Re: [Freesurfer] Infant Freesurfer exiting without error

[Zollei, Lilla,Ph.D.]

I included the list of FS labels with their IDs. When you know the 
correspondences, you should be able to use scripts / FS commands to change the 
labels automatically.
Lila

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of COLLEEN PLETCHER 

Sent: Tuesday, May 11, 2021 4:28 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Infant Freesurfer exiting without error


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Hello,

Getting a list of the labels would be fantastic! Also, when relabeling the 
segmentations, do you normally just do that by hand?

Thanks so much,

Colleen

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Sent: Thursday, May 6, 2021 4:14 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Infant Freesurfer exiting without error

Hi Colleen,
The segmentations just need to be relabled in order to match the labels that 
are produced by the infantFS pipeline. I am happy to send you a list of lables 
that get generated by our tool and then you can match those up with the ones 
that you get with FSL.
Best, Lilla

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of COLLEEN PLETCHER 

Sent: Tuesday, April 27, 2021 4:11 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Infant Freesurfer exiting without error


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Hi,

I was using FSL anat in order to do the initial segmentation for the --segfile 
input. I am not sure how to put FS aseg labels in something that is not a 
freesurfer aseg file. Can you offer any advice on how to do this?

Thanks so much for the help!

-Colleen

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Sent: Saturday, April 24, 2021 2:14 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Infant Freesurfer exiting without error

Hi Colleen,
Do you have all the FS aseg lables in your input segmentation file?
Lilla

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of COLLEEN PLETCHER 

Sent: Friday, April 23, 2021 3:01 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Infant Freesurfer exiting without error


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Hi,

Just checking in about this question. Please let me know if you need anything 
else from me!

Thanks,

Colleen

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of COLLEEN PLETCHER 

Sent: Tuesday, April 13, 2021 12:48 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Infant Freesurfer exiting without error


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Hello,

I have attached the log file and the command used is the first line, please let 
me know if you need anything else.

-Colleen

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Sent: Tuesday, April 13, 2021 12:33 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Infant Freesurfer exiting without error

Hi Colleen,

 Can you send the exact command that you used and also the log file for more 
information?

Best, Lilla

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of COLLEEN PLETCHER 

Sent: Tuesday, April 13, 2021 1:29 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Infant Freesurfer exiting without error


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Hi,

I am trying to run infant freesurfer using the --segfile and --masked options. 
When I attempt to run it, it runs for a bit and then I get this:


USAGE: mri_or   fname1 fname2 ..



After this, the program exits. I am not getting any error, so I am confused 
about why it is exiting suddenly?


Thank you very much!


-Colleen


FSinfant.xls
Description: FSinfant.xls
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[Freesurfer] how to visualize statistical maps in FS7.1?

[Bernardoni, Fabio]

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Dear Freesurfers

I recently moved to FS7.1 and I was trying to reproduce my workflow I had with 
FS5.3.

To visualize statistical maps, I had always used tksurfer. It seems, however, 
it is no longer maintained. 

When I launch it it fails to find out the tix, tcl, etc libraries. Following 
this thread:
https://secure-web.cisco.com/1v7sQGKZgCQ9d6BT0fUpIf9QvmP5selhkoGYWs1-X9TSsF6ebf9WkfXQKwNGkJnbQTNihRlUwkt3d_MtgGepc7G9MM_ZkCKisZX1hKBJ9twis_mX1rWvKXW84_u67FO-1Nf-Nw0XV4e4TaksCUTJbLoVykRInrujR5kv4RuP668hB4uZuRSUTzw5Wv0cdJpuX2G2CxoXrNGsfZPGI9wEQy2xuY0fWpzXbjw3A6IN30dlVGcFiz2RxbN4DmxS9mgJACyaWUAW4XrSh_mrEyukmaw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg66219.html

I tried to use tksurferfv.  However, when trying to overlay the sig.mgh output 
of mriglmfit, on an inflated fsaverage surface, the program shuts down, with 
this error:

freeview -f 
/usr/local/freesurfer/subjects/fsaverage/surf/lh.inflated:curvature=/usr/local/freesurfer/subjects/fsaverage/surf/lh.curv
 -viewport 3d
terminate called after throwing an instance of 'int'
Abort (core dumped)





What would you suggest to visualize statistical maps in FS7? Is my problem 
expected?

Thank you in advance for your attention

Fabio


Dr. Fabio Bernardoni
wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences
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Re: [Freesurfer] Απ: volume ROI to surface for cortical thickness

[M Pope]

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Hi Douglas,

I have a follow-up question regarding vol2surf. What is the best practice for 
quality control and checking the surface rendering of the ROI? Are there any 
protocols or suggestions? As slight changes in projfrac change the output by a 
large degree, it's difficult to assess what is the closest to the orginal 
volume ROI.

Thanks
Marianna

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: 10 May 2021 4:36 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Απ: volume ROI to surface for cortical thickness

For when your ROI is in fsaverage (or MNI152) space.

On 5/10/2021 12:34 PM, M Pope wrote:

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The labels are derived from ASHS- but yes they are registered to each subject 
seperately. Could I ask then what the tutorial refers to- for future reference? 
When is it best to go through fsaverage?

Thank you for the information

BW,
Marianna



Από: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 εκ μέρους του Douglas N. Greve 

Στάλθηκε: Δευτέρα, 10 Μαΐου 2021 4:30 μμ
Προς: freesurfer@nmr.mgh.harvard.edu 

Θέμα: Re: [Freesurfer] volume ROI to surface for cortical thickness

did you draw the labels on each subject separately? In that case there is no 
need to go through fsaverage.
Projfrac is the fractional distance between the white and pial surfaces (0.5 is 
half way)
projdist is the absolute distance (eg, 1.5 is 1.5mm)
Generally projfrac is preferred as it adapts to changes in thickness
In your case, you might want to use --projfrac-max where it will look over a 
range of projfrac values for the maximum. This might make your maps look better 
because it will be sampling the label or nothing.

On 5/10/2021 12:25 PM, M Pope wrote:

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Dear Freesurfer experts,



I have created volumetric ROIs of entorhinal cortex regions and have registered 
them to subjects’ native space (T1). I now wish to register them to the subject 
surface in order to get information such as cortical thickness- using 
mri_vol2surf and mri_segstats I believe.



I was looking at your tutorial regarding this VolumeRoiCorticalThickness - Free 
Surfer Wiki 
(harvard.edu)
 and had a few questions.

First of all- could you explain why you are going through fsaverage. Is there 
some kind of advantage to doing this procedure of registration, mri_vol2surf 
and then mri_surf2surf rather than just using mri_vol2surf with the subject 
space as the regheader?? When I tried through fsaverage as explained in the 
tutorial (following the exact same commands) the ROI appeared wrong in the 
surface and the thickness stats were incorrect.

Secondly, when doing the procedure as per the tutorial, do you mean that we 
have to register each subject's mask to the fsaverage- or only one, e.g a ROI 
derived from the subject-specific group template (we have one produced through 
ANTs).

Lastly- some explanation about how projfrac and projdist work would be very 
helpful. What numbers are considered best practice?



Thankyou,

Marianna Pope




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Re: [Freesurfer] Sulcal probability maps

[Fischl, Bruce]

Yes, if you store the pvals in the label file you can do this in freeview. 
Ruopeng: can you provide some instructions on this?
Thanks
Bruce

On May 12, 2021, at 7:28 PM, Kristi Drudik  
wrote:



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Hi Bruce,

Thanks to you help I was able to create surface probability maps of the 
likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the 
sulcus of interest (from 0% to 100%) (see attachment).

I have a quick question. Is there a way to represent this average .label file 
using a heat colour scale (as when you configure an overlay), where the least 
likely vertices are drawn in blue and the most likely vertices are drawn in red?

Thank you very much for your help!

Best,
Kristi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Fischl, Bruce
Sent: February 26, 2021 4:59 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Sulcal probability maps

mris_spherical_average will use the surface-based registration (?h.sphere.reg) 
to map the labels to whatever your output subject is and do the averaging in 
that space. You can specify fsaverage by -o fsaverage on the 
mris_spherical_average command line. You shouldn’t need to do anything other 
than draw the labels on the natives surface prior to running it

cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Kristi Drudik
Sent: Friday, February 26, 2021 4:20 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Sulcal probability maps


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My apologies, Bruce, now I’m more confused. We paint the sulci on the native 
surfaces in Freeview. Then we register them to fsaverage. We want to register 
them to fsaverage because we are interested in creating an average map that 
would represent the likelihood of each vertex on the FreeSurfer fsaverage 
surface belonging to the sulcus of interest (from 0% to 100%).

In brief, we can do this by converting the label registered to fsaverage to a 
volume (mri_label2vol) then to surface (mri_vol2surf) and adding the subjects 
together with mri_concat.

What I am wondering: Is there a more direct way to create probability per 
vertex maps using labels that have been registered to fsaverage?


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Fischl, Bruce
Sent: February 26, 2021 3:45 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Sulcal probability maps

Oh yes, that is your problem. mris_spherical_average assumes they are in 
subject space

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Kristi Drudik
Sent: Friday, February 26, 2021 2:52 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Sulcal probability maps


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It does not work when I load to the subject (see attachment).  I might add that 
the .label files that I am using originally have already been registered to 
fsaverage. Does that make a difference?


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Fischl, Bruce
Sent: February 26, 2021 2:46 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Sulcal probability maps

Can you load the label onto that subject also?

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Kristi Drudik
Sent: Friday, February 26, 2021 2:37 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Sulcal probability maps


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Hi Bruce,

I tried the command on one subject. The output does look like the input, 
however there vertices being picked up that shouldn’t be.

I’m working the Human Connectome Project data so I did not run recon-all myself.

Best,
Kristi

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Fischl, Bruce
Sent: February 26, 2021 12:28 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Sulcal probability maps

can you send the full screen output as text? Also, try it on 1 subject first. 
The output should look like the input. Generally this error means some of your 
surfaces are out of date (