[Freesurfer] Extracting values from a single vertex

[Nillo, Ryan Michael R]

External Email - Use Caution

Hi FreeSurfer users,


I want to extract thickness values at a single vertex. I searched on the 
support list and found an mris_convert command to use. However, the file I want 
to extract values from is a volume with multiple frames. When I try to use 
mris_convert on it, I only got the value at a vertex on the first frame. The 
goal is to set that vertex as a seed point and use the values as a regressor 
for glm. Is there a way to do this with FreeSurfer's commandline tools, or 
should I do this in Matlab?


Mahalo,


Ryan M Nillo

Staff Research Associate I

UCSF Department of Radiology and Biomedical Imaging
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Re: [Freesurfer] mris_apply_reg failing for area/volume

[James Michael Roe]

External Email - Use Caution

Hi Bruce

I realise that my last message made it sound as though the problem was fixed. 
However, I was only confirming that the files load fine in freeview (are not 
corrupted) as asked. 
The issue of many subs area and volume files failing to register when using 
--jac is still unsolved

Appreciate the support.

Thanks

James 


From: James Michael Roe
Sent: 31 October 2018 19:45
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume

Hi Bruce

Can confirm that both files (rh.area & rh.volume) load fine in freeview

Thanks for the help!

James

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: 29 October 2018 15:43
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume

Hi James

can you verify that the various files (e.g.
/cluster/projects/p23/projects/Memory_Project/James/AgeSym/long_recons_FXhemi/010_NDev/1000409_02_10_02_11.long.base_1000409_11/surf/rh.area)

are intact by loading them into freeview? For the area file you will of
course have to load it as an overlay not as a surface (since it isn't a
surface)

cheers
Bruce
On Mon, 29 Oct 2018, James Michael Roe wrote:

>
> External Email - Use Caution
>
>
> ​Dear freesurfer experts
>
>
>
> I’m running the following commands to register RH area and volume files per 
> sub to both hemispheres
> of a symmetrical template following Xhemi routines.
>
> The commands have already worked for many subs, but are failing to write the 
> target file for a
> number of others (and all run fine without the –-jac flag)
>
>
> #right to left
>
> mris_apply_reg \
>
> --src $SUBJECTS_DIR/$sub/surf/rh.area \
>
> --trg $concatdir/rh.lh.area.${sub}.${template}.nii.gz \
>
> --streg $SUBJECTS_DIR/$sub/xhemi/surf/lh.${template}.sphere.reg
> $SUBJECTS_DIR/${template}/surf/lh.sphere.reg \
>
> --jac
>
>
>
> #right to right
>
> mris_apply_reg \
>
> --src $SUBJECTS_DIR/$sub/surf/rh.area \
>
> --trg $concatdir/rh.rh.area.${sub}.${template}.nii.gz \
>
> --streg $SUBJECTS_DIR/$sub/surf/rh.${template}.sphere.reg
> $SUBJECTS_DIR/${template}/surf/rh.sphere.reg \
>
> --jac
>
>
>
>
> The error is not template-specific as the output is the same using 
> fsaverage_sym
>
> Attached is the log file.
>
>
>
> Thanks in advance!
>
>
>
>
> ​- James
>
>

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Re: [Freesurfer] help with subjects concatenation/dimension inconsistency error

[Barletta, Valeria]

Oh yeah... That could actually be the problem!
Thank you so much!
Vale

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, November 05, 2018 4:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] help with subjects concatenation/dimension 
inconsistency error

Hi Valeria

that means there is a mismatch between the surface overlay and the surface.
Maybe you sampled:

/autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/Ctrl034_R01_07/surf/overlay/rh.T1_mp2rage_depth0.5_fwhm3.mgh

to the surface then recreated the surfaces after editing?

cheers
Bruce


On Mon, 5 Nov 2018, Barletta, Valeria wrote:

> Dear FreeSurfers,
> I am trying to apply surface processes to concatenate my cohort, but for some 
> subjects I am getting this error:
>
> mri_surf2surf --srcsubject Ctrl034_R01_07 --srchemi rh --srcsurfreg
> sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg
> --tval
> /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/T1/allSubj/tmp.mris_preproc.61312/Ctrl034_R01_07.18.mgh
> --sval
> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/Ctrl034_R01_07/surf/overlay/rh.T1_mp2rage_depth0.5_fwhm3.mgh
> --noreshape --no-cortex ERROR: dimension inconsistency in source data
>   Number of surface vertices = 138446
>   Number of value vertices = 137970
> Source registration surface changed to sphere.reg
> Target registration surface changed to sphere.reg
> srcsubject = Ctrl034_R01_07
> srcval = 
> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/Ctrl034_R01_07/surf/overlay/rh.T1_mp2rage_depth0.5_fwhm3.mgh
> srctype=
> trgsubject = fsaverage
> trgval = 
> /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/T1/allSubj/tmp.mris_preproc.61312/Ctrl034_R01_07.18.mgh
> trgtype=
> srcsurfreg = sphere.reg
> trgsurfreg = sphere.reg
> srchemi= rh
> trghemi= rh
> frame  = 0
> fwhm-in= 0
> fwhm-out   = 0
> label-src  = (null)
> label-trg  = (null)
> OKToRevFaceOrder  = 1
> Reading source surface reg 
> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/Ctrl034_R01_07/surf/rh.sphere.reg
> Loading source data
>
>
> And the script running stops immediately after. I already tried to relaunch 
> the-autorecon2 -autorecon3command for those subjects, since we 
> already had this kind of issue in the past, but it didn't work.
> Do you have any idea of what could be the problem?
> Thank you very much,
> Valeria
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>
>
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Re: [Freesurfer] ICV normalization (longitudinal pipeline)

[Martin Reuter]

Hi Martin,

ICV is head size. It is unlikely that anything except head growth in children 
changes head size. I don’t know of drugs that do that ;-). 

So it is best to assume that head size is fixed for adults. Usually results 
should have less variance if you remove the noise from the ICV estimate, thus 
smaller p-values. Not sure what happens in your case, but I would not trust 
that.

(also how large is your dataset, how far apart are the time points, and what 
kind of treatment will change head size??)

Best, Martin



> On 1. Nov 2018, at 16:13, Martin Juneja  wrote:
> 
> Hello FS experts,
> 
> I am using longitudinal processing pipeline 
> (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing 
> ) to 
> calculate the cortical volume (CV) over a course of treatment (two 
> conditions: pre condition and post condition). In fact, I am interested in 
> comparing normalized CV (NCV) i.e. raw CV/ ICV between pre- and 
> post-condition.
> 
> (1). Now, longitudinal pipeline assumes that there is no change in ICV so it 
> gives me identical ICV for pre and post condition. That way, when I compared 
> NCV between pre and post condition, it gives me differences at significant 
> level of 0.16.
> (2). However, when I checked ICV (from cross-sectional pipeline i.e. each 
> time-point separately) and compared between pre and post-conditions, ICV 
> values are different. Its possible that these values could be different 
> because of treatment (may be !). When I compared NCV between pre and post 
> condition (calculated by dividing raw CV from longitudinal pipeline with ICV 
> values form cross-sectional pipeline), it gives me significant differences at 
> 0.02.
> 
> Could you please share your thoughts on this i.e. (a) whether I can use 
> approach 2 or (b) if I am using longitudinal pipeline, dividing raw CV from 
> longitudinal pipeline and dividing by ICV calculated from cross-sectional is 
> in correct way to do this analysis?
> 
> Thanks.
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Re: [Freesurfer] Triangular mesh sampling problem

[Bruce Fischl]

Hi yujunjie

we have code interenally that will do what you are asking, but no binary, 
sorry. You could download our source code and try to write your own, 
although it will be a bit of a project.


cheers
Bruce
On Tue, 6 Nov 2018, 1013364183 
wrote:




External Email - Use Caution

Dear FS
We now have high and low resolution images, we want to resample each triangular 
surface mesh
generated from low-resolution data onto the corresponding triangular surface 
mesh generated from
high-resolution data and vice versa as follows: For every vertex in a 
low-resolution surface mesh we
found the closest point on the high-resolution surface mesh (which typically 
fell within a triangle
face of the mesh), and defined a point at that location on the high-resolution 
surface mesh
(subsequently referred to as ??sparse?? meshes).What should we do to use 
freesurfer to do the above?

Thanks in advance

yours yujunjie

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Re: [Freesurfer] ?????? Recon-all run error

[Bruce Fischl]

does it occur if you run it outside of recon-all? Do you have enough free 
ram? If so, you can filedrop us the dataset and we can try to replicate and 
fit ix.


On Tue, 6 Nov 2018, 1013364183 wrote:



External Email - Use Caution

Dear Bruce,
  I found the error location in the recon-all.log folder. Here is the place 
where it went wrong??I
don't think it's the reason for insufficient memory..
  ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz % 4 == 0' 
failed.''
  This data is ok when we run with versions prior to freesurfer 6.0. But after 
we run the 6.0
version and set the expert file, this error will occur.Do I need to step 
through the instructions to
see the problem? How should this error be solved?

Thanks in advance

yours yujunjie

--  --
??: "Bruce Fischl";
: 2018??11??6??(??) 9:40
??: "Freesurfer support list";
: Re: [Freesurfer] Recon-all run error

that certainly looks like something is running out of ram. Can you run
the command that failed directly on the command line and see if it works?
Was anything else running on the machine at the time? We do report total
and free memory at the start of the recon in the recon-all.log file

cheers
Bruce
On Tue,
6 Nov 2018, 1013364183 wrote:

>
> External Email - Use Caution
>
> Dear FS,
> When we run ??recon-all?? with a 5GB high-resolution image, core dumped 
appears when the
mri_convert
> command is executed. The specific errors are as follows:
> /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: 29235 
Aborted (core dumped)
> mri_convert.bin "$@"
> ERROR: converting to minc
> We want to know if our high resolution image is too large for freesurfer to 
handle, or our
computer
> memory (64GB running memory) is limited.
>
> Thanks a lot in advance!
> yours sincerely,
> yu junjie
>
>
>
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Re: [Freesurfer] Desikan Atlas in volume space (ece ulug)

[Mcnorgan, Christopher]

External Email - Use Caution

Hi Ece,

I believe you will find a walkthrough of the steps to do exactly what you want 
done on my lab wiki:

http://ccnlab.psy.buffalo.edu/wiki/index.php/Annotation_Coordinates

Hope this helps,
Chris

/**
* Chris McNorgan
* Assistant Professor
* Department of Psychology
* University at Buffalo,
* The State University of New York
* http://ccnlab.buffalo.edu/
* Office: 716.645.0236
* Lab: 716.645.0222
**/

On Nov 6, 2018, at 12:00 PM, 
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Today's Topics:

  1. Ynt:  Ynt:  ?lt: Desikan Atlas in volume space (ece ulug)

From: ece ulug mailto:eceulu...@hotmail.com>>
Subject: [Freesurfer] Ynt: Ynt: İlt: Desikan Atlas in volume space
Date: November 6, 2018 at 6:37:17 AM EST
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>


External Email - Use Caution

Exactly. I cannot find in this file but i found lh.aparc.label and 
lh.aparc.annot files in freesurfer/subjects/fsaverage/label. Actually i told in 
my previous message. I need coordinates for generate caudalanteriorcingulate 
mask in coordinate system.




Gönderen: Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> adına 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
Gönderildi: 6 Kasım 2018 Salı 00:45
Kime: Freesurfer support list
Konu: Re: [Freesurfer] Ynt: İlt: Desikan Atlas in volume space

I don't think there is an lh.aparc.label file - I don't know what it
would be if it existed.

Maybe we can take a step back and you can let us know what you are trying
to achieve?

On Mon, 5 Nov 2018, ece ulug wrote:

>
> External Email - Use Caution
>
> Thanks for your reply doctor. Actually I want to access Desikan K. Atlas 
> coordinates as  x, y, z.
> (each regions. for example caudalanteriorcingulate).
>
>
> In that case, one expert said that ; the closest to what you want is probably
> $FREESURFER_HOME/subjects/fsaverage/surf/lh.aparc.label. You can open it with 
> a text editor. Then
> you should cross-check with 
> $FREESURFER_HOME/subjects/fsaverage/surf/lh.aparc.annot for the actual
> labels of those vertices. The .annot file can be opened in Matlab with the 
> read_annotation command
> from FreeSurfer.
>
>
> What do you recommend?
> Ece
>
> 
> Gönderen: Bruce Fischl 
> mailto:fis...@nmr.mgh.harvard.edu>> adına 
> freesurfer-boun...@nmr.mgh.harvard.edu
> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
> Gönderildi: 5 Kasım 2018 Pazartesi 20:18
> Kime: Freesurfer support list
> Konu: Re: [Freesurfer] İlt: Desikan Atlas in volume space
> Hi Ece
>
> for a given subject the Desikan parcellation is sampled into the volume
> alread in the file aparc+aseg.mgz in the subject's mri dir. Is that what
> you are looking for?
>
> cheers
> Bruce
>
> On Mon, 5 Nov 2018, ece ulug wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear Experts,
> >
> >
> > I am very beginner in Freesurfer, and I want to use 'read_annotation'
> > function but i don't know what is the next step. I added the Matlab
> > screenshoot.
> >
> >
> > Additionally; 'read_curv' function don't work in Matlab. I added it.
> >
> >
> > Thanks in advance
> >
> > Ece
> >
> >
> >
> >
>
>


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[Freesurfer] Ynt: Ynt: İlt: Desikan Atlas in volume space

[ece ulug]

External Email - Use Caution

Exactly. I cannot find in this file but i found lh.aparc.label and 
lh.aparc.annot files in freesurfer/subjects/fsaverage/label. Actually i told in 
my previous message. I need coordinates for generate caudalanteriorcingulate 
mask in coordinate system.




Gönderen: Bruce Fischl  adına 
freesurfer-boun...@nmr.mgh.harvard.edu 
Gönderildi: 6 Kasım 2018 Salı 00:45
Kime: Freesurfer support list
Konu: Re: [Freesurfer] Ynt: İlt: Desikan Atlas in volume space

I don't think there is an lh.aparc.label file - I don't know what it
would be if it existed.

Maybe we can take a step back and you can let us know what you are trying
to achieve?

On Mon, 5 Nov 2018, ece ulug wrote:

>
> External Email - Use Caution
>
> Thanks for your reply doctor. Actually I want to access Desikan K. Atlas 
> coordinates as  x, y, z.
> (each regions. for example caudalanteriorcingulate).
>
>
> In that case, one expert said that ; the closest to what you want is probably
> $FREESURFER_HOME/subjects/fsaverage/surf/lh.aparc.label. You can open it with 
> a text editor. Then
> you should cross-check with 
> $FREESURFER_HOME/subjects/fsaverage/surf/lh.aparc.annot for the actual
> labels of those vertices. The .annot file can be opened in Matlab with the 
> read_annotation command
> from FreeSurfer.
>
>
> What do you recommend?
> Ece
>
> 
> Gönderen: Bruce Fischl  adına 
> freesurfer-boun...@nmr.mgh.harvard.edu
> 
> Gönderildi: 5 Kasım 2018 Pazartesi 20:18
> Kime: Freesurfer support list
> Konu: Re: [Freesurfer] İlt: Desikan Atlas in volume space
> Hi Ece
>
> for a given subject the Desikan parcellation is sampled into the volume
> alread in the file aparc+aseg.mgz in the subject's mri dir. Is that what
> you are looking for?
>
> cheers
> Bruce
>
> On Mon, 5 Nov 2018, ece ulug wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear Experts,
> >
> >
> > I am very beginner in Freesurfer, and I want to use 'read_annotation'
> > function but i don't know what is the next step. I added the Matlab
> > screenshoot.
> >
> >
> > Additionally; 'read_curv' function don't work in Matlab. I added it.
> >
> >
> > Thanks in advance
> >
> > Ece
> >
> >
> >
> >
>
>
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