Re: [Freesurfer] segmentation help

[Nina Jacobsen]

Hi Dilip.

You have to place your files where the subject-directory points. If you dont 
change the directory yourself, this is under freesurfer/subjects.

For more info about recon all, see 
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-allhttps://surfer.nmr.mgh.harvard.edu/fswiki/recon-all

Nina.

Fra: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] på vegne af Dilip Puri 
[dilippurip...@gmail.com]
Sendt: 10. april 2017 07:46
Til: Freesurfer support list
Emne: Re: [Freesurfer] segmentation help

Hi,

To-do "recon-all" where should I keep all the files. I mean in which directory. 
What are the command lines?


Hope for response.


Thanks
Dilip

On Sun, Apr 9, 2017 at 7:18 PM, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:
Hi Dilip

you need to run your image through recon-all.

cheers
Bruce

On Sun, 9 Apr 2017, Dilip Puri
wrote:

> Hi all,
>
> I've 200 analyze7.5 format images(OASIS Dataset) and I want to segment
> HippoCampus.
>
> My input file xyz.img and output file will be like xyz_seg.img which
> contains only hippocampus image it like Grond Truth image for my original
> input image.
>
> Here is sample files including original and segmented mask link.
>
> Even I am very new to FREESURFER so I don't know the procedure to
> reconstruct the images.
>
>
> Kindly help me.
>
>
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Re: [Freesurfer] segmentation help

[Dilip Puri]

Hi,

To-do "recon-all" where should I keep all the files. I mean in which
directory. What are the command lines?


Hope for response.


Thanks
Dilip

On Sun, Apr 9, 2017 at 7:18 PM, Bruce Fischl 
wrote:

> Hi Dilip
>
> you need to run your image through recon-all.
>
> cheers
> Bruce
>
> On Sun, 9 Apr 2017, Dilip Puri
> wrote:
>
> > Hi all,
> >
> > I've 200 analyze7.5 format images(OASIS Dataset) and I want to segment
> > HippoCampus.
> >
> > My input file xyz.img and output file will be like xyz_seg.img which
> > contains only hippocampus image it like Grond Truth image for my original
> > input image.
> >
> > Here is sample files including original and segmented mask link.
> >
> > Even I am very new to FREESURFER so I don't know the procedure to
> > reconstruct the images.
> >
> >
> > Kindly help me.
> >
> >
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] A question regarding LUT/Freeview

[Ruopeng Wang]

The isosurface option is only for 3D display. It does not apply to 2D views. 
However, I have added option to select labels to display from the look up table 
in our latest development version. You can download the development build here:

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev 


Best,
Ruopeng

> On Apr 9, 2017, at 6:56 AM, amir hosein  wrote:
> 
> Dear Ruopeng,
> 
>  
> Thanks a lot for your reply.
> 
> I am sorry, but I still could not fix this.
> 
>  
> Do you mean a command like this:
> 
> freeview –v aparc+aseg.mgz:colormap=lut:isosurface=2032,2035
> 
>  
> I could not perform what I have in mind using this command. I want to 
> simultaneously show several different brain areas on a T1 image. The labels 
> are so different; as examples, one is 14, one is 100, and one is 1250.
> 
>  
> Currently I am extracting labels, and using MATLAB I overlay them on a T1 
> image.
> 
> I am sure Freesurfer should be able to nicely perform this, but this is not 
> resolved for me yet :)
> 
>  
> Many thanks again,
> 
> Amir
> 
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[Freesurfer] -hemi flag

[Nillo, Ryan Michael R]

Hi FreeSurfer users,

I am using FreeSurfer v5.3 and have noticed that when -hemi is used as a flag 
in recon-all, the half I did not specify is not present in wm.mgz. The full 
command is recon-all -autorecon2 -autorecon3 -hemi (l or r)h -subjid 
subject_name -sd SUBJECTS_DIR. After running, white matter is missing in the 
half of wm.mgz not specified under the -hemi flag, but the surfaces and 
segmentation in aparc+aseg are unaffected. Is this a bug?

Ryan Michael Nillo
UCSF Center for Radiology and Biomedical Imaging
Staff Research Associate


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[Freesurfer] create mask from cluster number?

[lindsay hanford]

Hello Freesurfer Developers,

The main point of my post is to determine whether its possible to create a
mask from a cluster ID run using a subset of the sample, and then use that
mask to extract cortical thickness values from a model run with the full
sample.

I am running a pretty basic cortical thickness- behavioural correlation
analysis with two groups using fsgd. Because I have a relatively small
sample size (just over 40 participants in each group) I wanted to restrict
my analysis to only regions that showed a relationship within the HC group.
I ran the model using mri_glmfit:

mri_glmfit --y HC.43.rh.10.mgh --fsgd Behav.fsgd --C v1.slope.mtx --surf
fsaverage rh --cortex --glmdir MCCB.HC.43.rh

Behav.fsgd setup:
GroupDescriptorFile 1
Title MaineffectofGroup
Class HC
Variables BehavMC
Input 128 HC -5
Input 132 HC 8
Input 192 HC -10
Input 193 HC -6
...

v1.slope.mtx:
0 1

*quick side question - in the past I was curious to see if this could test
positive and negative relationships. I tried two different contrasts: 0 1
and 0 -1 to test the positive and negative relationships, respectively,
however the results were the direct inverse of each other... it didn't show
negative slope relationships. I am curious if its possible to test for
negative relationships in freesurfer? How would you set up that contrast?

next, I used mri_surfcluster to generate image and table files:
mri_surfcluster --in HC.43.rh/v1.slope/sig.mgh --subject fsaverage --hemi
rh --surf pial --annot aparc --thmin 2 --ocn HC.43.rh/v1.slope/results.ocn.mgh
--sum HC.43.rh/v1.slope/results.sum.txt

my results.sum.txt file shows a number of clusters
ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZNVtxs   Annot
   13.719  163035270.33 57.7  -34.6  -21.5   234
 inferiortemporal
   23.499   22608217.35 33.2  -48.2  -15.1   230  fusiform
   33.1702804 93.01 42.1   22.1   23.9   132
 rostralmiddlefrontal

Would it be possible to create a mask defined by say "ClusterNo 1"?

Once the mask is created, I want to use it to extract the cortical
thickness values for all participants (including those that weren't used to
create the mask).. Is this possible? Can that be done using mri_segstats?

Let me know if you require any other details.
Freesurfer version:  freesurfer-Darwin-lion-stable-pub-v5.3.0


Thank you in advance,


Lindsay
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Re: [Freesurfer] segmentation help

[Bruce Fischl]

Hi Dilip

you need to run your image through recon-all.

cheers
Bruce

On Sun, 9 Apr 2017, Dilip Puri 
wrote:

> Hi all,
> 
> I've 200 analyze7.5 format images(OASIS Dataset) and I want to segment
> HippoCampus.
> 
> My input file xyz.img and output file will be like xyz_seg.img which
> contains only hippocampus image it like Grond Truth image for my original
> input image.
> 
> Here is sample files including original and segmented mask link.
> 
> Even I am very new to FREESURFER so I don't know the procedure to
> reconstruct the images.
> 
> 
> Kindly help me.
> 
>
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Re: [Freesurfer] A question regarding LUT/Freeview

[amir hosein]

Dear Ruopeng,



Thanks a lot for your reply.

I am sorry, but I still could not fix this.



Do you mean a command like this:

freeview –v aparc+aseg.mgz:colormap=lut:isosurface=2032,2035



I could not perform what I have in mind using this command. I want to
simultaneously show several different brain areas on a T1 image. The labels
are so different; as examples, one is 14, one is 100, and one is 1250.



Currently I am extracting labels, and using MATLAB I overlay them on a T1
image.

I am sure Freesurfer should be able to nicely perform this, but this is not
resolved for me yet :)



Many thanks again,

Amir
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[Freesurfer] QA Tool error when identifying aseg outliers

[Ladan Shahshahani]

Dear all,

I'm using QA_tools v1.2 to check the recon-all processes for my subjects.
I'm getting the following lines in my terminal window while performing QA
on some subjects:
Processing each subcortical label ...
(standard_in) 1: syntax error
(standard_in) 1: syntax error
(standard_in) 1: syntax error
(standard_in) 1: syntax error
(standard_in) 1: syntax error
(standard_in) 1: syntax error
(standard_in) 1: syntax error

summary log says that there are 0 outliers for this subject.
Is this because of the syntax error I get that no outliers are identified
or there are really no outliers in my data?

In the [Subject id]/scripts/recon_checker.log I see lines like the
following:
checking subcortical label: Epidermis, 0 +/- 0
checking subcortical label: Conn-Tissue, 0 +/- 0
checking subcortical label: SC-Fat/Muscle, 0 +/- 0
checking subcortical label: CSF-SA, 0 +/- 0
My question is what is  "0 +/-0" telling me? What does it represent?

Thanks in advance.

Bests,
Ladan
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