[Freesurfer] seed to seed replica of fsfast

[Lee, Erik Gordon]

Hi All,

I am trying to do some seed to seed functional connectivity calculations that 
replicate my analysis design in fsfast. I know FreeSurfer 6 has the fcseedcor 
function, but it appears that this requires a low pass filter, which is not a 
part of our processing stream. Also I don't think the fcseedcor function has 
any detrending which is a part of our analysis.

I am putting together a Matlab script to do this for me, and want to be sure 
that the steps are equivalent.

This is my normal mkanalysis-sess command:

mkanalysis-sess -analysis targ.2cm.rh -surface fsaverage rh -fwhm 6 -notask 
-taskreg target_2cm.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg 
-polyfit 5 -fsd rest -TR 3 -per-run -hpf .01 -tpexclude tpe_file -nuisreg 
global.waveform.dat 1

This is what I am doing in Matlab:

-First, I apply a polynomial detrending to all the seeds and nuisance 
regressors (first five components from vcsf and wm, first three from mcextreg, 
and one component of global signal), while ignoring any bad timepoints.
-Second, I make all signals evenly sampled again by applying a linear 
interpolation over missing timepoints for both the seeds and nuisance 
regressors.
-Third, I apply a high order high pass filter.
-Fourth, I get rid of all the timepoints that were generated from the linear 
interpolation (now post filtering).
-Fifth, I use a glm to regress all the nuisance variables from the ROI signals.
-Sixth compute the correlation coefficients between seeds using the residuals 
from the previous step.

How similar is that to what is done in fsfast? Any tips on what to change?

Thanks!
Erik
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[Freesurfer] Cropping of slices during recon-all

[Jerry Jeyachandra]

Hi Freesurfer team,

I have a compressed nifti file converted from DICOM that I am running through 
recon-all. From my understanding first mri_convert is run on the original nifti 
file in order to generate 001.mgz which is then averaged across multiple runs 
to make rawavg.mgz. Since I'm only using 1 run, rawavg.mgz should be equivalent 
to 001.mgz. Now I've noticed that compared to simply loading in the original 
NIFTI image, loading in rawavg.mgz produces a cropped version of the image 
where the bottom section (neck region and below) is cropped out. In addition 
the SI axis which used to be 255 voxels in height, is now shorter (different 
across individuals run through recon-all). With a set of voxel indices in the 
original NIFTI image, I'd like to find a corresponding set of voxel indices in 
the cropped rawavg.mgz. Does FreeSurfer store any information related to the 
cropping that is done, I expect that there is only a translational shift in the 
SI axis but I'd like to automatically extract this value for each individual 
I've run through recon-all.

Thanks,
Jerrold Jeyachandra
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Re: [Freesurfer] substract images

[John Anderson]

Fantastic!!

It is worked. Thank you very much for the great help!


 

Sent: Thursday, June 15, 2017 at 1:51 PM
From: "Bruce Fischl" 
To: "Freesurfer support list" 
Subject: Re: [Freesurfer] substract images

try:

mri_binarize mask.nii --min 0 --max .1 --o mask.rev.nii --binval 1
mri_mask T1.nii mask.rev.nii T1.masked.nii

cheers
Bruce

On Thu, 15 Jun 2017, John Anderson wrote:

> Hi Bruce, the mask is already binariz (min=0 ; max=1)
> I tried
> mri_mask T1.nii mask.nii output.nii
>  
> The output is a maked image meaning the structure behind the mask
>  
> I tried mri_binarize mask.nii --min 0 --max 1 output mask.nii then 
> mri_mask T1.nii output_mask.nii output.nii
>  
> And I still get the same output. What in behind the mask and what I want is
> T1 free of what in the mask. I am not sure what I am doing wrong. My
> appologies for asking to many times.
>  
>  
>  
>   Sent: Thursday, June 15, 2017 at 1:32 PM
> From: "Bruce Fischl" 
> To: "Freesurfer support list" 
> Subject: Re: [Freesurfer] substract images
> Hi Jon
>
> use mri_binarize on your initial mask to create a new one for mri_mask (use
> --min and --max to specify the input mask intensity ranges that you want to
> be "on"), then give that to mri_mask
>
> cheers
> Bruce
> On Thu, 15 Jun 2017, John Anderson wrote:
>
> > Thank you Dr Bruce
> >
> > mri_mask removes everything and leaves the areas behind the mask. And what
> I
> > want is the opposite.
> > For example with mri_mask if I have brain with skull and mask for skull
> > stripped brain then the output is skull stripped brain. What I want is the
> > opposite, the skull without the brain. I highly aprreciate any
> suggestion. 
> >   Sent: Thursday, June 15, 2017 at 1:19 PM
> > From: "Bruce Fischl" 
> > To: "Freesurfer support list" 
> > Subject: Re: [Freesurfer] substract images
> > Hi Jon
> >
> > mri_mask should do the trick
> >
> > cheers
> > Bruce
> > On Thu, 15 Jun 2017, John Anderson wrote:
> >
> > > Dear experts,
> > > I have image and mask and I want to subtract the mask from the image.
> > > Meaning I want to get image free of specific anatomical region. For
> > example,
> > >
> > > I have image T1.nii for the brain and mask for the thalamus. How can I
> > > remove the thalamus from the T1 image to get T1 image free of the
> > thalamus.
> > > Thanks you for any help
> > > Jon
> > >
> > >___
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> >
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Re: [Freesurfer] substract images

[Bruce Fischl]

try:

mri_binarize mask.nii --min 0 --max .1 --o mask.rev.nii --binval 1
mri_mask T1.nii mask.rev.nii T1.masked.nii

cheers
Bruce

On Thu, 15 Jun 2017, John Anderson wrote:


Hi Bruce, the mask is already binariz (min=0 ; max=1)
I tried
mri_mask T1.nii mask.nii output.nii
 
The output is a maked image meaning the structure behind the mask
 
I tried mri_binarize mask.nii --min 0 --max 1 output mask.nii then 
mri_mask T1.nii output_mask.nii output.nii
 
And I still get the same output. What in behind the mask and what I want is
T1 free of what in the mask. I am not sure what I am doing wrong. My
appologies for asking to many times.
 
 
 
  Sent: Thursday, June 15, 2017 at 1:32 PM
From: "Bruce Fischl" 
To: "Freesurfer support list" 
Subject: Re: [Freesurfer] substract images
Hi Jon

use mri_binarize on your initial mask to create a new one for mri_mask (use
--min and --max to specify the input mask intensity ranges that you want to
be "on"), then give that to mri_mask

cheers
Bruce
On Thu, 15 Jun 2017, John Anderson wrote:

> Thank you Dr Bruce
>
> mri_mask removes everything and leaves the areas behind the mask. And what
I
> want is the opposite.
> For example with mri_mask if I have brain with skull and mask for skull
> stripped brain then the output is skull stripped brain. What I want is the
> opposite, the skull without the brain. I highly aprreciate any
suggestion. 
>   Sent: Thursday, June 15, 2017 at 1:19 PM
> From: "Bruce Fischl" 
> To: "Freesurfer support list" 
> Subject: Re: [Freesurfer] substract images
> Hi Jon
>
> mri_mask should do the trick
>
> cheers
> Bruce
> On Thu, 15 Jun 2017, John Anderson wrote:
>
> > Dear experts,
> > I have image and mask and I want to subtract the mask from the image.
> > Meaning I want to get image free of specific anatomical region. For
> example,
> >
> > I have image T1.nii for the brain and mask for the thalamus. How can I
> > remove the thalamus from the T1 image to get T1 image free of the
> thalamus.
> > Thanks you for any help
> > Jon
> >
> >___
> 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 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] substract images

[John Anderson]

Hi Bruce, the mask is already binariz (min=0 ; max=1)

I tried

mri_mask T1.nii mask.nii output.nii

 

The output is a maked image meaning the structure behind the mask

 

I tried mri_binarize mask.nii --min 0 --max 1 output mask.nii then 

mri_mask T1.nii output_mask.nii output.nii

 

And I still get the same output. What in behind the mask and what I want is T1 free of what in the mask. I am not sure what I am doing wrong. My appologies for asking to many times.

 

 

 


 

Sent: Thursday, June 15, 2017 at 1:32 PM
From: "Bruce Fischl" 
To: "Freesurfer support list" 
Subject: Re: [Freesurfer] substract images

Hi Jon

use mri_binarize on your initial mask to create a new one for mri_mask (use
--min and --max to specify the input mask intensity ranges that you want to
be "on"), then give that to mri_mask

cheers
Bruce
On Thu, 15 Jun 2017, John Anderson wrote:

> Thank you Dr Bruce
>
> mri_mask removes everything and leaves the areas behind the mask. And what I
> want is the opposite.
> For example with mri_mask if I have brain with skull and mask for skull
> stripped brain then the output is skull stripped brain. What I want is the
> opposite, the skull without the brain. I highly aprreciate any suggestion. 
>   Sent: Thursday, June 15, 2017 at 1:19 PM
> From: "Bruce Fischl" 
> To: "Freesurfer support list" 
> Subject: Re: [Freesurfer] substract images
> Hi Jon
>
> mri_mask should do the trick
>
> cheers
> Bruce
> On Thu, 15 Jun 2017, John Anderson wrote:
>
> > Dear experts,
> > I have image and mask and I want to subtract the mask from the image.
> > Meaning I want to get image free of specific anatomical region. For
> example,
> >
> > I have image T1.nii for the brain and mask for the thalamus. How can I
> > remove the thalamus from the T1 image to get T1 image free of the
> thalamus.
> > Thanks you for any help
> > Jon
> >
> >___
> 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 Partners Compliance
> HelpLine at
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> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
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Re: [Freesurfer] Freesurfer parcelations of cortical regions in TrackVis

[Lilla Zollei]

Hi Cris,
As long as your parcellation file gets resampled into the diffusion space, 
you should not have any trouble reading it into TrackVis. When defining 
ROIs you can just select individual label values afterwards.

Lilla

On Thu, 15 Jun 2017, Leyton Moscoso, Cristian Eduardo wrote:


Hi Freesurfer’s and TrackVis experts

I am wondering if there is a way to import cortical parcelations mapped on a T1 
image in TrackVis.  I tried loading segmentation in TrackVis, but this does not 
allow me to see all parcelations in T1 as I can be done in Freeview. In 
TrackVis I need to upload them one by one. 

Thank you

Cris


Dr Cristian Leyton M Research Fellow in Neurology
Department of Neurology
Massachusetts General Hospital
Harvard Medical School
149  13th Street
Charlestown, MA 02129

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Re: [Freesurfer] viewing 3D surfaces

[Bruce Fischl]

seems like that is a good start


On Thu, 15 Jun 2017, Michael Davies wrote:



Thank you for your help Bruce. I have downloaded Unix_tutorial_FS_course. Is
there any others you could recommend?


Michael





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

Sent: 15 June 2017 17:03:19
To: Freesurfer support list
Subject: Re: [Freesurfer] viewing 3D surfaces  
I mean the /surf/lh.pial path has to be wrong, as that points to the root
where you wouldn't be allowed to put data. I guess surf/ worked for you,
but would only work if you were in the $SUBJECTS_DIR/$subject dir when you
issued the freeview command.

cheers
Bruce


On Thu, 15 Jun 2017, Michael
Davies wrote:

>
> Hello Bruce, how do you mean the path is wrong? I am curious as the data
> loaded just.
>
>
> Kind regards, Michael
>
>___
_
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Bruce Fischl
> 
> Sent: 15 June 2017 16:11:53
> To: Freesurfer support list
> Subject: Re: [Freesurfer] viewing 3D surfaces  
> Hi Michael
>
> I think you need to do a Unix tutorial. That path is wrong.
>
> cheers
> Bruce
>
>
> On Thu, 15 Jun
> 2017, Michael Davies wrote:
>
> >
> > Hi Bruce, i'm getting closer to opening it now. But the final command
> > /surf/lh.pial \ didnt work this time. Any further suggestions?
> >
> >
> > Kind regards, Michael
> >
> >
> > bash-4.1$ freesurfer_setup_freeview
> >  freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> 
> > Setting up environment for FreeSurfer/FS-FAST (and FSL)
> > FREESURFER_HOME   /usr/local/freesurfer_v6.0.0
> > FSFAST_HOME   /usr/local/freesurfer_v6.0.0/fsfast
> > FSF_OUTPUT_FORMAT nii.gz
> > SUBJECTS_DIR  /usr/local/freesurfer_v6.0.0/subjects
> > MNI_DIR   /usr/local/freesurfer_v6.0.0/mni
> > FSL_DIR   /usr/local/fsl
> > bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage
> > bash-4.1$ freeview -f \
> > > /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
>>>/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=infl
a
> t
> > ed_thickness:visible=0 \
> > > /surf/lh.inflated:visible=0 \
> > > /surf/lh.white:visible=0 \
> > > /surf/lh.pial \
> > > --viewport 3d
> > MRISread(/surf/lh.pial): could not open file
> > No such file or directory
> > MRISread failed
> > No such file or directory
> > ould not open file
> > bash-4.1$
> >
>>__
_
> _
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
> >  on behalf of Bruce Fischl
> > 
> > Sent: 15 June 2017 15:19:21
> > To: Freesurfer support list
> > Subject: Re: [Freesurfer] viewing 3D surfaces  
> > you are not calling freeview in this command. Try putting freeview at
the
> > start
> > On Thu, 15 Jun 2017, Michael Davies wrote:
> >
> > >
> > > Hi Bruce, i am still getting error messages. is there anything else i
> > could
> > > try doing?
> > >
> > > Kind regards, Michael
> > >
> > >
> > > bash-4.1$ freesurfer_setup_freeview
> > >  freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> > 
> > > Setting up environment for FreeSurfer/FS-FAST (and FSL)
> > > FREESURFER_HOME   /usr/local/freesurfer_v6.0.0
> > > FSFAST_HOME   /usr/local/freesurfer_v6.0.0/fsfast
> > > FSF_OUTPUT_FORMAT nii.gz
> > > SUBJECTS_DIR  /usr/local/freesurfer_v6.0.0/subjects
> > > MNI_DIR   /usr/local/freesurfer_v6.0.0/mni
> > > FSL_DIR   /usr/local/fsl
> > > bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage
> > > bash-4.1$ /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inf
l
> a
> > t
> > > ed_thickness:visible=0 \
> > > > /surf/lh.inflated:visible=0 \
> > > > /surf/lh.white:visible=0 \
> > > > /surf/lh.pial \
> > > > --viewport 3d
> > > bash: /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0: No
such
> > > file or directory
> > > bash-4.1$
> > >
> > >
> > >
>>>_
_
> _
> > _
> > > From: freesurfer-boun...@nmr.mgh.harvard.edu
> > >  on behalf of Bruce Fischl
> > > 
> > > Sent: 15 June 2017 14:11
> > > To: Freesurfer support list
> > > Subject: Re: [Freesurfer] viewing 3D surfaces  
> > > Hi Michael
> > >
> > > you need to have FreeSurfer in your path or nothing will work. Have
you
> > > sourced the FreeSurferEnv.sh file? Have you set FREESURFER_HOME in the
> > > environment?
> > >
> > > cheers
> > > Bruce
> > >
> > >
> > > On Thu, 15 Jun 2017, Michael Davies wrote:
> > >
> > > > 

Re: [Freesurfer] substract images

[Bruce Fischl]

Hi Jon

use mri_binarize on your initial mask to create a new one for mri_mask (use 
--min and --max to specify the input mask intensity ranges that you want to 
be "on"), then give that to mri_mask


cheers
Bruce
 On Thu, 15 Jun 2017, John Anderson wrote:


Thank you Dr Bruce

mri_mask removes everything and leaves the areas behind the mask. And what I
want is the opposite.
For example with mri_mask if I have brain with skull and mask for skull
stripped brain then the output is skull stripped brain. What I want is the
opposite, the skull without the brain. I highly aprreciate any suggestion. 
  Sent: Thursday, June 15, 2017 at 1:19 PM
From: "Bruce Fischl" 
To: "Freesurfer support list" 
Subject: Re: [Freesurfer] substract images
Hi Jon

mri_mask should do the trick

cheers
Bruce
On Thu, 15 Jun 2017, John Anderson wrote:

> Dear experts,
> I have image and mask and I want to subtract the mask from the image.
> Meaning I want to get image free of specific anatomical region. For
example,
>
> I have image T1.nii for the brain and mask for the thalamus. How can I
> remove the thalamus from the T1 image to get T1 image free of the
thalamus.
> Thanks you for any help
> Jon
>
>___
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http://www.partners.org/complianceline . If the e-mail was sent to you in
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Re: [Freesurfer] viewing 3D surfaces

[Michael Davies]

Thank you for your help Bruce. I have downloaded Unix_tutorial_FS_course. Is 
there any others you could recommend?


Michael





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

Sent: 15 June 2017 17:03:19
To: Freesurfer support list
Subject: Re: [Freesurfer] viewing 3D surfaces

I mean the /surf/lh.pial path has to be wrong, as that points to the root
where you wouldn't be allowed to put data. I guess surf/ worked for you,
but would only work if you were in the $SUBJECTS_DIR/$subject dir when you
issued the freeview command.

cheers
Bruce


On Thu, 15 Jun 2017, Michael
Davies wrote:

>
> Hello Bruce, how do you mean the path is wrong? I am curious as the data
> loaded just.
>
>
> Kind regards, Michael
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Bruce Fischl
> 
> Sent: 15 June 2017 16:11:53
> To: Freesurfer support list
> Subject: Re: [Freesurfer] viewing 3D surfaces
> Hi Michael
>
> I think you need to do a Unix tutorial. That path is wrong.
>
> cheers
> Bruce
>
>
> On Thu, 15 Jun
> 2017, Michael Davies wrote:
>
> >
> > Hi Bruce, i'm getting closer to opening it now. But the final command
> > /surf/lh.pial \ didnt work this time. Any further suggestions?
> >
> >
> > Kind regards, Michael
> >
> >
> > bash-4.1$ freesurfer_setup_freeview
> >  freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> 
> > Setting up environment for FreeSurfer/FS-FAST (and FSL)
> > FREESURFER_HOME   /usr/local/freesurfer_v6.0.0
> > FSFAST_HOME   /usr/local/freesurfer_v6.0.0/fsfast
> > FSF_OUTPUT_FORMAT nii.gz
> > SUBJECTS_DIR  /usr/local/freesurfer_v6.0.0/subjects
> > MNI_DIR   /usr/local/freesurfer_v6.0.0/mni
> > FSL_DIR   /usr/local/fsl
> > bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage
> > bash-4.1$ freeview -f \
> > > /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
> >>/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=infla
> t
> > ed_thickness:visible=0 \
> > > /surf/lh.inflated:visible=0 \
> > > /surf/lh.white:visible=0 \
> > > /surf/lh.pial \
> > > --viewport 3d
> > MRISread(/surf/lh.pial): could not open file
> > No such file or directory
> > MRISread failed
> > No such file or directory
> > ould not open file
> > bash-4.1$
> >
> >___
> _
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
> >  on behalf of Bruce Fischl
> > 
> > Sent: 15 June 2017 15:19:21
> > To: Freesurfer support list
> > Subject: Re: [Freesurfer] viewing 3D surfaces
> > you are not calling freeview in this command. Try putting freeview at the
> > start
> > On Thu, 15 Jun 2017, Michael Davies wrote:
> >
> > >
> > > Hi Bruce, i am still getting error messages. is there anything else i
> > could
> > > try doing?
> > >
> > > Kind regards, Michael
> > >
> > >
> > > bash-4.1$ freesurfer_setup_freeview
> > >  freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> > 
> > > Setting up environment for FreeSurfer/FS-FAST (and FSL)
> > > FREESURFER_HOME   /usr/local/freesurfer_v6.0.0
> > > FSFAST_HOME   /usr/local/freesurfer_v6.0.0/fsfast
> > > FSF_OUTPUT_FORMAT nii.gz
> > > SUBJECTS_DIR  /usr/local/freesurfer_v6.0.0/subjects
> > > MNI_DIR   /usr/local/freesurfer_v6.0.0/mni
> > > FSL_DIR   /usr/local/fsl
> > > bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage
> > > bash-4.1$ /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
> >>>/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=infl
> a
> > t
> > > ed_thickness:visible=0 \
> > > > /surf/lh.inflated:visible=0 \
> > > > /surf/lh.white:visible=0 \
> > > > /surf/lh.pial \
> > > > --viewport 3d
> > > bash: /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0: No such
> > > file or directory
> > > bash-4.1$
> > >
> > >
> > >
> >>__
> _
> > _
> > > From: freesurfer-boun...@nmr.mgh.harvard.edu
> > >  on behalf of Bruce Fischl
> > > 
> > > Sent: 15 June 2017 14:11
> > > To: Freesurfer support list
> > > Subject: Re: [Freesurfer] viewing 3D surfaces
> > > Hi Michael
> > >
> > > you need to have FreeSurfer in your path or nothing will work. Have you
> > > sourced the FreeSurferEnv.sh file? Have you set FREESURFER_HOME in the
> > > environment?
> > >
> > > cheers
> > > Bruce
> > >
> > >
> > > On Thu, 15 Jun 2017, Michael Davies wrote:
> > >
> > > > Hello, i am having problems accessing the 3D surfaces of my data. Is
> > there
> > > > any advice you could provide for me please?

Re: [Freesurfer] substract images

[John Anderson]

Thank you Dr Bruce


mri_mask removes everything and leaves the areas behind the mask. And what I want is the opposite.

For example with mri_mask if I have brain with skull and mask for skull stripped brain then the output is skull stripped brain. What I want is the opposite, the skull without the brain. I highly aprreciate any suggestion. 


 

Sent: Thursday, June 15, 2017 at 1:19 PM
From: "Bruce Fischl" 
To: "Freesurfer support list" 
Subject: Re: [Freesurfer] substract images

Hi Jon

mri_mask should do the trick

cheers
Bruce
On Thu, 15 Jun 2017, John Anderson wrote:

> Dear experts,
> I have image and mask and I want to subtract the mask from the image.
> Meaning I want to get image free of specific anatomical region. For example,
>
> I have image T1.nii for the brain and mask for the thalamus. How can I
> remove the thalamus from the T1 image to get T1 image free of the thalamus.
> Thanks you for any help
> Jon
>
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Re: [Freesurfer] substract images

[Bruce Fischl]

Hi Jon

mri_mask should do the trick

cheers
Bruce
On Thu, 15 Jun 2017, John Anderson wrote:


Dear experts,
I have image and mask and I want to subtract the mask from the image.
Meaning I want to get image free of specific anatomical region. For example,

I have image T1.nii for the brain and mask for the thalamus. How can I
remove the thalamus from the T1 image to get T1 image free of the thalamus.
Thanks you for any help
Jon

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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] substract images

[John Anderson]

Dear experts,
I have image and mask and I want to subtract the mask from the image. Meaning I want to get image free of specific anatomical region. For example,


I have image T1.nii for the brain and mask for the thalamus. How can I remove the thalamus from the T1 image to get T1 image free of the thalamus.

Thanks you for any help
Jon

___
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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.

Re: [Freesurfer] viewing 3D surfaces

[Bruce Fischl]

I mean the /surf/lh.pial path has to be wrong, as that points to the root 
where you wouldn't be allowed to put data. I guess surf/ worked for you, 
but would only work if you were in the $SUBJECTS_DIR/$subject dir when you 
issued the freeview command.


cheers
Bruce


On Thu, 15 Jun 2017, Michael 
Davies wrote:




Hello Bruce, how do you mean the path is wrong? I am curious as the data
loaded just.


Kind regards, Michael


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

Sent: 15 June 2017 16:11:53
To: Freesurfer support list
Subject: Re: [Freesurfer] viewing 3D surfaces  
Hi Michael

I think you need to do a Unix tutorial. That path is wrong.

cheers
Bruce


On Thu, 15 Jun
2017, Michael Davies wrote:

>
> Hi Bruce, i'm getting closer to opening it now. But the final command
> /surf/lh.pial \ didnt work this time. Any further suggestions?
>
>
> Kind regards, Michael
>
>
> bash-4.1$ freesurfer_setup_freeview
>  freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /usr/local/freesurfer_v6.0.0
> FSFAST_HOME   /usr/local/freesurfer_v6.0.0/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /usr/local/freesurfer_v6.0.0/subjects
> MNI_DIR   /usr/local/freesurfer_v6.0.0/mni
> FSL_DIR   /usr/local/fsl
> bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage
> bash-4.1$ freeview -f \
> > /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
>>/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=infla
t
> ed_thickness:visible=0 \
> > /surf/lh.inflated:visible=0 \
> > /surf/lh.white:visible=0 \
> > /surf/lh.pial \
> > --viewport 3d
> MRISread(/surf/lh.pial): could not open file
> No such file or directory
> MRISread failed
> No such file or directory
> ould not open file
> bash-4.1$
>
>___
_
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Bruce Fischl
> 
> Sent: 15 June 2017 15:19:21
> To: Freesurfer support list
> Subject: Re: [Freesurfer] viewing 3D surfaces  
> you are not calling freeview in this command. Try putting freeview at the
> start
> On Thu, 15 Jun 2017, Michael Davies wrote:
>
> >
> > Hi Bruce, i am still getting error messages. is there anything else i
> could
> > try doing?
> >
> > Kind regards, Michael
> >
> >
> > bash-4.1$ freesurfer_setup_freeview
> >  freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> 
> > Setting up environment for FreeSurfer/FS-FAST (and FSL)
> > FREESURFER_HOME   /usr/local/freesurfer_v6.0.0
> > FSFAST_HOME   /usr/local/freesurfer_v6.0.0/fsfast
> > FSF_OUTPUT_FORMAT nii.gz
> > SUBJECTS_DIR  /usr/local/freesurfer_v6.0.0/subjects
> > MNI_DIR   /usr/local/freesurfer_v6.0.0/mni
> > FSL_DIR   /usr/local/fsl
> > bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage
> > bash-4.1$ /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
>>>/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=infl
a
> t
> > ed_thickness:visible=0 \
> > > /surf/lh.inflated:visible=0 \
> > > /surf/lh.white:visible=0 \
> > > /surf/lh.pial \
> > > --viewport 3d
> > bash: /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0: No such
> > file or directory
> > bash-4.1$
> >
> >
> >
>>__
_
> _
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
> >  on behalf of Bruce Fischl
> > 
> > Sent: 15 June 2017 14:11
> > To: Freesurfer support list
> > Subject: Re: [Freesurfer] viewing 3D surfaces  
> > Hi Michael
> >
> > you need to have FreeSurfer in your path or nothing will work. Have you
> > sourced the FreeSurferEnv.sh file? Have you set FREESURFER_HOME in the
> > environment?
> >
> > cheers
> > Bruce
> >
> >
> > On Thu, 15 Jun 2017, Michael Davies wrote:
> >
> > > Hello, i am having problems accessing the 3D surfaces of my data. Is
> there
> > > any advice you could provide for me please?
> > > bash-4.1$ freeview -f \
/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=a
p
> a
> > r
> > > c.annot:name=pial_aparc:visible=0 \
/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:ove
r
> l
> > a
> > >
> y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
> > \
/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:vis
i
> b
> > l
> > > e=0 \
/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visibl
e
> =
> > 0
> > > \
> > > > /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial \
> > > > --viewport 3d
> > > bash: 

Re: [Freesurfer] viewing 3D surfaces

[Michael Davies]

Hello Bruce, how do you mean the path is wrong? I am curious as the data loaded 
just.


Kind regards, Michael


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

Sent: 15 June 2017 16:11:53
To: Freesurfer support list
Subject: Re: [Freesurfer] viewing 3D surfaces

Hi Michael

I think you need to do a Unix tutorial. That path is wrong.

cheers
Bruce


On Thu, 15 Jun
2017, Michael Davies wrote:

>
> Hi Bruce, i'm getting closer to opening it now. But the final command
> /surf/lh.pial \ didnt work this time. Any further suggestions?
>
>
> Kind regards, Michael
>
>
> bash-4.1$ freesurfer_setup_freeview
>  freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /usr/local/freesurfer_v6.0.0
> FSFAST_HOME   /usr/local/freesurfer_v6.0.0/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /usr/local/freesurfer_v6.0.0/subjects
> MNI_DIR   /usr/local/freesurfer_v6.0.0/mni
> FSL_DIR   /usr/local/fsl
> bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage
> bash-4.1$ freeview -f \
> > /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
> >/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflat
> ed_thickness:visible=0 \
> > /surf/lh.inflated:visible=0 \
> > /surf/lh.white:visible=0 \
> > /surf/lh.pial \
> > --viewport 3d
> MRISread(/surf/lh.pial): could not open file
> No such file or directory
> MRISread failed
> No such file or directory
> ould not open file
> bash-4.1$
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Bruce Fischl
> 
> Sent: 15 June 2017 15:19:21
> To: Freesurfer support list
> Subject: Re: [Freesurfer] viewing 3D surfaces
> you are not calling freeview in this command. Try putting freeview at the
> start
> On Thu, 15 Jun 2017, Michael Davies wrote:
>
> >
> > Hi Bruce, i am still getting error messages. is there anything else i
> could
> > try doing?
> >
> > Kind regards, Michael
> >
> >
> > bash-4.1$ freesurfer_setup_freeview
> >  freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> 
> > Setting up environment for FreeSurfer/FS-FAST (and FSL)
> > FREESURFER_HOME   /usr/local/freesurfer_v6.0.0
> > FSFAST_HOME   /usr/local/freesurfer_v6.0.0/fsfast
> > FSF_OUTPUT_FORMAT nii.gz
> > SUBJECTS_DIR  /usr/local/freesurfer_v6.0.0/subjects
> > MNI_DIR   /usr/local/freesurfer_v6.0.0/mni
> > FSL_DIR   /usr/local/fsl
> > bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage
> > bash-4.1$ /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
> >>/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=infla
> t
> > ed_thickness:visible=0 \
> > > /surf/lh.inflated:visible=0 \
> > > /surf/lh.white:visible=0 \
> > > /surf/lh.pial \
> > > --viewport 3d
> > bash: /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0: No such
> > file or directory
> > bash-4.1$
> >
> >
> >
> >___
> _
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
> >  on behalf of Bruce Fischl
> > 
> > Sent: 15 June 2017 14:11
> > To: Freesurfer support list
> > Subject: Re: [Freesurfer] viewing 3D surfaces
> > Hi Michael
> >
> > you need to have FreeSurfer in your path or nothing will work. Have you
> > sourced the FreeSurferEnv.sh file? Have you set FREESURFER_HOME in the
> > environment?
> >
> > cheers
> > Bruce
> >
> >
> > On Thu, 15 Jun 2017, Michael Davies wrote:
> >
> > > Hello, i am having problems accessing the 3D surfaces of my data. Is
> there
> > > any advice you could provide for me please?
> > > bash-4.1$ freeview -f \
> >>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=ap
> a
> > r
> > > c.annot:name=pial_aparc:visible=0 \
> >>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:over
> l
> > a
> > >
> y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
> > \
> >>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visi
> b
> > l
> > > e=0 \
> >>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visible
> =
> > 0
> > > \
> > > > /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial \
> > > > --viewport 3d
> > > bash: freeview: command not found
> > >
> > > Kind regards, Michael
> > >
> > >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > Freesurfer Info Page - Harvard University
> > mail.nmr.mgh.harvard.edu
> > To see the collection of prior 

Re: [Freesurfer] bvals and bvecs for tracula v6

[Yendiki, Anastasia]

Hi Marissa – Those things are not all required simultaneously. You should 
either specify a single file (if it’s the same for all scans you’re processing) 
or a list of files, but not both at the same time.

As far as errors go, there’s no way of guessing what’s going on without seeing 
the error. Please send the trac-all.log file  and your config file if you want 
help troubleshooting. Thanks!

a.y

From: 
>
 on behalf of Marissa Pifer 
>
Reply-To: Freesurfer support list 
>
Date: Thursday, June 15, 2017 at 12:20 PM
To: Freesurfer support list 
>
Subject: [Freesurfer] bvals and bvecs for tracula v6

Hi freesurfers,

I recently updated my freesurfer version from 5.3 to 6, and I'm running into a 
problem with the tracula dmrirc.example file. In the dmrirc.example file for 
v5.3, it required just the bvals and bvecs in a text file in the correct 
format. For v6, it now requires a bval files, bval list, bvec file and bvec 
list. Could you give me an example of what the bval list and bvec list would 
look like? I'm not sure what the difference is, and I've tried a few different 
things but cannot get tracula to run correctly due to there being an error with 
these inputs.

Marissa
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The information in this e-mail is intended only for the person to whom it is
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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.

[Freesurfer] bvals and bvecs for tracula v6

[Marissa Pifer]

Hi freesurfers,

I recently updated my freesurfer version from 5.3 to 6, and I'm running
into a problem with the tracula dmrirc.example file. In the dmrirc.example
file for v5.3, it required just the bvals and bvecs in a text file in the
correct format. For v6, it now requires a bval files, bval list, bvec file
and bvec list. Could you give me an example of what the bval list and bvec
list would look like? I'm not sure what the difference is, and I've tried a
few different things but cannot get tracula to run correctly due to there
being an error with these inputs.

Marissa
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Re: [Freesurfer] mris_anatomical_stats and cortical thickness {Disarmed} {Disarmed}

[Hilton, Benjamin Taylor]

Okay I think I found a fix, but wanted to run it by you to see if it makes 
sense and for anyone else who might have this problem.  I ran it with the 
thickness file specified under the -t argument, which I think makes it so that 
the program doesn't pick up anything that is subcortical when calculating the 
thickness average.  Now the values seem reasonable, and look similar to when I 
use the thickness as an overlay in freeview.  I'll post a sample of one of the 
commands I am running below.


mris_anatomical_stats -l s71765/label/rh.cluster-001.label -t 
s71765/surf/rh.thickness -b s71765 rh




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

Sent: Tuesday, June 13, 2017 1:52:58 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_anatomical_stats and cortical thickness 
{Disarmed}


how did you do the test of the group diffs?

On 6/12/17 7:37 PM, Hilton, Benjamin Taylor wrote:

I just loaded up the label on a single subject, looks like it is fine, it's in 
the same position and squarely on the surface, it's a little skinnier but I'm 
guessing that's the difference of overlaying it on the subject.  We tried 
looking at the ocn.dat file earlier and didn't find a significant difference 
between groups despite the output of mri_glmfit-sim (see this thread: 
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg53380.html)




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

 on behalf of Douglas Greve 

Sent: Friday, June 9, 2017 9:48:50 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_anatomical_stats and cortical thickness


Have you tried to view your label on the individual subject? If your original 
analysis was on cortical thickness, then there will be a *ocn*.dat file in the 
output with the values for each input subject and each cluster

On 6/6/17 10:14 AM, Taylor Hilton wrote:

Hi all,

I’m trying to extract individual cortical thickness values using the output of 
the annotation file from mri_glmfit-sim.  This worked well for the left 
hemisphere, we got values that were significantly different between groups we 
had specified in mri_glmfit, but for the right hemisphere we get all values of 
0 for the cortical thickness and mean curvature.  I’ll post the commands I’m 
running below.  Essentially I’m attempting to take the annot file from 
mri_glmfit-sim, convert it to a label, then put that label onto a subject 
(which may or may not be necessary), and pull out the anatomical stats using 
that label.  Below is the example code for one subject.  I did also confirm 
that the initial annot file, and the final subject label both sit on the right 
hemisphere when loading them up in freeview.  I’ll also attach the summary file 
from mri_glmfit-sim for the cluster and a sample recon-all log.

Any help is appreciated!

- Taylor H.
Lab Data Coordinator
LRDC, University of Pittsburgh

mri_annotation2label --subject fsaverage --hemi rh --outdir ./scripts 
--annotation 
archive/rh.PYS_Can3_2.glmdir/PYS_Can3_2/cache.th40.neg.sig.ocn.annot --label 1

mri_label2label --srcsubject fsaverage --srclabel scripts/rh.cluster-001.label 
--trglabel s72064/label/rh.cluster-001.label --trgsubject s72064 --hemi rh 
--regmethod surface

mris_anatomical_stats -l s72064/label/rh.cluster-001.label -b s72064 rh >> 
s72064/scripts/rh-cluster001.txt


Using TH3 vertex volume calc
Total face volume 228346
Total vertex volume 224557 (mask=0)

table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name

   86 64179  0.000 0.000 0.108 0.0181 0.1  
s72064/label/rh.cluster-001.label







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Re: [Freesurfer] viewing 3D surfaces

[Bruce Fischl]

Hi Michael

I think you need to do a Unix tutorial. That path is wrong.

cheers
Bruce


On Thu, 15 Jun 
2017, Michael Davies wrote:




Hi Bruce, i'm getting closer to opening it now. But the final command
/surf/lh.pial \ didnt work this time. Any further suggestions?


Kind regards, Michael


bash-4.1$ freesurfer_setup_freeview
 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer_v6.0.0
FSFAST_HOME   /usr/local/freesurfer_v6.0.0/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer_v6.0.0/subjects
MNI_DIR   /usr/local/freesurfer_v6.0.0/mni
FSL_DIR   /usr/local/fsl
bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage
bash-4.1$ freeview -f \
> /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
>/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflat
ed_thickness:visible=0 \
> /surf/lh.inflated:visible=0 \
> /surf/lh.white:visible=0 \
> /surf/lh.pial \
> --viewport 3d
MRISread(/surf/lh.pial): could not open file
No such file or directory
MRISread failed
No such file or directory
ould not open file
bash-4.1$


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

Sent: 15 June 2017 15:19:21
To: Freesurfer support list
Subject: Re: [Freesurfer] viewing 3D surfaces  
you are not calling freeview in this command. Try putting freeview at the
start
On Thu, 15 Jun 2017, Michael Davies wrote:

>
> Hi Bruce, i am still getting error messages. is there anything else i
could
> try doing?
>
> Kind regards, Michael
>
>
> bash-4.1$ freesurfer_setup_freeview
>  freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /usr/local/freesurfer_v6.0.0
> FSFAST_HOME   /usr/local/freesurfer_v6.0.0/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /usr/local/freesurfer_v6.0.0/subjects
> MNI_DIR   /usr/local/freesurfer_v6.0.0/mni
> FSL_DIR   /usr/local/fsl
> bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage
> bash-4.1$ /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
>>/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=infla
t
> ed_thickness:visible=0 \
> > /surf/lh.inflated:visible=0 \
> > /surf/lh.white:visible=0 \
> > /surf/lh.pial \
> > --viewport 3d
> bash: /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0: No such
> file or directory
> bash-4.1$
>
>
>
>___
_
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Bruce Fischl
> 
> Sent: 15 June 2017 14:11
> To: Freesurfer support list
> Subject: Re: [Freesurfer] viewing 3D surfaces  
> Hi Michael
>
> you need to have FreeSurfer in your path or nothing will work. Have you
> sourced the FreeSurferEnv.sh file? Have you set FREESURFER_HOME in the
> environment?
>
> cheers
> Bruce
>
>
> On Thu, 15 Jun 2017, Michael Davies wrote:
>
> > Hello, i am having problems accessing the 3D surfaces of my data. Is
there
> > any advice you could provide for me please?
> > bash-4.1$ freeview -f \
>>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=ap
a
> r
> > c.annot:name=pial_aparc:visible=0 \
>>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:over
l
> a
> >
y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
> \
>>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visi
b
> l
> > e=0 \
>>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visible
=
> 0
> > \
> > > /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial \
> > > --viewport 3d
> > bash: freeview: command not found
> >
> > Kind regards, Michael
> >
> >
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> ...
>
>
>
> The information in this e-mail is intended only for the person to whom it
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[Freesurfer] Freesurfer parcelations of cortical regions in TrackVis

[Leyton Moscoso, Cristian Eduardo]

Hi Freesurfer’s and TrackVis experts


I am wondering if there is a way to import cortical parcelations mapped on a T1 
image in TrackVis.  I tried loading segmentation in TrackVis, but this does not 
allow me to see all parcelations in T1 as I can be done in Freeview. In 
TrackVis I need to upload them one by one.

Thank you

Cris


Dr Cristian Leyton M
Research Fellow in Neurology
Department of Neurology
Massachusetts General Hospital
Harvard Medical School
149  13th Street
Charlestown, MA 02129

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Please think of our environment and only print this e-mail if necessary.

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Re: [Freesurfer] viewing 3D surfaces

[Michael Davies]

That did it :) thank you so much for your help!!


Kind regards, Michael


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ruopeng Wang 

Sent: 15 June 2017 15:48:31
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] viewing 3D surfaces

Remove the '/' in front of "surf".

On 06/15/2017 11:45 AM, Michael Davies wrote:

Hi Bruce, i'm getting closer to opening it now. But the final command 
/surf/lh.pial \ didnt work this time. Any further suggestions?


Kind regards, Michael


bash-4.1$ freesurfer_setup_freeview
 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer_v6.0.0
FSFAST_HOME   /usr/local/freesurfer_v6.0.0/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer_v6.0.0/subjects
MNI_DIR   /usr/local/freesurfer_v6.0.0/mni
FSL_DIR   /usr/local/fsl
bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage
bash-4.1$ freeview -f \
> /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
> /surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
>  \
> /surf/lh.inflated:visible=0 \
> /surf/lh.white:visible=0 \
> /surf/lh.pial \
> --viewport 3d
MRISread(/surf/lh.pial): could not open file
No such file or directory
MRISread failed
No such file or directory
ould not open file
bash-4.1$


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

 on behalf of Bruce Fischl 

Sent: 15 June 2017 15:19:21
To: Freesurfer support list
Subject: Re: [Freesurfer] viewing 3D surfaces

you are not calling freeview in this command. Try putting freeview at the
start
On Thu, 15 Jun 2017, Michael Davies wrote:

>
> Hi Bruce, i am still getting error messages. is there anything else i could
> try doing?
>
> Kind regards, Michael
>
>
> bash-4.1$ freesurfer_setup_freeview
>  freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /usr/local/freesurfer_v6.0.0
> FSFAST_HOME   /usr/local/freesurfer_v6.0.0/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /usr/local/freesurfer_v6.0.0/subjects
> MNI_DIR   /usr/local/freesurfer_v6.0.0/mni
> FSL_DIR   /usr/local/fsl
> bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage
> bash-4.1$ /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
> >/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflat
> ed_thickness:visible=0 \
> > /surf/lh.inflated:visible=0 \
> > /surf/lh.white:visible=0 \
> > /surf/lh.pial \
> > --viewport 3d
> bash: /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0: No such
> file or directory
> bash-4.1$
>
>
>
> 
> From: 
> freesurfer-boun...@nmr.mgh.harvard.edu
> 
>  on behalf of Bruce Fischl
> 
> Sent: 15 June 2017 14:11
> To: Freesurfer support list
> Subject: Re: [Freesurfer] viewing 3D surfaces
> Hi Michael
>
> you need to have FreeSurfer in your path or nothing will work. Have you
> sourced the FreeSurferEnv.sh file? Have you set FREESURFER_HOME in the
> environment?
>
> cheers
> Bruce
>
>
> On Thu, 15 Jun 2017, Michael Davies wrote:
>
> > Hello, i am having problems accessing the 3D surfaces of my data. Is there
> > any advice you could provide for me please?
> > bash-4.1$ freeview -f \
> >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=apa
> r
> > c.annot:name=pial_aparc:visible=0 \
> >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overl
> a
> > y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
> \
> >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visib
> l
> > e=0 \
> >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visible=
> 0
> > \
> > > /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial \
> > > --viewport 3d
> > bash: freeview: command not found
> >
> > Kind regards, Michael
> >
> >
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> Freesurfer Info Page - Harvard University
> mail.nmr.mgh.harvard.edu
> To see the collection of prior postings to the list, visit the Freesurfer
> Archives. A searchable 

Re: [Freesurfer] viewing 3D surfaces

[Michael Davies]

Hi Bruce, i'm getting closer to opening it now. But the final command 
/surf/lh.pial \ didnt work this time. Any further suggestions?


Kind regards, Michael


bash-4.1$ freesurfer_setup_freeview
 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer_v6.0.0
FSFAST_HOME   /usr/local/freesurfer_v6.0.0/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer_v6.0.0/subjects
MNI_DIR   /usr/local/freesurfer_v6.0.0/mni
FSL_DIR   /usr/local/fsl
bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage
bash-4.1$ freeview -f \
> /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
> /surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
>  \
> /surf/lh.inflated:visible=0 \
> /surf/lh.white:visible=0 \
> /surf/lh.pial \
> --viewport 3d
MRISread(/surf/lh.pial): could not open file
No such file or directory
MRISread failed
No such file or directory
ould not open file
bash-4.1$



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

Sent: 15 June 2017 15:19:21
To: Freesurfer support list
Subject: Re: [Freesurfer] viewing 3D surfaces

you are not calling freeview in this command. Try putting freeview at the
start
On Thu, 15 Jun 2017, Michael Davies wrote:

>
> Hi Bruce, i am still getting error messages. is there anything else i could
> try doing?
>
> Kind regards, Michael
>
>
> bash-4.1$ freesurfer_setup_freeview
>  freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /usr/local/freesurfer_v6.0.0
> FSFAST_HOME   /usr/local/freesurfer_v6.0.0/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /usr/local/freesurfer_v6.0.0/subjects
> MNI_DIR   /usr/local/freesurfer_v6.0.0/mni
> FSL_DIR   /usr/local/fsl
> bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage
> bash-4.1$ /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
> >/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflat
> ed_thickness:visible=0 \
> > /surf/lh.inflated:visible=0 \
> > /surf/lh.white:visible=0 \
> > /surf/lh.pial \
> > --viewport 3d
> bash: /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0: No such
> file or directory
> bash-4.1$
>
>
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Bruce Fischl
> 
> Sent: 15 June 2017 14:11
> To: Freesurfer support list
> Subject: Re: [Freesurfer] viewing 3D surfaces
> Hi Michael
>
> you need to have FreeSurfer in your path or nothing will work. Have you
> sourced the FreeSurferEnv.sh file? Have you set FREESURFER_HOME in the
> environment?
>
> cheers
> Bruce
>
>
> On Thu, 15 Jun 2017, Michael Davies wrote:
>
> > Hello, i am having problems accessing the 3D surfaces of my data. Is there
> > any advice you could provide for me please?
> > bash-4.1$ freeview -f \
> >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=apa
> r
> > c.annot:name=pial_aparc:visible=0 \
> >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overl
> a
> > y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
> \
> >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visib
> l
> > e=0 \
> >>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visible=
> 0
> > \
> > > /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial \
> > > --viewport 3d
> > bash: freeview: command not found
> >
> > Kind regards, Michael
> >
> >
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> Freesurfer Info Page - Harvard University
> mail.nmr.mgh.harvard.edu
> To see the collection of prior postings to the list, visit the Freesurfer
> Archives. A searchable archive which of messages PRIOR to March 2004 is at
> ...
>
>
>
> 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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The information in this e-mail is intended only for the person to whom it is

Re: [Freesurfer] viewing 3D surfaces

[Bruce Fischl]

you are not calling freeview in this command. Try putting freeview at the 
start

On Thu, 15 Jun 2017, Michael Davies wrote:



Hi Bruce, i am still getting error messages. is there anything else i could
try doing?

Kind regards, Michael


bash-4.1$ freesurfer_setup_freeview
 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer_v6.0.0
FSFAST_HOME   /usr/local/freesurfer_v6.0.0/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer_v6.0.0/subjects
MNI_DIR   /usr/local/freesurfer_v6.0.0/mni
FSL_DIR   /usr/local/fsl
bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage
bash-4.1$ /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
>/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflat
ed_thickness:visible=0 \
> /surf/lh.inflated:visible=0 \
> /surf/lh.white:visible=0 \
> /surf/lh.pial \
> --viewport 3d
bash: /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0: No such
file or directory
bash-4.1$




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

Sent: 15 June 2017 14:11
To: Freesurfer support list
Subject: Re: [Freesurfer] viewing 3D surfaces  
Hi Michael

you need to have FreeSurfer in your path or nothing will work. Have you
sourced the FreeSurferEnv.sh file? Have you set FREESURFER_HOME in the
environment?

cheers
Bruce


On Thu, 15 Jun 2017, Michael Davies wrote:

> Hello, i am having problems accessing the 3D surfaces of my data. Is there
> any advice you could provide for me please?
> bash-4.1$ freeview -f \
>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=apa
r
> c.annot:name=pial_aparc:visible=0 \
>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overl
a
> y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
\
>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visib
l
> e=0 \
>>/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visible=
0
> \
> > /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial \
> > --viewport 3d
> bash: freeview: command not found
>
> Kind regards, Michael
>
>
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Re: [Freesurfer] viewing 3D surfaces

[Michael Davies]

Hi Bruce, i am still getting error messages. is there anything else i could try 
doing?

Kind regards, Michael


bash-4.1$ freesurfer_setup_freeview
 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer_v6.0.0
FSFAST_HOME   /usr/local/freesurfer_v6.0.0/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer_v6.0.0/subjects
MNI_DIR   /usr/local/freesurfer_v6.0.0/mni
FSL_DIR   /usr/local/fsl
bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj1/fsaverage
bash-4.1$ /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
> /surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
>  \
> /surf/lh.inflated:visible=0 \
> /surf/lh.white:visible=0 \
> /surf/lh.pial \
> --viewport 3d
bash: /surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0: No such file 
or directory
bash-4.1$




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

Sent: 15 June 2017 14:11
To: Freesurfer support list
Subject: Re: [Freesurfer] viewing 3D surfaces

Hi Michael

you need to have FreeSurfer in your path or nothing will work. Have you
sourced the FreeSurferEnv.sh file? Have you set FREESURFER_HOME in the
environment?

cheers
Bruce


On Thu, 15 Jun 2017, Michael Davies wrote:

> Hello, i am having problems accessing the 3D surfaces of my data. Is there
> any advice you could provide for me please?
> bash-4.1$ freeview -f \
> >/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=apar
> c.annot:name=pial_aparc:visible=0 \
> >/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overla
> y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 \
> >/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visibl
> e=0 \
> >/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visible=0
> \
> > /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial \
> > --viewport 3d
> bash: freeview: command not found
>
> Kind regards, Michael
>
>
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University
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Re: [Freesurfer] Libnetcdf.so.6 error during mris_make_surfaces

[Lisa Kramarenko]

Hi,

sure, it's

freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP

thanks!

On 13 June 2017 at 19:38, Z K  wrote:

> Hello Lisa,
>
> Can you provide me with the contents of your
> FREESURFER_HOME/build-stamp.txt file
>
> On 06/12/2017 05:44 PM, Lisa Kramarenko wrote:
> > Hi,
> >
> > I am getting the following error when my HCP pipelines come to the
> > mris_make surfaces step:
> >
> > mris_make_surfaces: error while loading shared libraries:
> > libnetcdf.so.6: cannot open shared object file: No such file or directory
> >
> > I saw this response:
> > https://www.mail-archive.com/hcp-users@humanconnectome.org/msg02418.html
> > but the files are not available anymore and I cannot find where to
> > download it. I have Ubuntu 14.04 (64-bit). Do you have any idea about
> > what causes this problem and how to solve it?
> >
> > Thanks a lot!
> > Lisa
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
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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] viewing 3D surfaces

[Bruce Fischl]

Hi Michael

you need to have FreeSurfer in your path or nothing will work. Have you 
sourced the FreeSurferEnv.sh file? Have you set FREESURFER_HOME in the 
environment?

cheers
Bruce


On Thu, 15 Jun 2017, Michael Davies wrote:

> Hello, i am having problems accessing the 3D surfaces of my data. Is there
> any advice you could provide for me please?
> bash-4.1$ freeview -f \
> >/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=apar
> c.annot:name=pial_aparc:visible=0 \
> >/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overla
> y=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 \
> >/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visibl
> e=0 \
> >/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visible=0
> \
> > /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial \
> > --viewport 3d
> bash: freeview: command not found
> 
> Kind regards, Michael
> 
>
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[Freesurfer] volume, thickness and surface area analyses

[Lim, Lena]

Dear Freesurfer Experts,


A review questioned the validity of examining volume in addition to cortical 
thickness and surface area within the same study. In particular, he commented 
that "The volume is the product of the thickness and area  ...As the product of 
two Gaussian-distributed variables is not Gaussian-distributed, the volume is 
likely to violate assumptions of the statistical methods." Could you please 
kindly advice on this?





Many thanks,



Lena



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[Freesurfer] Cortical thickness differences displayed on surface

[Ismail Koubiyr]

Dear all,

I have performed cortical thickness analysis with FS 5.3 and have found
some differences in some areas ( I have used the --lobesStrict option).
Now, I would like to display the p-values I have found for each lobe on a
surface . Would anyone have any idea how to do it  ?
Many thanks,

Ismail
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[Freesurfer] Viewing 3D surfaces

[Michael Davies]

Hello, i am having problems loading the 3D surface for my data. I was wondering 
if you could provide any advice please? This is the command code i put into the 
terminal;


bash-4.1$ freeview 
-f/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0
 \
> /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
>  \
> /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visible=0
>  \
> /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visible=0 \
> /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial \
> --viewport 3d
bash: freeview: command not found
bash-4.1$


Kind regards, Michael

University of Birmingham
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[Freesurfer] DKT vs. DK Freesurfer atlases

[Gabor Perlaki]

Dear all,


I've found an article comparing DK and DKT atlas based automatic
segmentations to manual labels (Klein and Tourville, Front Neurosci. 2012;
6:171, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514540/). It seems
that using DKT40 works better than DK in most of the cortical regions
(based on Dice).
Does anybody know that the DKTatlas related results created by Freesurfer
(e.g. aparc.DKTatlas+aseg.mgz, lh.aparc.DKTatlas.stats) are based on the
same DKT40 atlas used in the article and whether the DKT40 atlas related
results were also created by Freesurfer in the article by Klein and
Tourville? Are the Freesurfer created results in lh.aparc.DKTatlas.stats
generally more reliable than the results in lh.aparc.stats?



-- 
Gabor Perlaki
research associate
Diagnostic Center of Pécs
H-7623 Pécs, Rét str. 2.
Tel.: 0036-30-2084367
E-mail: petzinger.ga...@gmail.com
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[Freesurfer] viewing 3D surfaces

[Michael Davies]

Hello, i am having problems accessing the 3D surfaces of my data. Is there any 
advice you could provide for me please?

bash-4.1$ freeview -f \
> /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0
>  \
> /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
>  \
> /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visible=0
>  \
> /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visible=0 \
> /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial \
> --viewport 3d
bash: freeview: command not found

Kind regards, Michael
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