Re: [Freesurfer] Hippocampus subfield LUT

[Douglas N. Greve]

Look in $FREESURFER/FreeSurferLUT.txt
This has those indices (and a lot more). If you want just the hippo SF 
indices, you can run something like

mri_segstats --seg hipposf.mgz --ctab-default --sum sum.dat
The indices will be in sum.dat

On 5/14/2024 11:04 AM, karl landheer wrote:


External Email - Use Caution

Hello, I am looking for the LUT which converts the indices in images 
like lh.hippoAmygLabels-T.v22.mgz to region name. Is this available 
anywhere? I can’t find it


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] Hippocampus subfield LUT

[karl landheer]

External Email - Use Caution

Hello, I am looking for the LUT which converts the indices in images like
lh.hippoAmygLabels-T.v22.mgz to region name. Is this available anywhere? I
can’t find it
___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Retinotopy error computing contrast matrices

[Mesquita, Tiago]

External Email - Use Caution

Hello Freesurfer Experts,

I find a way to do the analysis solving the contrast matrices problem, but I am 
not sure about this solution, mostly because the results don't look correct to 
me.


So basically my solution was replicate my 3 runs, and the second time calling 
it Eccen after the first 3 being polar. This time the contrast matrix was 
created without any issue and the analyse was done.

So I would like to know if the problem is on my "solution". And if is there any 
way of doing eccen and polar separately.
How should I proceed with this analysis since i use bars that swipe the visual 
field, from 8 different directions, i think the can be considered as both eccen 
and polar because I'm covering different angles and different eccentricities.



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Mesquita, Tiago 

Sent: 20 April 2024 14:29:19
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Retinotopy error computing contrast matrices


External Email - Use Caution

Hello FreeSurfer Developers,

I am trying to do a retinotopy analysis. My retinotopy has 8 bars, this bars 
swipe the visual field from the 8 possible directions (all multiple of 45 
degrees angle). One complete swipe takes 24 sec. I have 16 different positions 
per swipe. So I have tried using -retinotopy 24 (period of a complete swipe) or 
1.5 (period of each individual bar) in every case i always end up having the 
same error. For some reason Xcond = NaN (normalized). I tried eccen pos, eccen 
neg even polar neg and pos in my paradigm files and get always the same result.

Can someone help me? this is what i get:

Creating Design Matrix
 ... creation time =  0.006 sec
DoMCFit = 1
ntptot = 119, nX = 35, DOF = 84
Saving X matrix to ~/Project/Sess02/bold/rtopy.self.lh/pr001/Xtmp.mat
XCond = NaN (normalized)
Warning: Matrix is singular to working precision.
> In fast_selxavg3b (line 403)

Computing contrast matrices
Warning: Matrix is singular to working precision.
> In fast_selxavg3b (line 441)

Warning: Matrix is singular to working precision.
> In fast_selxavg3b (line 441)

OLS Beta Pass
  run 1t= 0.0
reading data ... 0.820008
Global Mean   146.10
Global In-Mask Mean = 146.104 (NaN)
Rescale Target = 100
RescaleFactor = 0.68
OLS Residual Pass
  run 1t= 0.0
reading data ... 0.776954
Saving rho1
Found 0 voxels with corrected AR1 > 0.90
Not Whitening
Warning: Matrix is singular to working precision.
> In fast_glmfit (line 54)
In fast_selxavg3b (line 999)

Found 7921 zero-valued voxels
Computing contrasts
Starting contrasts
eccen J=2 -
Warning: Matrix is singular to working precision.
> In fast_fratiow (line 86)
In fast_selxavg3b (line 1161)

Warning: Matrix is singular, close to singular or badly scaled. Results may be
inaccurate. RCOND = NaN.
> In fast_fratiow (line 86)
In fast_selxavg3b (line 1161)

Error using betainc
X must be in the interval [0,1].

Error in FTest (line 51)
p = betainc(z, dof2/2, dof1/2);

Error in fast_selxavg3b (line 1163)
pmat = FTest(dof1, dof2, Fmat);

If i look into the X.mat m betainc is filled witn NaN.

I have atteched my analysis info and X.mat.
Let me know if you need more informations about my analysis.

Best,

Tiago Mesquita
___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.