dear FS team,
>I was trying to do an analylisis  using mri_glmfit command. The
> analysis consists of two groups of patients and I wanted to know if
> there was an interaction between age and group. I wrote the following
> lines:
>
>mri_glmfit --table table1.txt --fsgd Descriptor.txt --C C1.txt
> --glmfir firstanalysis.glmdir
>
>
>- table1 was obtained afther command aparc2stats
>- C1 is the contrast matrix: 0 0 1 -1 0 0
>- Descriptor.txt if the design matrix:
>
>  GroupDescriptorFile 1
>  Title PatientsControls
>  Class Patient
>  Class Control
>  Variables Age IQ
>  InputNYU_0050985 Patient 13.09   90
>  InputNYU_0051099 Control 13.72   87
>  InputNYU_0051021 Patient 23.66   112
>  InputNYU_0051067 Control 23.65   116
>  InputNYU_0050996 Patient 15.81   100
>  InputNYU_0051104 Control 15.27   104
>   .
>   .
>   .
>
>
> I got this error:
> gdfRead(): reading Descriptor.txt
> ERROR: fio_FileHasCarriageReturn(): cannot open Descriptor.txt
>
>
> I created this matrix using text editor in Linux. Would yo know
> what is the problem?
> Thank you
>
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Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

[Ruopeng Wang]

Not sure if I followed. Does the look up table have the labels at all?

> On May 15, 2017, at 7:46 PM, Bruce Fischl  wrote:
> 
> hmm, not sure. Ruopeng?
> 
> On Mon, 15 May 2017, Lukas Pezenka wrote:
> 
>> Thank you. The tip about Christophe's parcellation was very helpful - I
>> can actually see the sulcal labels in freesurfer when loading
>> aparc.a2009s+aparc volume. Oddly enough, when I check the "show existing
>> labels only" box, none of them is displayed - I wonder why that is?
>> 
>> I should, in any case, be able to build the map now. Thank you!
>> 
>> Best regards,
>> 
>> Lukas
>> 
>> On 15.05.2017 18:38, Bruce Fischl wrote:
>>> no, they shouldn't be labeled as 0. You can create your own though,
>>> possibly using Christophe's parcellation instead of the aparc.annot
>>> (check in recon-all.cmd to see how to run it). Christophe's has sulci
>>> labeled separately so might be better for your purposes. Or you could
>>> create your own from your own label(s)
>>> On Mon, 15 May 2017, Lukas Pezenka
>>> wrote:
>>> 
 Hi Bruce,
 
 not sure - from what I see, sulci are labelled as 0 in the wmparc, are
 they not? In my understanding, only gyri are actually labelled... I
 might as well get that totally wrong, though, so sorry if I do...
 
 Best regards,
 
 Lukas
 
 
 On 15.05.2017 15:53, Bruce Fischl wrote:
> Hi Lukas
> 
> lh.sulc is not a surface - it's a scalar field over the surface. Have you
> looked at the wmparc? Does it not fill your needs?
> 
> cheers
> Bruce
> 
> 
> On Mon, 15
> May 2017, Lukas Pezenka wrote:
> 
>> Hi all,
>> 
>> here's my follow-up: I've now tried to use mris_fill on my lh.sulc.
>> However, I got the error message that "there are many more faces than
>> vertices". Running recon-all on this dataset takes 30+ hours on my
>> machine, hence I don't want to do it again unless it is absolutely
>> necessary.
>> 
>> Can anybody recommend another way (or a solution to either my
>> mri_surf2vol or mris_fill problems) of obtaining a binary sulcus mask?
>> I'm in desperate need of one..
>> 
>> Best regards,
>> 
>> Lukas
>> 
>> 
>> On 12.05.2017 16:18, Lukas Pezenka wrote:
>>> Hi all,
>>> 
>>> I need a volume that maps my sulci. So first I've run recon-all on my
>>> data. Worked like a charm. Visual verification in freeview shows that
>>> the inflated surface looks just about right (although it does not seem
>>> to be registered to the aparc+aseg volume). However, when I try to run
>>> mri_surf2vol, I get the error message "ERROR: cannot recognize the type
>>> of surf/lh.inflated".
>>> 
>>> My precise syntax was mri_surf2vol --o out.nii --identity casestudy2
>>> --surf inflated --hemi --lh --surfval surf/lh.inflated
>>> 
>>> Can anyone advise me on this?
>>> 
>>> Best regards,
>>> 
>>> Lukas
>>> 
>>> PS :I'm running on FS version 5.3.0.
>>> PPS: Is it possible to achieve this from freeview rather than from the
>>> command line?
>>> ___
>>> 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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>> 
>> 
>> 
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>> 
>> 
> 
> 


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Re: [Freesurfer] Medial Surface Problem

[Bronwyn Overs]

Hi Bruce,

Thank you for offering to take a look at this medial surface problem.

I have uploaded all of the relevant files to through the Martinos Centre 
FileDrop v2.0 to your email address (fis...@nmr.mgh.harvard.edu 
). Please let me know if you require any 
additional information.
Kind regards,
Bronwyn Overs
Research Assistant

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265

neura.edu.au  
  
 

> On 5 May 2017, at 8:25 am, Bruce Fischl  wrote:
> 
> if someone can upload a dataset as well as the exact coordinates of the 
> problem I'll take a look
> 
> cheers
> Bruce
> 
> On Fri, 5 May 2017, Yann Quidé wrote:
> 
>> Hi all,
>> We also have the same issue, any idea/suggestion?
>> Thanks.
>> Yann
>> 
>>  On 27 Apr 2017, at 9:43 am, Bronwyn Overs 
>>  wrote:
>> Hi Mailing List,
>> Still trying to solve the below medial surface problem. Does anyone
>> have any ideas?
>> Kind regards,
>> Bronwyn Overs
>> Research Assistant
>> Neuroscience Research Australia
>> Neuroscience Research Australia
>> Margarete Ainsworth Building
>> Barker Street Randwick Sydney NSW 2031 Australia
>> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265
>> neura.edu.au 
>> Follow @neuraustralia on twitter Follow NeuRA on facebook Subscribe to
>> the NeuRA Magazine
>> 
>>  On 28 Mar 2017, at 10:51 pm, Yann Quidé
>>   wrote:
>> Dear all,
>> I have an equivalent issue with my data. Any idea on how to fix
>> this?
>> Thanks.
>> Yann
>> 
>>  Begin forwarded message:
>> From: Bronwyn Overs 
>> Subject: Re: [Freesurfer] Medial Surface Problem
>> Date: 20 March 2017 10:28:37 am AEDT
>> To: Freesurfer support list
>> 
>> Reply-To: Freesurfer support list
>> 
>> Hello again mailing list,
>> Can anyone address the possible cause of the medial
>> surface problem shown below (overestimating of rh medial
>> surface, shows up in the long image and not the tp or base
>> images). Forgot to mention that I am using freesurfer v5.3
>> with an updated mris_make_surfaces binary (sourced from
>> the development versionat 
>> ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/cento
>> s6_x86_64/ ).
>> Here is the image again:
>> 
>> Kind regards,
>> Bronwyn Overs
>> Research Assistant
>> Neuroscience Research Australia
>> Neuroscience Research Australia
>> Margarete Ainsworth Building
>> Barker Street Randwick Sydney NSW 2031 Australia
>> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265
>> neura.edu.au 
>> Follow @neuraustralia on twitter Follow NeuRA on facebook
>> Subscribe to the NeuRA Magazine
>> 
>>  On 6 Mar 2017, at 1:17 pm, Bronwyn Overs
>>   wrote:
>> Hi mailing list,
>> I am currently processing a longitudinal image and
>> have come across a problem at the medial surface in
>> the long image (step 3). As you can see in the
>> attached image, the rh medial surface has been
>> significantly overestimated and extends into the lh
>> surface. This error showed up only in only 1 of the
>> 2 long images for this subject, and both the
>> time-point images and the base are perfectly fine.
>> Do you know why this is happening? 
>> 
>> Kind regards,
>> Bronwyn Overs
>> Research Assistant
>> Neuroscience Research Australia
>> Neuroscience Research Australia
>> Margarete Ainsworth Building
>> Barker Street Randwick Sydney NSW 2031 Australia
>> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265
>> neura.edu.au 
>> Follow @neuraustralia on twitter Follow NeuRA on
>> facebook Subscribe to the NeuRA Magazine
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>> 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.
>> ___
>> 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 

Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

[Bruce Fischl]

hmm, not sure. Ruopeng?

On Mon, 15 May 2017, Lukas Pezenka wrote:

> Thank you. The tip about Christophe's parcellation was very helpful - I
> can actually see the sulcal labels in freesurfer when loading
> aparc.a2009s+aparc volume. Oddly enough, when I check the "show existing
> labels only" box, none of them is displayed - I wonder why that is?
>
> I should, in any case, be able to build the map now. Thank you!
>
> Best regards,
>
> Lukas
>
> On 15.05.2017 18:38, Bruce Fischl wrote:
>> no, they shouldn't be labeled as 0. You can create your own though,
>> possibly using Christophe's parcellation instead of the aparc.annot
>> (check in recon-all.cmd to see how to run it). Christophe's has sulci
>> labeled separately so might be better for your purposes. Or you could
>> create your own from your own label(s)
>> On Mon, 15 May 2017, Lukas Pezenka
>> wrote:
>>
>>> Hi Bruce,
>>>
>>> not sure - from what I see, sulci are labelled as 0 in the wmparc, are
>>> they not? In my understanding, only gyri are actually labelled... I
>>> might as well get that totally wrong, though, so sorry if I do...
>>>
>>> Best regards,
>>>
>>> Lukas
>>>
>>>
>>> On 15.05.2017 15:53, Bruce Fischl wrote:
 Hi Lukas

 lh.sulc is not a surface - it's a scalar field over the surface. Have you
 looked at the wmparc? Does it not fill your needs?

 cheers
 Bruce


 On Mon, 15
 May 2017, Lukas Pezenka wrote:

> Hi all,
>
> here's my follow-up: I've now tried to use mris_fill on my lh.sulc.
> However, I got the error message that "there are many more faces than
> vertices". Running recon-all on this dataset takes 30+ hours on my
> machine, hence I don't want to do it again unless it is absolutely
> necessary.
>
> Can anybody recommend another way (or a solution to either my
> mri_surf2vol or mris_fill problems) of obtaining a binary sulcus mask?
> I'm in desperate need of one..
>
> Best regards,
>
> Lukas
>
>
> On 12.05.2017 16:18, Lukas Pezenka wrote:
>> Hi all,
>>
>> I need a volume that maps my sulci. So first I've run recon-all on my
>> data. Worked like a charm. Visual verification in freeview shows that
>> the inflated surface looks just about right (although it does not seem
>> to be registered to the aparc+aseg volume). However, when I try to run
>> mri_surf2vol, I get the error message "ERROR: cannot recognize the type
>> of surf/lh.inflated".
>>
>> My precise syntax was mri_surf2vol --o out.nii --identity casestudy2
>> --surf inflated --hemi --lh --surfval surf/lh.inflated
>>
>> Can anyone advise me on this?
>>
>> Best regards,
>>
>> Lukas
>>
>> PS :I'm running on FS version 5.3.0.
>> PPS: Is it possible to achieve this from freeview rather than from the
>> command line?
>> ___
>> 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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>
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[Freesurfer] decimate overlay

[Dorothy Sincasto]

Hi freesurfers,

I have an overlay with 4k vertices and I want to decimate it to 1k. This
overlay is actually an atlas with a label value for each vertex. My
surfaces will have 1k vertices and I need the overlay to 1k so I know which
areas each vertex belong to.

I tried to decimate the atlas.mgh but it gives me this error:

ERROR: MRISread: file
'/Users/dsinc35/Desktop/projects/parcellation/MMP_atlas_L.mgh' has 0
vertices! Probably trying to use a scalar data file as a surface!

Maybe there is a way to project it?

Any thoughts?

Thanks,

Dorothy
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[Freesurfer] Error reading FSGD file

[Laura Ferrero Montes]

  Dear FS team,
  I was trying to do an analylisis  using mri_glmfit command. The  
analysis consists of two groups of patients and I wanted to know if  
there was an interaction between age and group. I wrote the following  
lines:

  mri_glmfit --table table1.txt --fsgd Descriptor.txt --C C1.txt  
--glmfir firstanalysis.glmdir


  - table1 was obtained afther command aparc2stats
  - C1 is the contrast matrix: 0 0 1 -1 0 0
  - Descriptor.txt if the design matrix:

GroupDescriptorFile 1
Title PatientsControls
Class Patient
Class Control
Variables Age IQ
Input   NYU_0050985 Patient 13.09   90
Input   NYU_0051099 Control 13.72   87
Input   NYU_0051021 Patient 23.66   112
Input   NYU_0051067 Control 23.65   116
Input   NYU_0050996 Patient 15.81   100
Input   NYU_0051104 Control 15.27   104
 .
 .
 .


   I got this error:
   gdfRead(): reading Descriptor.txt
   ERROR: fio_FileHasCarriageReturn(): cannot open Descriptor.txt


   I created this matrix using text editor in Linux. Would yo know  
what is the problem?
   Thank you

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[Freesurfer] Cortical Thickness

[Limachia, Gaurang (NIH/NINDS) [F]]

Hello Freesurfer Experts,

I finished running the qdec analysis on our patient and healthy control 
populations. While looking at the clusters I am having a hard time telling 
which group -controls or patients have a larger cortical thickness?  
Additionally, I wanted to know if it would be possible to save the images 
created by qdec as a jpeg or png file. I would greatly appreciate your help.

Thanks,

Gaurang
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[Freesurfer] Freesurfer white matter outer edge to volume

[Gamaliz]

I need to create an image which overlaps the T1/mgz and the outer surface
of the white matter. How do I convert the surface into a mgz volume?


-- 
gAbE
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Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

[Lukas Pezenka]

Thank you. The tip about Christophe's parcellation was very helpful - I 
can actually see the sulcal labels in freesurfer when loading 
aparc.a2009s+aparc volume. Oddly enough, when I check the "show existing 
labels only" box, none of them is displayed - I wonder why that is?

I should, in any case, be able to build the map now. Thank you!

Best regards,

Lukas

On 15.05.2017 18:38, Bruce Fischl wrote:
> no, they shouldn't be labeled as 0. You can create your own though,
> possibly using Christophe's parcellation instead of the aparc.annot
> (check in recon-all.cmd to see how to run it). Christophe's has sulci
> labeled separately so might be better for your purposes. Or you could
> create your own from your own label(s)
> On Mon, 15 May 2017, Lukas Pezenka
> wrote:
>
>> Hi Bruce,
>>
>> not sure - from what I see, sulci are labelled as 0 in the wmparc, are
>> they not? In my understanding, only gyri are actually labelled... I
>> might as well get that totally wrong, though, so sorry if I do...
>>
>> Best regards,
>>
>> Lukas
>>
>>
>> On 15.05.2017 15:53, Bruce Fischl wrote:
>>> Hi Lukas
>>>
>>> lh.sulc is not a surface - it's a scalar field over the surface. Have you
>>> looked at the wmparc? Does it not fill your needs?
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Mon, 15
>>> May 2017, Lukas Pezenka wrote:
>>>
 Hi all,

 here's my follow-up: I've now tried to use mris_fill on my lh.sulc.
 However, I got the error message that "there are many more faces than
 vertices". Running recon-all on this dataset takes 30+ hours on my
 machine, hence I don't want to do it again unless it is absolutely
 necessary.

 Can anybody recommend another way (or a solution to either my
 mri_surf2vol or mris_fill problems) of obtaining a binary sulcus mask?
 I'm in desperate need of one..

 Best regards,

 Lukas


 On 12.05.2017 16:18, Lukas Pezenka wrote:
> Hi all,
>
> I need a volume that maps my sulci. So first I've run recon-all on my
> data. Worked like a charm. Visual verification in freeview shows that
> the inflated surface looks just about right (although it does not seem
> to be registered to the aparc+aseg volume). However, when I try to run
> mri_surf2vol, I get the error message "ERROR: cannot recognize the type
> of surf/lh.inflated".
>
> My precise syntax was mri_surf2vol --o out.nii --identity casestudy2
> --surf inflated --hemi --lh --surfval surf/lh.inflated
>
> Can anyone advise me on this?
>
> Best regards,
>
> Lukas
>
> PS :I'm running on FS version 5.3.0.
> PPS: Is it possible to achieve this from freeview rather than from the
> command line?
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] probability maps

[Trisanna Sprung-Much]

Hi Bruce

The maps are .mgz format and are % overlap (across 40 subjects). They were
generated using

-labels turned into surface overlay using mri_vol2surf
-then registered to fsaverage using mri_surf2surf
-then averaged within fsaverage space using mri_concat and then mris_fwhm
to smooth.

Best
Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Mon, May 15, 2017 at 2:53 PM, Bruce Fischl 
wrote:

> what format is your map of p-values in?
> On Mon, 15 May 2017, Trisanna
> Sprung-Much wrote:
>
> > Hi Bruce
> > I would not know where to start (not an avid matlab user) - what input
> would
> > be needed to be fed into matlab?
> >
> > Trisanna
> >
> > --
> > Ph.D. CandidateMcGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Mon, May 15, 2017 at 12:52 PM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu>
> > wrote:
> >   hmmm, should be pretty easy in matlab, no?
> >   On Mon, 15 May 2017, Trisanna
> >   Sprung-Much wrote:
> >
> >   > Hi there
> >   > I have generated some anatomical probabilistic maps as
> >   overlays on the
> >   > fsaverage pial surface. Is there a way to automatically find
> >   the vertex
> >   > coordinates of the vertex with the highest probability of
> >   overlap? Or does
> >   > this have to be done manually in Freeview?
> >   >
> >   > Many thanks
> >   >
> >   > Trisanna
> >   > --
> >   > Ph.D. CandidateMcGill University
> >   > Integrated Program in Neuroscience
> >   > Psychology
> >   >
> >   >
> >   >
> >   >
> >   ___
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Re: [Freesurfer] probability maps

[Bruce Fischl]

what format is your map of p-values in?
On Mon, 15 May 2017, Trisanna 
Sprung-Much wrote:

> Hi Bruce
> I would not know where to start (not an avid matlab user) - what input would
> be needed to be fed into matlab?
> 
> Trisanna
> 
> --
> Ph.D. CandidateMcGill University
> Integrated Program in Neuroscience
> Psychology
> 
> 
> On Mon, May 15, 2017 at 12:52 PM, Bruce Fischl 
> wrote:
>   hmmm, should be pretty easy in matlab, no?
>   On Mon, 15 May 2017, Trisanna
>   Sprung-Much wrote:
>
>   > Hi there
>   > I have generated some anatomical probabilistic maps as
>   overlays on the
>   > fsaverage pial surface. Is there a way to automatically find
>   the vertex
>   > coordinates of the vertex with the highest probability of
>   overlap? Or does
>   > this have to be done manually in Freeview?
>   >
>   > Many thanks
>   >
>   > Trisanna
>   > --
>   > Ph.D. CandidateMcGill University
>   > Integrated Program in Neuroscience
>   > Psychology
>   >
>   >
>   >
>   >
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Re: [Freesurfer] LME : longitudinal correlations between imaging and cognition scores

[Matthieu Vanhoutte]

Hi Martin,

Thank you. How should this variable be coded ? Should it be as age
covariate where age at baseline is used along all time points of each
subject ?

Could you provide me an example of design matrix, I don't manage to see
what does it look like to.

Best regards,
Matthieu


Le 14 mai 2017 8:08 PM, "Martin Reuter"  a
écrit :

Hi Matthieu,

yes, that is possible. Instead of group, you use a variable for your score
(and interaction etc). Sometimes it may also makes sense to use score
instead of time.

Best, Martin


> On 12 May 2017, at 10:51, Matthieu Vanhoutte 
wrote:
>
> Dear Freesurfer's experts,
>
> I have searched through the mailing list but haven't found any answer to
my question.
>
> Is it possible with LME model to make correlations between for example
cortical thickness surface data and cognition scores along time ? As it is
possible to test for interaction of group X time, is this also in the same
way feasible to test for coognition score X time on cortical thickness ?
>
> Many thanks for your advice !
>
> Best regards,
> Matthieu
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Re: [Freesurfer] probability maps

[Trisanna Sprung-Much]

Hi Bruce

I would not know where to start (not an avid matlab user) - what input
would be needed to be fed into matlab?

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Mon, May 15, 2017 at 12:52 PM, Bruce Fischl 
wrote:

> hmmm, should be pretty easy in matlab, no?
> On Mon, 15 May 2017, Trisanna
> Sprung-Much wrote:
>
> > Hi there
> > I have generated some anatomical probabilistic maps as overlays on the
> > fsaverage pial surface. Is there a way to automatically find the vertex
> > coordinates of the vertex with the highest probability of overlap? Or
> does
> > this have to be done manually in Freeview?
> >
> > Many thanks
> >
> > Trisanna
> > --
> > Ph.D. CandidateMcGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> >
> >
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[Freesurfer] Volumen for Aparc+aseg region 2 and 41

[Gamaliz]

Regions 2 and 41 are labeled as

Left-Cerebral-White-Matter

Right-Cerebral-White-Matter

respectively. However, there is no label in the aseg.stats,
wmparc.stats or xh.aparc.stats files.

The only label that seems to match it is the: CorticalWhiteMatterVol
in aseg.stats.

Where is the white matter (regions 2 and 4) volumes saved? is this
equivalent to the cortical white matter values?
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Re: [Freesurfer] probability maps

[Bruce Fischl]

hmmm, should be pretty easy in matlab, no?
On Mon, 15 May 2017, Trisanna 
Sprung-Much wrote:

> Hi there
> I have generated some anatomical probabilistic maps as overlays on the
> fsaverage pial surface. Is there a way to automatically find the vertex
> coordinates of the vertex with the highest probability of overlap? Or does
> this have to be done manually in Freeview?
> 
> Many thanks
> 
> Trisanna
> --
> Ph.D. CandidateMcGill University
> Integrated Program in Neuroscience
> Psychology
> 
> 
> 
>
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[Freesurfer] probability maps

[Trisanna Sprung-Much]

Hi there

I have generated some anatomical probabilistic maps as overlays on the
fsaverage pial surface. Is there a way to automatically find the vertex
coordinates of the vertex with the highest probability of overlap? Or does
this have to be done manually in Freeview?

Many thanks

Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
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Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

[Bruce Fischl]

no, they shouldn't be labeled as 0. You can create your own though, 
possibly using Christophe's parcellation instead of the aparc.annot 
(check in recon-all.cmd to see how to run it). Christophe's has sulci 
labeled separately so might be better for your purposes. Or you could 
create your own from your own label(s)
On Mon, 15 May 2017, Lukas Pezenka 
wrote:

> Hi Bruce,
>
> not sure - from what I see, sulci are labelled as 0 in the wmparc, are
> they not? In my understanding, only gyri are actually labelled... I
> might as well get that totally wrong, though, so sorry if I do...
>
> Best regards,
>
> Lukas
>
>
> On 15.05.2017 15:53, Bruce Fischl wrote:
>> Hi Lukas
>>
>> lh.sulc is not a surface - it's a scalar field over the surface. Have you
>> looked at the wmparc? Does it not fill your needs?
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 15
>> May 2017, Lukas Pezenka wrote:
>>
>>> Hi all,
>>>
>>> here's my follow-up: I've now tried to use mris_fill on my lh.sulc.
>>> However, I got the error message that "there are many more faces than
>>> vertices". Running recon-all on this dataset takes 30+ hours on my
>>> machine, hence I don't want to do it again unless it is absolutely
>>> necessary.
>>>
>>> Can anybody recommend another way (or a solution to either my
>>> mri_surf2vol or mris_fill problems) of obtaining a binary sulcus mask?
>>> I'm in desperate need of one..
>>>
>>> Best regards,
>>>
>>> Lukas
>>>
>>>
>>> On 12.05.2017 16:18, Lukas Pezenka wrote:
 Hi all,

 I need a volume that maps my sulci. So first I've run recon-all on my
 data. Worked like a charm. Visual verification in freeview shows that
 the inflated surface looks just about right (although it does not seem
 to be registered to the aparc+aseg volume). However, when I try to run
 mri_surf2vol, I get the error message "ERROR: cannot recognize the type
 of surf/lh.inflated".

 My precise syntax was mri_surf2vol --o out.nii --identity casestudy2
 --surf inflated --hemi --lh --surfval surf/lh.inflated

 Can anyone advise me on this?

 Best regards,

 Lukas

 PS :I'm running on FS version 5.3.0.
 PPS: Is it possible to achieve this from freeview rather than from the
 command line?
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[Freesurfer] Contrast matrix for PVR

[Sahil Bajaj]

Hi everyone,

>From FreeSurfer manual and discussion forum, I found that volume and LGI
can be correlated using mri_glmfit command with -pvr flag.

For that, my fsgd file has age, gender as covariates and the file is as
following:

GroupDescriptorFile 1

Class Male

Class Female

Variables Age

Inputzerek1 Male 21

Input zerek2 Male 25

etc.

My concern is:

To run mri_glmfit command, I am not sure how to define my contrast matrix
if I am interested in removing the effect of age and sex.

1st option I tried is: 0 0.5 0.5 0 1

Here, I think first 0 regresses out age, 0.5 0.5 should be averaging over
males and females and last 0 1 correlates between volume and LGI. But this
looks like it is not giving me correct correlations maps, although there is
no error.

2nd option I tried is: 0 0 0 0 1

This looks like its working and maps look correct to me but I want to make
sure this is the correct contrast matrix and I am not sure how this matrix
is regressing out age and gender or 1st option is correct contrast matrix?

Thank you so much !

Best,

Sahil
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Re: [Freesurfer] Maps showing correlations between structural measures

[Martin Juneja]

Thanks Dr. Greve.

Regarding 2nd question, I am not sure how authors in this paper:
http://www.sciencedirect.com/science/article/pii/S0166432815001837
performed FRD correction?
If we do not run FDR, then is sig.mgh output already FDR corrected as shown
in this paper?

Thanks for your valuable time.

On Mon, May 15, 2017 at 9:26 AM, Douglas N Greve 
wrote:

> I think your command lines are correct. I would not expect that swapping
> the y and pvr to give the same results. sig=-log10(p)=30 is not totally
> unreasonable. I don't understand #2. Why are you running FDR and cluster
> correction?
>
>
> On 05/11/2017 06:39 PM, Martin Juneja wrote:
> > In addition to that: I am always getting positive correlations (when I
> > load sig.mgh) every time i.e. even when I correlated thickness and
> > gyrification. None of the voxels/areas showing negative correlation
> > between any of the structural measures
> >
> > On Thu, May 11, 2017 at 11:26 AM, Martin Juneja  > > wrote:
> >
> > Hi Dr. Greve,
> >
> > I doubt these results because of following:
> >
> > (1). When I compare sig.mgh files created using following two
> > commands i.e. correlation between LGI and CV versus CV and LGI:
> > mri_glmfit --y Corr_CV_LGI/lh.LGI.10.mgh --fsgd CV_LGI.fsgd dods
> > --C Corr-VL-cor.mtx --surf fsaverage lh --cortex --glmdir
> > Corr_CV_LGI/lh.VL.glmdir --pvr Corr_CV_LGI/lh.CV.10.mgh
> > and
> > mri_glmfit --y Corr_CV_LGI/lh.vol.10.mgh --fsgd CV_LGI.fsgd dods
> > --C Corr-VL-cor.mtx --surf fsaverage lh --cortex --glmdir
> > Corr_CV_LGI/lh.VL.glmdir --pvr Corr_CV_LGI/lh.LGI.10.mgh
> >
> > (a). I do not get identical maps. Please find attached screen shot.
> > (b). Here, colorbar showing a value of around 30, does that
> > reflect -log10(p)? I am not sure if thats normal?
> >
> > (2). Assuming magnitude from colorbar is normal then I performed
> > FDR correction- I am assuming its same command as following as
> > mentioned in FS manual:
> > mri_glmfit-sim --glmdir Corr_CV_LGI/lh.VL.glmdir --cache 1.3 pos
> > --cwp 0.01 --2spaces
> >
> > After running FDR correction, cache.th13.pos.sig.cluster.mgh and
> > cache.th13.neg.sig.cluster.mgh, none of these are showing me any
> > significant clusters, instead its showing a constant magnitude
> > (same color) over whole brain?
> >
> > Thanks.
> > ​
> >
> >
> >
> >
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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] Maps showing correlations between structural measures

[Douglas N Greve]

I think your command lines are correct. I would not expect that swapping 
the y and pvr to give the same results. sig=-log10(p)=30 is not totally 
unreasonable. I don't understand #2. Why are you running FDR and cluster 
correction?


On 05/11/2017 06:39 PM, Martin Juneja wrote:
> In addition to that: I am always getting positive correlations (when I 
> load sig.mgh) every time i.e. even when I correlated thickness and 
> gyrification. None of the voxels/areas showing negative correlation 
> between any of the structural measures
>
> On Thu, May 11, 2017 at 11:26 AM, Martin Juneja  > wrote:
>
> Hi Dr. Greve,
>
> I doubt these results because of following:
>
> (1). When I compare sig.mgh files created using following two
> commands i.e. correlation between LGI and CV versus CV and LGI:
> mri_glmfit --y Corr_CV_LGI/lh.LGI.10.mgh --fsgd CV_LGI.fsgd dods
> --C Corr-VL-cor.mtx --surf fsaverage lh --cortex --glmdir
> Corr_CV_LGI/lh.VL.glmdir --pvr Corr_CV_LGI/lh.CV.10.mgh
> and
> mri_glmfit --y Corr_CV_LGI/lh.vol.10.mgh --fsgd CV_LGI.fsgd dods
> --C Corr-VL-cor.mtx --surf fsaverage lh --cortex --glmdir
> Corr_CV_LGI/lh.VL.glmdir --pvr Corr_CV_LGI/lh.LGI.10.mgh
>
> (a). I do not get identical maps. Please find attached screen shot.
> (b). Here, colorbar showing a value of around 30, does that
> reflect -log10(p)? I am not sure if thats normal?
>
> (2). Assuming magnitude from colorbar is normal then I performed
> FDR correction- I am assuming its same command as following as
> mentioned in FS manual:
> mri_glmfit-sim --glmdir Corr_CV_LGI/lh.VL.glmdir --cache 1.3 pos
> --cwp 0.01 --2spaces
>
> After running FDR correction, cache.th13.pos.sig.cluster.mgh and
> cache.th13.neg.sig.cluster.mgh, none of these are showing me any
> significant clusters, instead its showing a constant magnitude
> (same color) over whole brain?
>
> Thanks.
> ​
>
>
>
>
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Re: [Freesurfer] mri_glmfit mask.mgh for mri_surfcluster

[Ryan Muetzel]

Perfect --- Thank you! 

Ryan



> On May 15, 2017, at 6:09 PM, Douglas N Greve  
> wrote:
> 
> usually the fsaverage mask is fine. You can use mri_label2label with the 
> --outmask option to convert the ?h.cortex.label to a binary mask. You 
> can also pass surfcluster a label directly with the --clabel option
> 
> 
> On 05/14/2017 05:45 AM, Ryan Muetzel wrote:
>> Dear Experts,
>> 
>> This is partially a follow-up question to another thread related to 
>> the mask.mgh generated by mri_glmfit 
>> (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50691.html).
>> 
>> We would like to use the mri_surfcluster tool on a log10p map.  I’m 
>> wondering — for vertex-wise analyses that use freesurfer-specific 
>> output (e.g., thickness, surface area, lgi, etc, not FMRI or DTI 
>> data)….can we rely on a single mask image for each hemisphere that 
>> comes from the fsaverage ?h.cortex.label? Or, should we be creating a 
>> mask that is specific to a given analysis/dataset, as is done with 
>> mri_glmfit?
>> 
>> If the latter, is there a way to create this mask outside of mri_glmfit?
>> 
>> Thank you in advance for your time and help!
>> 
>> Best,
>> 
>> Ryan
>> 
>> 
>> 
>> ___
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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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> 
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Re: [Freesurfer] mri_glmfit mask.mgh for mri_surfcluster

[Douglas N Greve]

usually the fsaverage mask is fine. You can use mri_label2label with the 
--outmask option to convert the ?h.cortex.label to a binary mask. You 
can also pass surfcluster a label directly with the --clabel option


On 05/14/2017 05:45 AM, Ryan Muetzel wrote:
> Dear Experts,
>
> This is partially a follow-up question to another thread related to 
> the mask.mgh generated by mri_glmfit 
> (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50691.html).
>
> We would like to use the mri_surfcluster tool on a log10p map.  I’m 
> wondering — for vertex-wise analyses that use freesurfer-specific 
> output (e.g., thickness, surface area, lgi, etc, not FMRI or DTI 
> data)….can we rely on a single mask image for each hemisphere that 
> comes from the fsaverage ?h.cortex.label? Or, should we be creating a 
> mask that is specific to a given analysis/dataset, as is done with 
> mri_glmfit?
>
> If the latter, is there a way to create this mask outside of mri_glmfit?
>
> Thank you in advance for your time and help!
>
> Best,
>
> Ryan
>
>
>
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gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422

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Re: [Freesurfer] Calculating effect sizes using an older version of Freesurfer

[Douglas N Greve]

Try using the version 6 mri_glmfit. It will produce identical results 
and it will also create the pcc.mgh output


On 05/12/2017 12:02 PM, Clint Johns wrote:
> Using Freesurfer 5.3.0, we assessed correlations. between behavioral 
> measures (e.g., working memory, IQ) and grey matter thickness in a 
> single group of participants. We obtained some results - a significant 
> correlation between measure X and cortical thickness in, say, IFG. We 
> would like to include the Pearson's r or some other measure of the 
> effect size. Newer versions of Freesurfer allow this (pcc.mgh), but we 
> are not sure what to use. We have the contrast effect size file 
> gamma.mgh, and the gamma values are "C*beta, where beta are the 
> regression coefficients, so gamma is a type of regression coeff" (per 
> Doug G. in this old thread: 
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-April/045135.html 
> ).
>  
> So how do we use these values in a table? They're not Pearson's r, or 
> Cohen's d, obviously. Do we just label the column "peak contrast 
> effect size", naming the values after the gamma.mgh file?
>
> Thanks! (We're very confused.)
>
> clint
>
> -- 
> I remain...
>
> Clinton L. Johns, Ph.D.
> Research Scientist, Haskins Laboratories
> 300 George Street
> New Haven CT 06511
> speech: 203-865-6163 x240
> fax: 203-865-8963
> net: jo...@haskins.yale.edu 
>
>
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Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

[Douglas N Greve]

You need to use a valid output format like mgh, mgz, nii, etc (eg, 
surf/lh.inflated.mgh). Also, you should not run vol2surf mapping to the 
inflated surface as this surface is mostly outside the head. Use the 
default white surface and then visualize on the inflated only


On 05/12/2017 10:18 AM, Lukas Pezenka wrote:
> Hi all,
>
> I need a volume that maps my sulci. So first I've run recon-all on my
> data. Worked like a charm. Visual verification in freeview shows that
> the inflated surface looks just about right (although it does not seem
> to be registered to the aparc+aseg volume). However, when I try to run
> mri_surf2vol, I get the error message "ERROR: cannot recognize the type
> of surf/lh.inflated".
>
> My precise syntax was mri_surf2vol --o out.nii --identity casestudy2
> --surf inflated --hemi --lh --surfval surf/lh.inflated
>
> Can anyone advise me on this?
>
> Best regards,
>
> Lukas
>
> PS :I'm running on FS version 5.3.0.
> PPS: Is it possible to achieve this from freeview rather than from the
> command line?
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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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Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

[Lukas Pezenka]

Hi Bruce,

not sure - from what I see, sulci are labelled as 0 in the wmparc, are 
they not? In my understanding, only gyri are actually labelled... I 
might as well get that totally wrong, though, so sorry if I do...

Best regards,

Lukas


On 15.05.2017 15:53, Bruce Fischl wrote:
> Hi Lukas
>
> lh.sulc is not a surface - it's a scalar field over the surface. Have you
> looked at the wmparc? Does it not fill your needs?
>
> cheers
> Bruce
>
>
> On Mon, 15
> May 2017, Lukas Pezenka wrote:
>
>> Hi all,
>>
>> here's my follow-up: I've now tried to use mris_fill on my lh.sulc.
>> However, I got the error message that "there are many more faces than
>> vertices". Running recon-all on this dataset takes 30+ hours on my
>> machine, hence I don't want to do it again unless it is absolutely
>> necessary.
>>
>> Can anybody recommend another way (or a solution to either my
>> mri_surf2vol or mris_fill problems) of obtaining a binary sulcus mask?
>> I'm in desperate need of one..
>>
>> Best regards,
>>
>> Lukas
>>
>>
>> On 12.05.2017 16:18, Lukas Pezenka wrote:
>>> Hi all,
>>>
>>> I need a volume that maps my sulci. So first I've run recon-all on my
>>> data. Worked like a charm. Visual verification in freeview shows that
>>> the inflated surface looks just about right (although it does not seem
>>> to be registered to the aparc+aseg volume). However, when I try to run
>>> mri_surf2vol, I get the error message "ERROR: cannot recognize the type
>>> of surf/lh.inflated".
>>>
>>> My precise syntax was mri_surf2vol --o out.nii --identity casestudy2
>>> --surf inflated --hemi --lh --surfval surf/lh.inflated
>>>
>>> Can anyone advise me on this?
>>>
>>> Best regards,
>>>
>>> Lukas
>>>
>>> PS :I'm running on FS version 5.3.0.
>>> PPS: Is it possible to achieve this from freeview rather than from the
>>> command line?
>>> ___
>>> 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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>>
>>
>>
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Re: [Freesurfer] Create thresholded annotations without recon-all?

[Bruce Fischl]

it's the threshold that gives the labels the right surface area on 
average

cheers
Bruce
On Mon, 15 May 2017, Michael Bannert wrote:

> Dear Bruce,
>
> Thanks for you reply. I was just about to answer my own question in the
> same way :) This does seem to do what I want. Awesome!
> (see https://surfer.nmr.mgh.harvard.edu/fswiki/BrodmannAreaMaps)
>
> I was just wondering how the threshold is chosen to define each ROI?
>
> Best,
> Michael
>
>
> On 15/05/17 15:43, Bruce Fischl wrote:
>> Hi Michael
>>
>> I believe you can just run the -balabels switch, which should only take a
>> couple of minutes
>>
>> cheers
>> Bruce
>> On Mon, 15 May 2017, Michael Bannert wrote:
>>
>>> Dear FreeSurfer community,
>>>
>>> I would like to perform a ROI analysis using an anatomical mask. I was
>>> thinking of using the thresholded masks in the annotations file created
>>> from running recon-all.
>>>
>>> Now I noticed that a few of my older datasets do not seem to have
>>> thresholded annotation files, but only the unthresholded ones.
>>>
>>> Is it possible to create these files (e.g., l/rh.BA.tresh.annot) again
>>> without having to run recon-all over again? Maybe from manually
>>> thresholding the unthresholded annotation files (l/rh.BA.annot)?
>>>
>>> How would I go about this?
>>>
>>> Thanks and best,
>>> Michael
>>> ___
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>>>
>>>
>>>
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>>
>>
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>> properly
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Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

[Bruce Fischl]

Hi Lukas

lh.sulc is not a surface - it's a scalar field over the surface. Have you 
looked at the wmparc? Does it not fill your needs?

cheers
Bruce


On Mon, 15 
May 2017, Lukas Pezenka wrote:

> Hi all,
>
> here's my follow-up: I've now tried to use mris_fill on my lh.sulc.
> However, I got the error message that "there are many more faces than
> vertices". Running recon-all on this dataset takes 30+ hours on my
> machine, hence I don't want to do it again unless it is absolutely
> necessary.
>
> Can anybody recommend another way (or a solution to either my
> mri_surf2vol or mris_fill problems) of obtaining a binary sulcus mask?
> I'm in desperate need of one..
>
> Best regards,
>
> Lukas
>
>
> On 12.05.2017 16:18, Lukas Pezenka wrote:
>> Hi all,
>>
>> I need a volume that maps my sulci. So first I've run recon-all on my
>> data. Worked like a charm. Visual verification in freeview shows that
>> the inflated surface looks just about right (although it does not seem
>> to be registered to the aparc+aseg volume). However, when I try to run
>> mri_surf2vol, I get the error message "ERROR: cannot recognize the type
>> of surf/lh.inflated".
>>
>> My precise syntax was mri_surf2vol --o out.nii --identity casestudy2
>> --surf inflated --hemi --lh --surfval surf/lh.inflated
>>
>> Can anyone advise me on this?
>>
>> Best regards,
>>
>> Lukas
>>
>> PS :I'm running on FS version 5.3.0.
>> PPS: Is it possible to achieve this from freeview rather than from the
>> command line?
>> ___
>> 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] Create thresholded annotations without recon-all?

[Michael Bannert]

Dear Bruce,

Thanks for you reply. I was just about to answer my own question in the
same way :) This does seem to do what I want. Awesome!
(see https://surfer.nmr.mgh.harvard.edu/fswiki/BrodmannAreaMaps)

I was just wondering how the threshold is chosen to define each ROI?

Best,
Michael


On 15/05/17 15:43, Bruce Fischl wrote:
> Hi Michael
> 
> I believe you can just run the -balabels switch, which should only take a 
> couple of minutes
> 
> cheers
> Bruce
> On Mon, 15 May 2017, Michael Bannert wrote:
> 
>> Dear FreeSurfer community,
>>
>> I would like to perform a ROI analysis using an anatomical mask. I was
>> thinking of using the thresholded masks in the annotations file created
>> from running recon-all.
>>
>> Now I noticed that a few of my older datasets do not seem to have
>> thresholded annotation files, but only the unthresholded ones.
>>
>> Is it possible to create these files (e.g., l/rh.BA.tresh.annot) again
>> without having to run recon-all over again? Maybe from manually
>> thresholding the unthresholded annotation files (l/rh.BA.annot)?
>>
>> How would I go about this?
>>
>> Thanks and best,
>> Michael
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
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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 
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Re: [Freesurfer] Create thresholded annotations without recon-all?

[Bruce Fischl]

Hi Michael

I believe you can just run the -balabels switch, which should only take a 
couple of minutes

cheers
Bruce
On Mon, 15 May 2017, Michael Bannert wrote:

> Dear FreeSurfer community,
>
> I would like to perform a ROI analysis using an anatomical mask. I was
> thinking of using the thresholded masks in the annotations file created
> from running recon-all.
>
> Now I noticed that a few of my older datasets do not seem to have
> thresholded annotation files, but only the unthresholded ones.
>
> Is it possible to create these files (e.g., l/rh.BA.tresh.annot) again
> without having to run recon-all over again? Maybe from manually
> thresholding the unthresholded annotation files (l/rh.BA.annot)?
>
> How would I go about this?
>
> Thanks and best,
> Michael
> ___
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>
>
>
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[Freesurfer] New version FreeSurfer 6.0

[Lisa Delalande]

Hello everyone,

I would like to know if the new version of FreeSurfer bring a lot of
changes for the longitudinal procesing like recon-all and qcache ? I
started to processing them with FreeSurfer 5.3, Do you think I should start
again with FreeSurfer 6.0 ?

Thanks a lot in advance
Best regards

Lisa
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Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

[Lukas Pezenka]

Hi all,

here's my follow-up: I've now tried to use mris_fill on my lh.sulc. 
However, I got the error message that "there are many more faces than 
vertices". Running recon-all on this dataset takes 30+ hours on my 
machine, hence I don't want to do it again unless it is absolutely 
necessary.

Can anybody recommend another way (or a solution to either my 
mri_surf2vol or mris_fill problems) of obtaining a binary sulcus mask? 
I'm in desperate need of one..

Best regards,

Lukas


On 12.05.2017 16:18, Lukas Pezenka wrote:
> Hi all,
>
> I need a volume that maps my sulci. So first I've run recon-all on my
> data. Worked like a charm. Visual verification in freeview shows that
> the inflated surface looks just about right (although it does not seem
> to be registered to the aparc+aseg volume). However, when I try to run
> mri_surf2vol, I get the error message "ERROR: cannot recognize the type
> of surf/lh.inflated".
>
> My precise syntax was mri_surf2vol --o out.nii --identity casestudy2
> --surf inflated --hemi --lh --surfval surf/lh.inflated
>
> Can anyone advise me on this?
>
> Best regards,
>
> Lukas
>
> PS :I'm running on FS version 5.3.0.
> PPS: Is it possible to achieve this from freeview rather than from the
> command line?
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Re: [Freesurfer] illustration

[Iglesias Gonzalez, Eugenio]

Dear Julian,

Apologies if your message feel in the cracks.

If you want to visualize the atlas, you can use a (very buggy) program called 
kvlViewMeshCollectionWithGUI.

First, source Freesurfer and cd into the following directory:
cd $FREESURFER_HOME/average/hippoSF/atlas

Then, run the following command
kvlViewMeshCollectionWithGUI AtlasMesh.gz

Once the GUI has opened, selected Mesh Number: Reference mesh.

Finally, check “show summary” to produce the color-coded image.

Cheers,

/Eugenio


Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 12 May 2017, at 20:43, Julian Jäckle 
> wrote:

Dear all
I know that i’ve posted this question before, but yet nobody replied and we do 
really need an answer to close our project.
Your “Segmentation of hippocampal subfields” wiki article refers to the 
publication: “A computational atlas of the hippocampal formation using ex vivo, 
ultra-high resolution MRI: Application to adaptive segmentation of in vivo 
MRI“. Within the paper there are two figures No. 4 & 6 demonstrating the 
probabilistic atlas and mesh deformation. We do need to know how you created 
these illustrations.
I attached one of the images as an example
Thanks a lot
Julian


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[Freesurfer] Create thresholded annotations without recon-all?

[Michael Bannert]

Dear FreeSurfer community,

I would like to perform a ROI analysis using an anatomical mask. I was
thinking of using the thresholded masks in the annotations file created
from running recon-all.

Now I noticed that a few of my older datasets do not seem to have
thresholded annotation files, but only the unthresholded ones.

Is it possible to create these files (e.g., l/rh.BA.tresh.annot) again
without having to run recon-all over again? Maybe from manually
thresholding the unthresholded annotation files (l/rh.BA.annot)?

How would I go about this?

Thanks and best,
Michael
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