Re: [Freesurfer] Generating intermediate surfaces?

[Souheil Inati]

Hi Bruce,

Ahh, I knew there had to be a simple way.  I’ll give it a shot.

Thanks!
Souheil

btw, it’s not listed here: http://freesurfer.net/fswiki/FreeSurferCommands


> On Jan 22, 2017, at 10:49 PM, Bruce Fischl  wrote:
> 
> Hi Souheil
> 
> Check out mris_expand. It should do the trick. Give it a negative number to 
> get it to move into the whir matter
> Cheers
> Bruce
> 
>> On Jan 22, 2017, at 10:31 PM, Souheil Inati  wrote:
>> 
>> Hi All,
>> 
>> I would like to generate some surfaces a bit below the white surface (in the 
>> white matter) and at several locations between the white and pial surfaces.  
>> Having trouble finding enough on the wiki - I’m guessing it’s some 
>> combination of mris_make_surfaces and mris_inflate?
>> 
>> Any help would be greatly appreciated.
>> 
>> Thanks,
>> Souheil
>> 
>> 
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>> 
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Re: [Freesurfer] Generating intermediate surfaces?

[Bruce Fischl]

Hi Souheil

Check out mris_expand. It should do the trick. Give it a negative number to get 
it to move into the whir matter
Cheers
Bruce

> On Jan 22, 2017, at 10:31 PM, Souheil Inati  wrote:
> 
> Hi All,
> 
> I would like to generate some surfaces a bit below the white surface (in the 
> white matter) and at several locations between the white and pial surfaces.  
> Having trouble finding enough on the wiki - I’m guessing it’s some 
> combination of mris_make_surfaces and mris_inflate?
> 
> Any help would be greatly appreciated.
> 
> Thanks,
> Souheil
> 
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 


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[Freesurfer] Generating intermediate surfaces?

[Souheil Inati]

Hi All,

I would like to generate some surfaces a bit below the white surface (in the 
white matter) and at several locations between the white and pial surfaces.  
Having trouble finding enough on the wiki - I’m guessing it’s some combination 
of mris_make_surfaces and mris_inflate?

Any help would be greatly appreciated.

Thanks,
Souheil


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[Freesurfer] Extracting significant clusters after qdec analyses

[Katherine Damme]

Hello Everyone,

Is there a way to extract the significant clusters as masks from
significant group comparisons using qdec?

All I can seem to find is  mri_glmfit-sim which doesn't quite replicate the
QDEC FDR 0.05 output and doesn't seem to make anything that I could extract
as a label, or hand drawing an ROI.

I am working with a longitudinal model of cortical thickness, and would
like to extract the average thickness of each significant cluster to
understand the change in thickness.

Thank you.

Kate Damme
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Re: [Freesurfer] longitudinal tracula error

[Yendiki, Anastasia]

Hi Barbara - If you're using the 5.3 version, then you'll have to download the 
update from 2014:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

This should fix the problem. But if there's a version of the 6.0 beta that was 
having the same problem, please let me know (by sending the trac-all copy of 
that version) so I can fix that asap.

Thanks!

a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se]
Sent: Friday, January 20, 2017 7:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your quick reply. I've only tried version 6.0 to determine 
whether the error was possibly version-related, but that doesn’t seem to be the 
case… I'm actually working with version 5.3 so I'll send attach the 
trac-all.local-copy for that if that’s OK. Once again, thank you!

On 20 Jan 2017, at 23:52, Yendiki, Anastasia  wrote:

Hi Barbara - If you take out the "set baselist" part, you'll run the 
cross-sectional TRACULA stream, i.e., analyze each time point independently. So 
you want to leave that in to use the longitudinal TRACULA stream.

The base template itself (i.e., the median of the T1s of the time-points) may 
not be used, but the files under the base template's directory are used. 
Longitudinal TRACULA maps between the base space to the space of each DWI time 
point, as described in the paper.

Can you please attach the file scripts/trac-all.local-copy? Since there's no 
official 6.0 version yet but multiple beta versions of it, it's hard to know 
which one you used.

Thanks,
a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[freesurfer-boun...@nmr.mgh.harvard.edu]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se]
Sent: Friday, January 20, 2017 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] longitudinal tracula error

Dear FreeSurfer experts,

I’m running tracula on longitudinal data but I’ve encountered the following 
error at the “trac-all -prep” stage:  ERROR: flag ; unrecognized (see below)

trac-preproc -c /Documents/TRACULA/TEST/S0001.01_T1/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.cmd ;
ERROR: flag ; unrecognized

As an example, I defined the parameters in my dmrirc file as:
set subjlist = ( S0001.01_T1 \
   S0001.01_T2 \
   S0004.00_T1 \
   S0004.00_T2 )

set baselist = ( S0001.01 \
S0001.01 \
S0004.00 \
S0004.00 )

set dcmlist =  ( S0001.01_T1/DTI.nii \
S0001.01_T2/DTI.nii \
S0004.00_T1/DTI.nii \
S0004.00_T2/DTI.nii )

>From the mailing list, it seems a similar issue has been fixed in previous 
>updates but I have tried both version 5.3 and 6.0 and still get this error...

My tracula directory contains 3 directories per participant: 2 with the 
*.long.* output for timepoint 1 and 2, and a directory with the base. Including 
the base gives the error above, but if I take it out, it asks for it: ERROR: 
cannot find /Documents/TRACULA/TEST/S0001.01

>From what I understand, the base is not necessary to run any analysis, but it 
>has to be there anyhow (?): 
>https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg45332.html 
>Maybe I am understanding this incorrectly?

Since the base is used to create the longitudinal output (*long*), including 
the aparc+aseg.mgz file, and those are then used in tracula, I thought I could 
run things without it. I decided to take out the “set baselist” part from the 
configuration file — this way it seems to run fine (so far). But I assume it’s 
there for a reason so I’m not sure this is a solution at all...

Any help would be much appreciated!

Details:
1) freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
2) platform: CentOS release 6.8 (Final)
3) Operating system details (kernel name, release, version, etc.): Linux 
2.6.32-642.11.1.el6.x86_64 #1 SMP Fri Nov 18 19:25:05 UTC 2016 x86_64 x86_64 
x86_64 GNU/Linux
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[Freesurfer] Regarding: Habenula ROI

[Dr Sampada Sinha]

Dear freesurfer experts,

Is it possible to create Habenula as region of interest from fsaverage
(orig.mgz images) using tkmedit? I will be using following links to guide
me for creating Habenular region of interest

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI_tktools

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT

Thanks for your help.

Kind regards,

Sampada

-- 
Sampada
​Research medical scientist (B)​
Department of Geriatric Mental Health (DGMH)
King George Medical University
Lucknow-226003
​, Uttar Pradesh​
India
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