Re: [Freesurfer] Fwd: using CAT12 segmentation for PVC {Disarmed}
External Email - Use Caution Dear, Would there be another option to fix this? Kind regards Donatienne Op do 5 nov. 2020 om 17:38 schreef Donatienne Van Weehaeghe < donatiennevanweehae...@gmail.com>: > The subcortical structures were not delineated correctly, especially the > nucleus caudatus which had a lot of atrophy in this particular patient > group. > > Kind regards > Donatienne > > Op do 5 nov. 2020 om 15:50 schreef Douglas N. Greve < > dgr...@mgh.harvard.edu>: > >> I don't think CAT creates white or pial surfaces, so no. What is wrong >> with your FS analysis? >> >> On 11/5/2020 2:15 AM, Donatienne Van Weehaeghe wrote: >> >> External Email - Use Caution >> Dear, >> >> The segmentation using Freesurfer was incorrect, however we have a good >> segmentation from Cat 12. Can we use this segmentation for PVC in PETsurfer? >> >> Kind regards >> Donatienne >> >> ___ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1ZxmEs2Pk3BSMewoFlR47-yhqcFOo6DC4cKshyj4rTlsuLJB-lX2-17scYj6eyBy8oBx51BWPPWnmw4DO-O7Po_Pt_Qr3Zkz4ntxNcDfxQsDuqDehy6iRqGUj0Sl-aRPRaVNteXx6RxcYxuXYq1k7HTYDFAOjjbCtbmOn_fwXdxvUQbVjJb3zQlId77o_0NQnLn7qiEYvovXCcgSGHG2qtQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Fwd: using CAT12 segmentation for PVC {Disarmed}
External Email - Use Caution The subcortical structures were not delineated correctly, especially the nucleus caudatus which had a lot of atrophy in this particular patient group. Kind regards Donatienne Op do 5 nov. 2020 om 15:50 schreef Douglas N. Greve : > I don't think CAT creates white or pial surfaces, so no. What is wrong > with your FS analysis? > > On 11/5/2020 2:15 AM, Donatienne Van Weehaeghe wrote: > > External Email - Use Caution > Dear, > > The segmentation using Freesurfer was incorrect, however we have a good > segmentation from Cat 12. Can we use this segmentation for PVC in PETsurfer? > > Kind regards > Donatienne > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1JgAQlvSK79sdSjRzj76FwNDPzbnpDZLwDs4AnsLY36QhZryo9RS8zEq9pmxZYP2lUIrF_qfLqwNf5d43DfORXWGkonAXMLqtr6zn8nwKXoSV4Xakd2Fzbb0WZehCHhZ0jC-C7LQJmCgnpSpRPqW8BblcFVf-AsvBu5jikjez6invHtPwEcZQtk8gt0Y4413cL_HQ6s5I84LtV9pKBBpa8w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Fwd: using CAT12 segmentation for PVC
External Email - Use Caution Dear, The segmentation using Freesurfer was incorrect, however we have a good segmentation from Cat 12. Can we use this segmentation for PVC in PETsurfer? Kind regards Donatienne ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] pvc error
External Email - Use Caution
No, there is no unknown folder. I do not understand why he uses unknown
instead of the subject names specified in the text file. Also, the muller
gartner PVC correction works.
I created the suv.reg.lgta using the following command:
mri_coreg --targ
/Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/${word}/mri/brainmask.mgz
--mov
/Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/VT/Vt_all/${word}.nii
--reg
/Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/${word}/mri/suv.reg.lta
Thank you for your help.
Op vr 26 apr. 2019 om 17:08 schreef Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu>:
>
> Does that file actually exist? It seems to think that the subject name is
> "unknown", which is probably not right. How did you create suv.reg.lta?
> That file should have the name of the subject in it. Also, no need to
> specify the full path to the --seg (so, just --seg gtmseg.mgz is ok).
>
>
>
> On 4/26/2019 2:05 AM, Donatienne Van Weehaeghe wrote:
>
> External Email - Use Caution
> Dear Dough,
>
> The terminal output: HV_02_11_p2x7
> mghRead(/Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/unknown/mri/orig.mgz,
> -1): could not open file
> ERROR: loading
> /Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/unknown/mri/orig.mgz
> This is needed for RBV
>
> The command line: mri_gtmpvc --i
> /Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/VT/Vt_all/${word}_lin_T1.nii.gz
> --reg
> /Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/${word}/mri/suv.reg.lta
> --psf 5 --seg
> /Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/${word}/mri/gtmseg.mgz
> --default-seg-merge --auto-mask 5 0.01 --rbv --o
> /DATA_PETMR/data_donatienne/Boston_final_analysis/VT/Vt_all/${word}/PVC/gtmpvc.output.spmreg
> --no-rescale
>
> Kind regards
> Donatienne
>
> Op do 25 apr. 2019 om 17:44 schreef Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu>:
>
>> can you send command line and terminal output?
>>
>> On 4/25/19 10:37 AM, Donatienne Van Weehaeghe wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Dear freesurfer experts,
>> >
>> > I am running the rbv pvc correction on a mac system and encountered
>> > the following error.
>> >
>> >
>> mghRead(/Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/unknown/mri/orig.mgz,
>>
>> > -1): could not open file
>> >
>> > The subjects directory is
>> >
>> Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair,
>>
>> > the orig files are located in
>> >
>> Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/$subjectname
>> >
>> > Thank you!
>> >
>> > Kind regards
>> > Donatienne
>> >
>> > ___
>> > 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
> listfreesur...@nmr.mgh.harvard.eduhttps://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
Re: [Freesurfer] pvc error
External Email - Use Caution
Dear Dough,
The terminal output: HV_02_11_p2x7
mghRead(/Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/unknown/mri/orig.mgz,
-1): could not open file
ERROR: loading
/Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/unknown/mri/orig.mgz
This is needed for RBV
The command line: mri_gtmpvc --i
/Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/VT/Vt_all/${word}_lin_T1.nii.gz
--reg
/Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/${word}/mri/suv.reg.lta
--psf 5 --seg
/Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/${word}/mri/gtmseg.mgz
--default-seg-merge --auto-mask 5 0.01 --rbv --o
/DATA_PETMR/data_donatienne/Boston_final_analysis/VT/Vt_all/${word}/PVC/gtmpvc.output.spmreg
--no-rescale
Kind regards
Donatienne
Op do 25 apr. 2019 om 17:44 schreef Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu>:
> can you send command line and terminal output?
>
> On 4/25/19 10:37 AM, Donatienne Van Weehaeghe wrote:
> >
> > External Email - Use Caution
> >
> > Dear freesurfer experts,
> >
> > I am running the rbv pvc correction on a mac system and encountered
> > the following error.
> >
> >
> mghRead(/Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/unknown/mri/orig.mgz,
>
> > -1): could not open file
> >
> > The subjects directory is
> >
> Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair,
>
> > the orig files are located in
> >
> Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/$subjectname
> >
> > Thank you!
> >
> > Kind regards
> > Donatienne
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] pvc error
External Email - Use Caution Dear freesurfer experts, I am running the rbv pvc correction on a mac system and encountered the following error. mghRead(/Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/unknown/mri/orig.mgz, -1): could not open file The subjects directory is Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair, the orig files are located in Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/$subjectname Thank you! Kind regards Donatienne ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] VT images from pmod to freesurfer
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/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta
>> --hemi rh --projfrac 0.5 --o
>> /autof
Re: [Freesurfer] VT images from pmod to freesurfer
External Email - Use Caution
Dear,
The Freesurfer program generated the error after multiple comparison
corerction.
Thank you for your help.
Kind regards
Donatienne
Op vr 29 mrt. 2019 om 10:58 schreef Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu>:
> what program generated the error? What is the full command line for that
> program?
>
> On 3/21/19 12:49 PM, Donatienne Van Weehaeghe wrote:
>
> External Email - Use Caution
>
> Dear,
>
>
> I encountered a problem when going from pmod to freesurfer.
>
>
> I made Vt images in pmod using the logan plot, then I used the following
> commands to convert them to freesurfer space:
>
>
>
> #flirt -noresample -in
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${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/${word}gtmpvc.output.spmreg/rh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz
> --cortex --trgsubject fsaverage
>
>
>
> followed by smoothing, concatening and then a group comparison. However
> then I obtained the following error:
>
> ERROR: cannot find
> /usr/local/freesurfer/stable6_0_0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm37/pos/th13/mc-z.csd
>
>
> Kind regards
>
> Donatienne
>
> ___
> Freesurfer mailing
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] VT images from pmod to freesurfer
External Email - Use Caution
Dear,
I encountered a problem when going from pmod to freesurfer.
I made Vt images in pmod using the logan plot, then I used the following
commands to convert them to freesurfer space:
#flirt -noresample -in
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${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/${word}gtmpvc.output.spmreg/rh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz
--cortex --trgsubject fsaverage
followed by smoothing, concatening and then a group comparison. However
then I obtained the following error:
ERROR: cannot find
/usr/local/freesurfer/stable6_0_0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm37/pos/th13/mc-z.csd
Kind regards
Donatienne
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Re: [Freesurfer] Segmentation fault
External Email - Use Caution We just found the mistake. I created the SUVR images already in T1 space so I remade the lta files using the SUVR images and now it works. Kind regards Donatienne Van: freesurfer-boun...@nmr.mgh.harvard.edu namens Greve, Douglas N.,Ph.D. Verzonden: donderdag 14 maart 2019 17:17:54 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] Segmentation fault Can you send the command line with out variables and the full terminal output? On 3/14/19 8:48 AM, Donatienne Van Weehaeghe wrote: > > External Email - Use Caution > > Dear, > > > Apologies, this is a copy and paste error the full command was: > > > #mri_gtmpvc --i > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/SUVR/SUVR_cerebellum.nii.gz > --reg > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/suv.reg.lta > --psf 5 --seg > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/gtmseg.mgz > --default-seg-merge --auto-mask 5 0.01 --rbv --o > /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/PVC/gtmpvc.output.suvrcerebellum.spmreg > --no-rescale --threads 8 > > Kind regards > > Donatienne > > > // > > > *Van:* freesurfer-boun...@nmr.mgh.harvard.edu > namens Tim Schäfer > > *Verzonden:* woensdag 13 maart 2019 23:22:07 > *Aan:* Freesurfer support list > *Onderwerp:* Re: [Freesurfer] Segmentation fault > External Email - Use Caution > > > On March 13, 2019 at 9:18 PM Donatienne Van Weehaeghe > wrote: > > The code I tried to run: > > > > #mri_gtmpvc --i SUVR_cerebellum.nii.gz --reg suv.reg.lta --psf 5 > --seg /gtmseg.mgz --default-seg-merge --auto-mask 5 0.01 --rbv --o > gtmpvc.output.suvrcerebellum.spmreg --no-rescale --threads 8 > > > > Is that slash in the part '--seg /gtmseg.mgz' a copy & paste error? If > not: it is very likely that the file does not exist in that location. > > I'm not sure though whether that is the cause of the error. I would > rather expect a "file not found" error message instead of a seg fault > in that case. But it's worth checking. > > -- > Tim > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Segmentation fault
External Email - Use Caution Dear, Apologies, this is a copy and paste error the full command was: #mri_gtmpvc --i /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/SUVR/SUVR_cerebellum.nii.gz --reg /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/suv.reg.lta --psf 5 --seg /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/gtmseg.mgz --default-seg-merge --auto-mask 5 0.01 --rbv --o /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/PVC/gtmpvc.output.suvrcerebellum.spmreg --no-rescale --threads 8 Kind regards Donatienne Van: freesurfer-boun...@nmr.mgh.harvard.edu namens Tim Schäfer Verzonden: woensdag 13 maart 2019 23:22:07 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] Segmentation fault External Email - Use Caution > On March 13, 2019 at 9:18 PM Donatienne Van Weehaeghe > wrote: > The code I tried to run: > > #mri_gtmpvc --i SUVR_cerebellum.nii.gz --reg suv.reg.lta --psf 5 --seg > /gtmseg.mgz --default-seg-merge --auto-mask 5 0.01 --rbv --o > gtmpvc.output.suvrcerebellum.spmreg --no-rescale --threads 8 > Is that slash in the part '--seg /gtmseg.mgz' a copy & paste error? If not: it is very likely that the file does not exist in that location. I'm not sure though whether that is the cause of the error. I would rather expect a "file not found" error message instead of a seg fault in that case. But it's worth checking. -- Tim ___ 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] Segmentation fault
External Email - Use Caution Dear, I encountered the following error when I tried to run mri_gtmpvc -- rbv: Segmentation fault (core dumped) First I performed the PET to orig registration using spmregister, secondly I tried with the registration using mri_coreg but the error remained. I also redid the segmentation step gtmseg --s $word --xcerseg without fixing the problem. Can anyone help me with this problem? The code I tried to run: #mri_gtmpvc --i SUVR_cerebellum.nii.gz --reg suv.reg.lta --psf 5 --seg /gtmseg.mgz --default-seg-merge --auto-mask 5 0.01 --rbv --o gtmpvc.output.suvrcerebellum.spmreg --no-rescale --threads 8 Kind regards Donatienne ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
