[Freesurfer] Unequal size groups

[stdp82]

 
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  Hi 
  I’m using fs-fast to map the connectivity differences between 3 groups. My problem is unequally sized groups. In the sense that the first group consists of 40 subjects, the second of 190, and the third of 18. What solutions does FreeSurfer offer to handle this type of problem which affects the assumption of equal variances in tests like ANOVA? 
  Thanks 
    
  Stefano
 

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[Freesurfer] ScLimbic: error: could not allocate memory for slice 1 out of 256error: mri_convert --conform failed!

[stdp82]

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Hi list, the error is reported below.

Of note I have just runned, with success, ScLimbic for another study.

Thus, I do not understand which is the issue for this one.

Thanks

Stefano




mri_sclimbic_seg --i FOLDER --o FOLDER --write_volumes --write_qa_stats --etiv 
--conform

/Applications/freesurfer/7.3.2/sclimbic/python/scripts/mri_sclimbic_seg --i 
FOLDER --o FOLDER --write_volumes --write_qa_stats --etiv --conform

Excluding seg [853]Using CPUUsing 1 thread(s)Loaded lookup table 
/Applications/freesurfer/7.3.2/sclimbic/models/sclimbic.ctab

Loaded population stats 
/Applications/freesurfer/7.3.2/sclimbic/models/sclimbic.volstats.csv

Loaded model weights 
/Applications/freesurfer/7.3.2/sclimbic/models/sclimbic.fsm+ad.t1.nstd00-50.nstd32-50.h5

Computing etiv from scratchmri_convert --conform FOLDER/subjID.mgz 
/var/folders/vd/g4zth0dn6nldcx62m0l827srgn/T/tmpk6kr248m/nu.mgz reading 
from FOLDER/subjID.mgz...error: could not allocate memory for slice 1 out of 
256error: mri_convert --conform failed!
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Re: [Freesurfer] ERROR: fast_mat2vol

[stdp82]

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I have resolved by eliminating the option -nowhiten







It looks like the anatomical analysis is out of sync with the functional 
analysis. Is is possible that you ran the functional analysis, then edited the 
subject, then tried to rerun the analysis? If so, try running preproc-sess with 
-force to redo all the preprocessing.On 12/1/2022 12:45 PM, std...@virgilio.it 
wrote:
>  External Email - Use Caution I would extract the rs-fMRI timeseries 
> from Yeo’s Network components. I’m running: preproc-sess -s ${1} -fsd rest 
> -sliceorder up -surface self lhrh -fwhm 0 -per-runfcseed-config -wm -fcname 
> wm.dat -fsd rest -pca -cfg wm.config fcseed-sess -s ${1} -cfg 
> wm.configfcseed-config -vcsf -fcname vcsf.dat -fsd rest -pca -cfg 
> vcsf.configfcseed-sess -s ${1} -cfg vcsf.config mkanalysis-sess -analysis 
> fc.noseed.surf.lh -surface self lh -fwhm 0 -notask -nuisreg vcsf.dat 5 
> -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.67 -per-run 
> -hpf 0.01 -lpf 0.1 -nowhiten mkanalysis-sess -analysis fc.noseed.surf.rh 
> -surface self rh -fwhm 0 -notask -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 
> -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.67 -per-run -hpf 0.01 -lpf 0.1 
> -nowhitenThe line below produced this error: selxavg3-sess -s ${1} -a 
> fc.noseed.surf.lh -no-con-ok -svres Saving rho1 ERROR: fast_mat2vol: szvol 
> inconsistent with mat2d  nv = 151008, size(mat,2) = 142954  run 2t= 
> 1.6reading data ... 0.518631Temporally filteringSaving rho1 ERROR: 
> fast_mat2vol: szvol inconsistent with mat2d  nv = 151008, size(mat,2) = 
> 142954Found 0 voxels with corrected AR1 > 0.90Not WhiteningFound 8054 
> zero-valued voxelsComputing contrastsThe res folder in fc.noseed.surf.lh or 
> fc.noseed.surf.rh contains res-001.nii.gz 158KB res-002.nii.gz 158KB that 
> cannot be opended. Stefano 
> 
> 
> 
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[Freesurfer] ERROR: fast_mat2vol: szvol inconsistent with mat2d nv

[stdp82]

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I would extract the rs-fMRI timeseries from Yeo’s Network components. 




I’m running: 

preproc-sess -s ${1} -fsd rest -sliceorder up -surface self lhrh -fwhm 0 
-per-run

fcseed-config -wm -fcname wm.dat -fsd rest -pca -cfg wm.config 

fcseed-sess -s ${1} -cfg wm.config

fcseed-config -vcsf -fcname vcsf.dat -fsd rest -pca -cfg vcsf.config

fcseed-sess -s ${1} -cfg vcsf.config 

mkanalysis-sess -analysis fc.noseed.surf.lh -surface self lh -fwhm 0 -notask 
-nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest 
-TR 1.67 -per-run -hpf 0.01 -lpf 0.1 -nowhiten 

mkanalysis-sess -analysis fc.noseed.surf.rh -surface self rh -fwhm 0 -notask 
-nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest 
-TR 1.67 -per-run -hpf 0.01 -lpf 0.1 -nowhiten 

The line below produced this error: 

selxavg3-sess -s ${1} -a fc.noseed.surf.lh -no-con-ok -svres 

Saving rho1 ERROR: fast_mat2vol: szvol inconsistent with mat2d nv = 151008, 
size(mat,2) = 142954 run 2 t= 1.6reading data ... 0.518631Temporally 
filteringSaving rho1 ERROR: fast_mat2vol: szvol inconsistent with mat2d nv = 
151008, size(mat,2) = 142954

Found 0 voxels with corrected AR1 > 0.90Not WhiteningFound 8054 zero-valued 
voxelsComputing contrasts 

The res folder in fc.noseed.surf.lh or fc.noseed.surf.rh contains

 res-001.nii.gz 158KB 

res-002.nii.gz 158KB 

that cannot be opended. 

Thanks




Stefano 
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[Freesurfer] ERROR: fast_mat2vol

[stdp82]

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 I would extract the rs-fMRI timeseries from Yeo’s Network components. 


 I’m running: 
preproc-sess -s ${1} -fsd rest -sliceorder up -surface self lhrh -fwhm 0 
-per-runfcseed-config -wm -fcname wm.dat -fsd rest -pca -cfg wm.config 
fcseed-sess -s ${1} -cfg wm.configfcseed-config -vcsf -fcname vcsf.dat -fsd 
rest -pca -cfg vcsf.configfcseed-sess -s ${1} -cfg vcsf.config


 mkanalysis-sess -analysis fc.noseed.surf.lh -surface self lh -fwhm 0 -notask 
-nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest 
-TR 1.67 -per-run -hpf 0.01 -lpf 0.1 -nowhiten 
 mkanalysis-sess -analysis fc.noseed.surf.rh -surface self rh -fwhm 0 -notask 
-nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest 
-TR 1.67 -per-run -hpf 0.01 -lpf 0.1 -nowhiten 


 The line below produced this error: 


 selxavg3-sess -s ${1} -a fc.noseed.surf.lh -no-con-ok -svres 
Saving rho1

ERROR: fast_mat2vol: szvol inconsistent with mat2d  nv = 151008, size(mat,2) = 
142954  run 2t= 1.6reading data ... 0.518631Temporally filteringSaving rho1

ERROR: fast_mat2vol: szvol inconsistent with mat2d  nv = 151008, size(mat,2) = 
142954Found 0 voxels with corrected AR1 > 0.90Not WhiteningFound 8054 
zero-valued voxelsComputing contrasts

The res folder in fc.noseed.surf.lh or fc.noseed.surf.rh contains

 res-001.nii.gz 158KB 
 res-002.nii.gz 158KB 


 that cannot be opended. 


 Stefano ___
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[Freesurfer] time-series from Yeo's Network components

[stdp82]

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Hi list,

I  would extract the rs-fMRI time-series from spitted components of Yeo's 7 
Network Atlas (fsaverage5).

To this aim, I'm planning to convert the "fmcpr.odd.sm0.fsaverage.lh.nii.gz" 
(obtained by preproc-sess) on fsaverage5.

However, the fmcpr.odd.sm0.fsaverage.lh.nii.gz should still include some 
nuisance variables (CSF, the white matter, motion, first 4 time points).

To address this issue, is it corrected to apply the command lines reported 
below?

mkanalysis-sess -analysis fc.noseed.surf.lh -surface fsaverage lh -fwhm 0 
-notask -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg 
-fsd rest -TR 1.67 -per-run -hpf 0.01 -lpf 0.1 -nowhiten

mkanalysis-sess -analysis fc.noseed.surf.rh -surface fsaverage rh -fwhm 0 
-notask -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg 
-fsd rest -TR 1.67 -per-run -hpf 0.01 -lpf 0.1 -nowhiten

selxavg3-sess -s subj_folder_name -a fc.noseed.surf.lh -overwrite -no-con-ok 

selxavg3-sess -s subj_folder_name -a fc.noseed.surf.rh -overwrite -no-con-ok




Thanks

Stefano


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[Freesurfer] FS-FAST preprocessing of rs-fMRI data and extracting timeseries from Yeo's Networks

[stdp82]

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 I aim at FS-FAST preprocessing of rs-fMRI data and extracting timeseries from 
Yeo's Networks. 


 1 - I won’t perform a seed based analysis. 


 2 - I want to exclude the five sets of nuisance variables in mkanalysis-sess. 
Please could you check whether the command lines listed below are corrected for 
this aim? 


 mkanalysis-sess -analysis fc.noseed.surf.lh -surface fsaverage lh -fwhm 0 
-notask -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg 
-fsd rest -TR 1.67 -per-run -hpf 0.01 -lpf 0.1 -nowhiten -force 
mkanalysis-sess -analysis fc.noseed.surf.rh -surface fsaverage rh -fwhm 0 
-notask -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg 
-fsd rest -TR 1.67 -per-run -hpf 0.01 -lpf 0.1 -nowhiten -force 
selxavg3-sess -s subj_folder_name -a fc.noseed.surf.lh -overwrite -no-con-ok 
selxavg3-sess -s subj_folder_name -a fc.noseed.surf.rh -overwrite -no-con-ok 


 3 - I want to extract the timecourse, subject-by-subject, from each spitted 
Yeo's component. 


 The feature of produced "fc.noseed.surf" files are: 
type: nii 
dimensions: 163842 x 1 x 1 
voxel sizes: 1.00, 1.00, 1.00 


 I have tried to use 


 mri_segstats --slabel ${1} lh subj/label/Xcomponent --i 
${1}/rest/fc.noseed.surf.lh/meanfunc.nii.gz --sum /Xcomponent.sum.txt --avgwf 
Xcomponent.wav.txt 


 But an error of dimension mismatch between input volume and seg occurs. 
input 163842 1 1 
seg 116809 1 1 


 The input should be in fsaverage. Which is the correct average of set? And 
what do I do to run correctly at this step? 


 Thanks 



Stefano 

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[Freesurfer] ALL atlas and FS-FAST

[stdp82]

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Hi

is possible to use the AAL for connectivity analysis with FS-FAST?

How can I segment the subject GM according with the labels listed in the ALL 
atlas?

Thanks

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[Freesurfer] PCA

[stdp82]

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Dear list,

is possible to do a whole-brain, voxel-wise PCA analysis by FS-FAST?

Thanks


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[Freesurfer] mri_glmfit with pvr

[stdp82]

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Thanks

If I have 4 groups

GroupDescriptorFile 1
Title XXX
Class G1
Class G2
Class G3
Class G4

Input subj1 G1

Input subj2 G3

Input subj3 G2

Input subj4 G2

Input subj5 G4





Are the contrasts below corrected?

G1_only_thick 1 0 0 0

G2_only_thick 1 0 0 0

G3_only_thick 1 0 0 0

G4_only_thick 1 0 0 0

G1+G2-G3+G4_thick 0.5 0.5 -0.5 -0.5

G3+G4+G2+G1_thick -0.5 -0.5 0.5 0.5

G1+G2+G3+G4_thick 0.25 0.25 0.25 0.25

Thanks

Stefano





Yes, you use a "per-vertex map" (--pvr option to mri_glmfit). See, example, 
this thread 
https://secure-web.cisco.com/1951sWOE8h4m5NbLCNqMyCAH8IOXE-lQF7pVtK2O9WlGr4lhC_ZayJW3oVHincxLs53lKvn0Z-ft-svmipnYED9p-xyQou2z1oP685gnJy3DM4X5tON-4zkvd1sP1xWnF1nZd9lZy-XdrKD8EufxxsG-gOreUvYzG0cA8pE1W8jkaYloEpe1annxnW8XXl-kmnIHZf1--oFrTvMN64dAA6I2FO5CoCq1z-DrzvgSl3fP4l15sZISoKwYj68dddQJm69YYEODA7eKQ5rzp3VtndQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg18790.htmlOn
 6/3/2021 10:22 AM, std...@virgilio.it mailto:std...@virgilio.it wrote:


> External Email - Use Caution Hi, how can I perform vertex by vertex (surface) 
> analysis of covariance between functional connectivity data (FS-FAST) and 
> cortical thickness, regressing out the effect of groups?My mean concern is 
> how buid the fsgd file. Stefano
> 
Great news, thank you, Doug! Best, aga On 8/3/11 5:02 PM, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu wrote:


>Hi Aga, what you have done is correct, no need to include the pvr in the
>fsgd.
>doug
>
>Burzynska, Aga wrote:
>> Dear all,
>> I am trying to make group level analysis of functional data on the
>>surface and add per-vertex regressors (PVR, here: cortical thickness)
>>into the design. When I view the results I have the feeling that the PVR
>>is not really included in the model:
>>
>> I am using the command:
>> mri_glmfit --glmdir lh_output --y cope1_lh_4D.mgh --fsgd
>>Group1versusGroup2.fsgd  --pvr lh.thickness.10.mgh --C
>>Group1only_thickness.mat --C Group2only_thickness.mat --C
>>Group1minusGroup2_thickness.mat --C Group2minusGroup1_thickness.mat --C
>>Group1plusGroup2_thickness.mat
>>
>> where
>> cope1_lh_4D.mgh contains the concatenated sig.mgh images from the fixed
>>level analysis (combining the runs) for each participant
>> fsgd file contains:
>> GroupDescriptorFile 1
>> Title Group1versusGroup2
>> Class Group1 
>> Class Group2
>> Input 1109 Group1
>> Input 1110 Group1
>> Input  Group1
>> Input 1112 Group1
>> ...
>> Input 2280  Group2
>> Input 2282  Group2
>> Input 2283  Group2
>> Input 2284  Group2
>>
>> The PVR is a file containing thickness maps for each participant,
>>concatenated in the same order as for the functional data.
>>
>> So there are 2 main regressors (1 factor, 2 levels), but the contrast
>>files contain 3 regressors (the third one is the PVE), for instance:
>> Group1minusGroup2_thickness.mat contains  1 -1 0.
>>
>> Does it look correct?
>> Should the pvr regressor be included in the fsdg file? How can I do it?
>>
>> Thank you very much for your help,
>> Cheers,
>> Aga
>>
>> ___
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>>
>>
>>   
>
>-- 
>Douglas N. Greve, Ph.D.
>MGH-NMR Center
gr...@nmr.mgh.harvard.edu">>gr...@nmr.mgh.harvard.edu
>Phone Number: 617-724-2358
>Fax: 617-726-7422
>
>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>FileDrop: 
>http://secure-web.cisco.com/1sv09XhDGpKH6GdjRo4NvJdoe1IvIDCTTvOgKXpkc6HwNAe3Bxrv4derZ6AiKbGnv-0p8WN5rPJh6CsiFTAatsOwTZiOuoi3EEOqp5U9-wM4MtS7Hufp4RglpfBenXNlZMrszCcV8AyfMbsh-kSdZrbzPteg_iBo_PqDmgVvxqyMCCHW33f_eV5wCrKACoaY0qvJW4Ks0IbIHpvz24H23FpqGpDynYr_RsLdjwt3cty31dZHtHOihnkhutln4Z4DzgMZxcbX23pJW7dXVkMN7Qg/http%3A%2F%2Fwww.nmr.mgh.harvard.edu%2Ffacility%2Ffiledrop%2Findex.html
>
>
>
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>is
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>e-mail
>contains patient information, please contact the Partners Compliance
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[Freesurfer] mri_glmfit with pvr

[stdp82]

External Email - Use Caution

Thanks

If I have 4 groups

GroupDescriptorFile 1
Title XXX
Class G1
Class G2
Class G3
Class G4

Input subj1 G1

Input subj2 G3

Input subj3 G2

Input subj4 G2

Input subj5 G4




Are the contrasts below corrected?

G1_only_thick 1 0 0 0

G2_only_thick 1 0 0 0

G3_only_thick 1 0 0 0

G4_only_thick 1 0 0 0

G1+G2-G3+G4_thick 0.5 0.5 -0.5 -0.5

G3+G4+G2+G1_thick -0.5 -0.5 0.5 0.5

G1+G2+G3+G4_thick 0.25 0.25 0.25 0.25

Thanks

Stefano



Yes, you use a "per-vertex map" (--pvr option to mri_glmfit). See, example, 
this thread 
https://secure-web.cisco.com/1AQW2Zmfaui0gjHDqfC-62qKrikS49RYbR7pNeQeTr2onenw4VdfUzxAD-yIGZ-RWjvqJqELbkeBxh-eEoHsrsM5sjWYXowa55h5HmDwS2HP-LGyy4SFdxgEGV4R5lhBK0pMIf8VhbvlMkoZpaRCGO9sEsN89fc0rgzYL83HiJvCE6vviDul0-oFKliOXHXlXxdd6kqkmidKljGOb8tcDOZX_cjdrLsH7G0YoQYuiemfio9U_qVDhfkyDU2t5DWXRvlVbn_e9Nkc3DJ7h0XjhCA/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg18790.htmlOn
 6/3/2021 10:22 AM, std...@virgilio.it wrote:

> External Email - Use Caution Hi, how can I perform vertex by vertex (surface) 
> analysis of covariance between functional connectivity data (FS-FAST) and 
> cortical thickness, regressing out the effect of groups?My mean concern is 
> how buid the fsgd file. Stefano
> 

Great news, thank you, Doug! Best, aga On 8/3/11 5:02 PM, "Douglas N Greve" 
 wrote:

>Hi Aga, what you have done is correct, no need to include the pvr in the
>fsgd.
>doug
>
>Burzynska, Aga wrote:
>> Dear all,
>> I am trying to make group level analysis of functional data on the
>>surface and add per-vertex regressors (PVR, here: cortical thickness)
>>into the design. When I view the results I have the feeling that the PVR
>>is not really included in the model:
>>
>> I am using the command:
>> mri_glmfit --glmdir lh_output --y cope1_lh_4D.mgh --fsgd
>>Group1versusGroup2.fsgd  --pvr lh.thickness.10.mgh --C
>>Group1only_thickness.mat --C Group2only_thickness.mat --C
>>Group1minusGroup2_thickness.mat --C Group2minusGroup1_thickness.mat --C
>>Group1plusGroup2_thickness.mat
>>
>> where
>> cope1_lh_4D.mgh contains the concatenated sig.mgh images from the fixed
>>level analysis (combining the runs) for each participant
>> fsgd file contains:
>> GroupDescriptorFile 1
>> Title Group1versusGroup2
>> Class Group1 
>> Class Group2
>> Input 1109 Group1
>> Input 1110 Group1
>> Input  Group1
>> Input 1112 Group1
>> ...
>> Input 2280  Group2
>> Input 2282  Group2
>> Input 2283  Group2
>> Input 2284  Group2
>>
>> The PVR is a file containing thickness maps for each participant,
>>concatenated in the same order as for the functional data.
>>
>> So there are 2 main regressors (1 factor, 2 levels), but the contrast
>>files contain 3 regressors (the third one is the PVE), for instance:
>> Group1minusGroup2_thickness.mat contains  1 -1 0.
>>
>> Does it look correct?
>> Should the pvr regressor be included in the fsdg file? How can I do it?
>>
>> Thank you very much for your help,
>> Cheers,
>> Aga
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://secure-web.cisco.com/1eQw4HlVWpF4ZzzChk-hp9V02K-k7R250ksr-ZRpjXC5ESaaFuyzgAuTFAoGhyEgYrYKrou0EXi_1ri2KpbhLu0RDRiF8JbcjNXFPW9pDzwKVvda8OwJaDhfqmDKW60AffvShgjctqkjGDrtVh3d5g5ibXvHnKxBrCeDpGoDotLpWBCKfctMD7RKY5GYQlCh3Un1XOMnnDFI7_MF2lAwup2vGzl11XZ_ZrOq3M8ZZB588KJPu216UQ-0rXaUfyN9kqO2LvtMM_BKWPkbPWLv1wQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>
>>
>>   
>
>-- 
>Douglas N. Greve, Ph.D.
>MGH-NMR Center
>gr...@nmr.mgh.harvard.edu
>Phone Number: 617-724-2358
>Fax: 617-726-7422
>
>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>FileDrop: 
>http://secure-web.cisco.com/1C61OSNwGFU8-MmX4hWZetUP6ivnpYMPZsypGZ1hSjsNzy-brmGySww1ZGhhngrVj1qYbuwE6PRUUeJN-f9A8A1WZ7th0QNfdUhXE6D3hKAkvirUMUgcYjEpbpiqr5EEx-zEFztskyh0Z_s-qx-pZYihOqIa83wP01adMhu1ZWGzu3R2R5BlSU44Kyj-7-8tjs4X0m9YumA2POfACS1X8JuGCd9bbmRQnsPob9yGBPtkb0saYprAkjBM9vSEkN54Sqsr6uuBnkzUu9th-uPKp8g/http%3A%2F%2Fwww.nmr.mgh.harvard.edu%2Ffacility%2Ffiledrop%2Findex.html
>
>
>
>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://secure-web.cisco.com/1SUkt2fsByhbVkrjyleWea7U8vPw7dJUUjO3n73A05t_91lBe900zX8Xj5BXS5FVVIPhPdXp82Z6tn-yeqKFAhUFk_5StCCsEPSU9TJVMOayzf4j0KrCyoFNj-C2OGDP0xFemZL4QAwmVXf6LLrOE9uXSoUkhZAdqVKfMGyQ69ZkTVjm5-iFg90fsEAVNWEfQKIfNgsAMcDyfxfoi3sAh7AkPp30_dgubiPt_de-c2xl98NuTVZv4kCbN3juzQ9BiEeSE28aMxZczxiclrU7Fxg/http%3A%2F%2Fwww.partners.org%2Fcomplianceline
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[Freesurfer] nalysis of covariance between functional connectivity data (FS-FAST) and cortical thickness

[stdp82]

External Email - Use Caution

Hi,

how can I perform vertex by vertex (surface) analysis of covariance between 
functional connectivity data (FS-FAST) and cortical thickness, regressing out 
the effect of groups?

My mean concern is how buid the fsgd file.

Stefano___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Time courses and Yeo’s boundaries

[stdp82]

 
 External Email - Use Caution
  
   Hi,
  
  
   
  
  
   I have two questions please:
  
  
   
  
  
   Hi
  
  
   
  
  
   1. I’d like to extract the time courses of fMRI data from some selected ROIs.
  
  
   How can I do it? For Yeo’s ROI (splitted atlas) is better to do it on surface or operate in volume?
  
  
   
  
  
   2. I’m using version 6.0. Probably also due to Mac OS X update, I can not use tksurfer. The using freeview I can not overlap the Yeo’s bunduries on FAST results. Freeviewer overlaps colored dots to indetify the location of Yeo’s components.
  
  
   How can I do to overlap on FAST results Yeo’s bundaries?
  
  
   
  
  
   Best regard
  
 

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Re: [Freesurfer] vol2subfield single time course from multiple regions

[stdp82]

External Email - Use Caution

thanks!

> Il 18 maggio 2020 alle 16.23 Bruce Fischl < fis...@nmr.mgh.harvard.edu 
> mailto:fis...@nmr.mgh.harvard.edu > ha scritto:
> 
> 
> --replaceonly   \
> --replaceonly   \
> .
> .
> .
> 
> On Mon, 18 May 2020, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> 
> > > External Email - Use Caution
> > 
> > As reported in previous mails I have do it but with some problems.
> > 
> > Moreover, how can I do with multiple arguments (more than 2)?
> > 
> > > 
> > > Il 17 maggio 2020 alle 21.30 Bruce Fischl <
> > fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu > ha 
> > scritto:
> > 
> > 
> > Hi Stefano
> > 
> > --replaceonly takes two arguments - the label you want to replace 
> > and
> > the
> > one you want to replace it with
> > 
> > cheers
> > Bruce
> > 
> > 
> > On Sun, 17 May 2020, std...@virgilio.it mailto:std...@virgilio.it 
> > wrote:
> > 
> > > 
> > > External Email - Use Caution
> > 
> > just a kind reminder
> > 
> > many thanks
> > 
> > > 
> > > Il 15 maggio 2020 alle 1.05 std...@virgilio.it 
> mailto:std...@virgilio.it ha scritto:
> > 
> > > 
> > > mri_binarize --i
> > $SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz
> > --replaceonly 8204 --replaceonly 8205 --replaceonly 8206
> > --replaceonly 8217 --replaceonly 8218 --o
> > $SUBJECTS_DIR/R-Intralaminar.mgz
> > 
> > ERROR: Option 8205 unknown
> > 
> > 
> > mri_binarize --i $SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz
> > --replaceonly 8204 --replaceonly 8205 --replaceonly 8217
> > --replaceonly
> > 8218 --o $SUBJECTS_DIR/R-Intralaminar.mgz
> > 
> > ERROR: Option 8217 unknown
> > Il 14 maggio 2020 alle 17.39 "Douglas N. Greve"
> > < dgr...@mgh.harvard.edu mailto:dgr...@mgh.harvard.edu > ha scritto:
> > 
> > > 
> > > Just add more --replaceonly args
> > 
> > > 
> > > On 5/14/2020 10:38 AM, std...@virgilio.it 
> mailto:std...@virgilio.it wrote:
> > 
> > > 
> > > External Email - Use Caution
> > 
> > > 
> > > Moreover, how can I merge, with mri_binarize, more
> > thalamic regions?
> > 
> > > 
> > > e.g. 8204 8205 8206 8217 8218
> > 
> > > 
> > > Il 13 maggio 2020 alle 23.03 "Douglas N.
> > Greve" < dgr...@mgh.harvard.edu mailto:dgr...@mgh.harvard.edu > ha
> > scritto:
> > 
> > > 
> > > It problably means that seg 8130 does
> > not exist in the input mgz. Can you
> > confirm that it does?
> > 
> > > 
> > > On 5/13/2020 12:51 PM,
> > std...@virgilio.it mailto:std...@virgilio.it wrote:
> > 
> > > 
> > > External Email - Use
> > Caution
> > 
> > > 
> > > indeed. I would like to merge two
> > regions and extract the fMRI time serie.
> > if no difference is there, somewhat is
> > wrong. the L-VP file contains the same
> > information of ThalamicNuclei.v10.T1.
> > 
> > > 
> > > thanks
> > 
> > > 
> > > Il 13 maggio 2020 alle 17.02
> > "Douglas N. Greve"
> > < dgr...@mgh.harvard.edu mailto:dgr...@mgh.harvard.edu > ha
> > scritto:
> > 
> > > 
> > > That means there is no
> > difference
> > 
> > > 
> > > On 5/13/2020 10:47 AM,
> > std...@virgilio.it mailto:std...@virgilio.it wrote:
> > 
> > > 
> > > External Email - Use
> > Caution
> > 
> > > 
> > > is the command line ok?
> > 
> > > 
> > > by running
> > 
> > > 
> > > mri_binarize --i
> > ThalamicNuclei.v10.T1.mgz
> > --replace-only 8130 8133 --o
> > L-VP.mgz
> > 
> > > 
> > > mri_diff --po
> > mri/ThalamicNuclei.v10.T1.mgz
> > L-VP.mgz  
> > 
> > > 
> > > I obtain
> > diffcount 0
> > 
> > > 
> > > Il 12 maggio 2020 alle
> > 0.53
> > std...@virgilio.it mailto:std...@virgilio.it ha
> > scritto:
> > 
> > > 
> > > by running
> > mri_diff --po
> > mri/ThalamicNuclei.v10.T1.mgz
> > L-VP.mgz  
> > I obtain
> > diffcount 0
> > 
> > > 
> > > Il 11 maggio
> > 2020 alle 19.18
> > "Douglas N.
> > Greve"
> > < dgr...@mgh.harvard.edu mailto:dgr...@mgh.harvard.edu >
> > ha scritto:
> > 
> > > 
> > > Try running this
> > 

Re: [Freesurfer] vol2subfield single time course from multiple regions

[stdp82]

External Email - Use Caution

As reported in previous mails I have do it but with some problems.

Moreover, how can I do with multiple arguments (more than 2)?

> Il 17 maggio 2020 alle 21.30 Bruce Fischl < fis...@nmr.mgh.harvard.edu 
> mailto:fis...@nmr.mgh.harvard.edu > ha scritto:
> 
> 
> Hi Stefano
> 
> --replaceonly takes two arguments - the label you want to replace and the
> one you want to replace it with
> 
> cheers
> Bruce
> 
> 
> On Sun, 17 May 2020, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> 
> > > External Email - Use Caution
> > 
> > just a kind reminder
> > 
> > many thanks
> > 
> > 
> > > 
> > > Il 15 maggio 2020 alle 1.05 std...@virgilio.it 
> mailto:std...@virgilio.it ha scritto:
> > 
> > > 
> > > mri_binarize --i 
> $SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz
> > --replaceonly 8204 --replaceonly 8205 --replaceonly 8206
> > --replaceonly 8217 --replaceonly 8218 --o
> > $SUBJECTS_DIR/R-Intralaminar.mgz
> > 
> > ERROR: Option 8205 unknown
> > 
> > 
> > mri_binarize --i $SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz
> > --replaceonly 8204 --replaceonly 8205 --replaceonly 8217 
> > --replaceonly
> > 8218 --o $SUBJECTS_DIR/R-Intralaminar.mgz
> > 
> > ERROR: Option 8217 unknown
> > Il 14 maggio 2020 alle 17.39 "Douglas N. Greve"
> > < dgr...@mgh.harvard.edu mailto:dgr...@mgh.harvard.edu > ha scritto:
> > 
> > > 
> > > Just add more --replaceonly args
> > 
> > > 
> > > On 5/14/2020 10:38 AM, std...@virgilio.it 
> mailto:std...@virgilio.it wrote:
> > 
> > > 
> > > External Email - Use Caution
> > 
> > > 
> > > Moreover, how can I merge, with mri_binarize, more
> > thalamic regions?
> > 
> > > 
> > > e.g. 8204 8205 8206 8217 8218
> > 
> > 
> > > 
> > > Il 13 maggio 2020 alle 23.03 "Douglas N.
> > Greve" < dgr...@mgh.harvard.edu mailto:dgr...@mgh.harvard.edu > ha
> > scritto:
> > 
> > > 
> > > It problably means that seg 8130 does
> > not exist in the input mgz. Can you
> > confirm that it does?
> > 
> > > 
> > > On 5/13/2020 12:51 PM,
> > std...@virgilio.it mailto:std...@virgilio.it wrote:
> > 
> > > 
> > > External Email - Use
> > Caution
> > 
> > > 
> > > indeed. I would like to merge two
> > regions and extract the fMRI time serie.
> > if no difference is there, somewhat is
> > wrong. the L-VP file contains the same
> > information of ThalamicNuclei.v10.T1.
> > 
> > > 
> > > thanks
> > 
> > 
> > > 
> > > Il 13 maggio 2020 alle 17.02
> > "Douglas N. Greve"
> > < dgr...@mgh.harvard.edu mailto:dgr...@mgh.harvard.edu > ha
> > scritto:
> > 
> > > 
> > > That means there is no
> > difference
> > 
> > > 
> > > On 5/13/2020 10:47 AM,
> > std...@virgilio.it mailto:std...@virgilio.it wrote:
> > 
> > > 
> > > External Email - Use
> > Caution
> > 
> > > 
> > > is the command line ok?
> > 
> > > 
> > > by running
> > 
> > > 
> > > mri_binarize --i
> > ThalamicNuclei.v10.T1.mgz
> > --replace-only 8130 8133 --o
> > L-VP.mgz
> > 
> > > 
> > > mri_diff --po
> > mri/ThalamicNuclei.v10.T1.mgz
> > L-VP.mgz  
> > 
> > > 
> > > I obtain
> > diffcount 0
> > 
> > 
> > > 
> > > Il 12 maggio 2020 alle
> > 0.53
> > std...@virgilio.it mailto:std...@virgilio.it ha
> > scritto:
> > 
> > > 
> > > by running
> > mri_diff --po
> > mri/ThalamicNuclei.v10.T1.mgz
> > L-VP.mgz  
> > I obtain
> > diffcount 0
> > 
> > 
> > > 
> > > Il 11 maggio
> > 2020 alle 19.18
> > "Douglas N.
> > Greve"
> > < dgr...@mgh.harvard.edu mailto:dgr...@mgh.harvard.edu >
> > ha scritto:
> > 
> > > 
> > > Try running this
> > to see if there
> > is a difference
> > mri_diff --po
> > ThalamicNuclei.v10.T1.mgz
> > Left-Ventroposterior.mgz
> > Sometimes it is
> > not easy to see
> > a difference
> > that is just a
> > few voxels
> > 
> > > 
> > > On 5/11/2020
> > 3:02 AM,
> > std...@virgilio.it mailto:std...@virgilio.it
> > wrote:
> > 
> > > 
> > > External
> > Email -
> > 

Re: [Freesurfer] vol2subfield single time course from multiple regions

[stdp82]

External Email - Use Caution

just a kind reminder

many thanks


> Il 15 maggio 2020 alle 1.05 std...@virgilio.it ha scritto:
> 
> mri_binarize --i $SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz 
> --replaceonly 8204 --replaceonly 8205 --replaceonly 8206 --replaceonly 8217 
> --replaceonly 8218 --o $SUBJECTS_DIR/R-Intralaminar.mgz
> 
> ERROR: Option 8205 unknown
> 
> 
> mri_binarize --i $SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz 
> --replaceonly 8204 --replaceonly 8205 --replaceonly 8217 --replaceonly 8218 
> --o $SUBJECTS_DIR/R-Intralaminar.mgz
> 
> ERROR: Option 8217 unknown
> 
> > > Il 14 maggio 2020 alle 17.39 "Douglas N. Greve" 
>  ha scritto:
> > 
> > Just add more --replaceonly args
> > 
> > On 5/14/2020 10:38 AM, std...@virgilio.it mailto:std...@virgilio.it 
> > wrote:
> > 
> > > > > 
> > > External Email - Use Caution
> > > 
> > > Moreover, how can I merge, with mri_binarize, more thalamic 
> > > regions?
> > > 
> > > e.g. 8204 8205 8206 8217 8218
> > > 
> > > 
> > > > > > > Il 13 maggio 2020 alle 23.03 "Douglas N. Greve" 
> > >  mailto:dgr...@mgh.harvard.edu ha scritto:
> > > > 
> > > > It problably means that seg 8130 does not exist in the 
> > > > input mgz. Can you confirm that it does?
> > > > 
> > > > On 5/13/2020 12:51 PM, std...@virgilio.it 
> > > > mailto:std...@virgilio.it wrote:
> > > > 
> > > > > > > > > 
> > > > > External Email - Use Caution
> > > > > 
> > > > > indeed. I would like to merge two regions and 
> > > > > extract the fMRI time serie. if no difference is there, somewhat is 
> > > > > wrong. the L-VP file contains the same information of 
> > > > > ThalamicNuclei.v10.T1.
> > > > > 
> > > > > thanks
> > > > > 
> > > > > 
> > > > > > > > > > > Il 13 maggio 2020 alle 17.02 
> > > > > "Douglas N. Greve"  
> > > > > mailto:dgr...@mgh.harvard.edu ha scritto:
> > > > > > 
> > > > > > That means there is no difference
> > > > > > 
> > > > > > On 5/13/2020 10:47 AM, std...@virgilio.it 
> > > > > > mailto:std...@virgilio.it wrote:
> > > > > > 
> > > > > > > > > > > > > 
> > > > > > > External Email - Use Caution  
> > > > > > >   
> > > > > > > 
> > > > > > > is the command line ok?
> > > > > > > 
> > > > > > > by running
> > > > > > > 
> > > > > > > mri_binarize --i 
> > > > > > > ThalamicNuclei.v10.T1.mgz --replace-only 8130 8133 --o L-VP.mgz
> > > > > > > 
> > > > > > > mri_diff --po 
> > > > > > > mri/ThalamicNuclei.v10.T1.mgz L-VP.mgz  
> > > > > > > 
> > > > > > > I obtain
> > > > > > > diffcount 0
> > > > > > > 
> > > > > > > 
> > > > > > > 
> > > > > > > > > > > > > > > Il 12 maggio 2020 
> > > > > > > alle 0.53 std...@virgilio.it mailto:std...@virgilio.it ha scritto:
> > > > > > > > 
> > > > > > > > by running
> > > > > > > > mri_diff --po 
> > > > > > > > mri/ThalamicNuclei.v10.T1.mgz L-VP.mgz  
> > > > > > > > I obtain
> > > > > > > > diffcount 0
> > > > > > > > 
> > > > > > > > 
> > > > > > > > 
> > > > > > > > > > > > > > > > > Il 11 
> > > > > > > > maggio 2020 alle 19.18 "Douglas N. Greve" 
> > > > > > > >  mailto:dgr...@mgh.harvard.edu ha 
> > > > > > > > scritto:
> > > > > > > > > 
> > > > > > > > > Try running this to see 
> > > > > > > > > if there is a difference
> > > > > > > > > mri_diff --po 
> > > > > > > > > ThalamicNuclei.v10.T1.mgz Left-Ventroposterior.mgz
> > > > > > > > > Sometimes it is not easy 
> > > > > > > > > to see a difference that is just a few voxels
> > > > > > > > > 
> > > > > > > > > On 5/11/2020 3:02 AM, 
> > > > > > > > > std...@virgilio.it mailto:std...@virgilio.it wrote:
> > > > > > > > > 
> > > > > > > > > > > > > > > > > > > 
> > > > > > > > > > External 
> > > > > > > > > > Email - Use Caution
> > > > > > > > > > 
> > > > > > > > > > By visualizing the 
> > > > > > > > > > output by freeview, I found that it was the same of 
> > > > > > > > > > ThalamicNuclei.v10.T1.mgz.
> > > > > > > > > > 
> > > > > > > > > > Thanks
> > > > > > > > > > 
> > > > > > > > > >   

Re: [Freesurfer] vol2subfield single time course from multiple regions

[stdp82]

External Email - Use Caution

mri_binarize --i $SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz --replaceonly 8204 
--replaceonly 8205 --replaceonly 8206 --replaceonly 8217 --replaceonly 8218 --o 
$SUBJECTS_DIR/R-Intralaminar.mgz

ERROR: Option 8205 unknown


mri_binarize --i $SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz --replaceonly 8204 
--replaceonly 8205 --replaceonly 8217 --replaceonly 8218 --o 
$SUBJECTS_DIR/R-Intralaminar.mgz

ERROR: Option 8217 unknown

> Il 14 maggio 2020 alle 17.39 "Douglas N. Greve"  ha 
> scritto:
> 
> Just add more --replaceonly args
> 
> On 5/14/2020 10:38 AM, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> > > 
> > External Email - Use Caution
> > 
> > Moreover, how can I merge, with mri_binarize, more thalamic regions?
> > 
> > e.g. 8204 8205 8206 8217 8218
> > 
> > 
> > > > > Il 13 maggio 2020 alle 23.03 "Douglas N. Greve" 
> >  mailto:dgr...@mgh.harvard.edu ha scritto:
> > > 
> > > It problably means that seg 8130 does not exist in the input 
> > > mgz. Can you confirm that it does?
> > > 
> > > On 5/13/2020 12:51 PM, std...@virgilio.it 
> > > mailto:std...@virgilio.it wrote:
> > > 
> > > > > > > 
> > > > External Email - Use Caution
> > > > 
> > > > indeed. I would like to merge two regions and extract 
> > > > the fMRI time serie. if no difference is there, somewhat is wrong. the 
> > > > L-VP file contains the same information of ThalamicNuclei.v10.T1.
> > > > 
> > > > thanks
> > > > 
> > > > 
> > > > > > > > > Il 13 maggio 2020 alle 17.02 "Douglas N. 
> > > > Greve"  mailto:dgr...@mgh.harvard.edu ha 
> > > > scritto:
> > > > > 
> > > > > That means there is no difference
> > > > > 
> > > > > On 5/13/2020 10:47 AM, std...@virgilio.it 
> > > > > mailto:std...@virgilio.it wrote:
> > > > > 
> > > > > > > > > > > 
> > > > > > External Email - Use Caution
> > > > > > 
> > > > > > is the command line ok?
> > > > > > 
> > > > > > by running
> > > > > > 
> > > > > > mri_binarize --i ThalamicNuclei.v10.T1.mgz 
> > > > > > --replace-only 8130 8133 --o L-VP.mgz
> > > > > > 
> > > > > > mri_diff --po mri/ThalamicNuclei.v10.T1.mgz 
> > > > > > L-VP.mgz  
> > > > > > 
> > > > > > I obtain
> > > > > > diffcount 0
> > > > > > 
> > > > > > 
> > > > > > 
> > > > > > > > > > > > > Il 12 maggio 2020 alle 
> > > > > > 0.53 std...@virgilio.it mailto:std...@virgilio.it ha scritto:
> > > > > > > 
> > > > > > > by running
> > > > > > > mri_diff --po 
> > > > > > > mri/ThalamicNuclei.v10.T1.mgz L-VP.mgz  
> > > > > > > I obtain
> > > > > > > diffcount 0
> > > > > > > 
> > > > > > > 
> > > > > > > 
> > > > > > > > > > > > > > > Il 11 maggio 2020 
> > > > > > > alle 19.18 "Douglas N. Greve"  
> > > > > > > mailto:dgr...@mgh.harvard.edu ha scritto:
> > > > > > > > 
> > > > > > > > Try running this to see if 
> > > > > > > > there is a difference
> > > > > > > > mri_diff --po 
> > > > > > > > ThalamicNuclei.v10.T1.mgz Left-Ventroposterior.mgz
> > > > > > > > Sometimes it is not easy to see 
> > > > > > > > a difference that is just a few voxels
> > > > > > > > 
> > > > > > > > On 5/11/2020 3:02 AM, 
> > > > > > > > std...@virgilio.it mailto:std...@virgilio.it wrote:
> > > > > > > > 
> > > > > > > > > > > > > > > > > 
> > > > > > > > > External Email - 
> > > > > > > > > Use Caution
> > > > > > > > > 
> > > > > > > > > By visualizing the output 
> > > > > > > > > by freeview, I found that it was the same of 
> > > > > > > > > ThalamicNuclei.v10.T1.mgz.
> > > > > > > > > 
> > > > > > > > > Thanks
> > > > > > > > > 
> > > > > > > > > > > > > > > > > > >   
> > > > > > > > >   Il 11 maggio 2020 alle 
> > > > > > > > > 2.19 Bruce Fischl < fis...@nmr.mgh.harvard.edu 
> > > > > > > > > mailto:fis...@nmr.mgh.harvard.edu > ha scritto:
> > > > > > > > > > 
> > > > > > > > > > 
> > > > > > > > > > Hi Stefano
> > > > > > > > > > 
> > > > > > > > > > can you elaborate? 
> > > > > > > > > > Why do you suspect there is an error?
> > > > > > > > > > 
> > > > 

Re: [Freesurfer] vol2subfield single time course from multiple regions

[stdp82]

External Email - Use Caution

mri_segstats --seg $SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz --ctab-default 
--sum sum.dat --id 8130  

Using defalt ctab /Applications/freesurfer/FreeSurferColorLUT.txt



$Id: mri_segstats.c,v 1.122 2017/01/23 18:23:14 greve Exp $

cwd  

cmdline mri_segstats --seg $SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz 
--ctab-default --sum sum.dat --id 8130  

sysnameDarwin

hostname iMac.local

machinex86_64

user ...

whitesurfnamewhite

UseRobust0

Loading $SUBJECTS_DIR/mri/ThalamicNuclei.v10.T1.mgz

Voxel Volume is 0.125 mm^3

Generating list of segmentation ids

Found 1 segmentations

Computing statistics for each segmentation



Reporting on 0 segmentations

Using PrintSegStat

mri_segstats done



> Il 14 maggio 2020 alle 17.39 "Douglas N. Greve"  ha 
> scritto:
> 
> Try running
> mri_segstats --seg ThalamicNuclei.v10.T1.mgz --ctab-default --sum sum.dat 
> --id 8130
> And send the contents of sum.dat
> 
> 
> On 5/13/2020 7:37 PM, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> > > 
> > External Email - Use Caution
> > 
> > In the FreeSurferColorLUT.txt 8130 is the left VM.
> > 
> > The volume is correctly calculated in the VM of the subject.
> > 
> > I have tried with:
> > mri_binarize --i ThalamicNuclei.v10.T1.mgz --replaceonly 8126 8127 
> > --o L-VA.mgz
> > 
> > mri_diff --po ThalamicNuclei.v10.T1.mgz L-VA.mgz
> > 
> > diffcount 3389
> > 
> > Volumes differ in pixel data
> > 
> > maxdiff 1. at 104 61 88 0
> > 
> > 
> > It seems works fine. Agree?
> > 
> > The concern remains on L-VP.
> > 
> > 
> > 
> > 
> > 
> > > > > Il 13 maggio 2020 alle 23.03 "Douglas N. Greve" 
> >  mailto:dgr...@mgh.harvard.edu ha scritto:
> > > 
> > > It problably means that seg 8130 does not exist in the input 
> > > mgz. Can you confirm that it does?
> > > 
> > > On 5/13/2020 12:51 PM, std...@virgilio.it 
> > > mailto:std...@virgilio.it wrote:
> > > 
> > > > > > > 
> > > > External Email - Use Caution
> > > > 
> > > > indeed. I would like to merge two regions and extract 
> > > > the fMRI time serie. if no difference is there, somewhat is wrong. the 
> > > > L-VP file contains the same information of ThalamicNuclei.v10.T1.
> > > > 
> > > > thanks
> > > > 
> > > > 
> > > > > > > > > Il 13 maggio 2020 alle 17.02 "Douglas N. 
> > > > Greve"  mailto:dgr...@mgh.harvard.edu ha 
> > > > scritto:
> > > > > 
> > > > > That means there is no difference
> > > > > 
> > > > > On 5/13/2020 10:47 AM, std...@virgilio.it 
> > > > > mailto:std...@virgilio.it wrote:
> > > > > 
> > > > > > > > > > > 
> > > > > > External Email - Use Caution
> > > > > > 
> > > > > > is the command line ok?
> > > > > > 
> > > > > > by running
> > > > > > 
> > > > > > mri_binarize --i ThalamicNuclei.v10.T1.mgz 
> > > > > > --replace-only 8130 8133 --o L-VP.mgz
> > > > > > 
> > > > > > mri_diff --po mri/ThalamicNuclei.v10.T1.mgz 
> > > > > > L-VP.mgz  
> > > > > > 
> > > > > > I obtain
> > > > > > diffcount 0
> > > > > > 
> > > > > > 
> > > > > > 
> > > > > > > > > > > > > Il 12 maggio 2020 alle 
> > > > > > 0.53 std...@virgilio.it mailto:std...@virgilio.it ha scritto:
> > > > > > > 
> > > > > > > by running
> > > > > > > mri_diff --po 
> > > > > > > mri/ThalamicNuclei.v10.T1.mgz L-VP.mgz  
> > > > > > > I obtain
> > > > > > > diffcount 0
> > > > > > > 
> > > > > > > 
> > > > > > > 
> > > > > > > > > > > > > > > Il 11 maggio 2020 
> > > > > > > alle 19.18 "Douglas N. Greve"  
> > > > > > > mailto:dgr...@mgh.harvard.edu ha scritto:
> > > > > > > > 
> > > > > > > > Try running this to see if 
> > > > > > > > there is a difference
> > > > > > > > mri_diff --po 
> > > > > > > > ThalamicNuclei.v10.T1.mgz Left-Ventroposterior.mgz
> > > > > > > > Sometimes it is not easy to see 
> > > > > > > > a difference that is just a few voxels
> > > > > > > > 
> > > > > > > > On 5/11/2020 3:02 AM, 
> > > > > > > > std...@virgilio.it mailto:std...@virgilio.it wrote:
> > > > > > > > 
> > > > > > > > > > > > > > > > > 
> > > > > > > > > External Email - 
> > > > > > > > > Use Caution
> > > > > > > > > 
> > > > > > > > >

Re: [Freesurfer] vol2subfield single time course from multiple regions

[stdp82]

External Email - Use Caution

Moreover, how can I merge, with mri_binarize, more thalamic regions?

e.g. 8204 8205 8206 8217 8218


> Il 13 maggio 2020 alle 23.03 "Douglas N. Greve"  ha 
> scritto:
> 
> It problably means that seg 8130 does not exist in the input mgz. Can you 
> confirm that it does?
> 
> On 5/13/2020 12:51 PM, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> > > 
> > External Email - Use Caution
> > 
> > indeed. I would like to merge two regions and extract the fMRI time 
> > serie. if no difference is there, somewhat is wrong. the L-VP file contains 
> > the same information of ThalamicNuclei.v10.T1.
> > 
> > thanks
> > 
> > 
> > > > > Il 13 maggio 2020 alle 17.02 "Douglas N. Greve" 
> >  mailto:dgr...@mgh.harvard.edu ha scritto:
> > > 
> > > That means there is no difference
> > > 
> > > On 5/13/2020 10:47 AM, std...@virgilio.it 
> > > mailto:std...@virgilio.it wrote:
> > > 
> > > > > > > 
> > > > External Email - Use Caution
> > > > 
> > > > is the command line ok?
> > > > 
> > > > by running
> > > > 
> > > > mri_binarize --i ThalamicNuclei.v10.T1.mgz 
> > > > --replace-only 8130 8133 --o L-VP.mgz
> > > > 
> > > > mri_diff --po mri/ThalamicNuclei.v10.T1.mgz L-VP.mgz  
> > > > 
> > > > I obtain
> > > > diffcount 0
> > > > 
> > > > 
> > > > 
> > > > > > > > > Il 12 maggio 2020 alle 0.53 
> > > > std...@virgilio.it mailto:std...@virgilio.it ha scritto:
> > > > > 
> > > > > by running
> > > > > mri_diff --po mri/ThalamicNuclei.v10.T1.mgz 
> > > > > L-VP.mgz  
> > > > > I obtain
> > > > > diffcount 0
> > > > > 
> > > > > 
> > > > > 
> > > > > > > > > > > Il 11 maggio 2020 alle 19.18 
> > > > > "Douglas N. Greve"  
> > > > > mailto:dgr...@mgh.harvard.edu ha scritto:
> > > > > > 
> > > > > > Try running this to see if there is a 
> > > > > > difference
> > > > > > mri_diff --po ThalamicNuclei.v10.T1.mgz 
> > > > > > Left-Ventroposterior.mgz
> > > > > > Sometimes it is not easy to see a 
> > > > > > difference that is just a few voxels
> > > > > > 
> > > > > > On 5/11/2020 3:02 AM, std...@virgilio.it 
> > > > > > mailto:std...@virgilio.it wrote:
> > > > > > 
> > > > > > > > > > > > > 
> > > > > > > External Email - Use Caution  
> > > > > > >   
> > > > > > > 
> > > > > > > By visualizing the output by 
> > > > > > > freeview, I found that it was the same of 
> > > > > > > ThalamicNuclei.v10.T1.mgz.
> > > > > > > 
> > > > > > > Thanks
> > > > > > > 
> > > > > > > > > > > > > > >   
> > > > > > >   Il 11 maggio 2020 alle 2.19 Bruce Fischl < 
> > > > > > > fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu > ha 
> > > > > > > scritto:
> > > > > > > > 
> > > > > > > > 
> > > > > > > > Hi Stefano
> > > > > > > > 
> > > > > > > > can you elaborate? Why do you 
> > > > > > > > suspect there is an error?
> > > > > > > > 
> > > > > > > > cheers
> > > > > > > > Bruce
> > > > > > > > On Mon, 11 May
> > > > > > > > 2020, std...@virgilio.it 
> > > > > > > > mailto:std...@virgilio.it wrote:
> > > > > > > > 
> > > > > > > > 
> > > > > > > > > > > > > > > > >   
> > > > > > > >   External Email - Use Caution  
> > > > > > > >   
> > > > > > > > > 
> > > > > > > > > Please, could you check 
> > > > > > > > > the command line.
> > > > > > > > > I suspect that an error 
> > > > > > > > > is there.
> > > > > > > > > Thanks.
> > > > > > > > > Stefano
> > > > > > > > > 
> > > > > > > > > mri_binarize --i 
> > > > > > > > > ThalamicNuclei.v10.T1.mgz --replace-only 8130   8133 --o
> > > > > > > > > Left-Ventroposterior.mgz
> > > > > > > > > 
> > > > > > > > > 
> > > > > > > > > > > > > > > > > 
> > > > > > > > > > > > > > > > >   
> > > > > > > >   Il 30 aprile 2020 alle 18.51 "Douglas 
> > > > > > > > N. Greve"
> > > > > > > > > < 

Re: [Freesurfer] vol2subfield single time course from multiple regions

[stdp82]

External Email - Use Caution

In the FreeSurferColorLUT.txt 8130 is the left VM.

The volume is correctly calculated in the VM of the subject.

I have tried with:
mri_binarize --i ThalamicNuclei.v10.T1.mgz --replaceonly 8126 8127 --o L-VA.mgz

mri_diff --po ThalamicNuclei.v10.T1.mgz L-VA.mgz

diffcount 3389

Volumes differ in pixel data

maxdiff 1. at 104 61 88 0


It seems works fine. Agree?

The concern remains on L-VP.






> Il 13 maggio 2020 alle 23.03 "Douglas N. Greve"  ha 
> scritto:
> 
> It problably means that seg 8130 does not exist in the input mgz. Can you 
> confirm that it does?
> 
> On 5/13/2020 12:51 PM, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> > > 
> > External Email - Use Caution
> > 
> > indeed. I would like to merge two regions and extract the fMRI time 
> > serie. if no difference is there, somewhat is wrong. the L-VP file contains 
> > the same information of ThalamicNuclei.v10.T1.
> > 
> > thanks
> > 
> > 
> > > > > Il 13 maggio 2020 alle 17.02 "Douglas N. Greve" 
> >  mailto:dgr...@mgh.harvard.edu ha scritto:
> > > 
> > > That means there is no difference
> > > 
> > > On 5/13/2020 10:47 AM, std...@virgilio.it 
> > > mailto:std...@virgilio.it wrote:
> > > 
> > > > > > > 
> > > > External Email - Use Caution
> > > > 
> > > > is the command line ok?
> > > > 
> > > > by running
> > > > 
> > > > mri_binarize --i ThalamicNuclei.v10.T1.mgz 
> > > > --replace-only 8130 8133 --o L-VP.mgz
> > > > 
> > > > mri_diff --po mri/ThalamicNuclei.v10.T1.mgz L-VP.mgz  
> > > > 
> > > > I obtain
> > > > diffcount 0
> > > > 
> > > > 
> > > > 
> > > > > > > > > Il 12 maggio 2020 alle 0.53 
> > > > std...@virgilio.it mailto:std...@virgilio.it ha scritto:
> > > > > 
> > > > > by running
> > > > > mri_diff --po mri/ThalamicNuclei.v10.T1.mgz 
> > > > > L-VP.mgz  
> > > > > I obtain
> > > > > diffcount 0
> > > > > 
> > > > > 
> > > > > 
> > > > > > > > > > > Il 11 maggio 2020 alle 19.18 
> > > > > "Douglas N. Greve"  
> > > > > mailto:dgr...@mgh.harvard.edu ha scritto:
> > > > > > 
> > > > > > Try running this to see if there is a 
> > > > > > difference
> > > > > > mri_diff --po ThalamicNuclei.v10.T1.mgz 
> > > > > > Left-Ventroposterior.mgz
> > > > > > Sometimes it is not easy to see a 
> > > > > > difference that is just a few voxels
> > > > > > 
> > > > > > On 5/11/2020 3:02 AM, std...@virgilio.it 
> > > > > > mailto:std...@virgilio.it wrote:
> > > > > > 
> > > > > > > > > > > > > 
> > > > > > > External Email - Use Caution  
> > > > > > >   
> > > > > > > 
> > > > > > > By visualizing the output by 
> > > > > > > freeview, I found that it was the same of 
> > > > > > > ThalamicNuclei.v10.T1.mgz.
> > > > > > > 
> > > > > > > Thanks
> > > > > > > 
> > > > > > > > > > > > > > >   
> > > > > > >   Il 11 maggio 2020 alle 2.19 Bruce Fischl < 
> > > > > > > fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu > ha 
> > > > > > > scritto:
> > > > > > > > 
> > > > > > > > 
> > > > > > > > Hi Stefano
> > > > > > > > 
> > > > > > > > can you elaborate? Why do you 
> > > > > > > > suspect there is an error?
> > > > > > > > 
> > > > > > > > cheers
> > > > > > > > Bruce
> > > > > > > > On Mon, 11 May
> > > > > > > > 2020, std...@virgilio.it 
> > > > > > > > mailto:std...@virgilio.it wrote:
> > > > > > > > 
> > > > > > > > 
> > > > > > > > > > > > > > > > >   
> > > > > > > >   External Email - Use Caution  
> > > > > > > >   
> > > > > > > > > 
> > > > > > > > > Please, could you check 
> > > > > > > > > the command line.
> > > > > > > > > I suspect that an error 
> > > > > > > > > is there.
> > > > > > > > > Thanks.
> > > > > > > > > Stefano
> > > > > > > > > 
> > > > > > > > > mri_binarize --i 
> > > > > > > > > ThalamicNuclei.v10.T1.mgz --replace-only 8130   8133 --o
> > > > > > > > > Left-Ventroposterior.mgz
> > > > > > > > > 
> > > > > > > > > 
> > > > > > > 

Re: [Freesurfer] vol2subfield single time course from multiple regions

[stdp82]

External Email - Use Caution

indeed. I would like to merge two regions and extract the fMRI time serie. if 
no difference is there, somewhat is wrong. the L-VP file contains the same 
information of ThalamicNuclei.v10.T1.

thanks


> Il 13 maggio 2020 alle 17.02 "Douglas N. Greve"  ha 
> scritto:
> 
> That means there is no difference
> 
> On 5/13/2020 10:47 AM, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> > > 
> > External Email - Use Caution
> > 
> > is the command line ok?
> > 
> > by running
> > 
> > mri_binarize --i ThalamicNuclei.v10.T1.mgz --replace-only 8130 8133 
> > --o L-VP.mgz
> > 
> > mri_diff --po mri/ThalamicNuclei.v10.T1.mgz L-VP.mgz  
> > 
> > I obtain
> > diffcount 0
> > 
> > 
> > 
> > > > > Il 12 maggio 2020 alle 0.53 std...@virgilio.it 
> > mailto:std...@virgilio.it ha scritto:
> > > 
> > > by running
> > > mri_diff --po mri/ThalamicNuclei.v10.T1.mgz L-VP.mgz  
> > > I obtain
> > > diffcount 0
> > > 
> > > 
> > > 
> > > > > > > Il 11 maggio 2020 alle 19.18 "Douglas N. Greve" 
> > >  mailto:dgr...@mgh.harvard.edu ha scritto:
> > > > 
> > > > Try running this to see if there is a difference
> > > > mri_diff --po ThalamicNuclei.v10.T1.mgz 
> > > > Left-Ventroposterior.mgz
> > > > Sometimes it is not easy to see a difference that is 
> > > > just a few voxels
> > > > 
> > > > On 5/11/2020 3:02 AM, std...@virgilio.it 
> > > > mailto:std...@virgilio.it wrote:
> > > > 
> > > > > > > > > 
> > > > > External Email - Use Caution
> > > > > 
> > > > > By visualizing the output by freeview, I found 
> > > > > that it was the same of ThalamicNuclei.v10.T1.mgz.
> > > > > 
> > > > > Thanks
> > > > > 
> > > > > > > > > > > Il 11 
> > > > > maggio 2020 alle 2.19 Bruce Fischl < fis...@nmr.mgh.harvard.edu 
> > > > > mailto:fis...@nmr.mgh.harvard.edu > ha scritto:
> > > > > > 
> > > > > > 
> > > > > > Hi Stefano
> > > > > > 
> > > > > > can you elaborate? Why do you suspect there 
> > > > > > is an error?
> > > > > > 
> > > > > > cheers
> > > > > > Bruce
> > > > > > On Mon, 11 May
> > > > > > 2020, std...@virgilio.it 
> > > > > > mailto:std...@virgilio.it wrote:
> > > > > > 
> > > > > > 
> > > > > > > > > > > > >   
> > > > > >   External Email - Use Caution
> > > > > > > 
> > > > > > > Please, could you check the command 
> > > > > > > line.
> > > > > > > I suspect that an error is there.
> > > > > > > Thanks.
> > > > > > > Stefano
> > > > > > > 
> > > > > > > mri_binarize --i 
> > > > > > > ThalamicNuclei.v10.T1.mgz --replace-only 8130   8133 --o
> > > > > > > Left-Ventroposterior.mgz
> > > > > > > 
> > > > > > > 
> > > > > > > > > > > > > 
> > > > > > > > > > > > >   
> > > > > >   Il 30 aprile 2020 alle 18.51 "Douglas N. Greve"
> > > > > > > < dgr...@mgh.harvard.edu 
> > > > > > > mailto:dgr...@mgh.harvard.edu > ha scritto:
> > > > > > > 
> > > > > > > > > > > > > 
> > > > > > > > > > > > >   
> > > > > >   You can use mri_binarize --i ThalamicNuclei.v10.T1.mgz
> > > > > > > --replace-only segid segidreplace ... 
> > > > > > > --o newseg.mgz
> > > > > > > to create a new segmentation with 
> > > > > > > merged segments, then using
> > > > > > > vol2subfield with the newseg seg as 
> > > > > > > --sf
> > > > > > > 
> > > > > > > > > > > > > 
> > > > > > > > > > > > >   
> > > > > >   On 4/29/2020 7:57 PM, std...@virgilio.it 
> > > > > > mailto:std...@virgilio.it wrote:
> > > > > > > 
> > > > > > > > > > > > > 
> > > > > > > > > > > > >   
> > > > > >   External Email - Use Caution
> > > > > > > 
> > > > > > > > > > > > > 
> > > > > > > > > > > > >   
> > > > > >   Hi list,
> > > > > > > 
> > > > > > > > > > > > > 
> > > > > > > > > > > > >   
> > > > > >   

Re: [Freesurfer] vol2subfield single time course from multiple regions

[stdp82]

External Email - Use Caution

is the command line ok?

by running

mri_binarize --i ThalamicNuclei.v10.T1.mgz --replace-only 8130 8133 --o L-VP.mgz

mri_diff --po mri/ThalamicNuclei.v10.T1.mgz L-VP.mgz  

I obtain
diffcount 0



> Il 12 maggio 2020 alle 0.53 std...@virgilio.it ha scritto:
> 
> by running
> mri_diff --po mri/ThalamicNuclei.v10.T1.mgz L-VP.mgz  
> I obtain
> diffcount 0
> 
> 
> 
> > > Il 11 maggio 2020 alle 19.18 "Douglas N. Greve" 
>  ha scritto:
> > 
> > Try running this to see if there is a difference
> > mri_diff --po ThalamicNuclei.v10.T1.mgz Left-Ventroposterior.mgz
> > Sometimes it is not easy to see a difference that is just a few 
> > voxels
> > 
> > On 5/11/2020 3:02 AM, std...@virgilio.it mailto:std...@virgilio.it 
> > wrote:
> > 
> > > > > 
> > > External Email - Use Caution
> > > 
> > > By visualizing the output by freeview, I found that it was 
> > > the same of ThalamicNuclei.v10.T1.mgz.
> > > 
> > > Thanks
> > > 
> > > > > > > Il 11 maggio 2020 alle 2.19 Bruce 
> > > Fischl < fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu > 
> > > ha scritto:
> > > > 
> > > > 
> > > > Hi Stefano
> > > > 
> > > > can you elaborate? Why do you suspect there is an error?
> > > > 
> > > > cheers
> > > > Bruce
> > > > On Mon, 11 May
> > > > 2020, std...@virgilio.it mailto:std...@virgilio.it 
> > > > wrote:
> > > > 
> > > > 
> > > > > > > > > External 
> > > > Email - Use Caution
> > > > > 
> > > > > Please, could you check the command line.
> > > > > I suspect that an error is there.
> > > > > Thanks.
> > > > > Stefano
> > > > > 
> > > > > mri_binarize --i ThalamicNuclei.v10.T1.mgz 
> > > > > --replace-only 8130   8133 --o
> > > > > Left-Ventroposterior.mgz
> > > > > 
> > > > > 
> > > > > > > > > 
> > > > > > > > > Il 30 aprile 2020 
> > > > alle 18.51 "Douglas N. Greve"
> > > > > < dgr...@mgh.harvard.edu 
> > > > > mailto:dgr...@mgh.harvard.edu > ha scritto:
> > > > > 
> > > > > > > > > 
> > > > > > > > > You can use 
> > > > mri_binarize --i ThalamicNuclei.v10.T1.mgz
> > > > > --replace-only segid segidreplace ... --o 
> > > > > newseg.mgz
> > > > > to create a new segmentation with merged 
> > > > > segments, then using
> > > > > vol2subfield with the newseg seg as --sf
> > > > > 
> > > > > > > > > 
> > > > > > > > > On 4/29/2020 7:57 PM, 
> > > > std...@virgilio.it mailto:std...@virgilio.it wrote:
> > > > > 
> > > > > > > > > 
> > > > > > > > > External 
> > > > Email - Use Caution
> > > > > 
> > > > > > > > > 
> > > > > > > > > Hi list,
> > > > > 
> > > > > > > > > 
> > > > > > > > > vol2subfield --i 
> > > > fmcpr.nii.gz --reg register.dof6.lta --sf
> > > > > ThalamicNuclei.v10.T1.mgz --stats stats.dat 
> > > > > --avgwf
> > > > > avgwf.dat --avgwfvol avgwfvol.mgz --o 
> > > > > f2subf.nii.gz
> > > > > 
> > > > > > > > > 
> > > > > > > > > extracts the time 
> > > > course from each thalamic subregions.
> > > > > 
> > > > > > > > > 
> > > > > > > > > If I would like to 
> > > > merge multiple regions (e.g. --id 8115
> > > > > --id 8116) and extract a single time course from 
> > > > > them,
> > > > > which is the way?
> > > > > 
> > > > > > > > > 
> > > > > > > > > Thanks
> > > > > 
> > > > > 
> > > > > > > > > 
> > > > > > > > > Stefano
> > > > > 
> > > > > 
> > > > > 
> > > > > ___
> > > > > 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 
> > 

Re: [Freesurfer] vol2subfield single time course from multiple regions

[stdp82]

External Email - Use Caution

by running
mri_diff --po mri/ThalamicNuclei.v10.T1.mgz L-VP.mgz  
I obtain
diffcount 0



> Il 11 maggio 2020 alle 19.18 "Douglas N. Greve"  ha 
> scritto:
> 
> Try running this to see if there is a difference
> mri_diff --po ThalamicNuclei.v10.T1.mgz Left-Ventroposterior.mgz
> Sometimes it is not easy to see a difference that is just a few voxels
> 
> On 5/11/2020 3:02 AM, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> > > 
> > External Email - Use Caution
> > 
> > By visualizing the output by freeview, I found that it was the same 
> > of ThalamicNuclei.v10.T1.mgz.
> > 
> > Thanks
> > 
> > > > > Il 11 maggio 2020 alle 2.19 Bruce Fischl < 
> > fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu > ha scritto:
> > > 
> > > 
> > > Hi Stefano
> > > 
> > > can you elaborate? Why do you suspect there is an error?
> > > 
> > > cheers
> > > Bruce
> > > On Mon, 11 May
> > > 2020, std...@virgilio.it mailto:std...@virgilio.it wrote:
> > > 
> > > 
> > > > > > > External Email - Use 
> > > Caution
> > > > 
> > > > Please, could you check the command line.
> > > > I suspect that an error is there.
> > > > Thanks.
> > > > Stefano
> > > > 
> > > > mri_binarize --i ThalamicNuclei.v10.T1.mgz 
> > > > --replace-only 8130   8133 --o
> > > > Left-Ventroposterior.mgz
> > > > 
> > > > 
> > > > > > > 
> > > > > > > Il 30 aprile 2020 alle 18.51 
> > > "Douglas N. Greve"
> > > > < dgr...@mgh.harvard.edu mailto:dgr...@mgh.harvard.edu 
> > > > > ha scritto:
> > > > 
> > > > > > > 
> > > > > > > You can use mri_binarize --i 
> > > ThalamicNuclei.v10.T1.mgz
> > > > --replace-only segid segidreplace ... --o newseg.mgz
> > > > to create a new segmentation with merged segments, then 
> > > > using
> > > > vol2subfield with the newseg seg as --sf
> > > > 
> > > > > > > 
> > > > > > > On 4/29/2020 7:57 PM, 
> > > std...@virgilio.it mailto:std...@virgilio.it wrote:
> > > > 
> > > > > > > 
> > > > > > > External Email - Use 
> > > Caution
> > > > 
> > > > > > > 
> > > > > > > Hi list,
> > > > 
> > > > > > > 
> > > > > > > vol2subfield --i fmcpr.nii.gz 
> > > --reg register.dof6.lta --sf
> > > > ThalamicNuclei.v10.T1.mgz --stats stats.dat --avgwf
> > > > avgwf.dat --avgwfvol avgwfvol.mgz --o f2subf.nii.gz
> > > > 
> > > > > > > 
> > > > > > > extracts the time course from 
> > > each thalamic subregions.
> > > > 
> > > > > > > 
> > > > > > > If I would like to merge multiple 
> > > regions (e.g. --id 8115
> > > > --id 8116) and extract a single time course from them,
> > > > which is the way?
> > > > 
> > > > > > > 
> > > > > > > Thanks
> > > > 
> > > > 
> > > > > > > 
> > > > > > > Stefano
> > > > 
> > > > 
> > > > 
> > > > ___
> > > > 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
> > > 
> > > > > 
> > > 
> 
> 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 

Re: [Freesurfer] vol2subfield single time course from multiple regions

[stdp82]

External Email - Use Caution

By visualizing the output by freeview, I found that it was the same of 
ThalamicNuclei.v10.T1.mgz.

Thanks

> Il 11 maggio 2020 alle 2.19 Bruce Fischl < fis...@nmr.mgh.harvard.edu 
> mailto:fis...@nmr.mgh.harvard.edu > ha scritto:
> 
> 
> Hi Stefano
> 
> can you elaborate? Why do you suspect there is an error?
> 
> cheers
> Bruce
> On Mon, 11 May
> 2020, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> 
> > > External Email - Use Caution
> > 
> > Please, could you check the command line.
> > I suspect that an error is there.
> > Thanks.
> > Stefano
> > 
> > mri_binarize --i ThalamicNuclei.v10.T1.mgz --replace-only 8130   
> > 8133 --o
> > Left-Ventroposterior.mgz
> > 
> > 
> > > 
> > > Il 30 aprile 2020 alle 18.51 "Douglas N. Greve"
> > < dgr...@mgh.harvard.edu mailto:dgr...@mgh.harvard.edu > ha scritto:
> > 
> > > 
> > > You can use mri_binarize --i ThalamicNuclei.v10.T1.mgz
> > --replace-only segid segidreplace ... --o newseg.mgz
> > to create a new segmentation with merged segments, then using
> > vol2subfield with the newseg seg as --sf
> > 
> > > 
> > > On 4/29/2020 7:57 PM, std...@virgilio.it 
> mailto:std...@virgilio.it wrote:
> > 
> > > 
> > > External Email - Use Caution
> > 
> > > 
> > > Hi list,
> > 
> > > 
> > > vol2subfield --i fmcpr.nii.gz --reg register.dof6.lta --sf
> > ThalamicNuclei.v10.T1.mgz --stats stats.dat --avgwf
> > avgwf.dat --avgwfvol avgwfvol.mgz --o f2subf.nii.gz
> > 
> > > 
> > > extracts the time course from each thalamic subregions.
> > 
> > > 
> > > If I would like to merge multiple regions (e.g. --id 8115
> > --id 8116) and extract a single time course from them,
> > which is the way?
> > 
> > > 
> > > Thanks
> > 
> > 
> > > 
> > > Stefano
> > 
> > 
> > 
> > ___
> > 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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Re: [Freesurfer] vol2subfield single time course from multiple regions

[stdp82]

External Email - Use Caution

Please, could you check the command line.
I suspect that an error is there.
Thanks.
Stefano

mri_binarize --i ThalamicNuclei.v10.T1.mgz --replace-only 8130   8133 --o 
Left-Ventroposterior.mgz



> Il 30 aprile 2020 alle 18.51 "Douglas N. Greve"  ha 
> scritto:
> 
> You can use mri_binarize --i ThalamicNuclei.v10.T1.mgz --replace-only 
> segid segidreplace ... --o newseg.mgz
> to create a new segmentation with merged segments, then using 
> vol2subfield with the newseg seg as --sf
> 
> On 4/29/2020 7:57 PM, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> > > 
> > External Email - Use Caution
> > 
> > Hi list,
> > 
> > vol2subfield --i fmcpr.nii.gz --reg register.dof6.lta --sf 
> > ThalamicNuclei.v10.T1.mgz --stats stats.dat --avgwf avgwf.dat --avgwfvol 
> > avgwfvol.mgz --o f2subf.nii.gz
> > 
> > extracts the time course from each thalamic subregions.
> > 
> > If I would like to merge multiple regions (e.g. --id 8115 --id 
> > 8116) and extract a single time course from them, which is the way?
> > 
> > Thanks
> > 
> > 
> > Stefano
> > 
> > 
> > 
> > ___
> > 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
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 



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[Freesurfer] vol2subfield single time course from multiple regions

[stdp82]

External Email - Use Caution

Hi list,

vol2subfield --i fmcpr.nii.gz --reg register.dof6.lta --sf 
ThalamicNuclei.v10.T1.mgz --stats stats.dat --avgwf avgwf.dat --avgwfvol 
avgwfvol.mgz --o f2subf.nii.gz

extracts the time course from each thalamic subregions.

If I would like to merge multiple regions (e.g. --id 8115 --id 8116) and 
extract a single time course from them, which is the way?

Thanks


Stefano

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[Freesurfer] vol2subfield

[stdp82]

External Email - Use Caution

Hi list,

where/how should I add the file listed below?

https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/vol2subfield

Thanks___
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Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Time course thalamic subregions

[stdp82]

External Email - Use Caution

Yes, that's it. The memory should be ok, but I will do a check.

Anyway, is there a way to register the ThalamicNuclei.v10.T1 into EPI space? I 
would like to work in functional space.


> Il 29 agosto 2019 alle 0.32 "Greve, Douglas N.,Ph.D." 
>  ha scritto:
> 
> 
> Is that all the output it prints to the terminal? It might be exceeding 
> your available memory (it will need at least 10G). What does the limit 
> command return?
> 
> On 8/28/19 6:27 PM, std...@virgilio.it wrote:
> >
> > External Email - Use Caution
> >
> > In addition,
> >
> > a) to convert the time series data into the conformed space and 
> > viceversa, I have run the command line listed below:
> >
> > SUBJECTS_DIR=/media/DATA_NAS/ADNI_USB/Dati/
> > mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o 
> > f-in-anat.nii
> > mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o 
> > anat-in-func.nii --inv
> > Thus the command produce:
> >
> > fslinfo f-in-anat.nii
> > data_type FLOAT32
> > dim1 256
> > dim2 256
> > dim3 256
> > dim4 140
> > datatype 16
> > pixdim1 1.00
> > pixdim2 1.00
> > pixdim3 1.00
> > pixdim4 3.00
> > cal_max 0.
> > cal_min 0.
> > file_type NIFTI-1+
> >
> > I have also opt for --inv and obtained:
> >
> > fslinfo anat-in-func.nii
> > data_type FLOAT32
> > dim1 64
> > dim2 64
> > dim3 48
> > dim4 1
> > datatype 16
> > pixdim1 3.312500
> > pixdim2 3.312500
> > pixdim3 3.312500
> > pixdim4 1.00
> > cal_max 0.
> > cal_min 0.
> > file_type NIFTI-1+
> >
> > When I run
> > mri_segstats --seg mri/ThalamicNuclei.v10.T1.mgz --ctab 
> > /usr/local/freesurfer/FreeSurferColorLUT.txt --i f-in-anat.nii --avgwf 
> > prova --id 8103 --id 8104 --id 8105 --id 8106 --id 8108 --id 8109 --id 
> > 8110 --id 8111 --id 8112 --id 8113 --id 8115 --id 8116 --id 8117 --id 
> > 8118 --id 8119 --id 8120 --id 8121 --id 8122 --id 8123 --id 8125 --id 
> > 8126 --id 8127 --id 8128 --id 8129 --id 8130 --id 8133
> >
> > the process crash:
> > $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
> > cwd
> > cmdline mri_segstats --seg mri/ThalamicNuclei.v10.T1.mgz --ctab 
> > /usr/local/freesurfer/FreeSurferColorLUT.txt --i f-in-anat.nii --avgwf 
> > prova --id 8103 --id 8104 --id 8105 --id 8106 --id 8108 --id 8109 --id 
> > 8110 --id 8111 --id 8112 --id 8113 --id 8115 --id 8116 --id 8117 --id 
> > 8118 --id 8119 --id 8120 --id 8121 --id 8122 --id 8123 --id 8125 --id 
> > 8126 --id 8127 --id 8128 --id 8129 --id 8130 --id 8133
> > sysname Linux
> > hostname lab01
> > machine x86_64
> > UseRobust 0
> > Loading mri/ThalamicNuclei.v10.T1.mgz
> > Loading f-in-anat.nii
> > Killed
> >
> > Moreover, when I use
> > mri_vol2vol --reg register.dof6.lta --mov 
> > mri/ThalamicNuclei.v10.T1.nii.gz --fstarg --o 
> > ThalamicNuclei.v10.T1_struct2func.nii --interp nearest (with or 
> > without --inv)
> > the output is not unusable.
> >
> > Thanks
> >
> > Stefano
> >
> >
> >> Il 26 agosto 2019 alle 20.02 std...@virgilio.it ha scritto:
> >>
> >> Thanks. By specifying f-in-anat.nii as output the mri_vol2vol command 
> >> runs fine.
> >>
> >> How can I convert into the functional space the 
> >> ThalamicNuclei.v10.T1.mgz? Of note, to convert the orig.mgz I have 
> >> already added to the line --inv.
> >>
> >>
> >>> Il 26 agosto 2019 alle 15.35 "Greve, Douglas N.,Ph.D." 
> >>>  ha scritto:
> >>>
> >>> Is that all it prints out? BTW, you can just specify f-in-anat.nii 
> >>> as the output of mri_vol2vol, you never have to go into mgh format
> >>>
> >>> On 8/23/2019 5:20 PM, std...@virgilio.it  
> >>> wrote:
> 
>  External Email - Use Caution
> 
>  Hi,
> 
>  I have used:
> 
>  mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o 
>  f-in-anat.mgh
>  mri_binarize --i mri/ThalamicNuclei.v10.T1.mgz --min 8112 --max 
>  8114 --o merged_ROIs.nii.gz
>  mri_segstats --seg merged_ROIs.nii.gz --id 1 --i f-in-anat.mgh 
>  --avgwf time_course
> 
>  The error occurs when the followed command is running:
>  mri_convert.bin f-in-anat.mgh f-in-anat.nii.gz
>  $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
>  reading from f-in-anat.mgh...
>  /usr/local/freesurfer/bin/mri_convert: line 3: 29749 Killed
> 
>  Thanks
> 
> 
> > Il 12 aprile 2019 alle 20.42 "Greve, Douglas N.,Ph.D." 
> >   ha scritto:
> >
> > Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz 
> > --fstarg --o fmpr.conformed.mgz
> > Then use the conformed thalamic nuclei volume when running 
> > mri_segstats
> >
> > On 4/12/2019 1:46 PM, std...@virgilio.it 
> >  wrote:
> >>
> >> External Email - Use Caution
> >>
> >> Thanks!!
> >>
> >> Using mri_segstats, is the 
> >> input subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz?
> 

Re: [Freesurfer] New fsaverage

[stdp82]

External Email - Use Caution

Yes, that's it. The memory should be ok, but I will do a check.

Anyway, is there a way to register the ThalamicNuclei.v10.T1 into EPI space? I 
would like to work in functional space.



> Il 29 agosto 2019 alle 0.34 "Greve, Douglas N.,Ph.D." 
>  ha scritto:
> 
> 
> You can download dev from here
> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
> 
> 
> On 8/26/19 1:01 PM, Westeneng, H.J. wrote:
> >
> > External Email - Use Caution
> >
> > Dear FreeSurfer experts,
> >
> > It has previously been reported that vertex 40969 is the same as 
> > vertex 0, which creates a very large triangle in fsaverage (appearing 
> > as a defect in freeview) and is fixed in the development version. For 
> > our research we would very much appreciate to use the new fixed 
> > version of fsaverage. In the release notes 
> > (https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes) it has been 
> > mentioned that a post to this list is needed to get the new fsaverage 
> > version. I hope anyone can help me to get this new version.
> >
> > Kind regards,
> >
> > Henk-Jan
> >
> > 
> >
> > /De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is 
> > uitsluitend bestemd voor de geadresseerde. Indien u dit bericht 
> > onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de 
> > afzender direct te informeren door het bericht te retourneren. Het 
> > Universitair Medisch Centrum Utrecht is een publiekrechtelijke 
> > rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en 
> > Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van 
> > Koophandel voor Midden-Nederland onder nr. 30244197. /
> >
> > /Denk s.v.p aan het milieu voor u deze e-mail afdrukt. /
> >
> > 
> >
> > /This message may contain confidential information and is intended 
> > exclusively for the addressee. If you receive this message 
> > unintentionally, please do not use the contents but notify the sender 
> > immediately by return e-mail. University Medical Center Utrecht is a 
> > legal person by public law and is registered at the Chamber of 
> > Commerce for Midden-Nederland under no. 30244197. /
> >
> > /Please consider the environment before printing this e-mail. /
> >
> >
> > ___
> > 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] Time course thalamic subregions

[stdp82]

External Email - Use Caution

In addition,

a) to convert the time series data into the conformed space and viceversa, I 
have run the command line listed below:

SUBJECTS_DIR=/media/DATA_NAS/ADNI_USB/Dati/
mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o 
f-in-anat.nii
mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o 
anat-in-func.nii --inv
Thus the command produce:

fslinfo f-in-anat.nii
data_type FLOAT32
dim1 256
dim2 256
dim3 256
dim4 140
datatype 16
pixdim1 1.00
pixdim2 1.00
pixdim3 1.00
pixdim4 3.00
cal_max 0.
cal_min 0.
file_type NIFTI-1+

I have also opt for --inv and obtained:

fslinfo anat-in-func.nii
data_type FLOAT32
dim1 64
dim2 64
dim3 48
dim4 1
datatype 16
pixdim1 3.312500
pixdim2 3.312500
pixdim3 3.312500
pixdim4 1.00
cal_max 0.
cal_min 0.
file_type NIFTI-1+

When I run
mri_segstats --seg mri/ThalamicNuclei.v10.T1.mgz --ctab 
/usr/local/freesurfer/FreeSurferColorLUT.txt --i f-in-anat.nii --avgwf prova 
--id 8103 --id 8104 --id 8105 --id 8106 --id 8108 --id 8109 --id 8110 --id 8111 
--id 8112 --id 8113 --id 8115 --id 8116 --id 8117 --id 8118 --id 8119 --id 8120 
--id 8121 --id 8122 --id 8123 --id 8125 --id 8126 --id 8127 --id 8128 --id 8129 
--id 8130 --id 8133

the process crash:
$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd
cmdline mri_segstats --seg mri/ThalamicNuclei.v10.T1.mgz --ctab 
/usr/local/freesurfer/FreeSurferColorLUT.txt --i f-in-anat.nii --avgwf prova 
--id 8103 --id 8104 --id 8105 --id 8106 --id 8108 --id 8109 --id 8110 --id 8111 
--id 8112 --id 8113 --id 8115 --id 8116 --id 8117 --id 8118 --id 8119 --id 8120 
--id 8121 --id 8122 --id 8123 --id 8125 --id 8126 --id 8127 --id 8128 --id 8129 
--id 8130 --id 8133
sysname Linux
hostname lab01
machine x86_64
UseRobust 0
Loading mri/ThalamicNuclei.v10.T1.mgz
Loading f-in-anat.nii
Killed

Moreover, when I use
mri_vol2vol --reg register.dof6.lta --mov mri/ThalamicNuclei.v10.T1.nii.gz 
--fstarg --o ThalamicNuclei.v10.T1_struct2func.nii --interp nearest (with or 
without --inv)
the output is not unusable.

Thanks

Stefano


> Il 26 agosto 2019 alle 20.02 std...@virgilio.it ha scritto:
> 
> 
> Thanks. By specifying f-in-anat.nii as output the mri_vol2vol command 
> runs fine.
> 
> How can I convert into the functional space the 
> ThalamicNuclei.v10.T1.mgz? Of note, to convert the orig.mgz I have already 
> added to the line --inv.
> 
> 
> > > Il 26 agosto 2019 alle 15.35 "Greve, Douglas N.,Ph.D." 
>  ha scritto:
> > 
> > Is that all it prints out? BTW, you can just specify f-in-anat.nii 
> > as the output of mri_vol2vol, you never have to go into mgh format
> > 
> > On 8/23/2019 5:20 PM, std...@virgilio.it mailto:std...@virgilio.it 
> > wrote:
> > 
> > > > > 
> > > External Email - Use Caution
> > > 
> > > Hi,
> > > 
> > > I have used:
> > > 
> > > mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz 
> > > --fstarg --o f-in-anat.mgh
> > > mri_binarize --i mri/ThalamicNuclei.v10.T1.mgz --min 8112 
> > > --max 8114 --o merged_ROIs.nii.gz
> > > mri_segstats --seg merged_ROIs.nii.gz --id 1 --i 
> > > f-in-anat.mgh --avgwf time_course
> > > 
> > > The error occurs when the followed command is running:
> > > mri_convert.bin f-in-anat.mgh f-in-anat.nii.gz
> > > $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
> > > reading from f-in-anat.mgh...
> > > /usr/local/freesurfer/bin/mri_convert: line 3: 29749 Killed 
> > > 
> > > Thanks
> > > 
> > > 
> > > > > > > Il 12 aprile 2019 alle 20.42 "Greve, Douglas 
> > > N.,Ph.D."  mailto:dgr...@mgh.harvard.edu ha 
> > > scritto:
> > > > 
> > > > Use mri_vol2vol --reg register.dof6.lta --mov 
> > > > fmcpr.nii.gz --fstarg --o fmpr.conformed.mgz
> > > > Then use the conformed thalamic nuclei volume when 
> > > > running mri_segstats
> > > > 
> > > > On 4/12/2019 1:46 PM, std...@virgilio.it 
> > > > mailto:std...@virgilio.it wrote:
> > > > 
> > > > > > > > > 
> > > > > External Email - Use Caution
> > > > > 
> > > > > Thanks!!
> > > > > 
> > > > > Using mri_segstats, is the input 
> > > > > subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz?
> > > > > Or should I use the .odd like 
> > > > > fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz?
> > > > > 
> > > > > 
> > > > > > > > > > > Il 12 aprile 2019 alle 16.59 
> > > > > "Greve, Douglas N.,Ph.D."  
> > > > > mailto:dgr...@mgh.harvard.edu ha scritto:
> > > > > > 
> > > > > > You'll need to either convert the time 
> > > > > > series data into the conformed space or the segmentation into the 
> > > > > > 

Re: [Freesurfer] Time course thalamic subregions

[stdp82]

External Email - Use Caution

Thanks. By specifying f-in-anat.nii as output the mri_vol2vol command runs fine.

How can I convert into the functional space the ThalamicNuclei.v10.T1.mgz? Of 
note, to convert the orig.mgz I have already added to the line --inv.


> Il 26 agosto 2019 alle 15.35 "Greve, Douglas N.,Ph.D." 
>  ha scritto:
> 
> Is that all it prints out? BTW, you can just specify f-in-anat.nii as the 
> output of mri_vol2vol, you never have to go into mgh format
> 
> On 8/23/2019 5:20 PM, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> > > 
> > External Email - Use Caution
> > 
> > Hi,
> > 
> > I have used:
> > 
> > mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o 
> > f-in-anat.mgh
> > mri_binarize --i mri/ThalamicNuclei.v10.T1.mgz --min 8112 --max 
> > 8114 --o merged_ROIs.nii.gz
> > mri_segstats --seg merged_ROIs.nii.gz --id 1 --i f-in-anat.mgh 
> > --avgwf time_course
> > 
> > The error occurs when the followed command is running:
> > mri_convert.bin f-in-anat.mgh f-in-anat.nii.gz
> > $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
> > reading from f-in-anat.mgh...
> > /usr/local/freesurfer/bin/mri_convert: line 3: 29749 Killed 
> > 
> > Thanks
> > 
> > 
> > > > > Il 12 aprile 2019 alle 20.42 "Greve, Douglas N.,Ph.D." 
> >  mailto:dgr...@mgh.harvard.edu ha scritto:
> > > 
> > > Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz 
> > > --fstarg --o fmpr.conformed.mgz
> > > Then use the conformed thalamic nuclei volume when running 
> > > mri_segstats
> > > 
> > > On 4/12/2019 1:46 PM, std...@virgilio.it 
> > > mailto:std...@virgilio.it wrote:
> > > 
> > > > > > > 
> > > > External Email - Use Caution
> > > > 
> > > > Thanks!!
> > > > 
> > > > Using mri_segstats, is the input 
> > > > subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz?
> > > > Or should I use the .odd like 
> > > > fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz?
> > > > 
> > > > 
> > > > > > > > > Il 12 aprile 2019 alle 16.59 "Greve, 
> > > > Douglas N.,Ph.D."  
> > > > mailto:dgr...@mgh.harvard.edu ha scritto:
> > > > > 
> > > > > You'll need to either convert the time series 
> > > > > data into the conformed space or the segmentation into the functional 
> > > > > space. The first is probably better (it will create a huge file but 
> > > > > you can delete it when you are done). Use mri_vol2vol --reg 
> > > > > register.dof6.lta --mov fmcpr.nii.gz --fstarg --o fmpr.conformed.mgz
> > > > > Then use the conformed thalamic nuclei volume 
> > > > > when running mri_segstats
> > > > > 
> > > > > On 4/12/2019 7:39 AM, std...@virgilio.it 
> > > > > mailto:std...@virgilio.it wrote:
> > > > > 
> > > > > > > > > > > 
> > > > > > External Email - Use Caution
> > > > > > 
> > > > > > Hi list,
> > > > > > I would like to extract fMRI time series 
> > > > > > from the thalamic subregions that I obtained by the recent tool 
> > > > > > implemented in FS.
> > > > > > 
> > > > > > I have run
> > > > > > mri_segstats --seg 
> > > > > > subj/mri/ThalamicNuclei.v10.T1.mgz --ctab 
> > > > > > $FREESURFER_HOME/FreeSurferColorLUT.txt --i 
> > > > > > subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz --avgwf 
> > > > > > Time_Seriesfolder/ADNI011_HC.MNI --id 8120 --id 8121 --id 8122 --id 
> > > > > > 8123 --id 8220 --id 8221 --id 8222 --id 8223
> > > > > > 
> > > > > > The command produces this error:
> > > > > > ERROR: dimension mismatch between input 
> > > > > > volume and seg
> > > > > > input 76 76 93
> > > > > > seg 169 105 118
> > > > > > 
> > > > > > Please, I have other questions for you.
> > > > > > 
> > > > > > 1) At starting, I have used the command 
> > > > > > line reported below:
> > > > > > 
> > > > > > preproc-sess -sf sessid -fwhm 6 -surface 
> > > > > > fsaverage lhrh -mni305 -fsd rest -per-run -sliceorder odd
> > > > > > 
> > > > > > The -mni305-1mm could be more useful?
> > > > > > My raw-data are:
> > > > > > data_type UINT16
> > > > > > dim1 64
> > > > > > dim2 64
> > > > > > dim3 48
> > > > > > dim4 140
> > > > > > datatype 512
> > > > > > pixdim1 3.312500
> > > > > >   

Re: [Freesurfer] Time course thalamic subregions

[stdp82]

External Email - Use Caution

Hi,

I have used:

mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o 
f-in-anat.mgh
mri_binarize --i mri/ThalamicNuclei.v10.T1.mgz --min 8112 --max 8114 --o 
merged_ROIs.nii.gz
mri_segstats --seg merged_ROIs.nii.gz --id 1 --i f-in-anat.mgh --avgwf 
time_course

The error occurs when the followed command is running:
mri_convert.bin f-in-anat.mgh f-in-anat.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from f-in-anat.mgh...
/usr/local/freesurfer/bin/mri_convert: line 3: 29749 Killed 

Thanks


> Il 12 aprile 2019 alle 20.42 "Greve, Douglas N.,Ph.D." 
>  ha scritto:
> 
> Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o 
> fmpr.conformed.mgz
> Then use the conformed thalamic nuclei volume when running mri_segstats
> 
> On 4/12/2019 1:46 PM, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> > > 
> > External Email - Use Caution
> > 
> > Thanks!!
> > 
> > Using mri_segstats, is the input 
> > subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz?
> > Or should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or 
> > fmcpr.odd.sm6.mni305.2mm.nii.gz?
> > 
> > 
> > > > > Il 12 aprile 2019 alle 16.59 "Greve, Douglas N.,Ph.D." 
> >  mailto:dgr...@mgh.harvard.edu ha scritto:
> > > 
> > > You'll need to either convert the time series data into the 
> > > conformed space or the segmentation into the functional space. The first 
> > > is probably better (it will create a huge file but you can delete it when 
> > > you are done). Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz 
> > > --fstarg --o fmpr.conformed.mgz
> > > Then use the conformed thalamic nuclei volume when running 
> > > mri_segstats
> > > 
> > > On 4/12/2019 7:39 AM, std...@virgilio.it 
> > > mailto:std...@virgilio.it wrote:
> > > 
> > > > > > > 
> > > > External Email - Use Caution
> > > > 
> > > > Hi list,
> > > > I would like to extract fMRI time series from the 
> > > > thalamic subregions that I obtained by the recent tool implemented in 
> > > > FS.
> > > > 
> > > > I have run
> > > > mri_segstats --seg subj/mri/ThalamicNuclei.v10.T1.mgz 
> > > > --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i 
> > > > subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz --avgwf 
> > > > Time_Seriesfolder/ADNI011_HC.MNI --id 8120 --id 8121 --id 8122 --id 
> > > > 8123 --id 8220 --id 8221 --id 8222 --id 8223
> > > > 
> > > > The command produces this error:
> > > > ERROR: dimension mismatch between input volume and seg
> > > > input 76 76 93
> > > > seg 169 105 118
> > > > 
> > > > Please, I have other questions for you.
> > > > 
> > > > 1) At starting, I have used the command line reported 
> > > > below:
> > > > 
> > > > preproc-sess -sf sessid -fwhm 6 -surface fsaverage lhrh 
> > > > -mni305 -fsd rest -per-run -sliceorder odd
> > > > 
> > > > The -mni305-1mm could be more useful?
> > > > My raw-data are:
> > > > data_type UINT16
> > > > dim1 64
> > > > dim2 64
> > > > dim3 48
> > > > dim4 140
> > > > datatype 512
> > > > pixdim1 3.312500
> > > > pixdim2 3.312500
> > > > pixdim3 3.312500
> > > > pixdim4 3.00
> > > > cal_max 0.
> > > > cal_min 0.
> > > > file_type NIFTI-1+
> > > > 
> > > > 2) In the mri_segstats the input is 
> > > > subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz.
> > > > Do you agree? Conversely, should I use the .odd like 
> > > > fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz?
> > > > 
> > > > 3) If I interested to obtained the time course from a 
> > > > unique region expressing the merging of some thalamic regions (i.e. 
> > > > 8121plus 8122 plus 8123), which is the options that should I added?
> > > > 
> > > > Thanks,
> > > > 
> > > > Stefano
> > > > 
> > > > 
> > > > ___
> > > > 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
> > >  

Re: [Freesurfer] error matlab segmentHA

[stdp82]

External Email - Use Caution

I have reinstalled 2014 and runtime

the error persists:


Segmentation violation detected at Fri Jun7 11:59:05 2019



Configuration:

Crash Decoding : Disabled

Current Visual : Quartz

Default Encoding : ISO-8859-1

MATLAB Architecture: maci64

MATLAB Root: /Applications/freesurfer/MCRv84

MATLAB Version : 8.4.0.150421 (R2014b)

Operating System : Darwin 17.7.0 Darwin Kernel Version 17.7.0: Wed Apr 24 
21:17:24 PDT 2019; root:xnu-4570.71.45~1/RELEASE_X86_64 x86_64

Processor ID : x86 Family 6 Model 58 Stepping 9, GenuineIntel

Software OpenGL: 0

Virtual Machine: Java 1.7.0_55-b13 with Oracle Corporation Java HotSpot(TM) 
64-Bit Server VM mixed mode

Window System: Quartz

Fault Count: 2

Abnormal termination:

Segmentation violation

Register State (from fault):

RAX = 7fa9f08bc000RBX = 7fa9f08bc000

RCX = 7d4db2d0RDX = 00011493697e

RSP = 7fa9f08bc000RBP = 9b630d4db2d0

RSI = 7fa9f238f940RDI = 

R8 = 7fa9f0912e70 R9 = 7fa9f08bc000

R10 = 00012000976aR11 = 

R12 = 7d4db330R13 = 0001147843c7

R14 = 7d4db3a0R15 = 000120009777

RIP = 00011a3b1f40RFL = 7fa9f0912e70

CS = 9b6300305bc3 FS = 00012000976a GS = 7fa9f08bc1e8

Stack Trace (from fault):

[0] 0x00010a6efe64 
/Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00028260 
_ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+0052

[1] 0x00010a6f3a2a 
/Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00043562 
_ZN2fl4test17terminate_handledEv+0906

[2] 0x00010a6f3477 
/Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00042103 
_ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+0119

[3] 0x00011013db7a 
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00387962 
_Z32mnRunPathDependentInitializationv+3146

[4] 0x00011013de58 
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00388696 
_Z32mnRunPathDependentInitializationv+3880

[5] 0x00011013b733 
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00378675 
mnFatalSignalHandler+0275

[6] 0x7fff552c8f5a /usr/lib/system/libsystem_platform.dylib+8026 
_sigtramp+0026

[7] 0x0001147856f8 
/Applications/freesurfer/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03192568
 _ZN23JNI_ArgumentPusherVaArg7iterateEy+

[8] 0x000114775d67 
/Applications/freesurfer/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03128679
 jni_GetMethodID+0126

[9] 0x00011356e271 
/Applications/freesurfer/MCRv84//bin/maci64/libmwjmi.dylib+00160369 
_Z12mljGetMethodP7_jclassPKcS2_+0049

[ 10] 0x00011f864366 
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00598886 
_ZN2ui14JavaScreenData20getPrimaryScreenRectEv+0150

[ 11] 0x00011f869ef4 
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00622324 
_ZN10ScreenImpl13getScreenSizeEv+0036

[ 12] 0x00011f8682e2 
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00615138 
_ZNK2ui24RootScreenAndPointerImpl13getScreenSizeEv+0018

[ 13] 0x00011f86cf58 
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00634712 
_ZN2ui4Root17getScreenSizeImplEPN4mcos11COSPropInfoEPNS1_9COSClientEPNS1_12COSInterfaceE+0040

[ 14] 0x00011fca3d13 
/Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+05053715 
_ZN7hgutils6StubPIIN2ui4RootENS_15PropertyStorageIN8graphics8datatype8PositionENS_6NoModeENS_21NoSerializableStorage8getValueEPN4mcos12COSInterfaceE+0099

[ 15] 0x0008da6e 
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00371310 
_ZN4mcos13COSInterfaceI18igetDirectInternalEPNS_12COSInterfaceE+0110

[ 16] 0x00083c80 
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00330880 
_ZN4mcos13COSInterfaceI10igetDirectEPKNS_9COSClientEPNS_12COSInterfaceE+0128

[ 17] 0x000f312b 
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00786731 
_ZN4mcos28getValueOfKnownClassPropertyEP11mxArray_tagmPKS0_NS_15COSInterfacePtrEPKNS_9COSClientE+0411

[ 18] 0x000f4070 
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00790640 
_ZN4mcos16getPropertyValueEPKNS_9COSClientEPNS_8COSClassEPK11mxArray_tagPKcmPS5_+0416

[ 19] 0x000f4483 
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00791683 
_ZNK4mcos5GetMI6invokeEPKNS_9COSClientERiPNS_8COSValueEiPKS5_+0355

[ 20] 0x000dc1f2 
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00692722 
_ZN24OpaqueMethodCallMetaData11callCMethodEPN4mcos13COSMethodInfoEPP11mxArray_tagPKNS0_9COSClientE+0466

[ 21] 0x000def4e 
/Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00704334 

[Freesurfer] error matlab segmentHA

[stdp82]

External Email - Use Caution

I have installed matlab 2018b and removed 2014b.

When I run segmentHA_T1.sh the error reported below occurs:

MATLAB is exiting because of fatal error

/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 
37:3955 Killed: 9 
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
 $args

Darwin iMac-di-Stefano.local 17.7.0 Darwin Kernel Version 17.7.0: Wed Apr 24 
21:17:24 PDT 2019; root:xnu-4570.71.45~1/RELEASE_X86_64 x86_64

T1 hippocampal subfields exited with ERRORS at Tue Jun4 00:55:25 CEST 2019

For more details, see the log file 
/Applications/freesurfer/subjects/subj/scripts/hippocampal-subfields-T1.log

Please also take in account

segmentation violation detected at Tue Jun4 00:57:53 2019



Configuration:

Crash Decoding : Disabled

Current Visual : Quartz

Default Encoding : ISO-8859-1

MATLAB Architecture: maci64

MATLAB Root: /Applications/freesurfer/MCRv84

MATLAB Version : 8.4.0.150421 (R2014b)

MATLAB Version : 8.4.0.150421 (R2014b) 

Why it does not find 2018 version?

I have follow the guidelines at 
https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime 

Thanks

Stefano___
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[Freesurfer] Error in matlab with segmentHA_T1.sh

[stdp82]

External Email - Use Caution

I have installed matlab 2018b and removed 2014b.

When I run segmentHA_T1.sh the error reported below occurs:

MATLAB is exiting because of fatal error

/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 
37:3955 Killed: 9 
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
 $args

Darwin iMac-di-Stefano.local 17.7.0 Darwin Kernel Version 17.7.0: Wed Apr 24 
21:17:24 PDT 2019; root:xnu-4570.71.45~1/RELEASE_X86_64 x86_64

T1 hippocampal subfields exited with ERRORS at Tue Jun4 00:55:25 CEST 2019

For more details, see the log file 
/Applications/freesurfer/subjects/subj/scripts/hippocampal-subfields-T1.log


Please also take in account

segmentation violation detected at Tue Jun4 00:57:53 2019



Configuration:

Crash Decoding : Disabled

Current Visual : Quartz

Default Encoding : ISO-8859-1

MATLAB Architecture: maci64

MATLAB Root: /Applications/freesurfer/MCRv84

MATLAB Version : 8.4.0.150421 (R2014b)

MATLAB Version : 8.4.0.150421 (R2014b) 

Why it does not find 2018 version?

I have follow the guidelines at 
https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime 


Thanks

Stefano___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] error in matlab with segmentHA_T1.sh

[stdp82]

External Email - Use Caution

Please also take in account

segmentation violation detected at Tue Jun4 00:57:53 2019



Configuration:

Crash Decoding : Disabled

Current Visual : Quartz

Default Encoding : ISO-8859-1

MATLAB Architecture: maci64

MATLAB Root: /Applications/freesurfer/MCRv84

MATLAB Version : 8.4.0.150421 (R2014b)


MATLAB Version : 8.4.0.150421 (R2014b) 

Why it does not find 2018 version?

I have follow the guidelines at 
https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime  

> Il 4 giugno 2019 alle 7.59 std...@virgilio.it ha scritto:
> 
> 
> I have installed matlab 2018b and removed 2014b.
> 
> When I run segmentHA_T1.sh the error reported below occurs:
> 
> MATLAB is exiting because of fatal error
> 
> 
> /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: 
> line 37:3955 Killed: 9 
> "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
>  $args
> 
> Darwin iMac-di-Stefano.local 17.7.0 Darwin Kernel Version 17.7.0: Wed Apr 
> 24 21:17:24 PDT 2019; root:xnu-4570.71.45~1/RELEASE_X86_64 x86_64
> 
> T1 hippocampal subfields exited with ERRORS at Tue Jun4 00:55:25 CEST 2019
> 
> For more details, see the log file 
> /Applications/freesurfer/subjects/subj/scripts/hippocampal-subfields-T1.log
> 


 
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[Freesurfer] error in matlab with segmentHA_T1.sh

[stdp82]

External Email - Use Caution

I have installed matlab 2018b and removed 2014b.

When I run segmentHA_T1.sh the error reported below occurs:

MATLAB is exiting because of fatal error

/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 
37:3955 Killed: 9 
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
 $args

Darwin iMac-di-Stefano.local 17.7.0 Darwin Kernel Version 17.7.0: Wed Apr 24 
21:17:24 PDT 2019; root:xnu-4570.71.45~1/RELEASE_X86_64 x86_64

T1 hippocampal subfields exited with ERRORS at Tue Jun4 00:55:25 CEST 2019

For more details, see the log file 
/Applications/freesurfer/subjects/subj/scripts/hippocampal-subfields-T1.log___
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Re: [Freesurfer] Time course thalamic subregions

[stdp82]

External Email - Use Caution

Hi,

If I interested to obtained the time course from a unique region expressing the 
merging of thalamic regions (i.e. 8121 plus 8122 plus 8123), which is the 
options that should I added to mri_segstats?


> Il 12 aprile 2019 alle 20.42 "Greve, Douglas N.,Ph.D." 
>  ha scritto:
> 
> Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o 
> fmpr.conformed.mgz
> Then use the conformed thalamic nuclei volume when running mri_segstats
> 
> On 4/12/2019 1:46 PM, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> > > 
> > External Email - Use Caution
> > 
> > Thanks!!
> > 
> > Using mri_segstats, is the input 
> > subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz?
> > Or should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or 
> > fmcpr.odd.sm6.mni305.2mm.nii.gz?
> > 
> > 
> > > > > Il 12 aprile 2019 alle 16.59 "Greve, Douglas N.,Ph.D." 
> >  mailto:dgr...@mgh.harvard.edu ha scritto:
> > > 
> > > You'll need to either convert the time series data into the 
> > > conformed space or the segmentation into the functional space. The first 
> > > is probably better (it will create a huge file but you can delete it when 
> > > you are done). Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz 
> > > --fstarg --o fmpr.conformed.mgz
> > > Then use the conformed thalamic nuclei volume when running 
> > > mri_segstats
> > > 
> > > On 4/12/2019 7:39 AM, std...@virgilio.it 
> > > mailto:std...@virgilio.it wrote:
> > > 
> > > > > > > 
> > > > External Email - Use Caution
> > > > 
> > > > Hi list,
> > > > I would like to extract fMRI time series from the 
> > > > thalamic subregions that I obtained by the recent tool implemented in 
> > > > FS.
> > > > 
> > > > I have run
> > > > mri_segstats --seg subj/mri/ThalamicNuclei.v10.T1.mgz 
> > > > --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i 
> > > > subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz --avgwf 
> > > > Time_Seriesfolder/ADNI011_HC.MNI --id 8120 --id 8121 --id 8122 --id 
> > > > 8123 --id 8220 --id 8221 --id 8222 --id 8223
> > > > 
> > > > The command produces this error:
> > > > ERROR: dimension mismatch between input volume and seg
> > > > input 76 76 93
> > > > seg 169 105 118
> > > > 
> > > > Please, I have other questions for you.
> > > > 
> > > > 1) At starting, I have used the command line reported 
> > > > below:
> > > > 
> > > > preproc-sess -sf sessid -fwhm 6 -surface fsaverage lhrh 
> > > > -mni305 -fsd rest -per-run -sliceorder odd
> > > > 
> > > > The -mni305-1mm could be more useful?
> > > > My raw-data are:
> > > > data_type UINT16
> > > > dim1 64
> > > > dim2 64
> > > > dim3 48
> > > > dim4 140
> > > > datatype 512
> > > > pixdim1 3.312500
> > > > pixdim2 3.312500
> > > > pixdim3 3.312500
> > > > pixdim4 3.00
> > > > cal_max 0.
> > > > cal_min 0.
> > > > file_type NIFTI-1+
> > > > 
> > > > 2) In the mri_segstats the input is 
> > > > subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz.
> > > > Do you agree? Conversely, should I use the .odd like 
> > > > fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz?
> > > > 
> > > > 3) If I interested to obtained the time course from a 
> > > > unique region expressing the merging of some thalamic regions (i.e. 
> > > > 8121plus 8122 plus 8123), which is the options that should I added?
> > > > 
> > > > Thanks,
> > > > 
> > > > Stefano
> > > > 
> > > > 
> > > > ___
> > > > 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
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
 

Re: [Freesurfer] Time course thalamic subregions

[stdp82]

External Email - Use Caution

converting the time series data into the conformed space

mri_vol2vol --reg 
/Applications/freesurfer/subjects/fMRI_ADNI/subj/rest/001/register.dof6.lta 
--mov /Applications/freesurfer/subjects/fMRI_ADNI/subj/rest/001/fmcpr.nii.gz 
--fstarg --o subj/rest/001/fmpr.conformed.mgz

mri_segstats --seg $SUBJECTS_DIR/subj/mri/ThalamicNuclei.v10.T1.mgz --ctab 
$FREESURFER_HOME/FreeSurferColorLUT.txt --i subj/rest/001/fmpr.conformed.mgz 
--avgwf 
/Users/Stefano/Desktop/FS_FAST_ADNI_Results/Thalami_nuclei/Time_Series/subj.MNI 
--id 8103 --id 8104 --id 8105 --id 8106 --id 8108 --id 8109 --id 8110 --id 8111 
--id 8112 --id 8113 --id 8115 --id 8116 --id 8117 --id 8118 --id 8119 --id 8120 
--id 8121 --id 8122 --id 8123 --id 8125 --id 8126 --id 8127 --id 8128 --id 8129 
--id 8130 --id 8133

ERROR: dimension mismatch between input volume and seg

input 256 256 256

seg 169 105 118




> Il 12 aprile 2019 alle 20.42 "Greve, Douglas N.,Ph.D." 
>  ha scritto:
> 
> Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o 
> fmpr.conformed.mgz
> Then use the conformed thalamic nuclei volume when running mri_segstats
> 
> On 4/12/2019 1:46 PM, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> > > 
> > External Email - Use Caution
> > 
> > Thanks!!
> > 
> > Using mri_segstats, is the input 
> > subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz?
> > Or should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or 
> > fmcpr.odd.sm6.mni305.2mm.nii.gz?
> > 
> > 
> > > > > Il 12 aprile 2019 alle 16.59 "Greve, Douglas N.,Ph.D." 
> >  mailto:dgr...@mgh.harvard.edu ha scritto:
> > > 
> > > You'll need to either convert the time series data into the 
> > > conformed space or the segmentation into the functional space. The first 
> > > is probably better (it will create a huge file but you can delete it when 
> > > you are done). Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz 
> > > --fstarg --o fmpr.conformed.mgz
> > > Then use the conformed thalamic nuclei volume when running 
> > > mri_segstats
> > > 
> > > On 4/12/2019 7:39 AM, std...@virgilio.it 
> > > mailto:std...@virgilio.it wrote:
> > > 
> > > > > > > 
> > > > External Email - Use Caution
> > > > 
> > > > Hi list,
> > > > I would like to extract fMRI time series from the 
> > > > thalamic subregions that I obtained by the recent tool implemented in 
> > > > FS.
> > > > 
> > > > I have run
> > > > mri_segstats --seg subj/mri/ThalamicNuclei.v10.T1.mgz 
> > > > --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i 
> > > > subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz --avgwf 
> > > > Time_Seriesfolder/ADNI011_HC.MNI --id 8120 --id 8121 --id 8122 --id 
> > > > 8123 --id 8220 --id 8221 --id 8222 --id 8223
> > > > 
> > > > The command produces this error:
> > > > ERROR: dimension mismatch between input volume and seg
> > > > input 76 76 93
> > > > seg 169 105 118
> > > > 
> > > > Please, I have other questions for you.
> > > > 
> > > > 1) At starting, I have used the command line reported 
> > > > below:
> > > > 
> > > > preproc-sess -sf sessid -fwhm 6 -surface fsaverage lhrh 
> > > > -mni305 -fsd rest -per-run -sliceorder odd
> > > > 
> > > > The -mni305-1mm could be more useful?
> > > > My raw-data are:
> > > > data_type UINT16
> > > > dim1 64
> > > > dim2 64
> > > > dim3 48
> > > > dim4 140
> > > > datatype 512
> > > > pixdim1 3.312500
> > > > pixdim2 3.312500
> > > > pixdim3 3.312500
> > > > pixdim4 3.00
> > > > cal_max 0.
> > > > cal_min 0.
> > > > file_type NIFTI-1+
> > > > 
> > > > 2) In the mri_segstats the input is 
> > > > subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz.
> > > > Do you agree? Conversely, should I use the .odd like 
> > > > fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz?
> > > > 
> > > > 3) If I interested to obtained the time course from a 
> > > > unique region expressing the merging of some thalamic regions (i.e. 
> > > > 8121plus 8122 plus 8123), which is the options that should I added?
> > > > 
> > > > Thanks,
> > > > 
> > > > Stefano
> > > > 
> > > > 
> > > > ___
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu 
> > > > mailto:Freesurfer@nmr.mgh.harvard.edu
> > > > 
> > > > 

Re: [Freesurfer] Time course thalamic subregions

[stdp82]

External Email - Use Caution

Thanks!!

Using mri_segstats, is the input subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz?
Or should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or 
fmcpr.odd.sm6.mni305.2mm.nii.gz?


> Il 12 aprile 2019 alle 16.59 "Greve, Douglas N.,Ph.D." 
>  ha scritto:
> 
> You'll need to either convert the time series data into the conformed 
> space or the segmentation into the functional space. The first is probably 
> better (it will create a huge file but you can delete it when you are done). 
> Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o 
> fmpr.conformed.mgz
> Then use the conformed thalamic nuclei volume when running mri_segstats
> 
> On 4/12/2019 7:39 AM, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> > > 
> > External Email - Use Caution
> > 
> > Hi list,
> > I would like to extract fMRI time series from the thalamic 
> > subregions that I obtained by the recent tool implemented in FS.
> > 
> > I have run
> > mri_segstats --seg subj/mri/ThalamicNuclei.v10.T1.mgz --ctab 
> > $FREESURFER_HOME/FreeSurferColorLUT.txt --i 
> > subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz --avgwf 
> > Time_Seriesfolder/ADNI011_HC.MNI --id 8120 --id 8121 --id 8122 --id 8123 
> > --id 8220 --id 8221 --id 8222 --id 8223
> > 
> > The command produces this error:
> > ERROR: dimension mismatch between input volume and seg
> > input 76 76 93
> > seg 169 105 118
> > 
> > Please, I have other questions for you.
> > 
> > 1) At starting, I have used the command line reported below:
> > 
> > preproc-sess -sf sessid -fwhm 6 -surface fsaverage lhrh -mni305 
> > -fsd rest -per-run -sliceorder odd
> > 
> > The -mni305-1mm could be more useful?
> > My raw-data are:
> > data_type UINT16
> > dim1 64
> > dim2 64
> > dim3 48
> > dim4 140
> > datatype 512
> > pixdim1 3.312500
> > pixdim2 3.312500
> > pixdim3 3.312500
> > pixdim4 3.00
> > cal_max 0.
> > cal_min 0.
> > file_type NIFTI-1+
> > 
> > 2) In the mri_segstats the input is 
> > subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz.
> > Do you agree? Conversely, should I use the .odd like 
> > fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz?
> > 
> > 3) If I interested to obtained the time course from a unique region 
> > expressing the merging of some thalamic regions (i.e. 8121plus 8122 plus 
> > 8123), which is the options that should I added?
> > 
> > Thanks,
> > 
> > Stefano
> > 
> > 
> > ___
> > 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
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
 
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Time course thalamic subregions

[stdp82]

External Email - Use Caution

Hi list,
I would like to extract fMRI time series from the thalamic subregions that I 
obtained by the recent tool implemented in FS.

I have run
mri_segstats --seg subj/mri/ThalamicNuclei.v10.T1.mgz --ctab 
$FREESURFER_HOME/FreeSurferColorLUT.txt --i 
subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz --avgwf 
Time_Seriesfolder/ADNI011_HC.MNI --id 8120 --id 8121 --id 8122 --id 8123 --id 
8220 --id 8221 --id 8222 --id 8223

The command produces this error:
ERROR: dimension mismatch between input volume and seg
input 76 76 93
seg 169 105 118

Please, I have other questions for you.

1) At starting, I have used the command line reported below:

preproc-sess -sf sessid -fwhm 6 -surface fsaverage lhrh -mni305 -fsd rest 
-per-run -sliceorder odd

The -mni305-1mm could be more useful?
My raw-data are:
data_type UINT16
dim1 64
dim2 64
dim3 48
dim4 140
datatype 512
pixdim1 3.312500
pixdim2 3.312500
pixdim3 3.312500
pixdim4 3.00
cal_max 0.
cal_min 0.
file_type NIFTI-1+

2) In the mri_segstats the input is subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz.
Do you agree? Conversely, should I use the .odd like 
fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz?

3) If I interested to obtained the time course from a unique region expressing 
the merging of some thalamic regions (i.e. 8121plus 8122 plus 8123), which is 
the options that should I added?

Thanks,

Stefano
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Re: [Freesurfer] regions of Yeo 17 networks in fast

[stdp82]

External Email - Use CautionHi,please, could you suggest colortable for 7 network?Thanks!StefanoIl 27 marzo 2019 alle 16.10 Thomas Yeo  ha scritto:  External Email - Use Caution Hi Stefano,Did you see the colortable that Aihuiping attached? Does it work for you?Thanks,ThomasOn Wed, Mar 27, 2019 at 11:08 PM < std...@virgilio.it> wrote: Please see the attached file.Il 27 marzo 2019 alle 15.39 Thomas Yeo < ytho...@csail.mit.edu> ha scritto:  External Email - Use Caution Hi Stefano,Can you attach your updated colortable, so we can take a look?Thanks,ThomasOn Wed, Mar 27, 2019 at 10:27 PM < std...@virgilio.it> wrote: Yes the left hemisphere is fine.The error occurs again. The labels for posterior DMN and anterior DMN are the same and numbered like 1016 and 2016, despite I have modified the txt.ThanksStefanoIl 27 marzo 2019 alle 13.09 Thomas Yeo < ytho...@csail.mit.edu> ha scritto:  External Email - Use Caution Hi Stefano,Sorry. Can you confirm left hemisphere is ok? I think in this version of the annot file, the right hemisphere regions will start off as 2058, rather than 2001. So instead of numbering from 2001 to 2057, it should be from 2058 to 2114.Sorry about that. There are some intricacies between the annot format and mri_aparc2aseg that we were not aware of. We are trying to fix the issue now, but not so soon.  Regards,ThomasOn Wed, Mar 27, 2019 at 6:14 PM < std...@virgilio.it> wrote: I have renumbered and run:mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table Yeo2011_17Networks_renumbered.txtWhen I open the Yeo_17Net.mgz in freeview, the PCC portion of the DMN "2016 is visualized but labeled as rh_parahippocampal.What's happened?ThanksBest regards,StefanoIl 26 marzo 2019 alle 13.05 Thomas Yeo < ytho...@csail.mit.edu> ha scritto:  External Email - Use Caution Renumber for visualization purpose. Do you mean how to re-number in the colortable? Just open the colortable in a text editing software and edit.Thanks, ThomasOn Tue, Mar 26, 2019 at 6:44 PM < std...@virgilio.it> wrote: Thanks.Should I renumber for visualization purpose or for fs-fast?How can I do it?Il 26 marzo 2019 alle 4.01 Thomas Yeo < ytho...@csail.mit.edu> ha scritto:  Hi Stefano,Can I confirm that in Yeo_17Net.mgz, the left hemisphere parcels are 1001, 1002 to 1057? And the right hemisphere parcels are 2001, 2002, to 2057?If so, you will just need the right colortable to view the Yeo_17Net.mgz. We are currently generating a new colortable that should work for you. This might take a while.If you are in a hurry, you can download the colortable here ( https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt), but as you can see the range of values are not in the 1000-2000 range. So what you need to do is for the left hemisphere structures, you need to renumber them from 1 to 57 to 1001 to 1057. For the right hemisphere structures, you need to renumber them from 58 to 114 to 2001 to 2057.Regards,ThomasOn Sun, Mar 24, 2019 at 12:18 AM < std...@virgilio.it> wrote: Hi, my concern is the mri_aparc2aseg command line.In summary, I have done:mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000 mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annottkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgzThe output is correct by the color label is those of aparc.Probably the error is the match between the annotations and annot-table.Could you check the command lines, please?ThanksStefanoIl 10 marzo 2019 alle 21.15 "Greve, Douglas N.,Ph.D." < dgr...@mgh.harvard.edu> ha scritto:   Specify -seg Yeo_17Net.mgz (ie, don't include the full path). I don't know what is in that txt file. You can verify the segids by just bringing up the segmentation in freeview and clicking on a voxel. If you load the segmentation with that color table and everything looks ok, then the color table  is ok.  On 3/10/19 4:05 PM,  std...@virgilio.it wrote: External Email - Use CautionI will use freeview.Have you any suggestion on the use of fcseed-config option?Are you agree with the command line listed below?fcseed-config -segid ... -seg 

Re: [Freesurfer] regions of Yeo 17 networks in fast

[stdp82]

External Email - Use CautionThanks!By these command lines the analysis are going fine.mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.split_components.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi lh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.split_components.annot --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/Yeo2011_17network_SplitLabels_LUT_rh2058.txtIl 28 marzo 2019 alle 4.05 Ruby Kong  ha scritto:  Hi Stefano,We just figured out the issue. But there are a few things I might need to clarify with you:1) Yeo2011 original parcellation or Yeo2011 split labels versionMay I know which parcellation version you would like to use?We provide two different versions of Yeo2011 parcellation annot files:Version a. original parcellation: 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annotIn this version, each hemisphere contains 17 networks, for each hemisphere, the network labels start from 1 to 17 and medial wall area is indicated by 0.Version b. split labels version: 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.split_components.annotAs each network might contain multiple distributed components, therefore, we split all networks into multiple components, and re-label these components.In this version, each hemisphere contains 57 components, for left hemisphere, the component labels start from 1 to 57, for right hemisphere, the component labels start from 58 to 114.In one of your earliest email (Mar 9th), you were running this command:mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
The above command will project the Yeo2011 original parcellation (version a) to individual surface space.And then you run this one to project the parcellation from individual surface space to individual volumetric space:mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt --sval-annot yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot
there is a very weird flag -sval-annot, which is not a valid flag in mri_aparc2aseg. For this flag you are using Yeo2011 spilt labels version (version b). But for the correct flag -annot, you pass in the output from mri_surf2surf, which uses the Yeo2011 original parcellation (version a).2) freeview look up tablesMy colleague Aihuiping thought you are using the Yeo2011 split labels version (version b), therefore she passed you the look up table txt files which you can use to visualize version b (i.e. Yeo2011_17network_SplitLabels_LUT_rh2058.txt).But according to the commands in your last email, I assume you are actually using Yeo2011 original parcellation (version a). Therefore, the look up table txt file Yeo2011_17network_SplitLabels_LUT_rh2058.txt is not correct. That’s why you see the colors are wrongly mapped in freeview. If you would like to use version a, we can send you the look up table files for version a.3) Different input subjects for left and right hemisphereAccording to the commands in your last email, you are using subject subj as input for right hemisphere but subject ADNI001_AD for left hemisphere. It’s okay if you just want to do some quick test with different subjects, just want to confirm that you notice it. :)mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot --tval subj/label/rh.Yeo2011_17Networks_N1000

mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot --tval subj/label/lh.Yeo2011_17Networks_N1000
  Best,Ruby  On Thu, 28 Mar 2019 at 07:54, Thomas Yeo < ytho...@csail.mit.edu> wrote: Can you send us snapshots of what you are seeing? I am not sure what you mean by "labels of different colors that disagree with anatomical location and boundaries of the networks".On Thu, Mar 28, 2019 at 12:08 AM < std...@virgilio.it> wrote: My 

Re: [Freesurfer] regions of Yeo 17 networks in fast

[stdp82]

External Email - Use Caution

My apologies, the right hemisphere does not contain the color of each region 
but only an unique color. The left hemisphere contains labels of different 
colors that disagree with anatomical location and boundaries of the networks.
If I use the original ColorLUT cointained in freeview (at opening) the anatomy 
of the networks of the file that is computed by mri_aprac2seg is ok but the 
labels is wrong.

> Il 27 marzo 2019 alle 16.17 Thomas Yeo  ha scritto:
> 
> 
> External Email - Use Caution
> 
>  
> 
> Hi Stefano,
> 
> How are you using the colortable? Are you just passing it as a flag to 
> mri_aparc2aseg?
> 
> As far as I know (and I am NOT very knowledgeable, so I could be wrong), 
> the volumetric file (Yeo_17Net.mgz) does not contain the color information. 
> So when I said you should use the colortable, I meant you should use it with 
> the viewer. I am not sure about tkmedit, but for freeview, you can load your 
> volume and then also load your own colortable.
> 
> Regards,
> Thomas
> 
> On Wed, Mar 27, 2019 at 11:13 PM < std...@virgilio.it 
> mailto:std...@virgilio.it > wrote:
> 
> > > 
> > The problem persists.
> > 
> > We are sure that the command lines which I'm using are corrected?
> > 
> > mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh 
> > --sval-annot 
> > /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot
> >  --tval subj/label/rh.Yeo2011_17Networks_N1000
> > 
> > mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD 
> > --hemi lh --sval-annot 
> > /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
> >  --tval subj/label/lh.Yeo2011_17Networks_N1000
> > 
> > mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot 
> > Yeo2011_17Networks_N1000 --annot-table 
> > /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/Yeo2011_17network_SplitLabels_LUT_rh2058.txt
> > 
> > 
> > > > > Il 27 marzo 2019 alle 15.40 Aihuiping Xue < 
> > xueaihuip...@gmail.com mailto:xueaihuip...@gmail.com > ha scritto:
> > > 
> > > Hi Stefano,
> > > 
> > > I created a lookup table for your case. You can load your 
> > > .mgz file and try this lookup table in freeview. 
> > > 
> > > This is a temporary solution. We will modify the annot files 
> > > and provide another version of lookup table. But that will take some 
> > > time. I hope this lookup table can solve your problem for now.
> > > 
> > > Best Regards,
> > > XUE Aihuiping
> > > 
> > > < std...@virgilio.it mailto:std...@virgilio.it > 
> > > 于2019年3月27日周三 下午10:26写道：
> > > 
> > > > > > > 
> > > > Yes the left hemisphere is fine.
> > > > 
> > > > The error occurs again. The labels for posterior DMN 
> > > > and anterior DMN are the same and numbered like 1016 and 2016, despite 
> > > > I have modified the txt.
> > > > 
> > > > Thanks
> > > > 
> > > > Stefano
> > > > 
> > > > > > > > > Il 27 marzo 2019 alle 13.09 Thomas Yeo < 
> > > > ytho...@csail.mit.edu mailto:ytho...@csail.mit.edu > ha scritto:
> > > > > 
> > > > > 
> > > > > External Email - Use Caution
> > > > > 
> > > > >  
> > > > > 
> > > > > Hi Stefano,
> > > > > 
> > > > > Sorry. Can you confirm left hemisphere is ok? 
> > > > > 
> > > > > I think in this version of the annot file, the 
> > > > > right hemisphere regions will start off as 2058, rather than 2001. So 
> > > > > instead of numbering from 2001 to 2057, it should be from 2058 to 
> > > > > 2114.
> > > > > 
> > > > > Sorry about that. There are some intricacies 
> > > > > between the annot format and mri_aparc2aseg that we were not aware 
> > > > > of. We are trying to fix the issue now, but not so soon.  
> > > > > 
> > > > > Regards,
> > > > > Thomas
> > > > > 
> > > > > On Wed, Mar 27, 2019 at 6:14 PM < 
> > > > > std...@virgilio.it mailto:std...@virgilio.it > wrote:
> > > > > 
> > > > > > > > > > > 
> > > > > > I have renumbered and run:
> > > > > > 
> > > > > > mri_aparc2aseg --s subj --o 
> > > > > > subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 
> > > > > > --annot-table Yeo2011_17Networks_renumbered.txt
> > > > > > When I open the Yeo_17Net.mgz in freeview, 
> > > > > > the PCC portion of the DMN "2016 is visualized but labeled as 
> > > > > > rh_parahippocampal.
> > > > > > 
> > > > > >   

Re: [Freesurfer] regions of Yeo 17 networks in fast

[stdp82]

External Email - Use Caution

Additional issue: the colortable does not fit with the atlas and with anatomy 
of networks.

> Il 27 marzo 2019 alle 16.17 Thomas Yeo  ha scritto:
> 
> 
> External Email - Use Caution
> 
>  
> 
> Hi Stefano,
> 
> How are you using the colortable? Are you just passing it as a flag to 
> mri_aparc2aseg?
> 
> As far as I know (and I am NOT very knowledgeable, so I could be wrong), 
> the volumetric file (Yeo_17Net.mgz) does not contain the color information. 
> So when I said you should use the colortable, I meant you should use it with 
> the viewer. I am not sure about tkmedit, but for freeview, you can load your 
> volume and then also load your own colortable.
> 
> Regards,
> Thomas
> 
> On Wed, Mar 27, 2019 at 11:13 PM < std...@virgilio.it 
> mailto:std...@virgilio.it > wrote:
> 
> > > 
> > The problem persists.
> > 
> > We are sure that the command lines which I'm using are corrected?
> > 
> > mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh 
> > --sval-annot 
> > /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot
> >  --tval subj/label/rh.Yeo2011_17Networks_N1000
> > 
> > mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD 
> > --hemi lh --sval-annot 
> > /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
> >  --tval subj/label/lh.Yeo2011_17Networks_N1000
> > 
> > mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot 
> > Yeo2011_17Networks_N1000 --annot-table 
> > /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/Yeo2011_17network_SplitLabels_LUT_rh2058.txt
> > 
> > 
> > > > > Il 27 marzo 2019 alle 15.40 Aihuiping Xue < 
> > xueaihuip...@gmail.com mailto:xueaihuip...@gmail.com > ha scritto:
> > > 
> > > Hi Stefano,
> > > 
> > > I created a lookup table for your case. You can load your 
> > > .mgz file and try this lookup table in freeview. 
> > > 
> > > This is a temporary solution. We will modify the annot files 
> > > and provide another version of lookup table. But that will take some 
> > > time. I hope this lookup table can solve your problem for now.
> > > 
> > > Best Regards,
> > > XUE Aihuiping
> > > 
> > > < std...@virgilio.it mailto:std...@virgilio.it > 
> > > 于2019年3月27日周三 下午10:26写道：
> > > 
> > > > > > > 
> > > > Yes the left hemisphere is fine.
> > > > 
> > > > The error occurs again. The labels for posterior DMN 
> > > > and anterior DMN are the same and numbered like 1016 and 2016, despite 
> > > > I have modified the txt.
> > > > 
> > > > Thanks
> > > > 
> > > > Stefano
> > > > 
> > > > > > > > > Il 27 marzo 2019 alle 13.09 Thomas Yeo < 
> > > > ytho...@csail.mit.edu mailto:ytho...@csail.mit.edu > ha scritto:
> > > > > 
> > > > > 
> > > > > External Email - Use Caution
> > > > > 
> > > > >  
> > > > > 
> > > > > Hi Stefano,
> > > > > 
> > > > > Sorry. Can you confirm left hemisphere is ok? 
> > > > > 
> > > > > I think in this version of the annot file, the 
> > > > > right hemisphere regions will start off as 2058, rather than 2001. So 
> > > > > instead of numbering from 2001 to 2057, it should be from 2058 to 
> > > > > 2114.
> > > > > 
> > > > > Sorry about that. There are some intricacies 
> > > > > between the annot format and mri_aparc2aseg that we were not aware 
> > > > > of. We are trying to fix the issue now, but not so soon.  
> > > > > 
> > > > > Regards,
> > > > > Thomas
> > > > > 
> > > > > On Wed, Mar 27, 2019 at 6:14 PM < 
> > > > > std...@virgilio.it mailto:std...@virgilio.it > wrote:
> > > > > 
> > > > > > > > > > > 
> > > > > > I have renumbered and run:
> > > > > > 
> > > > > > mri_aparc2aseg --s subj --o 
> > > > > > subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 
> > > > > > --annot-table Yeo2011_17Networks_renumbered.txt
> > > > > > When I open the Yeo_17Net.mgz in freeview, 
> > > > > > the PCC portion of the DMN "2016 is visualized but labeled as 
> > > > > > rh_parahippocampal.
> > > > > > 
> > > > > > What's happened?
> > > > > > 
> > > > > > Thanks
> > > > > > 
> > > > > > Best regards,
> > > > > > 
> > > > > > Stefano
> > > > > > 
> > > > > > > > > > > > > Il 26 marzo 2019 alle 
> > > > > > 

Re: [Freesurfer] regions of Yeo 17 networks in fast

[stdp82]

External Email - Use Caution

Thanks the right hemiphere is ok, but the left no.

> Il 27 marzo 2019 alle 16.17 Thomas Yeo  ha scritto:
> 
> 
> External Email - Use Caution
> 
>  
> 
> Hi Stefano,
> 
> How are you using the colortable? Are you just passing it as a flag to 
> mri_aparc2aseg?
> 
> As far as I know (and I am NOT very knowledgeable, so I could be wrong), 
> the volumetric file (Yeo_17Net.mgz) does not contain the color information. 
> So when I said you should use the colortable, I meant you should use it with 
> the viewer. I am not sure about tkmedit, but for freeview, you can load your 
> volume and then also load your own colortable.
> 
> Regards,
> Thomas
> 
> On Wed, Mar 27, 2019 at 11:13 PM < std...@virgilio.it 
> mailto:std...@virgilio.it > wrote:
> 
> > > 
> > The problem persists.
> > 
> > We are sure that the command lines which I'm using are corrected?
> > 
> > mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh 
> > --sval-annot 
> > /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot
> >  --tval subj/label/rh.Yeo2011_17Networks_N1000
> > 
> > mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD 
> > --hemi lh --sval-annot 
> > /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
> >  --tval subj/label/lh.Yeo2011_17Networks_N1000
> > 
> > mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot 
> > Yeo2011_17Networks_N1000 --annot-table 
> > /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/Yeo2011_17network_SplitLabels_LUT_rh2058.txt
> > 
> > 
> > > > > Il 27 marzo 2019 alle 15.40 Aihuiping Xue < 
> > xueaihuip...@gmail.com mailto:xueaihuip...@gmail.com > ha scritto:
> > > 
> > > Hi Stefano,
> > > 
> > > I created a lookup table for your case. You can load your 
> > > .mgz file and try this lookup table in freeview. 
> > > 
> > > This is a temporary solution. We will modify the annot files 
> > > and provide another version of lookup table. But that will take some 
> > > time. I hope this lookup table can solve your problem for now.
> > > 
> > > Best Regards,
> > > XUE Aihuiping
> > > 
> > > < std...@virgilio.it mailto:std...@virgilio.it > 
> > > 于2019年3月27日周三 下午10:26写道：
> > > 
> > > > > > > 
> > > > Yes the left hemisphere is fine.
> > > > 
> > > > The error occurs again. The labels for posterior DMN 
> > > > and anterior DMN are the same and numbered like 1016 and 2016, despite 
> > > > I have modified the txt.
> > > > 
> > > > Thanks
> > > > 
> > > > Stefano
> > > > 
> > > > > > > > > Il 27 marzo 2019 alle 13.09 Thomas Yeo < 
> > > > ytho...@csail.mit.edu mailto:ytho...@csail.mit.edu > ha scritto:
> > > > > 
> > > > > 
> > > > > External Email - Use Caution
> > > > > 
> > > > >  
> > > > > 
> > > > > Hi Stefano,
> > > > > 
> > > > > Sorry. Can you confirm left hemisphere is ok? 
> > > > > 
> > > > > I think in this version of the annot file, the 
> > > > > right hemisphere regions will start off as 2058, rather than 2001. So 
> > > > > instead of numbering from 2001 to 2057, it should be from 2058 to 
> > > > > 2114.
> > > > > 
> > > > > Sorry about that. There are some intricacies 
> > > > > between the annot format and mri_aparc2aseg that we were not aware 
> > > > > of. We are trying to fix the issue now, but not so soon.  
> > > > > 
> > > > > Regards,
> > > > > Thomas
> > > > > 
> > > > > On Wed, Mar 27, 2019 at 6:14 PM < 
> > > > > std...@virgilio.it mailto:std...@virgilio.it > wrote:
> > > > > 
> > > > > > > > > > > 
> > > > > > I have renumbered and run:
> > > > > > 
> > > > > > mri_aparc2aseg --s subj --o 
> > > > > > subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 
> > > > > > --annot-table Yeo2011_17Networks_renumbered.txt
> > > > > > When I open the Yeo_17Net.mgz in freeview, 
> > > > > > the PCC portion of the DMN "2016 is visualized but labeled as 
> > > > > > rh_parahippocampal.
> > > > > > 
> > > > > > What's happened?
> > > > > > 
> > > > > > Thanks
> > > > > > 
> > > > > > Best regards,
> > > > > > 
> > > > > > Stefano
> > > > > > 
> > > > > > > > > > > > > Il 26 marzo 2019 alle 
> > > > > > 13.05 Thomas Yeo < ytho...@csail.mit.edu 
> > 

Re: [Freesurfer] regions of Yeo 17 networks in fast

[stdp82]

External Email - Use Caution

The problem persists.

We are sure that the command lines which I'm using are corrected?

> Il 27 marzo 2019 alle 16.10 Thomas Yeo  ha scritto:
> 
> Hi Stefano,
> 
> Did you see the colortable that Aihuiping attached? Does it work for you?
> 
> Thanks,
> Thomas
> 
> On Wed, Mar 27, 2019 at 11:08 PM < std...@virgilio.it 
> mailto:std...@virgilio.it > wrote:
> 
> > > 
> > Please see the attached file.
> > 
> > 
> > > > > Il 27 marzo 2019 alle 15.39 Thomas Yeo < 
> > ytho...@csail.mit.edu mailto:ytho...@csail.mit.edu > ha scritto:
> > > 
> > > 
> > > External Email - Use Caution
> > > 
> > >  
> > > 
> > > Hi Stefano,
> > > 
> > > Can you attach your updated colortable, so we can take a look?
> > > 
> > > Thanks,
> > > Thomas
> > > 
> > > On Wed, Mar 27, 2019 at 10:27 PM < std...@virgilio.it 
> > > mailto:std...@virgilio.it > wrote:
> > > 
> > > > > > > 
> > > > Yes the left hemisphere is fine.
> > > > 
> > > > The error occurs again. The labels for posterior DMN 
> > > > and anterior DMN are the same and numbered like 1016 and 2016, despite 
> > > > I have modified the txt.
> > > > 
> > > > Thanks
> > > > 
> > > > Stefano
> > > > 
> > > > > > > > > Il 27 marzo 2019 alle 13.09 Thomas Yeo < 
> > > > ytho...@csail.mit.edu mailto:ytho...@csail.mit.edu > ha scritto:
> > > > > 
> > > > > 
> > > > > External Email - Use Caution
> > > > > 
> > > > >  
> > > > > 
> > > > > Hi Stefano,
> > > > > 
> > > > > Sorry. Can you confirm left hemisphere is ok? 
> > > > > 
> > > > > I think in this version of the annot file, the 
> > > > > right hemisphere regions will start off as 2058, rather than 2001. So 
> > > > > instead of numbering from 2001 to 2057, it should be from 2058 to 
> > > > > 2114.
> > > > > 
> > > > > Sorry about that. There are some intricacies 
> > > > > between the annot format and mri_aparc2aseg that we were not aware 
> > > > > of. We are trying to fix the issue now, but not so soon.  
> > > > > 
> > > > > Regards,
> > > > > Thomas
> > > > > 
> > > > > On Wed, Mar 27, 2019 at 6:14 PM < 
> > > > > std...@virgilio.it mailto:std...@virgilio.it > wrote:
> > > > > 
> > > > > > > > > > > 
> > > > > > I have renumbered and run:
> > > > > > 
> > > > > > mri_aparc2aseg --s subj --o 
> > > > > > subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 
> > > > > > --annot-table Yeo2011_17Networks_renumbered.txt
> > > > > > When I open the Yeo_17Net.mgz in freeview, 
> > > > > > the PCC portion of the DMN "2016 is visualized but labeled as 
> > > > > > rh_parahippocampal.
> > > > > > 
> > > > > > What's happened?
> > > > > > 
> > > > > > Thanks
> > > > > > 
> > > > > > Best regards,
> > > > > > 
> > > > > > Stefano
> > > > > > 
> > > > > > > > > > > > > Il 26 marzo 2019 alle 
> > > > > > 13.05 Thomas Yeo < ytho...@csail.mit.edu 
> > > > > > mailto:ytho...@csail.mit.edu > ha scritto:
> > > > > > > 
> > > > > > > 
> > > > > > > External Email - Use Caution  
> > > > > > >   
> > > > > > > 
> > > > > > >  
> > > > > > > 
> > > > > > > Renumber for visualization purpose. 
> > > > > > > 
> > > > > > > Do you mean how to re-number in the 
> > > > > > > colortable? Just open the colortable in a text editing software 
> > > > > > > and edit.
> > > > > > > 
> > > > > > > Thanks,
> > > > > > > Thomas
> > > > > > > 
> > > > > > > On Tue, Mar 26, 2019 at 6:44 PM < 
> > > > > > > std...@virgilio.it mailto:std...@virgilio.it > wrote:
> > > > > > > 
> > > > > > > > > > > > > > > 
> > > > > > > > Thanks.
> > > > > > > > 
> > > > > > > > Should I renumber for 
> > > > > > > > visualization purpose or for fs-fast?
> > > > > > > > 
> > > > > > > > How can I do it?
> > > > > > > > 
> > > > > > > > 
> > > > > > > > > > > > > > > > > Il 26 
> > > > > > > > marzo 2019 alle 4.01 Thomas Yeo < ytho...@csail.mit.edu 
> > > > > > > > mailto:ytho...@csail.mit.edu > ha scritto:
> > > > > > > > > 
> > > > > > > > > Hi Stefano,
> > > > > > > > > 
> 

Re: [Freesurfer] regions of Yeo 17 networks in fast

[stdp82]

External Email - Use Caution

The problem persists.

We are sure that the command lines which I'm using are corrected?

mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh --sval-annot 
/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot
 --tval subj/label/rh.Yeo2011_17Networks_N1000

mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh 
--sval-annot 
/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
 --tval subj/label/lh.Yeo2011_17Networks_N1000

mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot 
Yeo2011_17Networks_N1000 --annot-table 
/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/Yeo2011_17network_SplitLabels_LUT_rh2058.txt


> Il 27 marzo 2019 alle 15.40 Aihuiping Xue  ha scritto:
> 
> Hi Stefano,
> 
> I created a lookup table for your case. You can load your .mgz file and 
> try this lookup table in freeview. 
> 
> This is a temporary solution. We will modify the annot files and provide 
> another version of lookup table. But that will take some time. I hope this 
> lookup table can solve your problem for now.
> 
> Best Regards,
> XUE Aihuiping
> 
> < std...@virgilio.it mailto:std...@virgilio.it > 于2019年3月27日周三 下午10:26写道：
> 
> > > 
> > Yes the left hemisphere is fine.
> > 
> > The error occurs again. The labels for posterior DMN and anterior 
> > DMN are the same and numbered like 1016 and 2016, despite I have modified 
> > the txt.
> > 
> > Thanks
> > 
> > Stefano
> > 
> > > > > Il 27 marzo 2019 alle 13.09 Thomas Yeo < 
> > ytho...@csail.mit.edu mailto:ytho...@csail.mit.edu > ha scritto:
> > > 
> > > 
> > > External Email - Use Caution
> > > 
> > >  
> > > 
> > > Hi Stefano,
> > > 
> > > Sorry. Can you confirm left hemisphere is ok? 
> > > 
> > > I think in this version of the annot file, the right 
> > > hemisphere regions will start off as 2058, rather than 2001. So instead 
> > > of numbering from 2001 to 2057, it should be from 2058 to 2114.
> > > 
> > > Sorry about that. There are some intricacies between the 
> > > annot format and mri_aparc2aseg that we were not aware of. We are trying 
> > > to fix the issue now, but not so soon.  
> > > 
> > > Regards,
> > > Thomas
> > > 
> > > On Wed, Mar 27, 2019 at 6:14 PM < std...@virgilio.it 
> > > mailto:std...@virgilio.it > wrote:
> > > 
> > > > > > > 
> > > > I have renumbered and run:
> > > > 
> > > > mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz 
> > > > --annot Yeo2011_17Networks_N1000 --annot-table 
> > > > Yeo2011_17Networks_renumbered.txt
> > > > When I open the Yeo_17Net.mgz in freeview, the PCC 
> > > > portion of the DMN "2016 is visualized but labeled as 
> > > > rh_parahippocampal.
> > > > 
> > > > What's happened?
> > > > 
> > > > Thanks
> > > > 
> > > > Best regards,
> > > > 
> > > > Stefano
> > > > 
> > > > > > > > > Il 26 marzo 2019 alle 13.05 Thomas Yeo < 
> > > > ytho...@csail.mit.edu mailto:ytho...@csail.mit.edu > ha scritto:
> > > > > 
> > > > > 
> > > > > External Email - Use Caution
> > > > > 
> > > > >  
> > > > > 
> > > > > Renumber for visualization purpose. 
> > > > > 
> > > > > Do you mean how to re-number in the colortable? 
> > > > > Just open the colortable in a text editing software and edit.
> > > > > 
> > > > > Thanks,
> > > > > Thomas
> > > > > 
> > > > > On Tue, Mar 26, 2019 at 6:44 PM < 
> > > > > std...@virgilio.it mailto:std...@virgilio.it > wrote:
> > > > > 
> > > > > > > > > > > 
> > > > > > Thanks.
> > > > > > 
> > > > > > Should I renumber for visualization purpose 
> > > > > > or for fs-fast?
> > > > > > 
> > > > > > How can I do it?
> > > > > > 
> > > > > > 
> > > > > > > > > > > > > Il 26 marzo 2019 alle 
> > > > > > 4.01 Thomas Yeo < ytho...@csail.mit.edu 
> > > > > > mailto:ytho...@csail.mit.edu > ha scritto:
> > > > > > > 
> > > > > > > Hi Stefano,
> > > > > > > 
> > > > > > > Can I confirm that in Yeo_17Net.mgz, 
> > > > > > > the left hemisphere parcels are 1001, 1002 to 1057? And the right 
> > > > > > > hemisphere parcels are 2001, 2002, to 2057?
> > > > > > > 
> > > > > > > If so, you will just need the right 
> > > > > > > colortable to view 

Re: [Freesurfer] regions of Yeo 17 networks in fast

[stdp82]

External Email - Use Caution

Please see the attached file.


> Il 27 marzo 2019 alle 15.39 Thomas Yeo  ha scritto:
> 
> 
> External Email - Use Caution
> 
>  
> 
> Hi Stefano,
> 
> Can you attach your updated colortable, so we can take a look?
> 
> Thanks,
> Thomas
> 
> On Wed, Mar 27, 2019 at 10:27 PM < std...@virgilio.it 
> mailto:std...@virgilio.it > wrote:
> 
> > > 
> > Yes the left hemisphere is fine.
> > 
> > The error occurs again. The labels for posterior DMN and anterior 
> > DMN are the same and numbered like 1016 and 2016, despite I have modified 
> > the txt.
> > 
> > Thanks
> > 
> > Stefano
> > 
> > > > > Il 27 marzo 2019 alle 13.09 Thomas Yeo < 
> > ytho...@csail.mit.edu mailto:ytho...@csail.mit.edu > ha scritto:
> > > 
> > > 
> > > External Email - Use Caution
> > > 
> > >  
> > > 
> > > Hi Stefano,
> > > 
> > > Sorry. Can you confirm left hemisphere is ok? 
> > > 
> > > I think in this version of the annot file, the right 
> > > hemisphere regions will start off as 2058, rather than 2001. So instead 
> > > of numbering from 2001 to 2057, it should be from 2058 to 2114.
> > > 
> > > Sorry about that. There are some intricacies between the 
> > > annot format and mri_aparc2aseg that we were not aware of. We are trying 
> > > to fix the issue now, but not so soon.  
> > > 
> > > Regards,
> > > Thomas
> > > 
> > > On Wed, Mar 27, 2019 at 6:14 PM < std...@virgilio.it 
> > > mailto:std...@virgilio.it > wrote:
> > > 
> > > > > > > 
> > > > I have renumbered and run:
> > > > 
> > > > mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz 
> > > > --annot Yeo2011_17Networks_N1000 --annot-table 
> > > > Yeo2011_17Networks_renumbered.txt
> > > > When I open the Yeo_17Net.mgz in freeview, the PCC 
> > > > portion of the DMN "2016 is visualized but labeled as 
> > > > rh_parahippocampal.
> > > > 
> > > > What's happened?
> > > > 
> > > > Thanks
> > > > 
> > > > Best regards,
> > > > 
> > > > Stefano
> > > > 
> > > > > > > > > Il 26 marzo 2019 alle 13.05 Thomas Yeo < 
> > > > ytho...@csail.mit.edu mailto:ytho...@csail.mit.edu > ha scritto:
> > > > > 
> > > > > 
> > > > > External Email - Use Caution
> > > > > 
> > > > >  
> > > > > 
> > > > > Renumber for visualization purpose. 
> > > > > 
> > > > > Do you mean how to re-number in the colortable? 
> > > > > Just open the colortable in a text editing software and edit.
> > > > > 
> > > > > Thanks,
> > > > > Thomas
> > > > > 
> > > > > On Tue, Mar 26, 2019 at 6:44 PM < 
> > > > > std...@virgilio.it mailto:std...@virgilio.it > wrote:
> > > > > 
> > > > > > > > > > > 
> > > > > > Thanks.
> > > > > > 
> > > > > > Should I renumber for visualization purpose 
> > > > > > or for fs-fast?
> > > > > > 
> > > > > > How can I do it?
> > > > > > 
> > > > > > 
> > > > > > > > > > > > > Il 26 marzo 2019 alle 
> > > > > > 4.01 Thomas Yeo < ytho...@csail.mit.edu 
> > > > > > mailto:ytho...@csail.mit.edu > ha scritto:
> > > > > > > 
> > > > > > > Hi Stefano,
> > > > > > > 
> > > > > > > Can I confirm that in Yeo_17Net.mgz, 
> > > > > > > the left hemisphere parcels are 1001, 1002 to 1057? And the right 
> > > > > > > hemisphere parcels are 2001, 2002, to 2057?
> > > > > > > 
> > > > > > > If so, you will just need the right 
> > > > > > > colortable to view the Yeo_17Net.mgz. We are currently generating 
> > > > > > > a new colortable that should work for you. This might take a 
> > > > > > > while.
> > > > > > > 
> > > > > > > If you are in a hurry, you can 
> > > > > > > download the colortable here ( 
> > > > > > > https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt),
> > > > > > >  but as you can see the range of values are not in the 1000-2000 
> > > > > > > range. So what you need to do is for the left hemisphere 
> > > > > > > structures, you need to renumber them from 1 to 57 to 1001 to 
> > > > > > > 1057. For the right hemisphere structures, you need to renumber 
> > > > > > > them from 58 to 114 to 2001 to 2057.
> > > > > > > 
> > > > > > > Regards,
> > > > > > > Thomas
> > > > > > > 
> > > > > > > 

Re: [Freesurfer] regions of Yeo 17 networks in fast

[stdp82]

External Email - Use Caution

Yes the left hemisphere is fine.

The error occurs again. The labels for posterior DMN and anterior DMN are the 
same and numbered like 1016 and 2016, despite I have modified the txt.

Thanks

Stefano

> Il 27 marzo 2019 alle 13.09 Thomas Yeo  ha scritto:
> 
> 
> External Email - Use Caution
> 
>  
> 
> Hi Stefano,
> 
> Sorry. Can you confirm left hemisphere is ok? 
> 
> I think in this version of the annot file, the right hemisphere regions 
> will start off as 2058, rather than 2001. So instead of numbering from 2001 
> to 2057, it should be from 2058 to 2114.
> 
> Sorry about that. There are some intricacies between the annot format and 
> mri_aparc2aseg that we were not aware of. We are trying to fix the issue now, 
> but not so soon.  
> 
> Regards,
> Thomas
> 
> On Wed, Mar 27, 2019 at 6:14 PM < std...@virgilio.it 
> mailto:std...@virgilio.it > wrote:
> 
> > > 
> > I have renumbered and run:
> > 
> > mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot 
> > Yeo2011_17Networks_N1000 --annot-table Yeo2011_17Networks_renumbered.txt
> > When I open the Yeo_17Net.mgz in freeview, the PCC portion of the 
> > DMN "2016 is visualized but labeled as rh_parahippocampal.
> > 
> > What's happened?
> > 
> > Thanks
> > 
> > Best regards,
> > 
> > Stefano
> > 
> > > > > Il 26 marzo 2019 alle 13.05 Thomas Yeo < 
> > ytho...@csail.mit.edu mailto:ytho...@csail.mit.edu > ha scritto:
> > > 
> > > 
> > > External Email - Use Caution
> > > 
> > >  
> > > 
> > > Renumber for visualization purpose. 
> > > 
> > > Do you mean how to re-number in the colortable? Just open the 
> > > colortable in a text editing software and edit.
> > > 
> > > Thanks,
> > > Thomas
> > > 
> > > On Tue, Mar 26, 2019 at 6:44 PM < std...@virgilio.it 
> > > mailto:std...@virgilio.it > wrote:
> > > 
> > > > > > > 
> > > > Thanks.
> > > > 
> > > > Should I renumber for visualization purpose or for 
> > > > fs-fast?
> > > > 
> > > > How can I do it?
> > > > 
> > > > 
> > > > > > > > > Il 26 marzo 2019 alle 4.01 Thomas Yeo < 
> > > > ytho...@csail.mit.edu mailto:ytho...@csail.mit.edu > ha scritto:
> > > > > 
> > > > > Hi Stefano,
> > > > > 
> > > > > Can I confirm that in Yeo_17Net.mgz, the left 
> > > > > hemisphere parcels are 1001, 1002 to 1057? And the right hemisphere 
> > > > > parcels are 2001, 2002, to 2057?
> > > > > 
> > > > > If so, you will just need the right colortable to 
> > > > > view the Yeo_17Net.mgz. We are currently generating a new colortable 
> > > > > that should work for you. This might take a while.
> > > > > 
> > > > > If you are in a hurry, you can download the 
> > > > > colortable here ( 
> > > > > https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt),
> > > > >  but as you can see the range of values are not in the 1000-2000 
> > > > > range. So what you need to do is for the left hemisphere structures, 
> > > > > you need to renumber them from 1 to 57 to 1001 to 1057. For the right 
> > > > > hemisphere structures, you need to renumber them from 58 to 114 to 
> > > > > 2001 to 2057.
> > > > > 
> > > > > Regards,
> > > > > Thomas
> > > > > 
> > > > > On Sun, Mar 24, 2019 at 12:18 AM < 
> > > > > std...@virgilio.it mailto:std...@virgilio.it > wrote:
> > > > > 
> > > > > > > > > > > 
> > > > > > Hi, my concern is the mri_aparc2aseg 
> > > > > > command line.
> > > > > > 
> > > > > > In summary, I have done:
> > > > > > 
> > > > > > mri_surf2surf --srcsubject fsaverage5 
> > > > > > --trgsubject subj --hemi rh --sval-annot 
> > > > > > /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot
> > > > > >  --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
> > > > > > mri_surf2surf --srcsubject fsaverage5 
> > > > > > --trgsubject ADNI001_AD --hemi lh --sval-annot 
> > > > > > /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
> > > > > >  --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000
> > > > > > 
> > > > > >  
> > > > > > 
> > > > > > mri_aparc2aseg --s subj --o 
> > > > > > subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 
> > > > > > 

Re: [Freesurfer] regions of Yeo 17 networks in fast

[stdp82]

External Email - Use Caution

I have renumbered and run:

mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot 
Yeo2011_17Networks_N1000 --annot-table Yeo2011_17Networks_renumbered.txt
When I open the Yeo_17Net.mgz in freeview, the PCC portion of the DMN "2016 is 
visualized but labeled as rh_parahippocampal.

What's happened?

Thanks

Best regards,

Stefano

> Il 26 marzo 2019 alle 13.05 Thomas Yeo  ha scritto:
> 
> 
> External Email - Use Caution
> 
>  
> 
> Renumber for visualization purpose. 
> 
> Do you mean how to re-number in the colortable? Just open the colortable 
> in a text editing software and edit.
> 
> Thanks,
> Thomas
> 
> On Tue, Mar 26, 2019 at 6:44 PM < std...@virgilio.it 
> mailto:std...@virgilio.it > wrote:
> 
> > > 
> > Thanks.
> > 
> > Should I renumber for visualization purpose or for fs-fast?
> > 
> > How can I do it?
> > 
> > 
> > > > > Il 26 marzo 2019 alle 4.01 Thomas Yeo < 
> > ytho...@csail.mit.edu mailto:ytho...@csail.mit.edu > ha scritto:
> > > 
> > > Hi Stefano,
> > > 
> > > Can I confirm that in Yeo_17Net.mgz, the left hemisphere 
> > > parcels are 1001, 1002 to 1057? And the right hemisphere parcels are 
> > > 2001, 2002, to 2057?
> > > 
> > > If so, you will just need the right colortable to view the 
> > > Yeo_17Net.mgz. We are currently generating a new colortable that should 
> > > work for you. This might take a while.
> > > 
> > > If you are in a hurry, you can download the colortable here ( 
> > > https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt),
> > >  but as you can see the range of values are not in the 1000-2000 range. 
> > > So what you need to do is for the left hemisphere structures, you need to 
> > > renumber them from 1 to 57 to 1001 to 1057. For the right hemisphere 
> > > structures, you need to renumber them from 58 to 114 to 2001 to 2057.
> > > 
> > > Regards,
> > > Thomas
> > > 
> > > On Sun, Mar 24, 2019 at 12:18 AM < std...@virgilio.it 
> > > mailto:std...@virgilio.it > wrote:
> > > 
> > > > > > > 
> > > > Hi, my concern is the mri_aparc2aseg command line.
> > > > 
> > > > In summary, I have done:
> > > > 
> > > > mri_surf2surf --srcsubject fsaverage5 --trgsubject subj 
> > > > --hemi rh --sval-annot 
> > > > /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot
> > > >  --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
> > > > mri_surf2surf --srcsubject fsaverage5 --trgsubject 
> > > > ADNI001_AD --hemi lh --sval-annot 
> > > > /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
> > > >  --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000
> > > > 
> > > >  
> > > > 
> > > > mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz 
> > > > --annot Yeo2011_17Networks_N1000 --annot-table 
> > > > /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annot
> > > > tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
> > > > 
> > > > The output is correct by the color label is those of 
> > > > aparc.
> > > > 
> > > > Probably the error is the match between the annotations 
> > > > and annot-table.
> > > > 
> > > > Could you check the command lines, please?
> > > > 
> > > > Thanks
> > > > 
> > > > Stefano
> > > > 
> > > > 
> > > > 
> > > > > > > > > Il 10 marzo 2019 alle 21.15 "Greve, 
> > > > Douglas N.,Ph.D." < dgr...@mgh.harvard.edu 
> > > > mailto:dgr...@mgh.harvard.edu > ha scritto:
> > > > > 
> > > > > Specify -seg Yeo_17Net.mgz (ie, don't include the 
> > > > > full path). I don't know what is in that txt file. You can verify the 
> > > > > segids by just bringing up the segmentation in freeview and clicking 
> > > > > on a voxel. If you load the segmentation with that color table and 
> > > > > everything looks ok, then the color table  is ok.
> > > > > 
> > > > > On 3/10/19 4:05 PM, std...@virgilio.it 
> > > > > mailto:std...@virgilio.it wrote:
> > > > > 
> > > > > > > > > > > 
> > > > > > External Email - Use Caution
> > > > > > 
> > > > > > I will use freeview.
> > > > > > 
> > > > > > Have you any suggestion on the use of 
> > > > > > fcseed-config option?
> > > > > > 
> > > 

Re: [Freesurfer] regions of Yeo 17 networks in fast

[stdp82]

External Email - Use Caution

mri_aparc2aseg --s subj --o sub/mri/Yeo_17Net.mgz --annot 
Yeo2011_17Networks_N1000 --annot-table 
/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt
freeview subj orig.mgz -ov subj/mri/Yeo_17Net.mgz

I am not sure that the command line sound fine.

When I open the files in freeview, the name of labels is the same of aparc2009.

> Il 26 marzo 2019 alle 4.01 Thomas Yeo  ha scritto:
> 
> Hi Stefano,
> 
> Can I confirm that in Yeo_17Net.mgz, the left hemisphere parcels are 
> 1001, 1002 to 1057? And the right hemisphere parcels are 2001, 2002, to 2057?
> 
> If so, you will just need the right colortable to view the Yeo_17Net.mgz. 
> We are currently generating a new colortable that should work for you. This 
> might take a while.
> 
> If you are in a hurry, you can download the colortable here ( 
> https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt),
>  but as you can see the range of values are not in the 1000-2000 range. So 
> what you need to do is for the left hemisphere structures, you need to 
> renumber them from 1 to 57 to 1001 to 1057. For the right hemisphere 
> structures, you need to renumber them from 58 to 114 to 2001 to 2057.
> 
> Regards,
> Thomas
> 
> On Sun, Mar 24, 2019 at 12:18 AM < std...@virgilio.it 
> mailto:std...@virgilio.it > wrote:
> 
> > > 
> > Hi, my concern is the mri_aparc2aseg command line.
> > 
> > In summary, I have done:
> > 
> > mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh 
> > --sval-annot 
> > /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot
> >  --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
> > mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD 
> > --hemi lh --sval-annot 
> > /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
> >  --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000
> > 
> >  
> > 
> > mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot 
> > Yeo2011_17Networks_N1000 --annot-table 
> > /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annot
> > tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
> > 
> > The output is correct by the color label is those of aparc.
> > 
> > Probably the error is the match between the annotations and 
> > annot-table.
> > 
> > Could you check the command lines, please?
> > 
> > Thanks
> > 
> > Stefano
> > 
> > 
> > 
> > > > > Il 10 marzo 2019 alle 21.15 "Greve, Douglas N.,Ph.D." < 
> > dgr...@mgh.harvard.edu mailto:dgr...@mgh.harvard.edu > ha scritto:
> > > 
> > > Specify -seg Yeo_17Net.mgz (ie, don't include the full path). 
> > > I don't know what is in that txt file. You can verify the segids by just 
> > > bringing up the segmentation in freeview and clicking on a voxel. If you 
> > > load the segmentation with that color table and everything looks ok, then 
> > > the color table  is ok.
> > > 
> > > On 3/10/19 4:05 PM, std...@virgilio.it 
> > > mailto:std...@virgilio.it wrote:
> > > 
> > > > > > > 
> > > > External Email - Use Caution
> > > > 
> > > > I will use freeview.
> > > > 
> > > > Have you any suggestion on the use of fcseed-config 
> > > > option?
> > > > 
> > > > Are you agree with the command line listed below?
> > > > 
> > > > fcseed-config -segid ... -seg 
> > > > $SUBJECTS_DIR/subj/mri/Yeo_17Net.mgz -fsd rest -mean -cfg 
> > > > lh.SEED.config -overwrite
> > > > 
> > > > My concerns are on -segids. Are the ids included in the 
> > > > file 
> > > > 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt?
> > > > 
> > > > How can I select a specific seed (id) to be used in 
> > > > -segids?
> > > > 
> > > > Thanks
> > > > 
> > > > Stefano
> > > > 
> > > > 
> > > > > > > > > 
> > > > > Il 10 marzo 2019 alle 17.17 Bruce Fischl 
> > > > >  mailto:fis...@nmr.mgh.harvard.edu ha 
> > > > > scritto:
> > > > > 
> > > > > Hi Stefano
> > > > > 
> > > > > is there a reason you are using tkmedit and not 
> > > > > freeview? We deprecated
> > > > > tkmedit a long time ago now
> > > > > 
> > > > > cheers
> > > > > Bruce
> > > > > 

Re: [Freesurfer] regions of Yeo 17 networks in fast

[stdp82]

External Email - Use Caution

Thanks.

Should I renumber for visualization purpose or for fs-fast?

How can I do it?


> Il 26 marzo 2019 alle 4.01 Thomas Yeo  ha scritto:
> 
> Hi Stefano,
> 
> Can I confirm that in Yeo_17Net.mgz, the left hemisphere parcels are 
> 1001, 1002 to 1057? And the right hemisphere parcels are 2001, 2002, to 2057?
> 
> If so, you will just need the right colortable to view the Yeo_17Net.mgz. 
> We are currently generating a new colortable that should work for you. This 
> might take a while.
> 
> If you are in a hurry, you can download the colortable here ( 
> https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt),
>  but as you can see the range of values are not in the 1000-2000 range. So 
> what you need to do is for the left hemisphere structures, you need to 
> renumber them from 1 to 57 to 1001 to 1057. For the right hemisphere 
> structures, you need to renumber them from 58 to 114 to 2001 to 2057.
> 
> Regards,
> Thomas
> 
> On Sun, Mar 24, 2019 at 12:18 AM < std...@virgilio.it 
> mailto:std...@virgilio.it > wrote:
> 
> > > 
> > Hi, my concern is the mri_aparc2aseg command line.
> > 
> > In summary, I have done:
> > 
> > mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh 
> > --sval-annot 
> > /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot
> >  --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
> > mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD 
> > --hemi lh --sval-annot 
> > /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
> >  --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000
> > 
> >  
> > 
> > mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot 
> > Yeo2011_17Networks_N1000 --annot-table 
> > /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annot
> > tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
> > 
> > The output is correct by the color label is those of aparc.
> > 
> > Probably the error is the match between the annotations and 
> > annot-table.
> > 
> > Could you check the command lines, please?
> > 
> > Thanks
> > 
> > Stefano
> > 
> > 
> > 
> > > > > Il 10 marzo 2019 alle 21.15 "Greve, Douglas N.,Ph.D." < 
> > dgr...@mgh.harvard.edu mailto:dgr...@mgh.harvard.edu > ha scritto:
> > > 
> > > Specify -seg Yeo_17Net.mgz (ie, don't include the full path). 
> > > I don't know what is in that txt file. You can verify the segids by just 
> > > bringing up the segmentation in freeview and clicking on a voxel. If you 
> > > load the segmentation with that color table and everything looks ok, then 
> > > the color table  is ok.
> > > 
> > > On 3/10/19 4:05 PM, std...@virgilio.it 
> > > mailto:std...@virgilio.it wrote:
> > > 
> > > > > > > 
> > > > External Email - Use Caution
> > > > 
> > > > I will use freeview.
> > > > 
> > > > Have you any suggestion on the use of fcseed-config 
> > > > option?
> > > > 
> > > > Are you agree with the command line listed below?
> > > > 
> > > > fcseed-config -segid ... -seg 
> > > > $SUBJECTS_DIR/subj/mri/Yeo_17Net.mgz -fsd rest -mean -cfg 
> > > > lh.SEED.config -overwrite
> > > > 
> > > > My concerns are on -segids. Are the ids included in the 
> > > > file 
> > > > 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt?
> > > > 
> > > > How can I select a specific seed (id) to be used in 
> > > > -segids?
> > > > 
> > > > Thanks
> > > > 
> > > > Stefano
> > > > 
> > > > 
> > > > > > > > > 
> > > > > Il 10 marzo 2019 alle 17.17 Bruce Fischl 
> > > > >  mailto:fis...@nmr.mgh.harvard.edu ha 
> > > > > scritto:
> > > > > 
> > > > > Hi Stefano
> > > > > 
> > > > > is there a reason you are using tkmedit and not 
> > > > > freeview? We deprecated
> > > > > tkmedit a long time ago now
> > > > > 
> > > > > cheers
> > > > > Bruce
> > > > > On Sun, 10 Mar 2019, std...@virgilio.it 
> > > > > mailto:std...@virgilio.it wrote:
> > > > > 
> > > > > > > > > > > 
> > > > > > External Email - Use Caution
> > > > > > 
> > > > > > Thanks.
> > > > > > 
> > > > > >   

Re: [Freesurfer] regions of Yeo 17 networks in fast

[stdp82]

External Email - Use Caution

Hi, my concern is the mri_aparc2aseg command line.

In summary, I have done:

mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh --sval-annot 
/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot
 --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh 
--sval-annot 
/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
 --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000

mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot 
Yeo2011_17Networks_N1000 --annot-table 
/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annot
tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz

The output is correct by the color label is those of aparc.

Probably the error is the match between the annotations and annot-table.

Could you check the command lines, please?

Thanks

Stefano



> Il 10 marzo 2019 alle 21.15 "Greve, Douglas N.,Ph.D." 
>  ha scritto:
> 
> Specify -seg Yeo_17Net.mgz (ie, don't include the full path). I don't 
> know what is in that txt file. You can verify the segids by just bringing up 
> the segmentation in freeview and clicking on a voxel. If you load the 
> segmentation with that color table and everything looks ok, then the color 
> table  is ok.
> 
> On 3/10/19 4:05 PM, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> > > 
> > External Email - Use Caution
> > 
> > I will use freeview.
> > 
> > Have you any suggestion on the use of fcseed-config option?
> > 
> > Are you agree with the command line listed below?
> > 
> > fcseed-config -segid ... -seg $SUBJECTS_DIR/subj/mri/Yeo_17Net.mgz 
> > -fsd rest -mean -cfg lh.SEED.config -overwrite
> > 
> > My concerns are on -segids. Are the ids included in the file 
> > 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt?
> > 
> > How can I select a specific seed (id) to be used in -segids?
> > 
> > Thanks
> > 
> > Stefano
> > 
> > 
> > > > > 
> > > Il 10 marzo 2019 alle 17.17 Bruce Fischl 
> > >  mailto:fis...@nmr.mgh.harvard.edu ha scritto:
> > > 
> > > Hi Stefano
> > > 
> > > is there a reason you are using tkmedit and not freeview? We 
> > > deprecated
> > > tkmedit a long time ago now
> > > 
> > > cheers
> > > Bruce
> > > On Sun, 10 Mar 2019, std...@virgilio.it 
> > > mailto:std...@virgilio.it wrote:
> > > 
> > > > > > > 
> > > > External Email - Use Caution
> > > > 
> > > > Thanks.
> > > > 
> > > > My error is in tkmedit
> > > > 
> > > > tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
> > > > 
> > > > Il 9 marzo 2019 alle 11.09 Thomas Yeo 
> > > >  mailto:ytho...@csail.mit.edu ha scritto:
> > > > 
> > > > External Email - Use Caution
> > > > 
> > > > Just to clarify, rh.Yeo2011_17Networks_N1000.annot 
> > > > looks fine, but Yeo_17Net.mgz is empty?
> > > > Your tkmedit command seems to assume Yeo_17Net.mgz is in
> > > > /Applications/freesurfer/subjects/subject_prova/. But 
> > > > shouldn't the output be in the mri folder?
> > > > 
> > > > On Sat, Mar 9, 2019 at 5:47 PM < std...@virgilio.it 
> > > > mailto:std...@virgilio.it > wrote:
> > > > 
> > > > External Email - Use Caution
> > > > 
> > > > I have run:
> > > > 
> > > > mri_surf2surf --srcsubject fsaverage5 --trgsubject 
> > > > subj--hemi rh 
> > > > --sval-annot/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo20
> > > > 11_17Networks_N1000.annot --tval 
> > > > $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
> > > > 
> > > > to check the output
> > > > 
> > > > tksurfer subj rh inflated -annot
> > > > 
> > > > $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot
> > > > 
> > > > My concern is here:
> > > > 
> > > > mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz 
> > > > --annot Yeo2011_17Networks_N1000
> > > > 
> > > > --annot-table/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLU
> > > > T_freeview.txt --sval-annot
> > > > 
> > > > yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot
> > > > 
> > > > tkmeditfv fsaverage orig.mgz -ov
> > > >  

Re: [Freesurfer] regions of Yeo 17 networks in fast

[stdp82]

External Email - Use Caution

I will use freeview.

Have you any suggestion on the use of fcseed-config option?

Are you agree with the command line listed below?

fcseed-config -segid ... -seg $SUBJECTS_DIR/subj/mri/Yeo_17Net.mgz -fsd rest 
-mean -cfg lh.SEED.config -overwrite

My concerns are on -segids. Are the ids included in the file 
1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt?

How can I select a specific seed (id) to be used in -segids?

Thanks

Stefano


> 
> Il 10 marzo 2019 alle 17.17 Bruce Fischl  ha 
> scritto:
> 
> Hi Stefano
> 
> is there a reason you are using tkmedit and not freeview? We deprecated
> tkmedit a long time ago now
> 
> cheers
> Bruce
> On Sun, 10 Mar 2019, std...@virgilio.it wrote:
> 
> > > 
> > External Email - Use Caution
> > 
> > Thanks.
> > 
> > My error is in tkmedit
> > 
> > tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
> > 
> > Il 9 marzo 2019 alle 11.09 Thomas Yeo  ha 
> > scritto:
> > 
> > External Email - Use Caution
> > 
> > Just to clarify, rh.Yeo2011_17Networks_N1000.annot looks fine, but 
> > Yeo_17Net.mgz is empty?
> > Your tkmedit command seems to assume Yeo_17Net.mgz is in
> > /Applications/freesurfer/subjects/subject_prova/. But shouldn't the 
> > output be in the mri folder?
> > 
> > On Sat, Mar 9, 2019 at 5:47 PM < std...@virgilio.it> wrote:
> > 
> > External Email - Use Caution
> > 
> > I have run:
> > 
> > mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh 
> > --sval-annot/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo20
> > 11_17Networks_N1000.annot --tval 
> > $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
> > 
> > to check the output
> > 
> > tksurfer subj rh inflated -annot
> > $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot
> > 
> > My concern is here:
> > 
> > mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot 
> > Yeo2011_17Networks_N1000
> > 
> > --annot-table/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLU
> > T_freeview.txt --sval-annot
> > 
> > yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot
> > 
> > tkmeditfv fsaverage orig.mgz -ov
> > /Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz
> > 
> > Yeo_17Net.mgz is empty.
> > 
> > Stefano
> > 
> > Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D."
> >  ha scritto:
> > 
> > You have to convert the annotation to a volume using mri_aparc2aseg
> > (look at recon-all.log for an example, but note that you'll need to
> > specify the output so that it does not overwrite). You'll then need 
> > to
> > look in the output segmentation and see what the segmentation ids 
> > are
> > 
> > On 3/7/19 4:13 PM, std...@virgilio.it wrote:
> > >
> > 
> > External Email - Use Caution
> > 
> > Hi list,
> > 
> > I'd like to use the regions included in Yeo 17 networks
> > 
> > (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_cluste
> > ring).
> > 
> > in FS-FAST.
> > 
> > Which is the command line to be used to create a segmentation in
> > $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd
> > like
> > to use it to run fcseed-config, specify -seg yourseg.mgz
> > -segid).
> > 
> > Thanks
> > 
> > Stefano
> > 
> > ___
> > 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
> > 
> > ___
> > Freesurfer mailing list
> > 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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Re: [Freesurfer] regions of Yeo 17 networks in fast

[stdp82]

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Thanks.

My error is in tkmedit

tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz



> Il 9 marzo 2019 alle 11.09 Thomas Yeo  ha scritto:
> 
> 
> External Email - Use Caution
> 
>  
> 
> Just to clarify, rh.Yeo2011_17Networks_N1000.annot looks fine, but 
> Yeo_17Net.mgz is empty?
> 
> Your tkmedit command seems to assume Yeo_17Net.mgz is in 
> /Applications/freesurfer/subjects/subject_prova/. But shouldn't the output be 
> in the mri folder?
> 
> 
> On Sat, Mar 9, 2019 at 5:47 PM < std...@virgilio.it 
> mailto:std...@virgilio.it > wrote:
> 
> > > 
> > External Email - Use Caution
> > 
> >  
> > 
> > I have run:
> > 
> > mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh 
> > --sval-annot 
> > /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot
> >  --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
> > 
> > to check the output
> > 
> > tksurfer subj rh inflated -annot 
> > $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot
> > 
> > 
> > My concern is here:
> > 
> > mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot 
> > Yeo2011_17Networks_N1000 --annot-table 
> > /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt
> >  --sval-annot 
> > yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot
> > 
> > 
> > tkmeditfv fsaverage orig.mgz -ov 
> > /Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz
> > 
> > Yeo_17Net.mgz is empty.
> > 
> > 
> > 
> > Stefano
> > 
> > > > > 
> > > Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." 
> > > mailto:dgr...@mgh.harvard.edu > ha scritto:
> > > 
> > > You have to convert the annotation to a volume using 
> > > mri_aparc2aseg
> > > (look at recon-all.log for an example, but note that you'll 
> > > need to
> > > specify the output so that it does not overwrite). You'll 
> > > then need to
> > > look in the output segmentation and see what the segmentation 
> > > ids are
> > > 
> > > On 3/7/19 4:13 PM, std...@virgilio.it 
> > > mailto:std...@virgilio.it wrote:
> > > >
> > > 
> > > > > > > 
> > > > External Email - Use Caution
> > > > 
> > > > Hi list,
> > > > 
> > > > I'd like to use the regions included in Yeo 17 networks
> > > > 
> > > > (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering).
> > > > 
> > > > in FS-FAST.
> > > > 
> > > > Which is the command line to be used to create a 
> > > > segmentation in
> > > > $SUBJECTS_DIR/$subject/mri in the same format as 
> > > > aseg.mgz? (I'd like
> > > > to use it to run fcseed-config, specify -seg 
> > > > yourseg.mgz -segid).
> > > > 
> > > > Thanks
> > > > 
> > > > Stefano
> > > > 
> > > > ___
> > > > 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@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] regions of Yeo 17 networks in fast

[stdp82]

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I have run:

mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh --sval-annot 
/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot
 --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000

to check the output

tksurfer subj rh inflated -annot 
$SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot


My concern is here:

mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot 
Yeo2011_17Networks_N1000 --annot-table 
/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt
 --sval-annot 
yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot


tkmeditfv fsaverage orig.mgz -ov 
/Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz

Yeo_17Net.mgz is empty.



Stefano

> 
> Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." 
>  ha scritto:
> 
> You have to convert the annotation to a volume using mri_aparc2aseg
> (look at recon-all.log for an example, but note that you'll need to
> specify the output so that it does not overwrite). You'll then need to
> look in the output segmentation and see what the segmentation ids are
> 
> On 3/7/19 4:13 PM, std...@virgilio.it wrote:
> >
> 
> > > 
> > External Email - Use Caution
> > 
> > Hi list,
> > 
> > I'd like to use the regions included in Yeo 17 networks
> > 
> > (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering).
> > 
> > in FS-FAST.
> > 
> > Which is the command line to be used to create a segmentation in
> > $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like
> > to use it to run fcseed-config, specify -seg yourseg.mgz -segid).
> > 
> > Thanks
> > 
> > Stefano
> > 
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> > > 
> ___
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Re: [Freesurfer] regions of Yeo 17 networks in fast

[stdp82]

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Hi Doug,

my apologies, I have tried to do it with some errors. Could you suggest the 
command line, please?

Stefano

> 
> Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." 
>  ha scritto:
> 
> You have to convert the annotation to a volume using mri_aparc2aseg
> (look at recon-all.log for an example, but note that you'll need to
> specify the output so that it does not overwrite). You'll then need to
> look in the output segmentation and see what the segmentation ids are
> 
> On 3/7/19 4:13 PM, std...@virgilio.it wrote:
> >
> 
> > > 
> > External Email - Use Caution
> > 
> > Hi list,
> > 
> > I'd like to use the regions included in Yeo 17 networks
> > 
> > (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering).
> > 
> > in FS-FAST.
> > 
> > Which is the command line to be used to create a segmentation in
> > $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like
> > to use it to run fcseed-config, specify -seg yourseg.mgz -segid).
> > 
> > Thanks
> > 
> > Stefano
> > 
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> > > 
> ___
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> 
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Re: [Freesurfer] regions of Yeo 17 networks in fast

[stdp82]

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Hi Bruce,

my apologies, I have tried to do it with some errors. Could you suggest the 
command line, please?

Stefano

> 
> Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." 
>  ha scritto:
> 
> You have to convert the annotation to a volume using mri_aparc2aseg
> (look at recon-all.log for an example, but note that you'll need to
> specify the output so that it does not overwrite). You'll then need to
> look in the output segmentation and see what the segmentation ids are
> 
> On 3/7/19 4:13 PM, std...@virgilio.it wrote:
> >
> 
> > > 
> > External Email - Use Caution
> > 
> > Hi list,
> > 
> > I'd like to use the regions included in Yeo 17 networks
> > 
> > (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering).
> > 
> > in FS-FAST.
> > 
> > Which is the command line to be used to create a segmentation in
> > $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like
> > to use it to run fcseed-config, specify -seg yourseg.mgz -segid).
> > 
> > Thanks
> > 
> > Stefano
> > 
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> > > 
> ___
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[Freesurfer] regions of Yeo 17 networks in fast

[stdp82]

External Email - Use Caution

Hi list,

I'd like to use the regions included in Yeo 17 networks 
(https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering).
in FS-FAST.

Which is the command line to be used to create a segmentation in 
$SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like to use it 
to run fcseed-config, specify -seg yourseg.mgz -segid).

Thanks

Stefano___
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Re: [Freesurfer] SUIT FS-FAST

[stdp82]

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Is available the segmentations for 601-628 to be used as seeds in functinal 
connectivity analysis by FS-FAST?

Thanks


Stefano


> Il 10 novembre 2018 alle 21.04 std...@virgilio.it ha scritto:
> 
> 
> Hi,
> 
> I'd like to run an analysis of the cerebellar FC by using FS-FAST. My 
> goal is to use SUIT masks as seeds. Is it possible? If yes, which si the best 
> way to import suit masks on FS?
> 
> Thank you
> 
> 
> Stefano
> 


 
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[Freesurfer] SUIT FS-FAST

[stdp82]

External Email - Use CautionHi,I'd like to run an analysis of the cerebellar FC by using FS-FAST. My goal is to use SUIT masks as seeds. Is it possible? If yes, which si the best way to import suit masks on FS?Thank youStefano
 
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[Freesurfer] Problem with new tool on thalamus segmentation

[stdp82]

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I'm reposting my questions that I have done some week ago because without your 
helpfulness is impossible to go ahead with my analysis.

1- I have installed dev version.
I have run the segmentThalamicNuclei.sh but .stats file has been not
produced in any subjects.

I have also try to re-run recon-all but without success.


2 - I have used FS-FAST previously.
However, when I use the thalami segmentation as seed

fcseed-config -segid 8103 -fcname L_AV.dat -fsd rest -mean -cfg mean.L_AV.config
fcseed-sess -sf sessid -cfg mean.L_AV.config

I obtain the error listed below:

Voxel Volume is 36.3469 mm^3

Generating list of segmentation ids

Found 1 segmentations

Computing statistics for each segmentation

Reporting on 0 segmentations

Using PrintSegStat

Computing spatial average of each frame

ERROR: no voxels found in segmentation


Please could you give me can help?

Thanks


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[Freesurfer] Problems with thalami nuclei segmentation

[stdp82]

External Email - Use Caution

Hi list,


1- I have run the segmentThalamicNuclei.sh but .stats file has been not 
produced in any subjects.

I have also try to re-run recon-all with dev version but fulling.


2 - Moreover, when I use the thalami segmentation as seed in FS-FAST I obtain 
the error listed below

fcseed-config -segid 8103 -fcname L_AV.dat -fsd rest -mean -cfg mean.L_AV.config
fcseed-sess -sf sessid -cfg mean.L_AV.config

Voxel Volume is 36.3469 mm^3

Generating list of segmentation ids

Found 1 segmentations

Computing statistics for each segmentation

Reporting on 0 segmentations

Using PrintSegStat

Computing spatial average of each frame

ERROR: no voxels found in segmentation



Please could you give me can help?



Stefano___
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[Freesurfer] segmentThalamicNuclei.sh do not produce .stats

[stdp82]

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Hi list,

the segmentThalamicNuclei.sh do not produce thalamic-nuclei.lh.v10.T1.stats.

All the other files are produced (ThalamicNuclei.v10.T1.volumes.txt/mgz).

The segmentation viewed by freeview is fine.

Thanks.


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[Freesurfer] ERROR: no voxels found in segmentation- Outputs of segmentThalamicNuclei.sh in FS-FAST

[stdp82]

External Email - Use Caution

Hi I'm using as seed in FS-FAST the outputs of segmentThalamicNuclei.sh.

However when I run

fcseed-config -segid 8103 -fcname L_AV.dat -fsd rest -mean -cfg mean.L_AV.config
fcseed-sess -sf sessid -cfg mean.L_AV.config

 

this error occurs:

Voxel Volume is 36.3469 mm^3

Generating list of segmentation ids

Found 1 segmentations

Computing statistics for each segmentation

Reporting on 0 segmentations

Using PrintSegStat

Computing spatial average of each frame

ERROR: no voxels found in segmentation___
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[Freesurfer] asegstats2table - env: python2: No such file or directory

[stdp82]

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I'm using last version dev with MacOS High Sierra 10.13.6.

I have run, for each subject:

segmentThalamicNuclei.sh

but when I run the command line "asegstats2table", I obtain:


env: python2: No such file or directory


Thanks


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[Freesurfer] FS-FAST and thalami nuclei

[stdp82]

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Hi list,

I would like to use as seed the output of segmentation of the thalamic nuclei 
in FS-FAST. Probably some nuclei may be too small to be used as seed. Are you 
agree? I wonder if to merge the outputs in 5-10 subregions (e.g. AV, MD, MC 
etc...) could be the most appropriate way. What do you advise?


Thanks

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Re: [Freesurfer] Problem to download dev version

[stdp82]

External Email - Use Caution

Thanks.

It seem to be fine.

Stefano


> Il 12 settembre 2018 alle 23.11 "Hoopes, Andrew"  ha 
> scritto:
> 
> 
> Hi Stefano, are you using this link - 
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-darwin-OSX-ElCapitan-dev.tar.gz
>  
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-darwin-OSX-ElCapitan-dev.tar.gz
>  ? You might have been trying to download the old OSX backup version that no 
> longer exists (and has now been removed from the disk)
> 
>  
> 
> best,
> 
> Andrew
> 
>  
> 
>  
> 
> From:  on behalf of 
> "std...@virgilio.it" 
> Reply-To: FS Help 
> Date: Wednesday, September 12, 2018 at 3:03 PM
> To: FS Help 
> Subject: [Freesurfer] Problem to download dev version
> 
>  
> 
 

> ___
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> is
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> e-mail
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> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
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[Freesurfer] Problem to download dev version

[stdp82]

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I'm tryining to download the Development Version (OSX) at:

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

When I click on "here", I push the "guess" botton but the operation is failing.

What do I do?

Thanks


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[Freesurfer] Latest dev version

[stdp82]

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Please could you send me the link to download the the dev version with thalamus 
segmentation?

Thanks


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[Freesurfer] Segmentation of thalamic nuclei - FreeSurferColorLUT

[stdp82]

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Hi list,
where can I find the list of regions that I obtain by trough the segmentation 
of thalamic nuclei? Are they in FreeSurferColorLUT? Which are the codes for 
right and left regions?
Thanks
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[Freesurfer] error in selxavg3-sess - mismatch TE

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Hi list,


I have run the FS-FAST analysis in line with the standard procedures that I use 
routinely.

With new data, selxavg3-sess produces an errror: there is a mis-matched between 
the TE in the analysis (=3) and the TE in the data (=0). I have cheched the 
data information by fslinfo as well as MELODIC and both the operations confirm 
the data have a TE=3 that matches with TE reported in mkanalysis-sess .

How is it possible? Please, could you help me?

Thanks


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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] Errors are occurring after FreeSurfer Installation

[stdp82]

External Email - Use Caution

This errors are occurring when we test FreeSurfer Installation on our server:

1) ubuntu01:/usr/local/freesurfer/subjects> mri_convert sample-001.mgz 
sample-001.nii.gz
mri_convert.bin sample-001.mgz sample-001.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from sample-001.mgz...
TR=7.25, TE=3.22, TI=600.00, flip angle=7.00
i_ras = (-0, -1, -0)
j_ras = (-0, 0, -1)
k_ras = (-1, 0, 0)
writing to sample-001.nii.gz...
niiWrite(): error opening file sample-001.nii.gz
ERROR: failure writing sample-001.nii.gz

2) ubuntu01:/usr/local/freesurfer/subjects> recon-all -i sample-001.nii.gz -s 
bert -all
mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert': 
Permission denied
mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert': 
Permission denied
mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert': 
Permission denied
cp: cannot create regular file 
'/usr/local/freesurfer/subjects/bert/scripts/build-stamp.txt': No such file or 
directory
cat: /usr/local/freesurfer/subjects/bert/scripts/build-stamp.txt: No such file 
or directory
INFO: FreeSurfer build stamps do not match
Subject Stamp:
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
/usr/local/freesurfer/subjects/bert/scripts/patchdir.txt: No such file or 
directory.

3) ubuntu01:/usr/local/freesurfer/subjects> freeview -v sample-001.mgz
freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open 
shared object file: No such file or directory


Thanks


Stefano
___
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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.

Re: [Freesurfer] Non-parametric correlation between FC and neuropsychological/volumetric outcomes

[stdp82]

External Email - Use Caution

Thanks.

I have sent you the tar by FileDrop.

Stefano

> 
> Il 7 maggio 2018 alle 22.23 "Douglas N. Greve"  
> ha scritto:
> 
> It should not have taken that long. If you want me to look, you can tar
> up the glmdir and send it to me on our filedrop (below). You can also
> use PALM. I've created a tool to assist in the interface
> 
> http://freesurfer.net/fswiki/FsPalm
> 
> On 05/07/2018 04:20 PM, std...@virgilio.it wrote:
> >
> >
> 
> > > 
> > Thanks.
> > 
> > I have about 40 subjects. The last run went ahead for five days. I
> > have killed it.
> > 
> > What's do you think about the use of PALM in my study (details are
> > listed in previous mails)?
> > 
> > Best regards,
> > 
> > Stefano
> > 
> > Il 7 maggio 2018 alle 19.48 "Douglas N. Greve"
> >  ha scritto:
> > 
> > It looks right. How many subjects do you have? You can also check
> > on the
> > progress by looking at the csd files in the glmdir/csd folder
> > 
> > On 05/03/2018 11:30 AM, std...@virgilio.it wrote:
> > >
> > 
> > Hi list,
> > 
> > I'm running the follow command lines:
> > 
> > 1) mri_glmfit --y ces.nii.gz --cortex --surf fsaverage rh --glmdir
> > MMSE.wls --nii.gz --fsgd g1v1_MMSE.fsgd dods --C intercept.mtx --C
> > slope.mtx --eres-save
> > 
> > 2) mri_glmfit-sim --glmdir MMSE.wls --perm 1000 2.0 abs --cwp 0.05
> > --bg 1 --3spaces
> > 
> > the computation N.2 (mri_glmfit-sim) is going ahead from two
> > days...
> > 
> > ...Poll 16733 job 1 Sun Apr 29 15:58:41 CEST 2018
> > 
> > I'm suspecting that some what in command lines is wrong... Please
> > could you check it?
> > 
> > Do you think that for my experimental question (I aiming to
> > perform a
> > within group correlatation between the thickness or FC and MMSE
> > scores) should I use also PALM within mri_glmfit-sim computation?
> > 
> > Thanks
> > 
> > Best regards
> > 
> > Stefano
> > 
> > Il 24 aprile 2018 alle 19.39 Douglas Greve
> > 
> > ha scritto:
> > 
> > Try permutation
> > 
> > 
> > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
> > 
> > On 4/24/18 8:21 AM, std...@virgilio.it
> > 
> > wrote:
> > >
> > >
> > 
> > Hi,
> > 
> > I'm performing a group analysis.
> > 
> > I would like to investigate a simple correlation
> > analysis within
> > group, aiming to map the clusters showing correlation
> > between the FC
> > and the neuropsychological test scores (e.g. MMSE).
> > Overall, the NPS
> > test have not a normal distribution of their scores
> > and, thus,
> > parametric computation should be discouraged.
> > 
> > Thanks
> > 
> > Stefano
> > 
> > >
> > 
> > Il 19 aprile 2018 alle 18.11 "Douglas N. Greve"
> > 
> >  ha
> > scritto:
> > 
> > I'm not sure what you mean. Can you elaborate? Is
> > this an
> > individual
> > analysis or a group analysis?
> > 
> > On 04/18/2018 10:10 AM, std...@virgilio.it
> >  wrote:
> > >
> > 
> > Hi list,
> > 
> > which the best way to perform a whole-brain
> > correlation of
> > the FC
> > assessed by FS-FAST with the volumetic or
> > neuropsychological outcomes?
> > Please note that my question is specifically
> > addressed to those
> > factors (neuropsycholgical scores or volume of
> > seed) did
> > not show a
> > normal distribution and that cannot be trasformed.
> > 
> > Thanks
> > 
> > Kind regards
> > 
> > Stefano
> > 
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> > The information in this e-mail is intended only
> > for the person
> > to whom it is
> > addressed. If you believe this e-mail was sent to
> > you in error
> > and the e-mail
> > contains 

Re: [Freesurfer] Non-parametric correlation between FC and neuropsychological/volumetric outcomes

[stdp82]

External Email - Use Caution

Thanks.

I have about 40 subjects. The last run went ahead for five days. I have killed 
it.

What's do you think about the use of PALM in my study (details are listed in 
previous mails)?

Best regards,


Stefano


> 
> Il 7 maggio 2018 alle 19.48 "Douglas N. Greve"  
> ha scritto:
> 
> It looks right. How many subjects do you have? You can also check on the
> progress by looking at the csd files in the glmdir/csd folder
> 
> On 05/03/2018 11:30 AM, std...@virgilio.it wrote:
> >
> 
> > > 
> > Hi list,
> > 
> > I'm running the follow command lines:
> > 
> > 1) mri_glmfit --y ces.nii.gz --cortex --surf fsaverage rh --glmdir
> > MMSE.wls --nii.gz --fsgd g1v1_MMSE.fsgd dods --C intercept.mtx --C
> > slope.mtx --eres-save
> > 
> > 2) mri_glmfit-sim --glmdir MMSE.wls --perm 1000 2.0 abs --cwp 0.05
> > --bg 1 --3spaces
> > 
> > the computation N.2 (mri_glmfit-sim) is going ahead from two days...
> > 
> > ...Poll 16733 job 1 Sun Apr 29 15:58:41 CEST 2018
> > 
> > I'm suspecting that some what in command lines is wrong... Please
> > could you check it?
> > 
> > Do you think that for my experimental question (I aiming to perform 
> > a
> > within group correlatation between the thickness or FC and MMSE
> > scores) should I use also PALM within mri_glmfit-sim computation?
> > 
> > Thanks
> > 
> > Best regards
> > 
> > Stefano
> > 
> > > > > 
> > > Il 24 aprile 2018 alle 19.39 Douglas Greve 
> > > 
> > > ha scritto:
> > > 
> > > Try permutation
> > > 
> > > 
> > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
> > > 
> > > On 4/24/18 8:21 AM, std...@virgilio.it 
> > > 
> > > wrote:
> > > >
> > > >
> > > 
> > > > > > > 
> > > > Hi,
> > > > 
> > > > I'm performing a group analysis.
> > > > 
> > > > I would like to investigate a simple correlation 
> > > > analysis within
> > > > group, aiming to map the clusters showing correlation 
> > > > between the FC
> > > > and the neuropsychological test scores (e.g. MMSE). 
> > > > Overall, the NPS
> > > > test have not a normal distribution of their scores 
> > > > and, thus,
> > > > parametric computation should be discouraged.
> > > > 
> > > > Thanks
> > > > 
> > > > Stefano
> > > > 
> > > > >
> > > > 
> > > > > > > > > 
> > > > > Il 19 aprile 2018 alle 18.11 "Douglas N. Greve"
> > > > >  
> > > > >  ha
> > > > > scritto:
> > > > > 
> > > > > I'm not sure what you mean. Can you elaborate? Is 
> > > > > this an
> > > > > individual
> > > > > analysis or a group analysis?
> > > > > 
> > > > > On 04/18/2018 10:10 AM, std...@virgilio.it
> > > > >  wrote:
> > > > > >
> > > > > 
> > > > > Hi list,
> > > > > 
> > > > > which the best way to perform a whole-brain 
> > > > > correlation of
> > > > > the FC
> > > > > assessed by FS-FAST with the volumetic or
> > > > > neuropsychological outcomes?
> > > > > Please note that my question is specifically 
> > > > > addressed to those
> > > > > factors (neuropsycholgical scores or volume of 
> > > > > seed) did
> > > > > not show a
> > > > > normal distribution and that cannot be trasformed.
> > > > > 
> > > > > Thanks
> > > > > 
> > > > > Kind regards
> > > > > 
> > > > > Stefano
> > > > > 
> > > > > ___
> > > > > 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
> > > > > 
> > > > 

Re: [Freesurfer] Non-parametric correlation between FC and neuropsychological/volumetric outcomes

[stdp82]

External Email - Use Caution

Hi list,

I'm running the follow command lines:

1) mri_glmfit --y ces.nii.gz --cortex --surf fsaverage rh --glmdir MMSE.wls 
--nii.gz --fsgd g1v1_MMSE.fsgd dods --C intercept.mtx --C slope.mtx --eres-save

2) mri_glmfit-sim --glmdir MMSE.wls --perm 1000 2.0 abs --cwp 0.05 --bg 1 
--3spaces

the computation N.2 (mri_glmfit-sim) is going ahead from two days...

...Poll 16733 job 1 Sun Apr 29 15:58:41 CEST 2018

I'm suspecting that some what in command lines is wrong... Please could you 
check it?

Do you think that for my experimental question (I aiming to perform a within 
group correlatation between the thickness or FC and MMSE scores) should I use 
also PALM within mri_glmfit-sim computation?

Thanks

Best regards


Stefano


> Il 24 aprile 2018 alle 19.39 Douglas Greve  ha 
> scritto:
> 
> 
> Try permutation
> 
> 
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
> 
> 
> 
> On 4/24/18 8:21 AM, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> > > 
> >   
> > 
> > Hi,
> > 
> > I'm performing a group analysis.
> > 
> > I would like to investigate a simple correlation analysis within 
> > group, aiming to map the clusters showing correlation between the FC and 
> > the neuropsychological test scores (e.g. MMSE). Overall, the NPS test have 
> > not a normal distribution of their scores and, thus, parametric computation 
> > should be discouraged.
> > 
> > Thanks
> > 
> > 
> > Stefano
> > 
> > > > > 
> > > 
> > > > > > > 
> > > > Il 19 aprile 2018 alle 18.11 "Douglas N. Greve" 
> > > >  mailto:dgr...@mgh.harvard.edu ha scritto:
> > > > 
> > > > I'm not sure what you mean. Can you elaborate? Is this 
> > > > an individual
> > > > analysis or a group analysis?
> > > > 
> > > > On 04/18/2018 10:10 AM, std...@virgilio.it 
> > > > mailto:std...@virgilio.it wrote:
> > > > >
> > > > 
> > > > > > > > > 
> > > > > Hi list,
> > > > > 
> > > > > which the best way to perform a whole-brain 
> > > > > correlation of the FC
> > > > > assessed by FS-FAST with the volumetic or 
> > > > > neuropsychological outcomes?
> > > > > Please note that my question is specifically 
> > > > > addressed to those
> > > > > factors (neuropsycholgical scores or volume of 
> > > > > seed) did not show a
> > > > > normal distribution and that cannot be trasformed.
> > > > > 
> > > > > Thanks
> > > > > 
> > > > > Kind regards
> > > > > 
> > > > > Stefano
> > > > > 
> > > > > ___
> > > > > 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
> > > > 
> > > > 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.
> > > > 
> > > > > > > 
> > > > > 
> > 
> >  
> > 
> > > > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu 
> > > mailto: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

Re: [Freesurfer] Non-parametric correlation between FC and neuropsychological/volumetric outcomes

[stdp82]

External Email - Use Caution

I'm running the follow command lines:

1) mri_glmfit --y ces.nii.gz --cortex --surf fsaverage rh --glmdir MMSE.wls 
--nii.gz --fsgd g1v1_MMSE.fsgd dods --C intercept.mtx --C slope.mtx --eres-save

2) mri_glmfit-sim --glmdir MMSE.wls --perm 1000 2.0 abs --cwp 0.05 --bg 1 
--3spaces

the computation N.2 (mri_glmfit-sim) is going ahead from two days...
...Poll 16733 job 1 Sun Apr 29 15:58:41 CEST 2018

I'm suspecting that some what in command lines is wrong...

Please could you check it?

Do you think that for my experimental question (I aiming to perform a within 
group correlatation between the thickness or FC and MMSE scores) should I use 
also PALM within mri_glmfit-sim computation?

Thanks

Best regards


Stefano

> Il 24 aprile 2018 alle 19.39 Douglas Greve  ha 
> scritto:
> 
> 
> Try permutation
> 
> 
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
> 
> 
> 
> On 4/24/18 8:21 AM, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> > > 
> >   
> > 
> > Hi,
> > 
> > I'm performing a group analysis.
> > 
> > I would like to investigate a simple correlation analysis within 
> > group, aiming to map the clusters showing correlation between the FC and 
> > the neuropsychological test scores (e.g. MMSE). Overall, the NPS test have 
> > not a normal distribution of their scores and, thus, parametric computation 
> > should be discouraged.
> > 
> > Thanks
> > 
> > 
> > Stefano
> > 
> > > > > 
> > > 
> > > > > > > 
> > > > Il 19 aprile 2018 alle 18.11 "Douglas N. Greve" 
> > > >  mailto:dgr...@mgh.harvard.edu ha scritto:
> > > > 
> > > > I'm not sure what you mean. Can you elaborate? Is this 
> > > > an individual
> > > > analysis or a group analysis?
> > > > 
> > > > On 04/18/2018 10:10 AM, std...@virgilio.it 
> > > > mailto:std...@virgilio.it wrote:
> > > > >
> > > > 
> > > > > > > > > 
> > > > > Hi list,
> > > > > 
> > > > > which the best way to perform a whole-brain 
> > > > > correlation of the FC
> > > > > assessed by FS-FAST with the volumetic or 
> > > > > neuropsychological outcomes?
> > > > > Please note that my question is specifically 
> > > > > addressed to those
> > > > > factors (neuropsycholgical scores or volume of 
> > > > > seed) did not show a
> > > > > normal distribution and that cannot be trasformed.
> > > > > 
> > > > > Thanks
> > > > > 
> > > > > Kind regards
> > > > > 
> > > > > Stefano
> > > > > 
> > > > > ___
> > > > > 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
> > > > 
> > > > 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.
> > > > 
> > > > > > > 
> > > > > 
> > 
> >  
> > 
> > > > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu 
> > > mailto: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
> > >

Re: [Freesurfer] Non-parametric correlation between FC and neuropsychological/volumetric outcomes

[stdp82]

External Email - Use Caution

Hi,

I'm performing a group analysis.

I would like to investigate a simple correlation analysis within group, aiming 
to map the clusters showing correlation between the FC and the 
neuropsychological test scores (e.g. MMSE). Overall, the NPS test have not a 
normal distribution of their scores and, thus, parametric computation should be 
discouraged.

Thanks


Stefano

> 
> 
> > > 
> > Il 19 aprile 2018 alle 18.11 "Douglas N. Greve" 
> >  ha scritto:
> > 
> > I'm not sure what you mean. Can you elaborate? Is this an individual
> > analysis or a group analysis?
> > 
> > On 04/18/2018 10:10 AM, std...@virgilio.it wrote:
> > >
> > 
> > > > > 
> > > Hi list,
> > > 
> > > which the best way to perform a whole-brain correlation of 
> > > the FC
> > > assessed by FS-FAST with the volumetic or neuropsychological 
> > > outcomes?
> > > Please note that my question is specifically addressed to 
> > > those
> > > factors (neuropsycholgical scores or volume of seed) did not 
> > > show a
> > > normal distribution and that cannot be trasformed.
> > > 
> > > Thanks
> > > 
> > > Kind regards
> > > 
> > > Stefano
> > > 
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > 
> > > > > 
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> > The information in this e-mail is intended only for the person to 
> > whom it is
> > addressed. If you believe this e-mail was sent to you in error and 
> > the e-mail
> > contains patient information, please contact the 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 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.
> 


 
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] Non-parametric correlation between FC and neuropsychological/volumetric outcomes

[stdp82]

External Email - Use Caution

> 

Hi,

group analysis.

I would like to perform a simple correlation analysis within group, aiming to 
map the clusters reporting the correlation between the FC and the seed volume 
or neuropsychological test scores (e.g. MMSE). Overall, the morphometric 
measures and NPS test scores do not shown a normal distribution and, thus, 
parametric computation should be discouraged.


Thanks


> 
> Il 19 aprile 2018 alle 18.11 "Douglas N. Greve"  
> ha scritto:
> 
> I'm not sure what you mean. Can you elaborate? Is this an individual
> analysis or a group analysis?
> 
> On 04/18/2018 10:10 AM, std...@virgilio.it wrote:
> >
> 
> > > 
> > Hi list,
> > 
> > which the best way to perform a whole-brain correlation of the FC
> > assessed by FS-FAST with the volumetic or neuropsychological 
> > outcomes?
> > Please note that my question is specifically addressed to those
> > factors (neuropsycholgical scores or volume of seed) did not show a
> > normal distribution and that cannot be trasformed.
> > 
> > Thanks
> > 
> > Kind regards
> > 
> > Stefano
> > 
> > ___
> > 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
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[Freesurfer] Non-parametric correlation between FC and neuropsychological/volumetric outcomes

[stdp82]

Hi list,

which the best way to perform a whole-brain correlation of the FC assessed by 
FS-FAST with the volumetic or neuropsychological outcomes?
Please note that my question is specifically addressed to those factors 
(neuropsycholgical scores or volume of seed) did not show a normal distribution 
and that cannot be trasformed.

Thanks

Kind regards


Stefano___
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Re: [Freesurfer] freeview for FS-FAST results

[stdp82]

Thanks.

My question is only for visualization purpose, not for statistics.

I would like to exclude from maps the clusters < 5 voxels.

Stefano

> 
> Il 5 marzo 2018 alle 21.42 Douglas N Greve  ha 
> scritto:
> 
> Set --cwp 1. This will keep all clusters regardless of size. Then look
> in the summary table and see where the cluster-wise p-value is for 5
> voxels or less, then rerun with that cwp. FYI, this is not a good way to
> correct for multple comparisson
> 
> On 03/05/2018 03:35 PM, std...@virgilio.it wrote:
> >
> 
> > > 
> > Hi list,
> > 
> > is it possible to avoid the clusters < 5 voxels using freeview for
> > FS-FAST results (mni.305) obtained after running mri_glmfit-sim
> > --glmdir my-glm.wls --grf?
> > 
> > Thanks
> > 
> > Kind regards
> > 
> > Stefano
> > 
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> > > 
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
> ___
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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] freeview for FS-FAST results

[stdp82]

Thanks, what's meaning FYI?

What do you advise?


> 
> Il 5 marzo 2018 alle 21.42 Douglas N Greve  ha 
> scritto:
> 
> Set --cwp 1. This will keep all clusters regardless of size. Then look
> in the summary table and see where the cluster-wise p-value is for 5
> voxels or less, then rerun with that cwp. FYI, this is not a good way to
> correct for multple comparisson
> 
> On 03/05/2018 03:35 PM, std...@virgilio.it wrote:
> >
> 
> > > 
> > Hi list,
> > 
> > is it possible to avoid the clusters < 5 voxels using freeview for
> > FS-FAST results (mni.305) obtained after running mri_glmfit-sim
> > --glmdir my-glm.wls --grf?
> > 
> > Thanks
> > 
> > Kind regards
> > 
> > Stefano
> > 
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> > > 
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
> ___
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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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[Freesurfer] freeview for FS-FAST results

[stdp82]

Hi list,

is it possible to avoid the clusters < 5 voxels using freeview for FS-FAST 
results (mni.305) obtained after running  mri_glmfit-sim --glmdir my-glm.wls 
--grf?

Thanks

Kind regards


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[Freesurfer] Region in Yeo_17Network_16 as seed in FS-FAST

[stdp82]

Hi list,

I should use the the region describing the mPFC in Yeo_17Network_16 (DMN) as a 
seed in FS-FAST (FC analysis)

How can I do to isolated this regions?

Thanks


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[Freesurfer] Question of fs-fast

[stdp82]

Hi list,

I wonder to know whether the FS-FAST tool is applicable on High Res Hippo fMRI 
images (175x60x175mm; 0.39x2x0.39mm).

In particular do you think that it could be possible to map the FC of a 
subfiled with the rest of the hippocampus?

If yes, have you particular advises on this issue.

Thanks


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Re: [Freesurfer] correlation between the FC (obtained by FS-FAST) and cortical thickness

[stdp82]

I have resolve the previous error (there was a typo in the fsdg file) but 
re-running I obtain this error:


Normalized matrix condition is 1

Matrix condition is 1

mghRead(/Applications/freesurfer/subjects/rh.GROUP.thickness.10B.mgh, -1): 
could not open file



fsgd file is:

GroupDescriptorFile 1 
Title All
Class Main
Input 032_XX Main
Input 047_XX Main
Input 049_XX Main
Input 060_XX Main


and I have two contrast (intercept 1 0; slope 0 1)


command line that runs:

mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --glmdir 
Thickness.wls --nii.gz --fsgd g1v1_thickness.fsgd --C intercept.mtx --C 
slope.mtx --pvr $SUBJECTS_DIR/rh.GROUP1.thickness.10B.mgh


> Il 5 febbraio 2018 alle 19.36 std...@virgilio.it ha scritto:
> 
> 
>  
> 
> I obtain this error: 
> 
> mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh 
> --glmdir Thickness.wls --nii.gz --fsgd g1v1_thickness.fsgd --C intercept.mtx 
> --C slope.mtx --pvr $SUBJECTS_DIR/rh.MCI.thickness.10B.mgh
> 
> Reading source surface 
> /Applications/freesurfer/subjects/fsaverage/surf/rh.white
> 
> gdfRead(): reading g1v1_thickness.fsgd
> 
> ERROR: fio_FileHasCarriageReturn(): cannot open g1v1_thickness.fsgd
> 
> 
> > > Il 5 febbraio 2018 alle 18.26 Douglas Greve 
>  ha scritto:
> > 
> > 
> > 
> > 
> > On 2/4/18 10:06 AM, std...@virgilio.it mailto:std...@virgilio.it 
> > wrote:
> > 
> > > > > 
> > > I have run:
> > > 
> > > 1)
> > > 
> > > mris_preproc --fsgd GROUP1.fsgd --target fsaverage --hemi rh 
> > > --meas thickness --out rh.GROUP1.thickness.00.mgh
> > > mri_surf2surf --hemi rh --s fsaverage --sval 
> > > rh.GROUP1.thickness.00.mgh --fwhm 10 --cortex --tval 
> > > rh.GROUP1.thickness.10B.mgh
> > > 
> > > > > looks good
> > 
> > > > > 
> > > 2)
> > > 
> > > mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface 
> > > fsaverage rh --glmdir Age.wls --nii.gz --fsgd g1v1_Age.fsgd --C 
> > > intercept.mtx --C slope.mtx --pvr rh.GROUP1.thickness.10B.mgh
> > > 
> > > The command line is correct?
> > > 
> > > > > Yes, though I'm not sure about the effect of using --wls and 
> > > --pvr. I guess it will be ok, I just have not used it.
> > 
> > > > > 
> > > 
> > > My concern is on the fsgd file.
> > > 
> > > I have 
> > > 
> > > GroupDescriptorFile 1
> > > Title All
> > > Class Main
> > > Variables thickness
> > > Input ADNI0XX_GROUP1 Main 
> > > Input ADNI0XY_GROUP1 Main 
> > > Input ADNI0YX.GROUP1 Main 
> > > ...
> > > 
> > > What I should add after Main if I would like to assess the 
> > > vertex by vertex correlation between FC (between seed and target vertex) 
> > > and thickness (in the target vertex)?
> > > 
> > > > > Don't represent the PVR in the FSGD file. You only need to 
> > > include items in the contrast matrix. Eg, for intercept use [1 0] and for 
> > > slope use [0 1] eventhough you only have a single class.
> > 
> > > > > 
> > > Should I add the path where is contained rh.thickness.mgh of 
> > > each subject?
> > > 
> > > > > No
> > 
> > > > > 
> > > Please give me an help because I did not find these 
> > > information using --help or mail list.
> > > 
> > > Thanks
> > > 
> > > 
> > > Stefano
> > > 
> > > 
> > > 
> > > Il 3 febbraio 2018 alle 19.55 Douglas Greve 
> > >  mailto:gr...@nmr.mgh.harvard.edu ha scritto:
> > > 
> > > 
> > > Yes, use the --pvr option to mri_glmfit (per-voxel 
> > > regressor). Search through the mail archives for an example on how to use 
> > > it
> > > 
> > > 
> > > On 2/3/18 12:10 PM, std...@virgilio.it 
> > > mailto:std...@virgilio.it wrote:
> > > 
> > > > > > > 
> > > > Hi list,
> > > > 
> > > > Is there a way to obtain a map that report the "vertex 
> > > > by vertex" correlation between the FC (obtained by FS-FAST) and 
> > > > cortical thickness?
> > > > 
> > > > Thanks
> > > > 
> > > > 
> > > > Stefano
> > > > 
> > > > 
> > > > 
> > > > ___
> > > > 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 
> > > > 

Re: [Freesurfer] correlation between the FC (obtained by FS-FAST) and cortical thickness

[stdp82]

I obtain this error: 

mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --glmdir 
Thickness.wls --nii.gz --fsgd g1v1_thickness.fsgd --C intercept.mtx --C 
slope.mtx --pvr $SUBJECTS_DIR/rh.MCI.thickness.10B.mgh

Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/rh.white

gdfRead(): reading g1v1_thickness.fsgd

ERROR: fio_FileHasCarriageReturn(): cannot open g1v1_thickness.fsgd


> Il 5 febbraio 2018 alle 18.26 Douglas Greve  ha 
> scritto:
> 
> 
> 
> 
> On 2/4/18 10:06 AM, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> > > 
> > I have run:
> > 
> > 1)
> > 
> > mris_preproc --fsgd GROUP1.fsgd --target fsaverage --hemi rh --meas 
> > thickness --out rh.GROUP1.thickness.00.mgh
> > mri_surf2surf --hemi rh --s fsaverage --sval 
> > rh.GROUP1.thickness.00.mgh --fwhm 10 --cortex --tval 
> > rh.GROUP1.thickness.10B.mgh
> > 
> > > looks good
> 
> > > 
> > 2)
> > 
> > mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage 
> > rh --glmdir Age.wls --nii.gz --fsgd g1v1_Age.fsgd --C intercept.mtx --C 
> > slope.mtx --pvr rh.GROUP1.thickness.10B.mgh
> > 
> > The command line is correct?
> > 
> > > Yes, though I'm not sure about the effect of using --wls and --pvr. I 
> > guess it will be ok, I just have not used it.
> 
> > > 
> > 
> > My concern is on the fsgd file.
> > 
> > I have 
> > 
> > GroupDescriptorFile 1
> > Title All
> > Class Main
> > Variables thickness
> > Input ADNI0XX_GROUP1 Main 
> > Input ADNI0XY_GROUP1 Main 
> > Input ADNI0YX.GROUP1 Main 
> > ...
> > 
> > What I should add after Main if I would like to assess the vertex 
> > by vertex correlation between FC (between seed and target vertex) and 
> > thickness (in the target vertex)?
> > 
> > > Don't represent the PVR in the FSGD file. You only need to include 
> > items in the contrast matrix. Eg, for intercept use [1 0] and for slope use 
> > [0 1] eventhough you only have a single class.
> 
> > > 
> > Should I add the path where is contained rh.thickness.mgh of each 
> > subject?
> > 
> > > No
> 
> > > 
> > Please give me an help because I did not find these information 
> > using --help or mail list.
> > 
> > Thanks
> > 
> > 
> > Stefano
> > 
> > 
> > 
> > Il 3 febbraio 2018 alle 19.55 Douglas Greve 
> >  mailto:gr...@nmr.mgh.harvard.edu ha scritto:
> > 
> > 
> > Yes, use the --pvr option to mri_glmfit (per-voxel regressor). 
> > Search through the mail archives for an example on how to use it
> > 
> > 
> > On 2/3/18 12:10 PM, std...@virgilio.it mailto:std...@virgilio.it 
> > wrote:
> > 
> > > > > 
> > > Hi list,
> > > 
> > > Is there a way to obtain a map that report the "vertex by 
> > > vertex" correlation between the FC (obtained by FS-FAST) and cortical 
> > > thickness?
> > > 
> > > Thanks
> > > 
> > > 
> > > Stefano
> > > 
> > > 
> > > 
> > > ___
> > > 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
> > > 
> > > 
> > > 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] One Group (One Factor), Two Covariates

[stdp82]

Thanks.

Only for I quick check of my understanding, if I'm using:


FSGD File (g1v1.fsgd)

GroupDescriptorFile 1

Title OSGM

Class Main

Variables Age

Input subject1 Main 30

Input subject2 Main 40

.


A) Contrast 1 (intercept.mtx) 1 0

B) Contrast 2 (slope.mtx) 0 1

Considering that my goal is to obtain a map reporting the significant clusters 
where the FC is positively/negatively associated with Age, is this contrast 
exact? Or it shows the clusters where la FC between seed and target regions is 
significant, regressing out the Age? This second case in not of my interest.
Please suggest a way to reach the first case.

Thanks


Stefano



> Il 5 febbraio 2018 alle 18.27 Douglas Greve  ha 
> scritto:
> 
> 
> If you have one class and two variables, then [0 1 0] and [0 0 1]
> 
> 
> On 2/4/18 10:23 AM, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> > > 
> > I would like to find where the functional connectivity is 
> > correlated to VARIABLE 1 regressing out the VARIABLE 2.
> > 
> > How I should set my contrast.mtx?
> > 
> > Thanks
> > 
> > 
> > Stefano
> > 
> > > > > Il 3 febbraio 2018 alle 19.57 Douglas Greve 
> >  mailto:gr...@nmr.mgh.harvard.edu ha scritto:
> > > 
> > > 
> > > 
> > > 
> > > On 2/2/18 7:47 AM, std...@virgilio.it 
> > > mailto:std...@virgilio.it wrote:
> > > 
> > > > > > > 
> > > > Hi list,
> > > > 
> > > > in reference to One Group (One Factor), Two Covariates
> > > > 
> > > > 
> > > > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V#Contrast2age.mtx
> > > > 
> > > > that has been applied on FS-FAST fcMRI data
> > > > 
> > > > I obtain three folder, respectively, for "main", 
> > > > "covariate 1", "covariate 2".
> > > > 
> > > > What's meaning the sig.nii.gz that it is produced by 
> > > > mri_glmfit in each folder?
> > > > Please correct my conclusions if they are wrong.
> > > > 
> > > > 1 - In the "Main" folder, the sig.nii.gz contains the 
> > > > results of One-sample t test regressing out the effect of the two 
> > > > covariates.
> > > > 
> > > > > > > Correct
> > > 
> > > > > > > 
> > > > 2 - In the "Covariate 1" folder, the sig.nii.gz 
> > > > contains the significant cluster that are associated with the covariate 
> > > > 1 regressing out the effect for the covariate 2.
> > > > 
> > > > > > > Yes (and the main)
> > > 
> > > > > > > 
> > > > 3 - In the "Covariate 2" folder, the sig.nii.gz 
> > > > contains the significant cluster that are associated with the covariate 
> > > > 2 regressing out the effect for the covariate 1.
> > > > 
> > > > > > > Yes (and regressing out the main)
> > > 
> > > > > > > 
> > > > Thanks
> > > > 
> > > > 
> > > > Stefano
> > > > 
> > > > 
> > > > 
> > > > 
> > > > 
> > > > ___
> > > > 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
> > > 
> > > 
> > > 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 
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> > > contains patient information, please contact the Partners 
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Re: [Freesurfer] One Group (One Factor), Two Covariates

[stdp82]

I would like to find where the functional connectivity is correlated to 
VARIABLE 1 regressing out the VARIABLE 2.

How I should set my contrast.mtx?

Thanks


Stefano

> Il 3 febbraio 2018 alle 19.57 Douglas Greve  ha 
> scritto:
> 
> 
> 
> 
> On 2/2/18 7:47 AM, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> > > 
> > Hi list,
> > 
> > in reference to One Group (One Factor), Two Covariates
> > 
> > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V#Contrast2age.mtx
> > 
> > that has been applied on FS-FAST fcMRI data
> > 
> > I obtain three folder, respectively, for "main", "covariate 1", 
> > "covariate 2".
> > 
> > What's meaning the sig.nii.gz that it is produced by mri_glmfit in 
> > each folder?
> > Please correct my conclusions if they are wrong.
> > 
> > 1 - In the "Main" folder, the sig.nii.gz contains the results of 
> > One-sample t test regressing out the effect of the two covariates.
> > 
> > > Correct
> 
> > > 
> > 2 - In the "Covariate 1" folder, the sig.nii.gz contains the 
> > significant cluster that are associated with the covariate 1 regressing out 
> > the effect for the covariate 2.
> > 
> > > Yes (and the main)
> 
> > > 
> > 3 - In the "Covariate 2" folder, the sig.nii.gz contains the 
> > significant cluster that are associated with the covariate 2 regressing out 
> > the effect for the covariate 1.
> > 
> > > Yes (and regressing out the main)
> 
> > > 
> > Thanks
> > 
> > 
> > Stefano
> > 
> > 
> > 
> > 
> > 
> > ___
> > 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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Re: [Freesurfer] correlation between the FC (obtained by FS-FAST) and cortical thickness

[stdp82]

I have run:

1)

mris_preproc --fsgd GROUP1.fsgd --target fsaverage --hemi rh --meas thickness 
--out rh.GROUP1.thickness.00.mgh
mri_surf2surf --hemi rh --s fsaverage --sval rh.GROUP1.thickness.00.mgh --fwhm 
10 --cortex --tval rh.GROUP1.thickness.10B.mgh

2)

mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --glmdir 
Age.wls --nii.gz --fsgd g1v1_Age.fsgd --C intercept.mtx --C slope.mtx --pvr 
rh.GROUP1.thickness.10B.mgh

The command line is correct?


My concern is on the fsgd file.

I have 

GroupDescriptorFile 1
Title All
Class Main
Variables thickness
Input ADNI0XX_GROUP1 Main 
Input ADNI0XY_GROUP1 Main 
Input ADNI0YX.GROUP1 Main 
...

What I should add after Main if I would like to assess the vertex by vertex 
correlation between FC (between seed and target vertex) and thickness (in the 
target vertex)?

Should I add the path where is contained rh.thickness.mgh of each subject?

Please give me an help because I did not find these information using --help or 
mail list.

Thanks


Stefano



Il 3 febbraio 2018 alle 19.55 Douglas Greve  ha 
scritto:


Yes, use the --pvr option to mri_glmfit (per-voxel regressor). Search through 
the mail archives for an example on how to use it


On 2/3/18 12:10 PM, std...@virgilio.it mailto:std...@virgilio.it wrote:

> 
> Hi list,
> 
> Is there a way to obtain a map that report the "vertex by vertex" 
> correlation between the FC (obtained by FS-FAST) and cortical thickness?
> 
> Thanks
> 
> 
> Stefano
> 
> 
> 
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> 

> 


 

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[Freesurfer] Fwd: Re: One Group (One Factor), Two Covariates

[stdp82]

Thanks.what do I do if I would like to maintain the effect of "main" in the points 2 and 3.Best regardsStefano
 --- Begin Message ---



On 2/2/18 7:47 AM, std...@virgilio.it wrote:


Hi list,

in reference to One Group (One Factor), Two Covariates

https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V#Contrast2age.mtx

that has been applied on FS-FAST fcMRI data

I obtain three folder, respectively, for "main", "covariate 1", 
"covariate 2".


What's meaning the sig.nii.gz that it is produced by mri_glmfit in 
each folder?

Please correct my conclusions if they are wrong.

1 - In the "Main" folder, the sig.nii.gz contains the results of 
One-sample t test regressing out the effect of the two covariates.



Correct


2 - In the "Covariate 1" folder, the sig.nii.gz contains the 
significant cluster that are associated with the covariate 1 
regressing out the effect for the covariate 2.



Yes (and the main)


3 - In the "Covariate 2" folder, the sig.nii.gz contains the 
significant cluster that are associated with the covariate 2 
regressing out the effect for the covariate 1.



Yes (and regressing out the main)


Thanks


Stefano

*
*

*
*



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[Freesurfer] correlation between the FC (obtained by FS-FAST) and cortical thickness

[stdp82]

Hi list,

Is there a way to obtain a map that report the "vertex by vertex" correlation 
between the FC (obtained by FS-FAST) and cortical thickness?

Thanks


Stefano___
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[Freesurfer] One Group (One Factor), Two Covariates

[stdp82]

Hi list,

in reference to One Group (One Factor), Two Covariates

https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V#Contrast2age.mtx

that has been applied on FS-FAST fcMRI data

I obtain three folder, respectively, for "main", "covariate 1", "covariate 2".

What's meaning the sig.nii.gz that it is produced by mri_glmfit in each folder?
Please correct my conclusions if they are wrong.

1 - In the "Main" folder, the sig.nii.gz contains the results of One-sample t 
test regressing out the effect of the two covariates.

2 - In the "Covariate 1" folder, the sig.nii.gz contains the significant 
cluster that are associated with the covariate 1 regressing out the effect for 
the covariate 2.

3 - In the "Covariate 2" folder, the sig.nii.gz contains the significant 
cluster that are associated with the covariate 2 regressing out the effect for 
the covariate 1.

Thanks


Stefano


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Re: [Freesurfer] Error using chol - FS-FAST selxavg3-sess

[stdp82]

I have done the changes did you suggested:


mkanalysis-sess -analysis fc.rhipposeed.mni305 -mni305 -fwhm 6 -notask -taskreg 
R_Hippocampus.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 
-mcextreg -fsd rest -TR 3 -per-run -hpf 0.01 -lpf 0.1 -force


but the error persists:


GLS Beta Pass 

  run 1t= 0.0

Temporally filtering

GLS Residual Pass 

  run 1t= 0.0

Temporally filtering

Error using chol

Matrix must be positive definite.

Error in fast_selxavg3b (line 947)

Wseg = inv(chol(toeplitz(acfrun))');

>> --


IMPORTANT

Please take in account that before to update the MacOs system to version 11, 
the command run on the same data independently, if I choose -hpf 0.01 -lpf 0.1 
or viceversa.


> Il 5 gennaio 2018 alle 17.17 Douglas Greve  ha 
> scritto:
> 
> 
> You need to swap the values of the hpf and lpf. The way you have it,  you 
> are essentially filtering out everything above .01 Hz, which probably leaves 
> almost no signal
> 
> 
> On 1/3/18 3:00 PM, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> > > 
> > mkanalysis-sess -analysis fc.lhamgseed.surf.lh -surface fsaverage 
> > lh -fwhm 6 -notask -taskreg L_Amygdala.dat 1 -nuisreg vcsf.dat 5 -nuisreg 
> > wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 3 -per-run -hpf 0.1 
> > -lpf 0.01
> > 
> > Thanks
> > 
> > > > > Il 31 dicembre 2017 alle 22.34 Douglas Greve 
> >  mailto:gr...@nmr.mgh.harvard.edu ha scritto:
> > > 
> > > 
> > > What is your mkanalysis-sess command line?
> > > 
> > > 
> > > On 12/28/17 8:53 AM, std...@virgilio.it 
> > > mailto:std...@virgilio.it wrote:
> > > 
> > > > > > > 
> > > > Running the "selxavg3-sess -s" command line in FS-FAST 
> > > > for seed-based functional connectivity analysis
> > > > 
> > > > the following errors occurred:
> > > > 
> > > > --
> > > > 
> > > > Temporally filtering
> > > > 
> > > > Error using chol
> > > > 
> > > > Matrix must be positive definite.
> > > > 
> > > > Error in fast_selxavg3b (line 947)
> > > > 
> > > > Wseg = inv(chol(toeplitz(acfrun))');
> > > > 
> > > > --
> > > > 
> > > > 
> > > > Thanks
> > > > 
> > > > Stefano
> > > > 
> > > > 
> > > > 
> > > > ___
> > > > 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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> > > mailto: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 
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> > > sender and properly
> > > dispose of the e-mail.
> > > 
> > > > > 
> > > 


 

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Re: [Freesurfer] Error using chol - FS-FAST selxavg3-sess

[stdp82]

mkanalysis-sess -analysis fc.lhamgseed.surf.lh -surface fsaverage lh -fwhm 6 
-notask -taskreg L_Amygdala.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 
-polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 3 -per-run -hpf 0.1 -lpf 0.01

Thanks

> Il 31 dicembre 2017 alle 22.34 Douglas Greve  ha 
> scritto:
> 
> 
> What is your mkanalysis-sess command line?
> 
> 
> On 12/28/17 8:53 AM, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> > > 
> > Running the "selxavg3-sess -s" command line in FS-FAST for 
> > seed-based functional connectivity analysis
> > 
> > the following errors occurred:
> > 
> > --
> > 
> > Temporally filtering
> > 
> > Error using chol
> > 
> > Matrix must be positive definite.
> > 
> > Error in fast_selxavg3b (line 947)
> > 
> > Wseg = inv(chol(toeplitz(acfrun))');
> > 
> > --
> > 
> > 
> > Thanks
> > 
> > Stefano
> > 
> > 
> > 
> > ___
> > 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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Re: [Freesurfer] Error using chol - FS-FAST selxavg3-sess

[stdp82]

mkanalysis-sess -analysis fc.lhamgseed.surf.lh -surface fsaverage lh -fwhm 6 
-notask -taskreg L_Amygdala.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 
-polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 3 -per-run -hpf 0.1 -lpf 0.01

> Il 1 gennaio 2018 alle 18.49 Douglas Greve  ha 
> scritto:
> 
> 
> I meant your mkanalysis-sess command, not your selxavg3-sess command
> 
> 
> On 1/1/18 12:36 PM, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> > > 
> > selxavg3-sess -sf sessid -a fc.rhamgseed.surf.rh
> > 
> > I have already used this command line many times, previously, using 
> > other labels.
> > It has always worked well.
> > I wonder if that error could be come from the update of my computer 
> > by macOS 1.
> > Thanks
> > Stefano
> > 
> > 
> > 
> > > > > Il 31 dicembre 2017 alle 22.34 Douglas Greve 
> >  mailto:gr...@nmr.mgh.harvard.edu ha scritto:
> > > 
> > > 
> > > What is your mkanalysis-sess command line?
> > > 
> > > 
> > > On 12/28/17 8:53 AM, std...@virgilio.it 
> > > mailto:std...@virgilio.it wrote:
> > > 
> > > > > > > 
> > > > Running the "selxavg3-sess -s" command line in FS-FAST 
> > > > for seed-based functional connectivity analysis
> > > > 
> > > > the following errors occurred:
> > > > 
> > > > --
> > > > 
> > > > Temporally filtering
> > > > 
> > > > Error using chol
> > > > 
> > > > Matrix must be positive definite.
> > > > 
> > > > Error in fast_selxavg3b (line 947)
> > > > 
> > > > Wseg = inv(chol(toeplitz(acfrun))');
> > > > 
> > > > --
> > > > 
> > > > 
> > > > Thanks
> > > > 
> > > > Stefano
> > > > 
> > > > 
> > > > 
> > > > ___
> > > > 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
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> > > mailto: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 
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> > > sender and properly
> > > dispose of the e-mail.
> > > 
> > > > > 
> > > 


 

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Re: [Freesurfer] Error using chol - FS-FAST selxavg3-sess

[stdp82]

selxavg3-sess -sf sessid -a fc.rhamgseed.surf.rh

I have already used this command line many times, previously, using other 
labels.
It has always worked well.
I wonder if that error could be come from the update of my computer by macOS 1.
Thanks
Stefano



> Il 31 dicembre 2017 alle 22.34 Douglas Greve  ha 
> scritto:
> 
> 
> What is your mkanalysis-sess command line?
> 
> 
> On 12/28/17 8:53 AM, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> > > 
> > Running the "selxavg3-sess -s" command line in FS-FAST for 
> > seed-based functional connectivity analysis
> > 
> > the following errors occurred:
> > 
> > --
> > 
> > Temporally filtering
> > 
> > Error using chol
> > 
> > Matrix must be positive definite.
> > 
> > Error in fast_selxavg3b (line 947)
> > 
> > Wseg = inv(chol(toeplitz(acfrun))');
> > 
> > --
> > 
> > 
> > Thanks
> > 
> > Stefano
> > 
> > 
> > 
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> > 
> > > 


 

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[Freesurfer] Error using chol - FS-FAST selxavg3-sess

[stdp82]

Running the "selxavg3-sess -s" command line in FS-FAST for seed-based 
functional connectivity analysis

the following errors occurred:

--

Temporally filtering

Error using chol

Matrix must be positive definite.

Error in fast_selxavg3b (line 947)

Wseg = inv(chol(toeplitz(acfrun))');

--


Thanks

Stefano___
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[Freesurfer] cut-off clusters size

[stdp82]

Hi,
I wonder if there is a consensus to thershold the size of clusters obtained by 
FS-FAST after FDR correction?To cut-off clusters size>10-15 mm2 should be good? 
or do you advise more than?
ThanksStefano ___
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