[Freesurfer] mris_preproc error

[Barletta, Valeria]

Hi Freesurfers,
I used the command mris_preproc to have all the surfaces of my cohort 
concatenated in fs average and I obtained this error message from several of my 
subjects:

#@# 3/11 MS073_R01_05/Bay8_3T/fs/MS073_R01_05 Fri May 11 14:24:58 EDT 2018 
--
---
mri_surf2surf --srcsubject MS073_R01_05/Bay8_3T/fs/MS073_R01_05 --srchemi lh 
--srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg 
sphere.reg --tval 
/autofs/space/alicudi_002/users/mscat/users/valeria/CMEt2star/11Subj/tmp.mris_preproc.10346/MS073_R01_05.Bay8_3T.fs.MS073_R01_05.3.mgh
 --sval 
/autofs/space/alicudi_002/users/mscat/users/gabriel/R01_Automatic/MS073_R01_05/Bay8_3T/fs/MS073_R01_05/surf/overlay/lh.MS073_R01_05-t2star_05iso_corr_disco_r0.8_depth0.5_fwhm3.mgh
 --noreshape --no-cortex
ERROR: dimension inconsistency in source data
   Number of surface vertices = 124277
   Number of value vertices = 124470
Source registration surface changed to sphere.reg
Target registration surface changed to sphere.reg
srcsubject = MS073_R01_05/Bay8_3T/fs/MS073_R01_05
srcval = 
/autofs/space/alicudi_002/users/mscat/users/gabriel/R01_Automatic/MS073_R01_05/Bay8_3T/fs/MS073_R01_05/surf/overlay/lh.MS073_R01_05-t2star_05iso_corr_disco_r0.8_depth0.5_fwhm3.mgh
srctype= 
trgsubject = fsaverage
trgval = 
/autofs/space/alicudi_002/users/mscat/users/valeria/CMEt2star/11Subj/tmp.mris_preproc.10346/MS073_R01_05.Bay8_3T.fs.MS073_R01_05.3.mgh
trgtype= 
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi= lh
trghemi= lh
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/gabriel/R01_Automatic//MS073_R01_05/Bay8_3T/fs/MS073_R01_05/surf/lh.sphere.reg
Loading source data


I saw that the problem could be related with the sphere file and I tried 
re-running -autorecon2 and -autorecon3 but it did not solve the problem.
Could you please help me out with this?
Thank you,
Valeria
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[Freesurfer] mris_preproc error

[Barletta, Valeria]

Hi Freesurfers,
I sent this help request some days ago but had some problems in receiving the 
reply because of mailing list subscription issues...
Sorry for submitting this request again:

I used the command mris_preproc to have all the surfaces of my cohort 
concatenated in fs average and I obtained this error message from several of my 
subjects:

#@# 3/11 MS073_R01_05/Bay8_3T/fs/MS073_R01_05 Fri May 11 14:24:58 EDT 2018 
--
---
mri_surf2surf --srcsubject MS073_R01_05/Bay8_3T/fs/MS073_R01_05 --srchemi lh 
--srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg 
sphere.reg --tval 
/autofs/space/alicudi_002/users/mscat/users/valeria/CMEt2star/11Subj/tmp.mris_preproc.10346/MS073_R01_05.Bay8_3T.fs.MS073_R01_05.3.mgh
 --sval 
/autofs/space/alicudi_002/users/mscat/users/gabriel/R01_Automatic/MS073_R01_05/Bay8_3T/fs/MS073_R01_05/surf/overlay/lh.MS073_R01_05-t2star_05iso_corr_disco_r0.8_depth0.5_fwhm3.mgh
 --noreshape --no-cortex
ERROR: dimension inconsistency in source data
   Number of surface vertices = 124277
   Number of value vertices = 124470
Source registration surface changed to sphere.reg
Target registration surface changed to sphere.reg
srcsubject = MS073_R01_05/Bay8_3T/fs/MS073_R01_05
srcval = 
/autofs/space/alicudi_002/users/mscat/users/gabriel/R01_Automatic/MS073_R01_05/Bay8_3T/fs/MS073_R01_05/surf/overlay/lh.MS073_R01_05-t2star_05iso_corr_disco_r0.8_depth0.5_fwhm3.mgh
srctype=
trgsubject = fsaverage
trgval = 
/autofs/space/alicudi_002/users/mscat/users/valeria/CMEt2star/11Subj/tmp.mris_preproc.10346/MS073_R01_05.Bay8_3T.fs.MS073_R01_05.3.mgh
trgtype=
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi= lh
trghemi= lh
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/gabriel/R01_Automatic//MS073_R01_05/Bay8_3T/fs/MS073_R01_05/surf/lh.sphere.reg
Loading source data


I saw that the problem could be related with the sphere file and I tried 
re-running -autorecon2 and -autorecon3 but it did not solve the problem.
Could you please help me out with this?
Thank you,
Valeria

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[Freesurfer] partial volume correction

[Barletta, Valeria]

Hi Freesurfers,
We are trying to apply the PVC process to our PET images.
We proceeded through step3 as indicated on fswiki, and obtained the files:
- gtm.nii
- nopvc.nii
- mgx.gm.nii
How can we obtain the corrected uptake values from these files?
Can we obtain a corrected volume file for voxel based analysis?

Thanks for your help,
Valeria
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[Freesurfer] brain parenchymal fraction

[Barletta, Valeria]

Dear Freesurfers,
I need to extract the brain parenchymal fraction to check brain atrophy in my 
patients.
The BPF is defined as "the ratio of brain parenchymal tissue volume to the 
total volume contained within the brain surface contour".
In the text file aseg.stats, I found this info:  
# Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1052408.00, mm^3
# Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume 
Without Ventricles, 1032104.00, mm^3
# Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation 
Volume Without Ventricles from Surf, 1030608.836503, mm^3

Can I extract the BPF from those, or is any of them the BPF?

Thank you,
Valeria
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Re: [Freesurfer] brain parenchymal fraction

[Barletta, Valeria]

I guess it means the surface of the whole brain, including infratentorial 
structures.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[dgr...@mgh.harvard.edu]
Sent: Thursday, July 26, 2018 3:58 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] brain parenchymal fraction

you'll have to be more specific about what "brain surface contour" means.

On 7/26/18 3:46 PM, Barletta, Valeria wrote:
> Dear Freesurfers,
> I need to extract the brain parenchymal fraction to check brain atrophy in my 
> patients.
> The BPF is defined as "the ratio of brain parenchymal tissue volume to the 
> total volume contained within the brain surface contour".
> In the text file aseg.stats, I found this info:
> # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1052408.00, 
> mm^3
> # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume 
> Without Ventricles, 1032104.00, mm^3
> # Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation 
> Volume Without Ventricles from Surf, 1030608.836503, mm^3
>
> Can I extract the BPF from those, or is any of them the BPF?
>
> Thank you,
> Valeria
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[Freesurfer] error in longitudinal stream command

[Barletta, Valeria]

Dear Freesurfers,
I am trying to re-launch a longitudinal time point after edits by using the 
command:

recon-all -long MS069_R01_01_Bay8_3T_03102014.long.MS069_base MS069_base -all

But I am obtaining this type of error:

Unmatched ".

I also tried to launch it on Launchpad but I have an error all the same and the 
process immediately aborts.
Do you know what could be the reason?
Thank you,
Valeria


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Re: [Freesurfer] error in longitudinal stream command

[Barletta, Valeria]

Hi Martin, thanks for your reply.
I tried to re-type the command in the shell but I still have the error.
I don't know what you mean with system install, but we are using the version 
5.3 and this is the path, if it can help:
/autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-stable5_3_0-05152013

Thank you!
Valeria

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Martin Reuter 
[mreu...@nmr.mgh.harvard.edu]
Sent: Wednesday, August 29, 2018 12:14 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] error in longitudinal stream command

Hi Valeria,

what version of FS are you using (also is it a local install or the
system install)?

Also try to re-type the command in the shell (don't run it from a
script) could be that there are invisible characters , like tab etc
from copy paste that mess things up.

Best, Martin


On Wed, 2018-08-29 at 13:51 +, Barletta, Valeria wrote:
> Dear Freesurfers,
> I am trying to re-launch a longitudinal time point after edits by
> using the command:
>
> recon-all -long MS069_R01_01_Bay8_3T_03102014.long.MS069_base
> MS069_base -all
>
> But I am obtaining this type of error:
>
> Unmatched ".
>
> I also tried to launch it on Launchpad but I have an error all the
> same and the process immediately aborts.
> Do you know what could be the reason?
> Thank you,
> Valeria
>
>
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>
>
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[Freesurfer] help with subjects concatenation/dimension inconsistency error

[Barletta, Valeria]

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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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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[Freesurfer] glm analysis

[Barletta, Valeria]

Dear Freesurfers,

I am trying to run a GLM analysis with 3 groups (1)long disease duration MS, 
2)short disease duration MS, 3)healthy controls) and 1 variable (age).


According to the formula provided on freewiki:

N classes (N of variables + 1),

 is this contrast matrix correct?


1 -1 0 0 0 0

1 0 -1 0 0 0


thank you,

Valeria
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Re: [Freesurfer] glm analysis

[Barletta, Valeria]

Dear Freesurfers,

I am trying to run a GLM analysis with 3 groups (1)long disease duration MS, 
2)short disease duration MS, 3)healthy controls) and 1 variable (age).


According to the formula provided on freewiki:

N classes (N of variables + 1),

 is this contrast matrix correct?


1 -1 0 0 0 0

1 0 -1 0 0 0


thank you,

Valeria



From: Barletta, Valeria
Sent: Friday, December 7, 2018 2:23:10 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: glm analysis


Dear Freesurfers,

I am trying to run a GLM analysis with 3 groups (1)long disease duration MS, 
2)short disease duration MS, 3)healthy controls) and 1 variable (age).


According to the formula provided on freewiki:

N classes (N of variables + 1),

 is this contrast matrix correct?


1 -1 0 0 0 0

1 0 -1 0 0 0


thank you,

Valeria
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[Freesurfer] error while running trac-preproc

[Barletta, Valeria]

Dear Freesurfers,

I am trying to run the command trac-all -prep -c but I'm getting this error:


error while loading shared libraries: libnetcdf.so.6: cannot open shared object 
file: No such file or directory


Can you help me?

Thank you,

Vale
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Re: [Freesurfer] GLM - correction for multiple comparisons

[Barletta, Valeria]

There are no negative clusters in abs.

I tried to apply the permutation but it says it requires an orthogonal matrix.

Right now I am using this:

-1 1 0 0

How would my orthogonal matrix look like?

Thanks,

Vale


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

Sent: Thursday, February 14, 2019 12:14:27 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] GLM - correction for multiple comparisons

It is certainly possible. Are some of the clusters in abs negative?
Also, I would strongly recommend using permutation if you are using such
a low clusterwise threshold. See
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
The monte carlo simulation is not valid at such low thresholds


On 2/14/19 11:50 AM, Barletta, Valeria wrote:
>
> Dear Freesurfers,
>
> I am performing a GLM analysis on two groups (patients versus
> controls) and one variable (age).
>
> We are using the following option to correct for multiple comparisons:
>
>
> mri_glmfit-sim --glmdir
> ${glm_dir}/${hemi}_contrast-${contrast}_${surfname_t1} --cache 1.3 pos/abs
>
>
> Is it normal to have those 2 different results when using pos or abs
> option? (see screenshots)
>
> Thank you!
>
> Vale
>
>
>
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[Freesurfer] surface cortical lesions mask --> annotation file ???

[Barletta, Valeria]

Dear Freesurfers,

I need to extract annotation files from my cortical lesion masks projected to 
the surface.

Do you know whether this is possible?

Thank you,

Valeria
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Re: [Freesurfer] surface cortical lesions mask --> annotation file ???

[Barletta, Valeria]

Yes sure,
I need to extract values from discrete cortical lesions, but I have masks of 
all lesions together projected to the cortical surface.

I have a script that can provide me values for every single lesion separately, 
but this script works on annotation files.

Is it possible to create an annotation file for the lesion masks? They are in   
.mgh   format



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

Sent: Thursday, February 14, 2019 3:28:44 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface cortical lesions mask --> annotation file ???

not sure what you mean, can you elaborate?

On 2/14/19 2:05 PM, Barletta, Valeria wrote:
>
> Dear Freesurfers,
>
> I need to extract annotation files from my cortical lesion masks
> projected to the surface.
>
> Do you know whether this is possible?
>
> Thank you,
>
> Valeria
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] surface cortical lesions mask --> annotation file ???

[Barletta, Valeria]

Ok thank you, it works but there is a problem... The command mris_label2annot 
requires a ColorTable file.

As I tried to use FreeSurferColorLUT.txtI got a list of all regions I did 
not need.

What kind a ColorTable file shall I provide to create an annotation file for 
cortical lesions only?

Thank you,

Vale


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

Sent: Thursday, February 14, 2019 3:37:28 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface cortical lesions mask --> annotation file ???

You can make separate labels (mri_cor2label with --surf option), then
use mris_label2annot

On 2/14/19 3:32 PM, Barletta, Valeria wrote:
>
> Yes sure,
> I need to extract values from discrete cortical lesions, but I have
> masks of all lesions together projected to the cortical surface.
>
> I have a script that can provide me values for every single lesion
> separately, but this script works on annotation files.
>
> Is it possible to create an annotation file for the lesion masks? They
> are in   .mgh  format
>
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Greve, Douglas
> N.,Ph.D. 
> *Sent:* Thursday, February 14, 2019 3:28:44 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] surface cortical lesions mask -->
> annotation file ???
> not sure what you mean, can you elaborate?
>
> On 2/14/19 2:05 PM, Barletta, Valeria wrote:
> >
> > Dear Freesurfers,
> >
> > I need to extract annotation files from my cortical lesion masks
> > projected to the surface.
> >
> > Do you know whether this is possible?
> >
> > Thank you,
> >
> > Valeria
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] surface cortical lesions mask --> annotation file ???

[Barletta, Valeria]

Ok I did and inserted only this:

#No. Label Name:R   G   B   A

1   Left-Cerebral-Exterior  70  130 180 0

since I binarized the lesion masks and when creating the label I assigned value 
1 (with the option --id 1). Is it correct?
Thanks,
Vale

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

Sent: Friday, February 15, 2019 1:56:50 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface cortical lesions mask --> annotation file ???

you have to create your own. Use FreeSurferColorsLUT.txt as your template

On 2/15/19 1:08 PM, Barletta, Valeria wrote:

Ok thank you, it works but there is a problem... The command mris_label2annot 
requires a ColorTable file.

As I tried to use FreeSurferColorLUT.txtI got a list of all regions I did 
not need.

What kind a ColorTable file shall I provide to create an annotation file for 
cortical lesions only?

Thank you,

Vale


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Greve, Douglas N.,Ph.D. 
<mailto:dgr...@mgh.harvard.edu>
Sent: Thursday, February 14, 2019 3:37:28 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] surface cortical lesions mask --> annotation file ???

You can make separate labels (mri_cor2label with --surf option), then
use mris_label2annot

On 2/14/19 3:32 PM, Barletta, Valeria wrote:
>
> Yes sure,
> I need to extract values from discrete cortical lesions, but I have
> masks of all lesions together projected to the cortical surface.
>
> I have a script that can provide me values for every single lesion
> separately, but this script works on annotation files.
>
> Is it possible to create an annotation file for the lesion masks? They
> are in   .mgh  format
>
>
> 
> *From:* 
> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>  on behalf of Greve, Douglas
> N.,Ph.D. <mailto:dgr...@mgh.harvard.edu>
> *Sent:* Thursday, February 14, 2019 3:28:44 PM
> *To:* freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Re: [Freesurfer] surface cortical lesions mask -->
> annotation file ???
> not sure what you mean, can you elaborate?
>
> On 2/14/19 2:05 PM, Barletta, Valeria wrote:
> >
> > Dear Freesurfers,
> >
> > I need to extract annotation files from my cortical lesion masks
> > projected to the surface.
> >
> > Do you know whether this is possible?
> >
> > Thank you,
> >
> > Valeria
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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[Freesurfer] surf2vol ERROR

[Barletta, Valeria]

Dear all,

I am trying to register surfaces to a volume by this command:

mri_surf2vol --subject MS089_R01_29 --hemi rh --rh.MS089_R01_29.subjspace.mgh 
--hemi lh --surfval lh.MS089_R01_29.subjspace.mgh --o CME_MS089_R01_29.nii.gz 
--merge combined-CL.nii.gz --trgsubj MS089_R01_29


And am obtaining this error:

ERROR: Option --trgsubject unknown


That is actually the name of my subject in $FREESURFER_HOME

Also, I do not have a registration file so I used the option --trgsubject

Is this correct? Why am I getting that error?

Thanks,

Vale


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Re: [Freesurfer] surf2vol ERROR

[Barletta, Valeria]

Oh I just used that option instead of providing a registration file, which I 
don't have.
I need to turn the two surfaces into a single volume.

Get Outlook for Android<https://aka.ms/ghei36>


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

Sent: Saturday, February 16, 2019 6:58:46 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] surf2vol ERROR

Hi Vale

mri_surf2vol is to take take from the surface to the volume within one
subject. Why do you need a trgsubject? You can compute the registration
with e.g. bbregister. Maybe I'm not understanding what you are trying to
do

cheers
Bruce

On Sat, 16 Feb 2019, Barletta, Valeria wrote:

>
> Dear all,
>
> I am trying to register surfaces to a volume by this command:
>
> mri_surf2vol --subject MS089_R01_29 --hemi rh --rh.MS089_R01_29.subjspace.mgh 
> --hemi lh --surfval
> lh.MS089_R01_29.subjspace.mgh --o CME_MS089_R01_29.nii.gz --merge 
> combined-CL.nii.gz --trgsubj
> MS089_R01_29
>
>
> And am obtaining this error:
>
> ERROR: Option --trgsubject unknown
>
>
> That is actually the name of my subject in $FREESURFER_HOME
>
> Also, I do not have a registration file so I used the option --trgsubject
>
> Is this correct? Why am I getting that error?
>
> Thanks,
>
> Vale
>
>
>
>
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Re: [Freesurfer] surf2vol ERROR

[Barletta, Valeria]

I need to turn my lh and rh .mgh files (they are in the subject's space) to a 
single .nii.gz file. Does this process require a registration? I actually tried 
to use --identity instead of --trgsubject, but I got the same error, "Option 
--identity unknown"


Get Outlook for Android<https://aka.ms/ghei36>


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

Sent: Sunday, February 17, 2019 10:56:33 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] surf2vol ERROR

but do you need a registration? What space do you want the volume to be
in? If the standard FS "conformed" space you don't need a regisration (you
can specify --identity  Oh I just used that option instead of providing a registration file, which I 
> don't have.
> I need to turn the two surfaces into a single volume.
>
> Get Outlook for Android
>
> __
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Bruce
> Fischl 
> Sent: Saturday, February 16, 2019 6:58:46 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] surf2vol ERROR
> Hi Vale
>
> mri_surf2vol is to take take from the surface to the volume within one
> subject. Why do you need a trgsubject? You can compute the registration
> with e.g. bbregister. Maybe I'm not understanding what you are trying to
> do
>
> cheers
> Bruce
>
> On Sat, 16 Feb 2019, Barletta, Valeria wrote:
>
> >
> > Dear all,
> >
> > I am trying to register surfaces to a volume by this command:
> >
> > mri_surf2vol --subject MS089_R01_29 --hemi rh 
> > --rh.MS089_R01_29.subjspace.mgh --hemi lh --surfval
> > lh.MS089_R01_29.subjspace.mgh --o CME_MS089_R01_29.nii.gz --merge 
> > combined-CL.nii.gz --trgsubj
> > MS089_R01_29
> >
> >
> > And am obtaining this error:
> >
> > ERROR: Option --trgsubject unknown
> >
> >
> > That is actually the name of my subject in $FREESURFER_HOME
> >
> > Also, I do not have a registration file so I used the option --trgsubject
> >
> > Is this correct? Why am I getting that error?
> >
> > Thanks,
> >
> > Vale
> >
> >
> >
> >
>
>
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Re: [Freesurfer] surf2vol ERROR

[Barletta, Valeria]

Ha ok I had read it on freewiki and it was --identify

https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol

Looks like it's working now, thanks!
Vale

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

Sent: Sunday, February 17, 2019 2:05:58 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] surf2vol ERROR

you have a typo. It's not "-identify" it is "--identity"

On Sun, 17 Feb
2019, Barletta, Valeria wrote:

>
> Sure... There is also a screenshot attached
>
>
> panarea:/autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3 
> $
> panarea:/autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3 
> $ mri_surf2vol
> --subject MS089_R01_29 --hemi rh 
> --surfval/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/surf2vol/M
> S089_R01_29/rh.MS089_R01_29.subjspace.mgh --hemi lh 
> --surfval/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/surf2vol/M
> S089_R01_29/lh.MS089_R01_29.subjspace.mgh 
> --o/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/surf2vol/M
> S089_R01_29/CME_MS089_R01_29.nii.gz --merge
> /autofs/space/alicudi_002/users/mscat/users/celine/lesion_mask/MS089_R01_29/combined-CL.nii.gz
> --regheader MS089_R01_29
> ERROR: Option --regheader unknown
>
> panarea:/autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3 
> $ mri_surf2vol
> --subject MS089_R01_29 --hemi rh 
> --surfval/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/surf2vol/M
> S089_R01_29/rh.MS089_R01_29.subjspace.mgh --hemi lh 
> --surfval/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/surf2vol/M
> S089_R01_29/lh.MS089_R01_29.subjspace.mgh 
> --o/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/surf2vol/M
> S089_R01_29/CME_MS089_R01_29.nii.gz --merge
> /autofs/space/alicudi_002/users/mscat/users/celine/lesion_mask/MS089_R01_29/combined-CL.nii.gz
> --trgsubject MS089_R01_29
> ERROR: Option --trgsubject unknown
>
> panarea:/autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3 
> $ mri_surf2vol
> --subject MS089_R01_29 --hemi rh 
> --surfval/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/surf2vol/M
> S089_R01_29/rh.MS089_R01_29.subjspace.mgh --hemi lh 
> --surfval/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/surf2vol/M
> S089_R01_29/lh.MS089_R01_29.subjspace.mgh 
> --o/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/surf2vol/M
> S089_R01_29/CME_MS089_R01_29.nii.gz --merge
> /autofs/space/alicudi_002/users/mscat/users/celine/lesion_mask/MS089_R01_29/combined-CL.nii.gz
> --identify MS089_R01_29
> ERROR: Option --identify unknown
>
>
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of
> Bruce Fischl 
> Sent: Sunday, February 17, 2019 11:08:41 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] surf2vol ERROR
> can you send us the full command line and screen output? You should not
> need a registration
>
> cheers
> Bruce
> On Sun, 17 Feb 2019, Barletta, Valeria wrote:
>
> > I need to turn my lh and rh .mgh files (they are in the subject's space) to 
> > a single .nii.gz file.
> Does
> > this process require a registration? I actually tried to use --identity 
> > instead of --trgsubject,
> but I got
> > the same error, "Option --identity unknown"
> >
> >
> > Get Outlook for Android
> >
> >___
> ___
> > From: freesurfer-boun...@nmr.mgh.harvard.edu 
> >  on behalf of
> Bruce
> > Fischl 
> > Sent: Sunday, February 17, 2019 10:56:33 AM
> > To: Freesurfer support list
> > Subject: Re: [Freesurfer] surf2vol ERROR
> > but do you need a registration? What space do you want the volume to be
> > in? If the standard FS "conformed" space you don't need a regisration (you
> > can specify --identity  > with --reg or --lta. In any case, mri_surf2vol has pretty good
> > documentation (thanks Doug!). Check out mri_surf2vol --help
> >
> > cheers
> > Bruce
> >
> >
> > On
> > Sun, 17 Feb 2019, Barletta, Valeria wrote:
> >
> > > Oh I just used that option instead of providing a registration file, 
> > > which I don't hav

[Freesurfer] clusters annotation file in surface

[Barletta, Valeria]

Dear Freesurfers,

I have a 3D volume mask of cortical lesions with 8 different clusters (8 
cortical lesions).

I projected this mask to the cortex and obtained a .mgh file with the command 
vol2surf:

mri_vol2surf --src $path_to_lesion/$subj/combined-$lesion.nii.gz --out 
$path_to_output/$subj/surf/$hemi".surf_combined-"$lesion".mgh" --projfrac-avg 
-0.1 1 0.05 --hemi $hemi --regheader $subj


Now I need to extract label files from this surface file, one label for each 
cluster, and then an annotation file summarizing all the label files.

How can I do this?

Thanks,

Vale





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[Freesurfer] Fw: clusters annotation file in surface - ERROR

[Barletta, Valeria]

Thank you Doug,

As you suggested, I tried to use that command

(mris_seg2annot --seg lh.surf_combined-magn_CL_fwhm1.mgh --s MS072_R01_04 
--hemi lh --ctab MS072_R01_04.txt --o lh.cortical_les.annot)

but I got this error on tksurfer:

Successfully parsed tksurfer.tcl
reading white matter vertex locations...
% reading colortable from annotation file...
colortable with 7 entries read (originally MS072_R01_04.txt)
Found embedded color table in annotation.
131940 vertices did not have an annotation!
surfer: WARNING: no labels imported; annotation was empty


I attach my color table file...


Thanks for your help,

Vale



___


>Greve, Douglas N.,Ph.D. DGREVE at mgh.harvard.edu 
><mailto:freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20clusters%20annotation%20file%20in%20surface&In-Reply-To=%3C2b8a798d-7cff-1db2-4508-51e52751f3eb%40mgh.harvard.edu%3E>
>Tue Feb 19 16:33:32 EST 2019

>You can create an annotation with mris_seg2annot (you basically have a
>surface-based segmentation). Run it with --help to get more info
>including examples. You will need to create your own color table

On 2/19/19 3:21 PM, Barletta, Valeria wrote:
>
> Dear Freesurfers,
>
> I have a 3D volume mask of cortical lesions with 8 different clusters
> (8 cortical lesions).
>
> I projected this mask to the cortex and obtained a .mgh file with the
> command vol2surf:
>
> mri_vol2surf --src $path_to_lesion/$subj/combined-$lesion.nii.gz --out
> $path_to_output/$subj/surf/$hemi".surf_combined-"$lesion".mgh"
> --projfrac-avg -0.1 1 0.05 --hemi $hemi --regheader $subj
>
>
> Now I need to extract label files from this surface file, one
> label for each cluster, and then an annotation file summarizing all
> the label files.
>
> How can I do this?
>
> Thanks,
>
> Vale




From: Barletta, Valeria
Sent: Tuesday, February 19, 2019 3:21 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: clusters annotation file in surface


Dear Freesurfers,

I have a 3D volume mask of cortical lesions with 8 different clusters (8 
cortical lesions).

I projected this mask to the cortex and obtained a .mgh file with the command 
vol2surf:

mri_vol2surf --src $path_to_lesion/$subj/combined-$lesion.nii.gz --out 
$path_to_output/$subj/surf/$hemi".surf_combined-"$lesion".mgh" --projfrac-avg 
-0.1 1 0.05 --hemi $hemi --regheader $subj


Now I need to extract label files from this surface file, one label for each 
cluster, and then an annotation file summarizing all the label files.

How can I do this?

Thanks,

Vale





#$Id: FreeSurferColorLUT.txt,v 1.70.2.7 2012/08/27 17:20:08 nicks Exp $

#No. Label Name:R   G   B   A

0   Unknown 0   0   0   0
1   Lesion1 70  130 180 0
2   Lesion2 245 245 245 0
3   Lesion3 205 62  78  0
4   Lesion4 120 18  134 0
5   Lesion5 196 58  250 0
6   Lesion6 0   148 0   0
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[Freesurfer] problem with mri_surfcluster

[Barletta, Valeria]

Dear Freesurfers,

I am trying to obtain clusters of vertices whit a certain value over a 
threshold inside a lesion mask projected to the surface, with the command:


mri_surfcluster --subject MS075_R01_07_R1year --hemi lh --in 
lh.MS075_R01_07_R1year.subjspace.mgh --surf lh.pial --mask 
lh.surf_magn_CL02_fwhm1.mgh --thmax 49.95807 --thmin 1 --sign pos --minarea 
0.01 --sum summary.txt

But I obtain this result saying there are no vertices in my mask.

thsign = pos, id = 1
version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $
hemi   = lh
srcid  = 
/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/49_subjects/CME_all/lh.MS075_R01_07_R1year.subjspace.mgh
srcsubjid  = MS075_R01_07_R1year
srcsurf= lh.pial
srcframe   = 0
thsign = pos
thmin  = 1
thmax  = 49.9581
fdr= -1
minarea= 0.01
xfmfile= talairach.xfm
nth = -1
sumfile  = 
/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/49_subjects/SINGLE_LESION/MS075_R01_07_R1year/summary.txt
subjectsdir= 
/autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3
FixMNI = 1
Found 0 vertices in mask


Can you help me figure out why?

Thanks,
Vale



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Re: [Freesurfer] problem with mri_surfcluster

[Barletta, Valeria]

I want to extract clusters within the cortical lesion mask in which the vertex 
values are below 49.95

The values are in the file lh.MS075_R01_07_R1year.subjspace.mgh


Thanks,

Vale


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

Sent: Monday, May 20, 2019 2:46:54 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] problem with mri_surfcluster

How did you choose thresholds of 1 and 49.95? In general, you don't need
to set --thmax. If you input is a binary mask, then you should set
--thmin to somethiing below 1 (eg, 0.5)

On 5/20/19 2:40 PM, Barletta, Valeria wrote:
>
> Dear Freesurfers,
>
> I am trying to obtain clusters of vertices whit a certain value over a
> threshold inside a lesion mask projected to the surface, with the command:
>
>
> mri_surfcluster --subject MS075_R01_07_R1year --hemi lh --in
> lh.MS075_R01_07_R1year.subjspace.mgh --surf lh.pial --mask
> lh.surf_magn_CL02_fwhm1.mgh --thmax 49.95807 --thmin 1 --sign pos
> --minarea 0.01 --sum summary.txt
>
> But I obtain this result saying there are no vertices in my mask.
>
> thsign = pos, id = 1
> version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $
> hemi   = lh
> srcid  =
> /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/49_subjects/CME_all/lh.MS075_R01_07_R1year.subjspace.mgh
>
> srcsubjid  = MS075_R01_07_R1year
> srcsurf= lh.pial
> srcframe   = 0
> thsign = pos
> thmin  = 1
> thmax  = 49.9581
> fdr= -1
> minarea= 0.01
> xfmfile= talairach.xfm
> nth = -1
> sumfile  =
> /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/49_subjects/SINGLE_LESION/MS075_R01_07_R1year/summary.txt
> subjectsdir=
> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3
> FixMNI = 1
> Found 0 vertices in mask
>
>
> Can you help me figure out why?
>
> Thanks,
> Vale
>
>
>
>
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[Freesurfer] question on surface analysis

[Barletta, Valeria]

Dear Freesurfer,

I have a surface file containing values of a cortical myelination index 
(rh.MS075_CME.mgh), and a lesion mask (rh.surf_CL03.mgh)


What I need to do is:

- Masking the surface file with the lesion mask, to create a new lesion mask 
that contains the myelination index values from rh.MS075_CME.mgh;

- Assess the percentage (or also the absolute number) of vertices that are 
under a certain threshold of myelination index values whithin the new lesion 
mask.


What is the best way to do this?


Thank you,

Vale
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Re: [Freesurfer] question on surface analysis

[Barletta, Valeria]

That is a great solution, thank you!


How exactly can I apply this whole thing to .mgh surface-based files?

I cannot convert them to .nii and I think mri_binarize and mri_segstats work 
only on volumes.


Thanks,

Vale



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

Sent: Wednesday, May 22, 2019 10:47:19 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] question on surface analysis



On 5/22/2019 10:19 AM, Barletta, Valeria wrote:

Dear Freesurfer,

I have a surface file containing values of a cortical myelination index 
(rh.MS075_CME.mgh), and a lesion mask (rh.surf_CL03.mgh)


What I need to do is:

- Masking the surface file with the lesion mask, to create a new lesion mask 
that contains the myelination index values from rh.MS075_CME.mgh;

Try
mri_mask rh.MS075_CME.mgh rh.surf_CL03.mgh  rh.MS075_CME.mask.mgh

- Assess the percentage (or also the absolute number) of vertices that are 
under a certain threshold of myelination index values whithin the new lesion 
mask.

You can use mri_binarize to create a mask of the myelination map (use --min and 
--max to spec the range), then use mri_segstats inputing the binarized mask 
with --seg and using --id 1. In the output summary file (--sum sumfile), the 
"number of voxels" will be the number of vertices; this could be modified to 
give the surface area instead.


What is the best way to do this?


Thank you,

Vale



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[Freesurfer] XL defect in recon-all

[Barletta, Valeria]

Dear Freesurfers,

I tried to launch  "recon-all -all" for an high-resolution 7T 0.75 isotropic 
MEMPRAGE, but the process got stuck on a XL defect in rh, numbered 54, 
measuring over 20,000 voxels!!


How do I check, and eventually fix, this defect?


Thank you,

Vale
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Re: [Freesurfer] XL defect in recon-all

[Barletta, Valeria]

That would be great. However, I am launching recon-all -all by entering the 
environment for freesurfer 6 in my terminal (we still have version 5_3 
installed in our computers). So there is no way I can copy the files from the 
2nd link in the folder $FREESURFER_HOME/bin (I have no access to that folder).

Is there another way to apply the command -conf2hires without having version 6 
installed?


Thank you,

Vale


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

Sent: Thursday, May 23, 2019 3:46:30 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] XL defect in recon-all

You can look at this tutorial
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview

But if you are using high res, I would run high res stream I put
together for the HCP:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/

On 5/23/19 2:59 PM, Barletta, Valeria wrote:
>
> Dear Freesurfers,
>
> I tried to launch  "recon-all -all" for an high-resolution 7T 0.75
> isotropic MEMPRAGE, but the process got stuck on a XL defect in rh,
> numbered 54, measuring over 20,000 voxels!!
>
>
> How do I check, and eventually fix, this defect?
>
>
> Thank you,
>
> Vale
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] question on surface analysis

[Barletta, Valeria]

It worked perfectly, thank you!!


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

Sent: Wednesday, May 22, 2019 1:22:30 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] question on surface analysis

mri_binarize and mri_segstats will work on any mgh or nii files. Note
that because something is an mgh or nii file does not mean it is volume
or surface based. Eg, if you
mri_convert lh.thickness lh.thickness.nii.gz
you will have a nifti file with number of columns = number of vertices,
1 row, and 1 column. So it looks like a volume in that it has columns,
row, and slices, but the underlying data is interpreted as a
surface-based map

On 5/22/19 12:33 PM, Barletta, Valeria wrote:
>
> That is a great solution, thank you!
>
>
> How exactly can I apply this whole thing to .mgh surface-based files?
>
> I cannot convert them to .nii and I think mri_binarize and
> mri_segstats work only on volumes.
>
>
> Thanks,
>
> Vale
>
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Greve, Douglas
> N.,Ph.D. 
> *Sent:* Wednesday, May 22, 2019 10:47:19 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] question on surface analysis
>
>
> On 5/22/2019 10:19 AM, Barletta, Valeria wrote:
>>
>> Dear Freesurfer,
>>
>> I have a surface file containing values of a cortical myelination
>> index (rh.MS075_CME.mgh), and a lesion mask (rh.surf_CL03.mgh)
>>
>>
>> What I need to do is:
>>
>> - Masking the surface filewith the lesion mask, to create a new
>> lesion mask that contains the myelination index values from
>> rh.MS075_CME.mgh;
>>
> Try
> mri_mask rh.MS075_CME.mgh rh.surf_CL03.mgh rh.MS075_CME.mask.mgh
>>
>> - Assess the percentage (or also the absolute number) of vertices
>> that are under a certain threshold of myelination
>> index values whithin the new lesion mask.
>>
> You can use mri_binarize to create a mask of the myelination map (use
> --min and --max to spec the range), then use mri_segstats inputing the
> binarized mask with --seg and using --id 1. In the output summary file
> (--sum sumfile), the "number of voxels" will be the number of
> vertices; this could be modified to give the surface area instead.
>>
>>
>> What is the best way to do this?
>>
>>
>> Thank you,
>>
>> Vale
>>
>>
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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[Freesurfer] how to obtain a mean .mgh file

[Barletta, Valeria]

Dear Freesurfers,

Is there a way to turn N .mgh files in to a single output .mgh file in which 
each vertex is the mean of the corresponding vertices in my input files?

For example, input  lh.Ctrl029.fsaverage.mgh ,  lh.Ctrl030.fsaverage.mgh , 
lh.Ctrl031.fsaverage.mgh , lh.Ctrl032.fsaverage.mgh >>> output 
lh.mean.fsaverage.mgh


Thanks,

Vale
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[Freesurfer] incompatible vertex number ???

[Barletta, Valeria]

Dear Freesurfers,
I am getting this type of error in the Terminal when I open my images on 
Freesurfer:

MRISreadNewCurvature: incompatible vertex number in file 
/autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSTAT_MS_001_B/surf/lh.curv
No such file or directory
could not read curvature from curv
No such file or directory
mpatible vertex number in file 
/autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSTAT_MS_001_B/surf/lh.curv


I can still visualize and modify the images, but I noticed that recon-all 
autorecon2-wm for wm edits is not working. Are these two things related?

Thank you,
Vale


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Re: [Freesurfer] incompatible vertex number ???

[Barletta, Valeria]

That final surfaces where not modified, but maybe that is because I was missing 
-autorecon3 in my command.


Shall I re-launch "recon-all -all" to fix that problem with lh.curv?


Thank you,

Vale


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

Sent: Friday, June 14, 2019 12:02:30 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] incompatible vertex number ???

Hi Vale

that typically means that recon-all was rerun and not completed. WHen you
say autorecon2-wm is not working what do you mean?
cheers
BruceOn Fri, 14 Jun 2019,
Barletta, Valeria wrote:

>
> Dear Freesurfers,
> I am getting this type of error in the Terminal when I open my images on 
> Freesurfer:
>
> MRISreadNewCurvature: incompatible vertex number in file
> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSTAT_MS_001_B/surf/lh.curv
> No such file or directory
> could not read curvature from curv
> No such file or directory
> mpatible vertex number in file
> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSTAT_MS_001_B/surf/lh.curv
>
>
> I can still visualize and modify the images, but I noticed that recon-all 
> autorecon2-wm for wm edits
> is not working. Are these two things related?
>
> Thank you,
> Vale
>
>
>
>
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Re: [Freesurfer] problem with reconstruction

[Barletta, Valeria]

Yes that would be awesome.

I am using the Martinos file drop, hope it is ok.

Thank you,

Vale


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

Sent: Wednesday, June 19, 2019 4:55:53 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] problem with reconstruction

Hi Vale

do you want to tar, gzip and ftp us that entire subject dir so we can
take a look?
cheers
Bruce
On Wed, 19 Jun 2019, Barletta, Valeria wrote:

>
> Dear Freesurfers,
>
>
> I am having issues with a reconstruction which is giving me giant defects 
> that I cannot correct (see
> screenshots).
>
> I tried to work on the wm and also to use the command
>
> recon-all -subject NIMMS02_2year_recon -T2 T2SPACE.nii.gz -T2pial -autorecon3
>
> ... to correct using T2 images.
>
> Nothing worked. This never happened to me except this time.
>
> Any suggestions?
>
>
> Thank you a lot,
>
> Vale
>
>
>
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[Freesurfer] total cortical area

[Barletta, Valeria]

Dear Freesurfers,

Where in the /mri/stats folder can I find the total cortical surface in mm2?

Is it in the ?h.aparc.stats or in the ?h.curv.stats?


Thank you,

Valeria
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[Freesurfer] Freesurfer's last version installation

[Barletta, Valeria]

Dear Freesurfers,
We need to install the last version of Freesurfer, but we need to keep the wm 
edits that we made with version 5.3
How can this be done? Is there any specific command?

Thanks a lot,
Vale
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[Freesurfer] question on mris_calc - re-submitting

[Barletta, Valeria]

From: Barletta, Valeria
Sent: Friday, September 27, 2019 12:30 PM
To: freesurfer-boun...@nmr.mgh.harvard.edu 

Subject: question on mris_calc

Dear Freesurfers,
I am trying to perform an operation with .mgh files by using mris_calc. This is 
my operation:

(image1 - image2)
___
  (image2)

First I am using the command:

mris_calc -o $hemi.FILE1.mgh $hemi.image1.mgh sub $hemi.image2.mgh

And then:

mris_calc -o $hemi.FILE2.mgh $hemi.FILE1.mgh div $hemi.image2.mgh

Is this procedure correct?

Also, I have read this information about the command mris_calc functions: 
"Note:  and  should typically be generated on the same subject"
But actually, my image1 belongs to a single subject, while image2 is a mean of 
images from many different subjects (obtained using mri_concat --mean).
Is mris_calc going to work in this case?

Thank you very much for your help,
Valeria
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Re: [Freesurfer] Question on GLM - correlation

[Barletta, Valeria]

I did what you suggested in your previous email:

> That does not have the pvr in it. You can extract the pvr for that
> vertex and add it as a column to the X matrix with
> pvr = fast_vol2mat(MRIread('pvr.mgz'));
> pvrvtx = pvr(:,vertexno+1);

Which file shall I look like for the single voxel?



From: Greve, Douglas N.,Ph.D. 
Sent: Thursday, December 5, 2019 12:40 PM
To: Barletta, Valeria ; Freesurfer support list 

Subject: Re: [Freesurfer] Question on GLM - correlation



On 12/4/19 11:51 AM, Barletta, Valeria wrote:
> Ok I did it and did not get any .mgh file as a result.
Did what?
>
> At this point I wonder, what is the best model to check for
> correlation between my continuous outcome CME.mgh and the continuous
> variable ficvf.mgh?
> Shall I include ficvf.mgh as a regressor (pvr) and use the Contrast  1
> 0 0   or shall I use a completely different method?
>
> Thanks, sorry for the long interaction...
> 
> *From:* Greve, Douglas N.,Ph.D. 
> *Sent:* Tuesday, December 3, 2019 3:18 PM
> *To:* Barletta, Valeria ; Freesurfer
> support list 
> *Subject:* Re: [Freesurfer] Question on GLM - correlation
> That does not have the pvr in it. You can extract the pvr for that
> vertex and add it as a column to the X matrix with
> pvr = fast_vol2mat(MRIread('pvr.mgz'));
> pvrvtx = pvr(:,vertexno+1);
>
> ps. Please remember to post to the list
>
> On 12/3/2019 1:29 PM, Barletta, Valeria wrote:
>> Ok done. This is the Xg.mat
>> 129
>>  144
>>  138
>>  147
>>  134
>>  125
>>  130
>>  122
>>  152
>>  131
>>  137
>>  142
>>  128
>>  139
>>  144
>>  144
>>  132
>>  132
>>  136
>>  147
>>  152
>> And the cond(Xg'*Xg) is again: 3.0555e+04
>> Looks like there is no extra column for the pvr in the Xg.mat
>>
>>
>> 
>> *From:* Greve, Douglas N.,Ph.D. 
>> <mailto:dgr...@mgh.harvard.edu>
>> *Sent:* Tuesday, December 3, 2019 11:03 AM
>> *To:* Barletta, Valeria 
>> <mailto:vbarle...@mgh.harvard.edu>; Freesurfer support list
>>  <mailto:freesurfer@nmr.mgh.harvard.edu>
>> *Subject:* Re: [Freesurfer] Question on GLM - correlation
>> I'm not sure those condition numbers include the pvr. Try loading the
>> Xg.mat into matlab and computing
>> cond(Xg'*Xg)
>> Make sure Xg has the extra column for the pvr
>>
>> On 12/3/2019 10:42 AM, Barletta, Valeria wrote:
>>> Ok it worked.
>>> So I tried with a non-zero vertex and I got:
>>> Normalized matrix condition is 81.1382
>>> Matrix condition is 30558.5
>>> Found 149926 points in label.
>>> Found 149926 voxels in mask
>>> Saving mask to
>>> /autofs/space/lipari_001/users/valeria/NODDI/GLM//GLM_CME_ficvf_doug/rh_contrast-MS_CME_all_FIS_ICA1/mask.mgh
>>> Reshaping mriglm->mask...
>>> search space = 74490.928733
>>> DOF = 18
>>> Dumping voxel 1024 0 0 to
>>> /autofs/space/lipari_001/users/valeria/NODDI/GLM//GLM_CME_ficvf_doug/rh_contrast-MS_CME_all_FIS_ICA1/voxdump-1024-0-0
>>>
>>> ...and with a zero vertex and got:
>>> Normalized matrix condition is 81.1382
>>> Matrix condition is 30558.5
>>> Found 149926 points in label.
>>> Found 149926 voxels in mask
>>> Saving mask to
>>> /autofs/space/lipari_001/users/valeria/NODDI/GLM//GLM_CME_ficvf_doug2/rh_contrast-MS_CME_all_FIS_ICA1/mask.mgh
>>> Reshaping mriglm->mask...
>>> search space = 74490.928733
>>> DOF = 18
>>> Dumping voxel 150252 0 0 to
>>> /autofs/space/lipari_001/users/valeria/NODDI/GLM//GLM_CME_ficvf_doug2/rh_contrast-MS_CME_all_FIS_ICA1/voxdump-150252-0-0
>>>
>>>
>>>
>>> 
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>>> 
>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve,
>>> Douglas N.,Ph.D. 
>>> <mailto:dgr...@mgh.harvard.edu>
>>> *Sent:* Monday, December 2, 2019 2:56 PM
>>> *To:* freesurfer@nmr.mgh.harvard.edu
>>> <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>  <mailto:freesurfer@nmr.m

[Freesurfer] bias correction on 7T MEMPRAGE

[Barletta, Valeria]

Dear Freesurfers,
I am trying to apply the bias correction on the 7T MEMPRAGE through the unified 
segmentation algorithm on SPM12, as a primary step to do the submillimetric 
recon on Freesurfer, as you suggested here:
https://surfer.nmr.mgh.harvard.edu/fswiki/HighFieldRecon

For some reason, I cannot set the Bias FWHM to 18 on the SPM12 interface. Also, 
not sure how to use the 5D image that I obtain from the process.

Have you ever done this before? Any tips?

Thanks a lot,
Vale
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[Freesurfer] question on partial volume correction

[Barletta, Valeria]

Dear Freesurfers,
We need to analyze PET data after correcting for partial volume effect in the 
cortex, white matter and subarachnoid space. Is Freesurfer's partial volume 
correction working on all these areas or only the grey matter volume and 
surface? Is there a way to use gtmseg on the white matter and outside the pial 
surface?

Thanks a lot,

Valeria Barletta, MD
Massachusetts General Hospital
149 13th Street, Charlestown MA 02129
(617)-724-8823
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[Freesurfer] question on partial volume correction

[Barletta, Valeria]

Dear Freesurfers,
We need to analyze PET data after correcting for partial volume effect in the 
cortex, white matter and subarachnoid space. Is Freesurfer's partial volume 
correction working on all these areas or only the grey matter volume and 
surface? Is there a way to use gtmseg on the white matter and outside the pial 
surface?

Thanks a lot,

Valeria Barletta, MD
Massachusetts General Hospital
149 13th Street, Charlestown MA 02129
(617)-724-8823
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Re: [Freesurfer] question on partial volume correction

[Barletta, Valeria]

Yes I need the lh and rh cerebral WM for sure, but not just the values, also an 
image.
And I need also a corrected image for the extra cerebral CSF. How can I get 
that?

Thank you very much,

Valeria Barletta, MD
Massachusetts General Hospital
149 13th Street, Charlestown MA 02129
(617)-724-8823

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

Sent: Thursday, May 21, 2020 10:32 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] question on partial volume correction

It will certainly do cortex. We do not have a segmentation for subarachnoid 
spaces. Or are you just talking about extra cerebral CSF? We do have a 
segmentation for xCSF, but it is not the most beautiful thing in the world. For 
WM, the GTM will give you a PVC corrected value for the entire lh and rh 
cerebral WM (and cerebellar) segments. Is that all you need?

On 5/19/2020 11:36 AM, Barletta, Valeria wrote:
Dear Freesurfers,
We need to analyze PET data after correcting for partial volume effect in the 
cortex, white matter and subarachnoid space. Is Freesurfer's partial volume 
correction working on all these areas or only the grey matter volume and 
surface? Is there a way to use gtmseg on the white matter and outside the pial 
surface?

Thanks a lot,

Valeria Barletta, MD
Massachusetts General Hospital
149 13th Street, Charlestown MA 02129
(617)-724-8823



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[Freesurfer] mri_glmfit masking strategy

[Barletta, Valeria]

Hello Freesurfers,
I need to perform a GLM in 25 patients versus 19 controls but I need the 
comparison to be done only on normal appearing cortex (in patients), thus 
excluding cortical lesions.

  *   Is it possible to concatenate binary masks projected to surface? What 
command shall I use?
  *   If I use the option --mask for mri_glmfit, will I obtain the same type of 
output with the only difference that clusters are looked for in the 
concatenated masks?

Thank you,

Valeria Barletta, MD
Massachusetts General Hospital
149 13th Street, Charlestown MA 02129
(617)-724-8823
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[Freesurfer] question on GLM

[Barletta, Valeria]

Good evening Freesurfers!
I am building a GLM with 4 classes (control_F, control_M, patient_F, patient_M) 
to check for differences in cortical thickness between patients and control 
accounting for the effect of gender and age on cortical thickness.

How should my contrast be?

Thanks a lot,

Valeria Barletta, MD
Massachusetts General Hospital
149 13th Street, Charlestown MA 02129
(617)-724-8823
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[Freesurfer] question on GLM

[Barletta, Valeria]

Good morning Freesurfers!
I am building a GLM with 4 classes (control_F, control_M, patient_F, patient_M) 
to check for differences in cortical thickness between patients and control 
accounting for the effect of gender and age on cortical thickness.

How should my contrast be?

Thanks a lot,

Valeria Barletta, MD
Massachusetts General Hospital
149 13th Street, Charlestown MA 02129
(617)-724-8823
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Re: [Freesurfer] question on GLM

[Barletta, Valeria]

Thanks. And what about the effect of age?
Thank you,

Valeria Barletta, MD
Massachusetts General Hospital
149 13th Street, Charlestown MA 02129
(617)-724-8823

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

Sent: Monday, January 25, 2021 5:24 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] question on GLM

0 0 0 0 0.5 0.5 -0.5 -0.5
will compute control-patient slope accounting for gender




On 1/8/2021 7:49 AM, Barletta, Valeria wrote:

Good morning Freesurfers!
I am building a GLM with 4 classes (control_F, control_M, patient_F, patient_M) 
to check for differences in cortical thickness between patients and control 
accounting for the effect of gender and age on cortical thickness.

How should my contrast be?

Thanks a lot,

Valeria Barletta, MD
Massachusetts General Hospital
149 13th Street, Charlestown MA 02129
(617)-724-8823



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[Freesurfer] WM volume

[Barletta, Valeria]

Dear Freesurfers,
In what file inside the patient_name/stats folder do I find the total white 
matter volume?
In the file "aseg.stats" there is something called lh/rh "cortical white matter 
volume", is that the right value to look at?

Thank you,

Valeria Barletta, MD
Massachusetts General Hospital
149 13th Street, Charlestown MA 02129
(617)-724-8823
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Re: [Freesurfer] WM volume

[Barletta, Valeria]

Thanks a lot. One more thing, is the total brain volume "BrainSegVolNotVent, 
Brain Segmentation Volume Without Ventricles" ?

Valeria Barletta, MD
Massachusetts General Hospital
149 13th Street, Charlestown MA 02129
(617)-724-8823

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

Sent: Tuesday, February 23, 2021 9:10 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] WM volume

Yes, that is the right value. We changed the name of it in more recent versions 
to CerebralWhiteMatter

On 2/22/2021 4:12 PM, Barletta, Valeria wrote:
Dear Freesurfers,
In what file inside the patient_name/stats folder do I find the total white 
matter volume?
In the file "aseg.stats" there is something called lh/rh "cortical white matter 
volume", is that the right value to look at?

Thank you,

Valeria Barletta, MD
Massachusetts General Hospital
149 13th Street, Charlestown MA 02129
(617)-724-8823



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[Freesurfer] TRACULA exited with ERROR /home/vbarletta/ants-2.5.4/bin/antsRegistrationSyNQuick.sh: Permission denied.

[Barletta, Valeria]

Dear Freesurfers,
Do you know how to fix this error in trac-all? (I'm using Ubuntu 18.04)

#@# Inter-subject registration Wed Dec  4 22:37:52 CET 2024
/home/vbarletta/ants-2.5.4/bin/antsRegistrationSyNQuick.sh -d 3 -m 
trac/R01121_SCAN/dmri/dtifit_FA.nii.gz -f 
/home/vbarletta/tester/freesurfer/trctrain/hcp/MGH35_HCP_FA_template.nii.gz -o 
trac/R01121_SCAN/dmri/xfms/diff2syn
/home/vbarletta/ants-2.5.4/bin/antsRegistrationSyNQuick.sh: Permission denied.

trac-preproc exited with ERRORS at Wed Dec  4 22:37:52 CET 2024

Alternatively, is there a way to run Tracula without using ants?

Thank you for your help,
Valeria

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[Freesurfer] errore with tracula: eddy_openmp: Command not found.

[Barletta, Valeria]

Dear Freesurfers,
I am trying to run trac-all on Freesurfer 7.4.1 but I am obtaining this output:

eddy_openmp --imain=trac/R01121_SCAN/dmri/dwi_orig_las.nii.gz 
--mask=trac/R01121_SCAN/dmri/lowb_orig_las_brain_mask.nii.gz 
--bvecs=trac/R01121_SCAN/dmri/dwi_orig_las.bvecs 
--bvals=trac/R01121_SCAN/dmri/dwi_orig_las.bvals 
--acqp=trac/R01121_SCAN/dmri/acqp.txt --index=trac/R01121_SCAN/dmri/index.txt 
--data_is_shelled --out=trac/R01121_SCAN/dmri/dwi
eddy_openmp: Command not found.
Linux LAPTOP-OH2647G1 5.15.167.4-microsoft-standard-WSL2 #1 SMP Tue Nov 5 
00:21:55 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Tue Dec  3 20:11:28 CET 2024

Can you please help me understand the problem? Is that related to my FSL 
version?
Thank you,
Valeria
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[Freesurfer] TRACULA error /bin/tcsh: bad interpreter: No such file or directory

[Barletta, Valeria]

Hello Freesurfers,
I am trying to launch trac-all -prep on Ubuntu 22 but I am getting this error:

-bash: /home/local/PARTNERS/vb922/freesurfer/bin/trac-all: /bin/tcsh: bad 
interpreter: No such file or directory

Can you please help me figure out what is going on?

Thank you,
Valeria
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[Freesurfer] preparing config file to run Tracula

[Barletta, Valeria]

Dear Freesurfers,
I am setting up the configuration file to run Tracula preproc. I have some 
doubts on certain variables...

  *
pedir: on my DTI protocol I have "PhaseEncodingDirection": "j-",so I assume it 
is AP
  *
epifactor : I took it from  "EchoTrainLength": 48
  *
echospacing: shall I take it from "DwellTime": 2.5e-06? In which format should 
I write it in the file?

Thank you,
Valeria

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[Freesurfer] preparing config file for Tracula

[Barletta, Valeria]

Dear Freesurfers,
I am setting up the configuration file to run Tracula preproc. I have some 
doubts on some variables...

  *
pedir: on my DTI protocol I have "PhaseEncodingDirection": "j-",so I assume it 
is AP
  *
epifactor : I took it from  "EchoTrainLength": 48
  *
echospacing: shall I take it from "DwellTime": 2.5e-06? Should that be 
indicated in seconds or milliseconds?

Thank you,
Valeria


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