Re: [Freesurfer] White matter surface don't change after editing

[Cong]

> Hi Dear Bruce
>  Thanks very much for your reply, I  improved min_border_white to 100, 
> the lh.white line shrinks but still is far out in some area,  and I notice 
> many topological defect appears as a result.
>  I failed to upload subject through ftp, it's always appear an error 
> called "550 Failed to change directory", so I send a subject to you through 
> FileDrop. Can you receive a file named Cong2Bruce.zip? 
>  Thanks again for your help.
> 
> Best Wishes
> Cong Chen
>> Date: Thu, 8 Sep 2016 10:12:29 -0400 (EDT)
>> From: Bruce Fischl > >
>> Hi Cong
>> 
>> you could try using expert options to modify the mris_make_surfaces 
>> parameters. It looks like you white surface is too far out. Try 
>> increasing min_border_white and/or increasing max_gray. If you can't get it 
>> working feel free to upload the entire subject dir and we will take a look
>> 
>> cheers
>> Bruce
>> 
>> 
>> On Thu, 8 Sep 2016, Cong wrote:
>> 
>> Hi dear all
>> I attach a new picture to illustrate this problem.  I erased some voxels 
>> in wm.mgz and rerun. The lh.orig(blue line) looks well, but lh.white(yellow 
>> line) don?t along the white surface in some area. Could anyone give me some 
>> advice? Thanks very much.
>> 
>> Best wishes
>> Cong Chen
>> 
>> 
>> Date: Sun, 4 Sep 2016 15:15:42 +0800
>> From: Cong <3110103...@zju.edu.cn >
>> Subject: [Freesurfer] White matter surface don't change after editing
>> 
>> Dear freesurfer team?
>>  I have some MRI images from a GE scanner,  it seems that images? quality is 
>> poor because grey matter is bright in so much area and these grey matter is 
>> included in wm.mgz. So I deleted wrong voxels in wm.mgz by freeview and 
>> rerun through command ? recon-all -autorecon2-wm -autorecon3 -subjid 
>> subjname?. But ?h.white (yellow line) don?t change after rerunning as you 
>> can see in the attached picture.  Is this problem caused by deleting too 
>> many voxels and how to fix it?  Thanks very much.
>> 
>> Regards
>> Cong Chen
> 

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[Freesurfer] Projecting processed 4D functional data to individual surfaces

[Jared Zimmerman]

Hi All,

I'm trying to project some processed resting-state data onto the surface to run 
some surface based parcellations, and I'm running into a bit of difficulty.  
Basically I'm using bbregister to register my functional to the T1, then 
mri_vol2surf to project to the surface with the following pseudocode:

bbregister --s subjID --mov /mov_dir/subjID_example_func_brain.nii.gz \
 --reg /mov_dir/coreg/fs_ep2struct_fsl.dat \
 --init-fsl --bold

mri_vol2surf --src /mov_dir/filtered_func_residuals.nii.gz \ 
 --out /mov_dir/filtered_func_residuals_fs6_lh_6mm_noreshape.mgh \
 --srcreg /coreg/fs_ep2struct_fsl.dat --hemi lh \
 --surf white --projfrac 0.5 --icoorder 6 --fwhm 6 --out_type mgh --noreshape


The registration looks pretty good after I run bbregister, but what I get out 
from the mri_vol2surf seems weird.  First of all, the dimensions are 112745 x 1 
x 1 x 120, which seems odd. I'm forcing no reshaping, and from the help page it 
seems like the x-dim should be 40962 for icoorder=6.  I have 120 frames in my 
input data, so that seems to be right, but I'm not sure where this dimension is 
coming from.  I've also tried it with icoorder=4 and I get the same 
x-dim=112745 when I'm expecting 2562.  I've also run these commands with 
various iterations e.g. reshaping, no smoothing, no projfrac, and I get the 
same thing every time.

I'm also wondering how I should view these files to confirm that the surface 
projection has worked as I expect it if/when I am able to get the dimensions to 
be correct.  I cannot open any of the projected functional files in either 
freeview or tksurfer, so it will be helpful to know how I might be able to view 
these time-series on the surface after I've succeeded in projecting them to 
that space.

Any advice would be much appreciated


Thanks,
Jared
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Re: [Freesurfer] mris_calc cluster infos

[Rudolph Pienaar]

'mris_calc' is designed to perform be a simple "calculator" that 
performs a set of operations between two operands of the same type. 
These operands are either 3D structures (like volumes) or 1D arrays 
(like curvature files). You can add/subtract/multiply/divide/etc two 
operands.


How would you want to use 'mris_calc' on groups? When you say "mris_calc 
doesn't have a .log as output" do you mean you'd like to use mris_calc 
on two "log" files? Can you explain more what you are trying to do?


Best

-=R


On 18/09/16 10:55, Nick Corriveau Lecavalier wrote:
>
> Hi Freesurfer team,
>
>
> I have a 2 Group (MCI, CTL) x 2 (Time1, Time2) protocol. As suggested 
> in an earlier discussion, I measured the rate atrophy for each group 
> between my two time points. Then I applied the clusterwise correction 
> for multiple comparison, which give a lot of information about each 
> group (for example, number of clusters, # of voxels, regions where 
> there's a significant difference).
>
>
> Then I used mris_calc to compute the difference between my groups.
>
>
> My question is: Is there a way to obtain the same informations on the 
> group difference? Since mris_calc doesn't have a .log as output, I 
> can't compute mris_glmfit-sim on it and I cannot get any infos on the 
> cluster summary.
>
>
> Regards,
>
>
> 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] Gaussian curvature or Mean curvature

[Hanbyul Cho]

Dear Bruce Fischl,

Thank you for your help.

Best Regards,

Han Byul Cho

On Fri, Sep 16, 2016 at 8:27 PM, Bruce Fischl 
wrote:

> Hi Han
>
> the ?h.curv files are the mean curvature of the white matter surface with
> a Gaussian smoothing kernel applied to it over space. The ?h.curv.pial is
> the same thing for the pial surface. The ?h.inflated.H is the (unsmoothed)
> curvature of the inflated surface, and the ?h.inflated.K is the same but
> Gaussian curvature.
>
>
> cheers
> Bruce
>
>
> On Fri, 16 Sep 2016, Hanbyul Cho wrote:
>
> Dear Bruce Fischl,
>>
>> Thank you for your explanation.
>>
>> I think I could not yet fully understand the 'curv' files.
>> After processed this command,
>> recon-all -s  -i  -all
>>
>> the output files were follow as,
>> surf/?h.curv
>> surf/?h.curv.pial
>> surf/?h.inflated.H
>> surf/?h.inflated.K
>>
>> I wonder all these output files contained 'spatially smoothed mean
>> curvature'.
>>
>> Could I know that the meaning of 'spatially smoothed' ?
>> Are these output files difference from the output of 'mris_curvature'
>> command?
>>
>>
>> I saw the values that
>> stats/?h.aparc.stats   and
>> stats/?h.aparc.a2009s.stats
>> contained the 'integrated rectified Mean curvature' and 'integrated
>> rectified Gaussian curvature'.
>>
>> I wonder these values were if the average curvature of vertices in each
>> region, or other computed values using different atlas parcellation level.
>>
>> I appreciate your help.
>>
>> Best Wishes,
>>
>> Han.
>>
>> On Fri, Sep 16, 2016 at 4:37 PM, Bruce Fischl > >
>> wrote:
>>   Hi Han
>>
>>   the files ?h.curv contain the spatially smoothed mean curvature.
>>   You can compute the mean or Gaussian (or principal) curvatures
>>   of any surface using the mris_curvature command.
>>
>>   cheers
>>   Bruce
>>
>>
>>
>>
>>   On Fri, 16 Sep 2016, Hanbyul Cho wrote:
>>
>> Dear FreeSurfer Team,
>>
>>
>> I heard that FreeSurfer could calculate the Gaussian
>> curvature and Mean
>> curvature by vertex level.
>>
>> Do the computed curvature values be saved as the
>> subject/surf/lh.curv  or
>> rh.curv  files?
>>
>>
>> When I prepared the generated mass-univariate data,
>> I used the mris_preproc
>> with [--meas curv] option, not [--meas thickness].
>>
>> mris_preproc --qdec-long qdec.table.dat --target
>> study_average --hemi lh
>> --meas curv--out lh.curv.mgh
>>
>> I wonder this option is right usage to analyze the
>> cortical curvature. And I
>> wonder the 'curv' is what specific value is meaning.
>>
>>
>> If I want to designate the specific curvature
>> values(Gaussian or Mean
>> curvature ) to analyze by vertex level, how can I
>> use the [--meas] option?
>>
>>
>> Thank you,
>>
>> Best wishes,
>>
>> Han.
>>
>>
>>
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Re: [Freesurfer] Display FSL PALM(permutation) stats in freeview

[Ajay Kurani]

Hi Anderson,
   My full design contrasts are below:

/ContrastName1 HC > Grp1
/ContrastName2 HC < Grp1
/ContrastName3 HC > Grp2
/ContrastName4 HC < Grp2
/ContrastName5 Grp1 > Grp2
/ContrastName6 Grp1 < Grp2
/ContrastName7 M > F
/ContrastName8 M < F
/ContrastName9 HC/Grp1 M/F Interaction
/ContrastName10 HC/Grp2 M/F Interaction
/ContrastName11 Grp1/Grp2 M/F Interaction
/NumWaves 9
/NumPoints 11
/Matrix
1 1 -1 -1 0 0 0 0 0
-1 -1 1 1 0 0 0 0 0
1 1 0 0 -1 -1 0 0 0
-1 -1 0 0 1 1 0 0 0
0 0 1 1 -1 -1 0 0 0
0 0 -1 -1 1 1 0 0 0
1 -1 1 -1 1 -1 0 0 0
-1 1 -1 1 -1 1 0 0 0
1 -1 -1 1 0 0 0 0 0
1 -1 0 0 -1 1 0 0 0
0 0 1 -1 -1 1 0 0 0

My colums correspond to the following:
EV1:HC-M
EV2:HC-F
EV3:Grp1-M
EV4:Grp1-F
EV5:Grp2-M
EV6:Grp2-F
EV7:Age
EV8:Education
EV9:Disease Severity

In the folder I was running the analysis I put the lh.thickness.10mm.mgz,
rh.thickness.10mm.mgz, lh.white (fsaverage), rh.white (fsaverage),
lh.mask.mgh (taken from running qdec initially), rh.mask.mgh (taken from
running qdec initially).

I initially ran palm_hemimerge lh* within matlab
Then from a terminal I ran the following command:

palm -i bh.thickness.10mm.mgz -d design.mat -t design.con -o bh.thickness
-n 500 -approx tail -corrcon -s bh.white -T -tfce2D -logp -m bh.mask.mgz
-nouncorrected

The command ran fully.  When I loaded contrast 6 I found no results on the
pial surface, however the white matter surface (where the mask was) was
speckled all over with no cluster.

If there is a location,I can upload the stats file if that is easier.

Thanks,
Ajay

On Sat, Sep 17, 2016 at 10:03 PM, Ajay Kurani 
wrote:

> Hi Anderson,
>Thanks for the help.  When viewing my results they looked very
> strange.  Upon further investigation it looks as though the mask I supplied
> to PALM was a white matter mask (mask.mgh from running qdec initially)
> created when I ran qdec.  I assumed this would be the whole cortex but I
> was wrong.  Therefore it seems to only run permutation testing on the
> surface of the white matter.  Due to the fact that it is unsmoothed white
> matter, I think this is why we see some speckling bleeding through near the
> boundaries
>
> In order to do permutation testing accurately for surface based cortical
> thickness, would the mask need to be a volume file which is between the
> pial and white matter surfaces or would it just need to be the pial surface
> (lh.pial / rh.pial), or something else?  Any suggestions on the best way to
> create this?
>
> Thanks,
> Ajay
>
> On Sat, Sep 17, 2016 at 1:03 PM, Ajay Kurani 
> wrote:
>
>> Hi Anderson,
>>Thanks for the help.  When viewing my results they looked very
>> strange.  Upon further investigation it looks as though the mask I supplied
>> to PALM was a white matter mask (mask.mgh from running qdec initially)
>> created when I ran qdec.  I assumed this would be the whole cortex but I
>> was wrong.  Therefore it seems to only run permutation testing on the
>> surface of the white matter as seen in the attached photo.  Due to the fact
>> that it is unsmoothed white matter, I think this is why we see some
>> speckling bleeding through near the boundaries
>>
>> In order to do permutation testing accurately for surface based cortical
>> thickness, would the mask need to be a volume file which is between the
>> pial and white matter surfaces or would it just need to be the pial surface
>> (lh.pial / rh.pial), or something else?  Any suggestions on the best way to
>> create this?
>>
>> Thanks,
>> Ajay
>>
>>
>>
>>
>> On Thu, Sep 15, 2016 at 1:46 PM, Ajay Kurani 
>> wrote:
>>
>>> Hello Freesurfer Experts,
>>>I was running permutation simulations on cortical thickness data and
>>> I had an issue with non-orthogonal covariates with mri_glmfit-sim -perm.  I
>>> then tried FSL's PALM which is an extension of randomize to calculate
>>> threshold free stats.  I saved the output as logp(which is similar to qdec
>>> I believe), however I have not been able to load the stats files
>>> correctly.  The output of palm is lh.thickness_tfce.mgz for my various
>>> contrasts.
>>>
>>> 1) Is .mgz the proper format for the stats files or do I need to convert
>>> this to another type like .mgh etc?
>>>
>>> 2) Can I display this in freeview or is another program needed?  I also
>>> tried tksurfer but when I loaded the stats file as an overlay nothing
>>> displayed.  I want to make sure that the stats is loaded as an overlay in
>>> freeview/tksurfer and if so, do I need to select anything special so that
>>> it scales the logp values correctly?
>>>
>>> Thanks,
>>> Ajay
>>>
>>
>>
>
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[Freesurfer] Anatomy File Orientation Question

[Sepeta, Leigh]

Hi all,

I am trying to bring my FreeSurfer brainmask into SPM and then to coregister it 
(along with some ROIs from FreeSurfer) to the same subject's mprage already 
processed (coregistered to functional data) in SPM. To do this, I used:

mri_convert brainmask.mgz brainmask.nii.gz (then used gunzip)

and then looked at the brainmask and mprage in SPM and they both seem to be 
oriented correctly (left is left, right is right for each one--using anatomical 
landmarks as the guide). However, in reading up on this topic, many people 
advise using commands like these (often with RAS) when converting mgz to nii:

 mri_convert --in_type mgz --out_type nii --out_orientation RAS  brainmask.mgz 
brainmask.nii.gz

OR

 mri_convert --out_orientation RAS  -rt nearest --reslice_like   

OR

mri_convert -rl rawavg.mgz -rt nearest brainmask.mgz brainmask.nii.gz


Are any of the options (-rl, RAS, etc) in the last 3 commands listed necessary 
when going between mgz/nii for freesurfer to spm analyses if you know that the 
mgz and nii files are in the same orientation?

Thank you,
Leigh




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Re: [Freesurfer] FoV in additional scan

[Iglesias Gonzalez, Eugenio]

It does perform a registration, but this requires a decent initial alignment.


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


On 19 Sep 2016, at 14:43, pierre deman 
> wrote:

Does it perform a coregistration automatically when specified two images or is 
it better to perform it before running the recon-all ?

On Mon, Sep 19, 2016 at 3:34 PM, Iglesias Gonzalez, Eugenio 
> wrote:
Hi Renate,
as long as the additional scan is more or less aligned with the T1 in physical 
coordinates (i.e., they appear decently aligned when you open them in 
Freeview), you should be fine and not need to do anything.
Cheers,
/E

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


On 19 Sep 2016, at 14:31, Vaz pandolfo, Renata 
> wrote:

Dear Eugenio,

We have another question about the Hippo Sf Segmentation with an additional 
scan.

Some of our additional scans (FLAIRs or T2s) have a bigger field of view as 
compared to the T1 (ex.: they cover more of the neck almost up to the shoulders 
of the subjects, while the T1 has the "normal" FoV).

Should the additional scan be cropped or  preprocessed in any way (ex.: bias 
field correction)?  And if so, should we process the T1 in the same way or is 
it generally recommended to just use the raw images?

Thank you!

Renata


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Re: [Freesurfer] FoV in additional scan

[Vaz pandolfo, Renata]

Okay, thanks!

Best,

Renata

On Mon, Sep 19, 2016 at 3:34 PM, Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:

> Hi Renate,
> as long as the additional scan is more or less aligned with the T1 in
> physical coordinates (i.e., they appear decently aligned when you open them
> in Freeview), you should be fine and not need to do anything.
> Cheers,
> /E
>
> Juan Eugenio Iglesias
> Senior Research Fellow
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
>
>
> On 19 Sep 2016, at 14:31, Vaz pandolfo, Renata  wrote:
>
> Dear Eugenio,
>
> We have another question about the Hippo Sf Segmentation with an
> additional scan.
>
> Some of our additional scans (FLAIRs or T2s) have a bigger field of view
> as compared to the T1 (ex.: they cover more of the neck almost up to the
> shoulders of the subjects, while the T1 has the "normal" FoV).
>
> Should the additional scan be cropped or  preprocessed in any way (ex.:
> bias field correction)?  And if so, should we process the T1 in the same
> way or is it generally recommended to just use the raw images?
>
> Thank you!
>
> Renata
>
>
>
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Re: [Freesurfer] FoV in additional scan

[Iglesias Gonzalez, Eugenio]

Hi Renate,
as long as the additional scan is more or less aligned with the T1 in physical 
coordinates (i.e., they appear decently aligned when you open them in 
Freeview), you should be fine and not need to do anything.
Cheers,
/E

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


On 19 Sep 2016, at 14:31, Vaz pandolfo, Renata 
> wrote:

Dear Eugenio,

We have another question about the Hippo Sf Segmentation with an additional 
scan.

Some of our additional scans (FLAIRs or T2s) have a bigger field of view as 
compared to the T1 (ex.: they cover more of the neck almost up to the shoulders 
of the subjects, while the T1 has the "normal" FoV).

Should the additional scan be cropped or  preprocessed in any way (ex.: bias 
field correction)?  And if so, should we process the T1 in the same way or is 
it generally recommended to just use the raw images?

Thank you!

Renata

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Re: [Freesurfer] FoV in additional scan

[pierre deman]

Does it perform a coregistration automatically when specified two images or
is it better to perform it before running the recon-all ?

On Mon, Sep 19, 2016 at 3:34 PM, Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:

> Hi Renate,
> as long as the additional scan is more or less aligned with the T1 in
> physical coordinates (i.e., they appear decently aligned when you open them
> in Freeview), you should be fine and not need to do anything.
> Cheers,
> /E
>
> Juan Eugenio Iglesias
> Senior Research Fellow
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
>
>
> On 19 Sep 2016, at 14:31, Vaz pandolfo, Renata  wrote:
>
> Dear Eugenio,
>
> We have another question about the Hippo Sf Segmentation with an
> additional scan.
>
> Some of our additional scans (FLAIRs or T2s) have a bigger field of view
> as compared to the T1 (ex.: they cover more of the neck almost up to the
> shoulders of the subjects, while the T1 has the "normal" FoV).
>
> Should the additional scan be cropped or  preprocessed in any way (ex.:
> bias field correction)?  And if so, should we process the T1 in the same
> way or is it generally recommended to just use the raw images?
>
> Thank you!
>
> Renata
>
>
>
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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
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> HelpLine at
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> dispose of the e-mail.
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[Freesurfer] FoV in additional scan

[Vaz pandolfo, Renata]

Dear Eugenio,

We have another question about the Hippo Sf Segmentation with an additional
scan.

Some of our additional scans (FLAIRs or T2s) have a bigger field of view as
compared to the T1 (ex.: they cover more of the neck almost up to the
shoulders of the subjects, while the T1 has the "normal" FoV).

Should the additional scan be cropped or  preprocessed in any way (ex.:
bias field correction)?  And if so, should we process the T1 in the same
way or is it generally recommended to just use the raw images?

Thank you!

Renata
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Re: [Freesurfer] FLAIR for hippo subfield segmentation with an additional scan

[pierre deman]

ok thanks.

Cheers,
Pierre

On Mon, Sep 19, 2016 at 3:17 PM, Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:

> Yes, you have so specify it separately.
> Cheers,
> /Eugenio
>
>
> Juan Eugenio Iglesias
> Senior Research Fellow
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
>
>
> On 19 Sep 2016, at 14:13, pierre deman  wrote:
>
> Hi,
>
> I have a short question about the additional T2 scan as well.
>
> If I perform the full recon-all;
> recon-all -s mySubject -i myT1.nii -T2 myT2.nii -T2pial -all
> -hippocampal-subfields-T1T2
> do I still have to precise myT2scan.nii.gz T2 for using the t2 for the
> hippocampal subfields as well ? or it will automatically take the t2
> precised for the t2pial ?
>
> Cheers,
> Pierre
>
> On Mon, Sep 5, 2016 at 4:13 PM, Iglesias, Eugenio 
> wrote:
>
>> The same one; just change the input file and the analysis ID
>>
>> - T2:   recon-all -s mySubject -hippocampal-subfields-T1T2
>> myT2scan.nii.gz  T2
>>
>> - FLAIR: recon-all -s mySubject -hippocampal-subfields-T1T2
>> myFLAIRscan.nii.gz  FLAIR
>>
>> Cheers,
>>
>> /Eugenio
>>
>> Juan Eugenio Iglesias
>> Senior Research Fellow
>> Translational Imaging Group
>> University College London
>> http://www.jeiglesias.com
>> http://cmictig.cs.ucl.ac.uk/
>>
>>
>> On 5 Sep 2016, at 15:10, Vaz pandolfo, Renata  wrote:
>>
>> Dear FS experts,
>>
>> I have a question about the "segmentation with an additional scan - 
>> multispectral segmentation"
>> on the hippocampal sf segmentation, FS dev. 6.0.
>>
>> For controls on which I had already run recon-all -all, I added the T2 
>> sequence with the following
>> command:
>>
>>
>> recon-all -s  \
>> -hippocampal-subfields-T1T2  
>>
>> Now, if I want to do the same thing with FLAIR as the additional input, 
>> which flag should I use?
>>
>> Thank you,
>>
>> Renata
>>
>>
>>
>> ___
>> 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.
>>
>>
>
>
> --
> DEMAN Pierre
> Mobile : +33 7 82 57 80 94
>
>
>


-- 
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Mobile : +33 7 82 57 80 94
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Re: [Freesurfer] FLAIR for hippo subfield segmentation with an additional scan

[Iglesias Gonzalez, Eugenio]

Yes, you have so specify it separately.
Cheers,
/Eugenio


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


On 19 Sep 2016, at 14:13, pierre deman 
> wrote:

Hi,

I have a short question about the additional T2 scan as well.

If I perform the full recon-all;
recon-all -s mySubject -i myT1.nii -T2 myT2.nii -T2pial -all 
-hippocampal-subfields-T1T2
do I still have to precise myT2scan.nii.gz T2 for using the t2 for the 
hippocampal subfields as well ? or it will automatically take the t2 precised 
for the t2pial ?

Cheers,
Pierre

On Mon, Sep 5, 2016 at 4:13 PM, Iglesias, Eugenio 
> wrote:
The same one; just change the input file and the analysis ID

- T2:   recon-all -s mySubject -hippocampal-subfields-T1T2 myT2scan.nii.gz  
T2

- FLAIR: recon-all -s mySubject -hippocampal-subfields-T1T2 myFLAIRscan.nii.gz  
FLAIR

Cheers,

/Eugenio

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


On 5 Sep 2016, at 15:10, Vaz pandolfo, Renata 
> wrote:


Dear FS experts,


I have a question about the "segmentation with an additional scan - 
multispectral segmentation"
on the hippocampal sf segmentation, FS dev. 6.0.

For controls on which I had already run recon-all -all, I added the T2 sequence 
with the following
command:

recon-all -s  \
-hippocampal-subfields-T1T2  


Now, if I want to do the same thing with FLAIR as the additional input, which 
flag should I use?

Thank you,

Renata


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--
DEMAN Pierre
Mobile : +33 7 82 57 80 94

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Re: [Freesurfer] FLAIR for hippo subfield segmentation with an additional scan

[pierre deman]

Hi,

I have a short question about the additional T2 scan as well.

If I perform the full recon-all;
recon-all -s mySubject -i myT1.nii -T2 myT2.nii -T2pial -all
-hippocampal-subfields-T1T2
do I still have to precise myT2scan.nii.gz T2 for using the t2 for the
hippocampal subfields as well ? or it will automatically take the t2
precised for the t2pial ?

Cheers,
Pierre

On Mon, Sep 5, 2016 at 4:13 PM, Iglesias, Eugenio 
wrote:

> The same one; just change the input file and the analysis ID
>
> - T2:   recon-all -s mySubject -hippocampal-subfields-T1T2
> myT2scan.nii.gz  T2
>
> - FLAIR: recon-all -s mySubject -hippocampal-subfields-T1T2
> myFLAIRscan.nii.gz  FLAIR
>
> Cheers,
>
> /Eugenio
>
> Juan Eugenio Iglesias
> Senior Research Fellow
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
>
>
> On 5 Sep 2016, at 15:10, Vaz pandolfo, Renata  wrote:
>
> Dear FS experts,
>
> I have a question about the "segmentation with an additional scan - 
> multispectral segmentation"
> on the hippocampal sf segmentation, FS dev. 6.0.
>
> For controls on which I had already run recon-all -all, I added the T2 
> sequence with the following
> command:
>
>
> recon-all -s  \
> -hippocampal-subfields-T1T2  
>
> Now, if I want to do the same thing with FLAIR as the additional input, which 
> flag should I use?
>
> Thank you,
>
> Renata
>
>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
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> HelpLine at
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> properly
> dispose of the e-mail.
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[Freesurfer] make_average_volume problems

[Claudia Dacquino]

Hi all,
I'm trying making average volume from a set of subjects after making
average-subject, but I get this error line:

mghWrite(/home/Admin/Scrivania/SUBJ/average/tmp/make_average_vol-tmp-7513/orig-subj1/.mgh,
-1): could not open file

And then:

Applying LTAtransformInterp (resample_type 1)
writing to
/home/Admin/Scrivania/SUBJ/average/tmp/make_average_vol-tmp-7513/orig-subj1.mgh...
ERROR: failure writing
/home/Admin/Scrivania/SUBJ/average/tmp/make_average_vol-tmp-7513/orig-subj1/.mgh
/home/Admin/Scrivania/SUBJ
ERROR: mri_convert failed.

I'm quite sure my partition is not full and I have permissions.
Any ideas?

Thanks a lot.
Claudia



-- 

Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia

Laboratorio di Neuropsichiatria

Dipartimento di Neurologia Clinica e Comportamentale

IRCCS Fondazione Santa Lucia

via Ardeatina 306 - 00179 Roma

Tel. +39 (0)6 51501358

Fax +39 (0)6 51501575

web: http://www.neuropsichiatrialab.com

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[Freesurfer] Course in Advanced Neuroimaging (Barcelona)

[Erick Canales]

Dear colleagues,



I am pleased to announce our upcoming Course in Advanced Neuroimaging held
annually in Barcelona. It takes a practical approach and does not require
qualifications or previous experience in neuroimaging. It will be taught in
Spanish.



The multidisciplinary programme provides thorough training in the analysis
of brain images from different MRI modalities and data modeling techniques,
including voxel-based morphometry, cortical thickness, diffusion tensor
imaging and fibre tracking, functional MRI and brain connectivity, as well
as the statistical methods behind these techniques including elements of
meta-analysis, and more.



The course consists of a four-month online theoretical module (starting on
October 17th) and a period of practical face-to-face training (split
between two days in November and two weeks at the end of April) held in
Barcelona.



For further information, please visit the website: www.cursoneuroimagen.com


Best regards,

Erick J. Canales-Rodríguez, Joaquim Radua and Raymond Salvador



FIDMAG Research Foundation and Sociedad Española de Neuroimagen

*www.fidmag.com *
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[Freesurfer] Antwort: Re: Dev builds not found

[j . oschwald]

Hi Freesurfer users,

I have the same problem as Leila - I am in need of the latest dev build and 
would really appreciate if someone could put it on another site where we could 
download it as long as the server is down.

Hope that is possible!
Best wishes
Jessica

-freesurfer-boun...@nmr.mgh.harvard.edu schrieb: -
An: "freesurfer@nmr.mgh.harvard.edu" 
Von: Leila Reddy 
Gesendet von: freesurfer-boun...@nmr.mgh.harvard.edu
Datum: 18.09.2016 22:38
Betreff: Re: [Freesurfer] Dev builds not found

Hi Bruce,
Thanks for your reply. 

Does anyone on the list have access to the tar file of the latest dev build 
that they could put on some other site or in a public Dropbox folder? I totally 
changed my system and don't have a working version of Freesurfer/FS-FAST 
anymore and am pretty much stuck. Otherwise, do you think I should try to 
install an older version of perl?

Sorry to cause you trouble,
Thanks,
Leila
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Re: [Freesurfer] Display FSL PALM(permutation) stats in freeview

[Anderson M. Winkler]

Hi Ajay,

The mask is a file of the "curvature" type, that is, it contains vertexwise
data, and should mask out the "unknown" region (that region in the medial
aspect that is not cortex and is there to ensure the topology is the same
as that of a sphere). The mask can alternatively be a .mgz file as a
pseudo-volume, still with the same number of vertices as the input data and
surface.

Although I'm not seeing your input files, I believe your mask is fine,
otherwise PALM would have failed even before starting the permutations. I'd
think there is something else going on. Could you show the full design,
contrasts, and command line used?

All the best,

Anderson


On 18 September 2016 at 04:03, Ajay Kurani  wrote:

> Hi Anderson,
>Thanks for the help.  When viewing my results they looked very
> strange.  Upon further investigation it looks as though the mask I supplied
> to PALM was a white matter mask (mask.mgh from running qdec initially)
> created when I ran qdec.  I assumed this would be the whole cortex but I
> was wrong.  Therefore it seems to only run permutation testing on the
> surface of the white matter.  Due to the fact that it is unsmoothed white
> matter, I think this is why we see some speckling bleeding through near the
> boundaries
>
> In order to do permutation testing accurately for surface based cortical
> thickness, would the mask need to be a volume file which is between the
> pial and white matter surfaces or would it just need to be the pial surface
> (lh.pial / rh.pial), or something else?  Any suggestions on the best way to
> create this?
>
> Thanks,
> Ajay
>
> On Sat, Sep 17, 2016 at 1:03 PM, Ajay Kurani 
> wrote:
>
>> Hi Anderson,
>>Thanks for the help.  When viewing my results they looked very
>> strange.  Upon further investigation it looks as though the mask I supplied
>> to PALM was a white matter mask (mask.mgh from running qdec initially)
>> created when I ran qdec.  I assumed this would be the whole cortex but I
>> was wrong.  Therefore it seems to only run permutation testing on the
>> surface of the white matter as seen in the attached photo.  Due to the fact
>> that it is unsmoothed white matter, I think this is why we see some
>> speckling bleeding through near the boundaries
>>
>> In order to do permutation testing accurately for surface based cortical
>> thickness, would the mask need to be a volume file which is between the
>> pial and white matter surfaces or would it just need to be the pial surface
>> (lh.pial / rh.pial), or something else?  Any suggestions on the best way to
>> create this?
>>
>> Thanks,
>> Ajay
>>
>>
>>
>>
>> On Thu, Sep 15, 2016 at 1:46 PM, Ajay Kurani 
>> wrote:
>>
>>> Hello Freesurfer Experts,
>>>I was running permutation simulations on cortical thickness data and
>>> I had an issue with non-orthogonal covariates with mri_glmfit-sim -perm.  I
>>> then tried FSL's PALM which is an extension of randomize to calculate
>>> threshold free stats.  I saved the output as logp(which is similar to qdec
>>> I believe), however I have not been able to load the stats files
>>> correctly.  The output of palm is lh.thickness_tfce.mgz for my various
>>> contrasts.
>>>
>>> 1) Is .mgz the proper format for the stats files or do I need to convert
>>> this to another type like .mgh etc?
>>>
>>> 2) Can I display this in freeview or is another program needed?  I also
>>> tried tksurfer but when I loaded the stats file as an overlay nothing
>>> displayed.  I want to make sure that the stats is loaded as an overlay in
>>> freeview/tksurfer and if so, do I need to select anything special so that
>>> it scales the logp values correctly?
>>>
>>> Thanks,
>>> Ajay
>>>
>>
>>
>
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