Re: [Freesurfer] VT images from pmod to freesurfer

2019-03-29 Thread Donatienne Van Weehaeghe 
External Email - Use Caution

#mri_glmfit --glmdir
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/concatenate/PVC_proj0.5_lh
--y
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/concatenate/all.lh.mgx.ctxgm.fsaverage.pvc.VT.sm06.proj-0.5.nii.gz
--surface fsaverage lh --fsgd
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/FSGD/fsgd_all_VT
--C
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/FSGD/group.diff.mtx
#mri_glmfit --glmdir
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/concatenate/PVC_proj0.5_rh
--y
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/concatenate/all.rh.mgx.ctxgm.fsaverage.pvc.VT.sm06.proj-0.5.nii.gz
--surface fsaverage lh --fsgd
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/FSGD/fsgd_all_VT
--C
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/FSGD/group.diff.mtx


#mri_glmfit-sim --glmdir
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/concatenate/PVC_proj0.5_lh
--cache 2.0 pos --cwp 0.05 --2spaces
#mri_glmfit-sim --glmdir
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/concatenate/PVC_proj0.5_rh
--cache 1.3 pos --cwp 0.05 --2spaces


Op vr 29 mrt. 2019 om 11:08 schreef Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu>:

> What is the full command line for that program?
>
> On 3/29/19 11:01 AM, Donatienne Van Weehaeghe wrote:
>
> External Email - Use Caution
> Dear,
>
> The Freesurfer program generated the error after multiple comparison
> corerction.
>
> Thank you for your help.
>
> Kind regards
> Donatienne
>
> Op vr 29 mrt. 2019 om 10:58 schreef Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu>:
>
>> what program generated the error? What is the full command line for that
>> program?
>>
>> On 3/21/19 12:49 PM, Donatienne Van Weehaeghe wrote:
>>
>> External Email - Use Caution
>>
>> Dear,
>>
>>
>> I encountered a problem when going from pmod to freesurfer.
>>
>>
>> I made Vt images in pmod using the logan plot, then I used the following
>> commands to convert them to freesurfer space:
>>
>>
>>
>> #flirt -noresample -in
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.nii
>> -ref
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/T1-2mm_skullstripped.nii.gz
>> -applyxfm -init
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/SUVR/SUV.lrrev_lin_T1.mat
>> -out
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii
>>
>> #3dresample -master
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/occipital.nii.gz
>> -inset
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.nii
>> -prefix
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii
>>
>>
>>
>> Then I did partial volume correction using this command:
>>
>> #mri_gtmpvc --i
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii
>> --reg Vt.reg.lta --psf 5 --seg
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/gtmseg.mgz
>> --default-seg-merge --auto-mask 5 0.01 --rbv --o
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg
>> --no-rescale --threads 8
>>
>>
>>
>>
>>
>> Then I did surface projection:
>>
>> #mri_vol2surf --mov
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rbv.nii.gz
>> --reg
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta
>> --hemi lh --projfrac 0.5 --o
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/lh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz
>> --cortex --trgsubject fsaverage
>>
>> #mri_vol2surf --mov
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rbv.nii.gz
>> --reg
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta
>> --hemi rh --projfrac 0.5 --o
>> /autof

Re: [Freesurfer] VT images from pmod to freesurfer

2019-03-29 Thread Greve, Douglas N.,Ph.D. 
What is the full command line for that program?

On 3/29/19 11:01 AM, Donatienne Van Weehaeghe wrote:

External Email - Use Caution

Dear,

The Freesurfer program generated the error after multiple comparison corerction.

Thank you for your help.

Kind regards
Donatienne

Op vr 29 mrt. 2019 om 10:58 schreef Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>>:
what program generated the error? What is the full command line for that 
program?

On 3/21/19 12:49 PM, Donatienne Van Weehaeghe wrote:

External Email - Use Caution
Dear,

I encountered a problem when going from pmod to freesurfer.

I made Vt images in pmod using the logan plot, then I used the following 
commands to convert them to freesurfer space:

#flirt -noresample -in 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.nii
 -ref 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/T1-2mm_skullstripped.nii.gz
 -applyxfm -init 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/SUVR/SUV.lrrev_lin_T1.mat
 -out 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii
#3dresample -master 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/occipital.nii.gz
  -inset 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.nii
 -prefix 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii

Then I did partial volume correction using this command:
#mri_gtmpvc --i 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii
 --reg Vt.reg.lta --psf 5 --seg 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/gtmseg.mgz
 --default-seg-merge --auto-mask 5 0.01 --rbv --o 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg
 --no-rescale --threads 8


Then I did surface projection:
#mri_vol2surf --mov 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rbv.nii.gz
 --reg 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta
 --hemi lh --projfrac 0.5 --o 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/lh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz
 --cortex --trgsubject fsaverage
#mri_vol2surf --mov 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rbv.nii.gz
 --reg 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta
 --hemi rh --projfrac 0.5 --o 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz
 --cortex --trgsubject fsaverage

followed by smoothing, concatening and then a group comparison. However then I 
obtained the following error:
ERROR: cannot find 
/usr/local/freesurfer/stable6_0_0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm37/pos/th13/mc-z.csd

Kind regards
Donatienne



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Re: [Freesurfer] VT images from pmod to freesurfer

2019-03-29 Thread Donatienne Van Weehaeghe 
External Email - Use Caution

Dear,

The Freesurfer program generated the error after multiple comparison
corerction.

Thank you for your help.

Kind regards
Donatienne

Op vr 29 mrt. 2019 om 10:58 schreef Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu>:

> what program generated the error? What is the full command line for that
> program?
>
> On 3/21/19 12:49 PM, Donatienne Van Weehaeghe wrote:
>
> External Email - Use Caution
>
> Dear,
>
>
> I encountered a problem when going from pmod to freesurfer.
>
>
> I made Vt images in pmod using the logan plot, then I used the following
> commands to convert them to freesurfer space:
>
>
>
> #flirt -noresample -in
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.nii
> -ref
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/T1-2mm_skullstripped.nii.gz
> -applyxfm -init
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/SUVR/SUV.lrrev_lin_T1.mat
> -out
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii
>
> #3dresample -master
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/occipital.nii.gz
> -inset
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.nii
> -prefix
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii
>
>
>
> Then I did partial volume correction using this command:
>
> #mri_gtmpvc --i
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii
> --reg Vt.reg.lta --psf 5 --seg
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/gtmseg.mgz
> --default-seg-merge --auto-mask 5 0.01 --rbv --o
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg
> --no-rescale --threads 8
>
>
>
>
>
> Then I did surface projection:
>
> #mri_vol2surf --mov
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rbv.nii.gz
> --reg
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta
> --hemi lh --projfrac 0.5 --o
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/lh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz
> --cortex --trgsubject fsaverage
>
> #mri_vol2surf --mov
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rbv.nii.gz
> --reg
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta
> --hemi rh --projfrac 0.5 --o
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz
> --cortex --trgsubject fsaverage
>
>
>
> followed by smoothing, concatening and then a group comparison. However
> then I obtained the following error:
>
> ERROR: cannot find
> /usr/local/freesurfer/stable6_0_0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm37/pos/th13/mc-z.csd
>
>
> Kind regards
>
> Donatienne
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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Re: [Freesurfer] VT images from pmod to freesurfer

2019-03-29 Thread Greve, Douglas N.,Ph.D. 
what program generated the error? What is the full command line for that 
program?

On 3/21/19 12:49 PM, Donatienne Van Weehaeghe wrote:

External Email - Use Caution
Dear,

I encountered a problem when going from pmod to freesurfer.

I made Vt images in pmod using the logan plot, then I used the following 
commands to convert them to freesurfer space:

#flirt -noresample -in 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.nii
 -ref 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/T1-2mm_skullstripped.nii.gz
 -applyxfm -init 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/SUVR/SUV.lrrev_lin_T1.mat
 -out 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii
#3dresample -master 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/occipital.nii.gz
  -inset 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.nii
 -prefix 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii

Then I did partial volume correction using this command:
#mri_gtmpvc --i 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii
 --reg Vt.reg.lta --psf 5 --seg 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/gtmseg.mgz
 --default-seg-merge --auto-mask 5 0.01 --rbv --o 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg
 --no-rescale --threads 8


Then I did surface projection:
#mri_vol2surf --mov 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rbv.nii.gz
 --reg 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta
 --hemi lh --projfrac 0.5 --o 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/lh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz
 --cortex --trgsubject fsaverage
#mri_vol2surf --mov 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rbv.nii.gz
 --reg 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta
 --hemi rh --projfrac 0.5 --o 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz
 --cortex --trgsubject fsaverage

followed by smoothing, concatening and then a group comparison. However then I 
obtained the following error:
ERROR: cannot find 
/usr/local/freesurfer/stable6_0_0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm37/pos/th13/mc-z.csd

Kind regards
Donatienne



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[Freesurfer] VT images from pmod to freesurfer

2019-03-21 Thread Donatienne Van Weehaeghe 
External Email - Use Caution

Dear,


I encountered a problem when going from pmod to freesurfer.


I made Vt images in pmod using the logan plot, then I used the following
commands to convert them to freesurfer space:



#flirt -noresample -in
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.nii
-ref
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/T1-2mm_skullstripped.nii.gz
-applyxfm -init
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/SUVR/SUV.lrrev_lin_T1.mat
-out
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii

#3dresample -master
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/occipital.nii.gz
-inset
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.nii
-prefix
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii



Then I did partial volume correction using this command:

#mri_gtmpvc --i
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii
--reg Vt.reg.lta --psf 5 --seg
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/gtmseg.mgz
--default-seg-merge --auto-mask 5 0.01 --rbv --o
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg
--no-rescale --threads 8





Then I did surface projection:

#mri_vol2surf --mov
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rbv.nii.gz
--reg
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta
--hemi lh --projfrac 0.5 --o
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/lh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz
--cortex --trgsubject fsaverage

#mri_vol2surf --mov
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rbv.nii.gz
--reg
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta
--hemi rh --projfrac 0.5 --o
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz
--cortex --trgsubject fsaverage



followed by smoothing, concatening and then a group comparison. However
then I obtained the following error:

ERROR: cannot find
/usr/local/freesurfer/stable6_0_0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm37/pos/th13/mc-z.csd


Kind regards

Donatienne
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