Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] LGI index error
by Lorenzo Ferri 09 Dec '18

09 Dec '18

External Email - Use Caution > Dear Freesurfer expert > > I am trying to compute LGI with Mac OS. I am a beginner of FS. > I could connect free surfer to Matlab path, but when I run LGI it generate this error that i can not understand > > mris_fill -c -r 1 lh.pial /Applications/freesurfer/subjects/bianchi/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz > ================= > reading surface from lh.pial... > dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address > Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib > Expected in: /usr/lib/libSystem.B.dylib > > dyld: Symbol not found: ___emutls_get_address > Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib > Expected in: /usr/lib/libSystem.B.dylib > > Abort > ERROR: mris_fill -c -r 1 lh.pial /Applications/freesurfer/subjects/bianchi/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz failed! > > Any suggestions > Thanks > > Lorenzo >

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Fwd: fcseedcor output
by Sara Jafakesh 08 Dec '18

08 Dec '18

External Email - Use Caution -----Original Message----- From: "Sara Jafakesh" <S.Jafakesh(a)sutech.ac.ir> To: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> Date: Sat, 08 Dec 2018 12:21:06 +0330 Subject: Re: fcseedcor output hi, I send the entire email chain: Can? you send the full terminal output? On 12/05/2018 01:25 AM, Sara Jafakesh wrote: > > ????????External Email - Use Caution > > > Dear freesurfer experts, > I want to calculate corrolation between two seeds with > freesurfer-linux-centos6_x86_64_stable_pub-v6 .after using > fcseed-config and fcseed-sess, I used fcseedcor. the command > that I trying to run is as follow: > fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed > lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg > 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat > but the output of fcseedcor is not dat file ( the > connectivity matrix for my result 2*2 matrix) as it has been > explained in the fcssedcor help. the output is just the log > file named seedcor2.dat.log. although it has been done > without error. > I really dont know what is the problem. > I would be grateful if you could help me. > best regards, > sara hi sara, can you include the entire email chain so that I can see the context? On 12/7/18 4:19 PM, Sara Jafakesh wrote: External Email - Use Caution Dear Dr.GREVE , thank you for your reply my full terminal output is: [user at localhost subjects]$ fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat Sat Dec 1 18:05:11 IRST 2018 setenv SUBJECTS_DIR /home/user/freesurfer/subjects cd /home/user/freesurfer/subjects /home/user/freesurfer/fsfast/bin/fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c $Id: fcseedcor,v 1.3 2015/12/10 22:51:29 zkaufman Exp $ Linux localhost.localdomain 2.6.32-642.el6.x86_64 #1 SMP Tue May 10 17:27:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux ------- matlab output -------------------- matlab: Command not found. Started at Sat Dec 1 18:05:11 IRST 2018 Ended at Sat Dec 1 18:05:12 IRST 2018 Fcseedcor-Run-Time-Sec 1 Fcseedcor-Run-Time-Hours 0.00 fcseedcor Done best, sara -----Original Message----- From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> To: Sara Jafakesh <S.Jafakesh(a)sutech.ac.ir>, "87fc6eef-18d0-2f7d-99f5-eb8a79707c5c(a)mgh.harvard.edu" <87fc6eef-18d0-2f7d-99f5-eb8a79707c5c(a)mgh.harvard.edu> Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Date: Fri, 7 Dec 2018 22:33:49 +0000 Subject: Re: fcseedcor output hi sara, can you include the entire email chain so that I can see the context? On 12/7/18 4:19 PM, Sara Jafakesh wrote: External Email - Use Caution Dear Dr.GREVE , thank you for your reply my full terminal outpou is : [user@localhost subjects]$ fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat Sat Dec 1 18:05:11 IRST 2018 setenv SUBJECTS_DIR /home/user/freesurfer/subjects cd /home/user/freesurfer/subjects /home/user/freesurfer/fsfast/bin/fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c $Id: fcseedcor,v 1.3 2015/12/10 22:51:29 zkaufman Exp $ Linux localhost.localdomain 2.6.32-642.el6.x86_64 #1 SMP Tue May 10 17:27:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux ------- matlab output -------------------- matlab: Command not found. Started at Sat Dec 1 18:05:11 IRST 2018 Ended at Sat Dec 1 18:05:12 IRST 2018 Fcseedcor-Run-Time-Sec 1 Fcseedcor-Run-Time-Hours 0.00 fcseedcor Done best, sara 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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回复：回复： ?????? Calculated thickness
by 1013364183 08 Dec '18

08 Dec '18

External Email - Use Caution Dear Tim, I have used chmod to give this file permission. I want to know because this instruction is no longer available? yours yujunjie ---原始邮件--- 发件人: "ts+ml"<ts+ml(a)rcmd.org> 发送时间: 2018年12月9日(星期日) 凌晨1:15 收件人: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; 主题: Re: [Freesurfer]回复： ?????? Calculated thickness External Email - Use Caution Just to be sure, could you also post the output of the following command: who am i; ls -ld /usr/local/freesurfer/subjects/groupstudy/ I suspect that you do not have write access to /usr/local/. Unless you are running FreeSurfer as root (which you definitely should not do), you should not be allowed to write into /usr/. I suggest you try changing the output directory to some place where definitely have write access. You could do something like this: mkdir ~/groupstudy/ mris_surface_stats -nsmooth 60 -surf_name $SUBJECTS_DIR/1001/surf/lh.white -out_name ~/groupstudy/lh_std_10.mgh -absmean ~/groupstudy/lh_absmean_10.mgh -mean ~/groupstudy/lh_mean_10.mgh -absstd ~/groupstudy/lh_absstd_10.mgh /usr/local/freesurfer/subjects/1001/surf/lh.thickness_diff.mgh Best, Tim > On December 8, 2018 at 2:08 PM 1013364183 <yujunjie828(a)qq.com> wrote: > > > External Email - Use Caution > > Dear Bruce, > I run the following command: > > mris_surface_stats -nsmooth 60 -surf_name $SUBJECTS_DIR/1001/surf/lh.white -out_name $SUBJECTS_DIR/groupstudy/lh_std_10.mgh -absmean $SUBJECTS_DIR/groupstudy/lh_absmean_10.mgh -mean $SUBJECTS_DIR/groupstudy/lh_mean_10. Mgh -absstd $SUBJECTS_DIR/groupstudy/lh_absstd_10.mgh /usr/local/freesurfer/subjects/1001/surf/lh.thickness_diff.mgh > > > The results are as follows: > Perform 60 steps of smoothing of input data > Using /usr/local/freesurfer/subjects/groupstudy/lh_std_10.mgh as output file > Using /usr/local/freesurfer/subjects/groupstudy/lh_absmean_10.mgh as output file for abs-mean > Using /usr/local/freesurfer/subjects/groupstudy/lh_mean_10.mgh as output file for mean > Using /usr/local/freesurfer/subjects/groupstudy/lh_absstd_10.mgh as output file for std-of-abs-mean > Reading /usr/local/freesurfer/subjects/1001/surf/lh.thickness_diff.mgh... > Smooth input data by 60 steps > Stats over surface (318651 vertices): mean = 0.0888528, std = 0.334772, absmean = 0.23932, absstd = 0.250386 > > > > But I did not get the generated mgh file.Is this what is the reason? > > > > yours yujunjie > > > > ------------------ 原始邮件 ------------------ > 发件人: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu>; > 发送时间: 2018年12月8日(星期六) 凌晨1:16 > 收件人: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; > > 主题: Re: [Freesurfer] ?????? Calculated thickness > > > > Hi yujunjie > > in general if you want our help you have to give us more information. We > need for example the full command line you ran and the full output of it > (in text, not a screen shot!) > > cheers > Bruce > On Sat, 8 Dec 2018, 1013364183 wrote: > > > > > External Email - Use Caution > > > > The problem is in the fourth step of ThicknessRepeatibility - mris_surface_stats > > > > > > ------------------ ???????? ------------------ > > ??????: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu>; > > ????????: 2018??12??8??(??????) ????0:57 > > ??????: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; > > ????: Re: [Freesurfer] Calculated thickness > > > > Hi yujunjie > > > > you can use mris_distance_transform -vol to compute a volumetric map of > > distances to the surface if that is what you want. > > > > cheers > > Bruce > > On Fri, 7 Dec 2018, > > 1013364183 wrote: > > > > > > > > External Email - Use Caution > > > > > > Dear FS?? > > > I now have two different surfaces, the two surfaces have intersecting parts, I want to calculate > > > their signed distance, what should I do?I want to calculate the thick std and mean mgh files > > through > > > mris_surface_stats, but there is no output. What is the reason? > > > > > > yours yujunjie > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________… > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Tim 0176 84273709 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Calculated thickness
by 1013364183 08 Dec '18

08 Dec '18

External Email - Use Caution Dear FS， I now have two different surfaces, the two surfaces have intersecting parts, I want to calculate their signed distance, what should I do?I want to calculate the thick std and mean mgh files through mris_surface_stats, but there is no output. What is the reason? yours yujunjie

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Re: [Freesurfer] fcseedcor output
by Sara Jafakesh 08 Dec '18

08 Dec '18

External Email - Use Caution > Dear freesurfer experts, > I want to calculate corrolation between two seeds with > freesurfer-linux-centos6_x86_64_stable_pub-v6 .after using > fcseed-config and fcseed-sess, I used fcseedcor. the command > that I trying to run is as follow: > fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed > lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg > 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat > but the output of fcseedcor is not dat file ( the > connectivity matrix for my result 2*2 matrix) as it has been > explained in the fcssedcor help. the output is just the log > file named seedcor2.dat.log. although it has been done > without error. > I really dont know what is the problem. > I would be grateful if you could help me. > best regards, > sara Can? you send the full terminal output? On 12/05/2018 01:25 AM, Sara Jafakesh wrote: > > ????????External Email - Use Caution Dear Dr.GREVE , thank you for your reply my full terminal output is: [user at localhost subjects]$ fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat Sat Dec 1 18:05:11 IRST 2018 setenv SUBJECTS_DIR /home/user/freesurfer/subjects cd /home/user/freesurfer/subjects /home/user/freesurfer/fsfast/bin/fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c $Id: fcseedcor,v 1.3 2015/12/10 22:51:29 zkaufman Exp $ Linux localhost.localdomain 2.6.32-642.el6.x86_64 #1 SMP Tue May 10 17:27:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux ------- matlab output -------------------- matlab: Command not found. Started at Sat Dec 1 18:05:11 IRST 2018 Ended at Sat Dec 1 18:05:12 IRST 2018 Fcseedcor-Run-Time-Sec 1 Fcseedcor-Run-Time-Hours 0.00 fcseedcor Done best, sara hi sara, can you include the entire email chain so that I can see the context? On 12/7/18 4:19 PM, Sara Jafakesh wrote: External Email - Use Caution hi, I send the entire email chain. thank you, sara.

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extracting the version of FreeSurfer used to process some data
by David Groppe 07 Dec '18

07 Dec '18

External Email - Use Caution Hi FreeSurfers, I'm working with some data that has been collected and processed with FreeSurfer over several years. Consequently, some individuals have been processed with different versions of FreeSurfer. Is there a file in an individual's subject directory that specifies which version of FreeSurfer was used to create it? much thanks, -David

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fcseedcor output
by Sara Jafakesh 07 Dec '18

07 Dec '18

External Email - Use Caution Dear Dr.GREVE , thank you for your reply my full terminal outpou is : [user@localhost subjects]$ fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat Sat Dec 1 18:05:11 IRST 2018 setenv SUBJECTS_DIR /home/user/freesurfer/subjects cd /home/user/freesurfer/subjects /home/user/freesurfer/fsfast/bin/fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c $Id: fcseedcor,v 1.3 2015/12/10 22:51:29 zkaufman Exp $ Linux localhost.localdomain 2.6.32-642.el6.x86_64 #1 SMP Tue May 10 17:27:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux ------- matlab output -------------------- matlab: Command not found. Started at Sat Dec 1 18:05:11 IRST 2018 Ended at Sat Dec 1 18:05:12 IRST 2018 Fcseedcor-Run-Time-Sec 1 Fcseedcor-Run-Time-Hours 0.00 fcseedcor Done best, sara

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Re: [Freesurfer] fsaverage6 FS6
by Sanfelici, Rachele 07 Dec '18

07 Dec '18

External Email - Use Caution Thanks Bruce, this is my command line (note that because of a different organization of the data, the subject dir is /Data/48/ and the subject is MRI_sMRI_fs_reconall_fs_reconall_gcv6s): mri_surf2surf --srcsubject MRI_sMRI_fs_reconall_fs_reconall_gcv6s --srcsurfval /Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.pial_lgi.fsaverage6.mgh --trgsubject MRI_sMRI_fs_reconall_fs_reconall_gcv6s --trgsurfval /Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.pial_lgi.fwhm5.fsaverage6.mgh --surfreg sphere.reg --hemi lh --fwhm 5 so I could use the fsaverage6/surf/lh.sphere.reg for the --surfreg flag instead, right? But then I would need to copy and rename it in the subject folder, is that correct? Thanks a lot! Rachele ________________________________________ Von: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> im Auftrag von Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Gesendet: Freitag, 7. Dezember 2018 19:14 An: Freesurfer support list Betreff: Re: [Freesurfer] fsaverage6 FS6 Hi Rachele what is your command line? The ?h.sphere.reg is in register with fsaverage, but it looks like your data has been mapped to the fsaverage6 subject (which has 40962), but you are specifying the individual subject surface. If that is the case, use the fsaverage6 surface instead cheers Bruce On Fri, 7 Dec 2018, Sanfelici, Rachele wrote: > External Email - Use Caution > > Many thanks Doug, that worked! > > Now that I resampled my data I'm having the next issue: smoothing. > I'm using mri_surf2surf specifying the same source and target subject (resampled to fsaverage6), but apparently to skip the registration I need to also specify the ?h.sphere.reg. I get this error: > > Reading source surface reg /Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.sphere.reg > Loading source data > ERROR: dimension inconsistency in source data > Number of surface vertices = 151901 > Number of value vertices = 40962 > > Which I guess it's because the sphere is not "registered" to fsaverage6, right? > My solution would be to copy and rename fsaverage6 ?h.sphere.reg to the subject directory to bypass this problem. Can you please confirm that this approach is valid? Or otherwise would you have a better solution? > > Thanks a lot in advance! > Rachele > > ________________________________________ > Von: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> im Auftrag von Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu> > Gesendet: Donnerstag, 6. Dezember 2018 18:33 > An: freesurfer(a)nmr.mgh.harvard.edu > Betreff: Re: [Freesurfer] fsaverage6 FS6 > > Try using mris_apply_reg. The command line is simpler (but otherwise > gives the same result). > > On 12/06/2018 11:44 AM, Sanfelici, Rachele wrote: >> >> External Email - Use Caution >> >> Dear FreeSurfer experts, >> >> >> I am encountering a problem when trying to downsample to fsaverage6 >> with FreeSurfer v.6.(see below): >> >> >> mri_surf2surf --srcsubject MRI_sMRI_fs_reconall_fs_reconall_gcv6s >> --srchemi lh --srcsurfreg fsaverage6.sphere.reg --trgsubject >> fsaverage6 --trghemi lh --trgsurfreg sphere.reg --tval >> ./tmp.mris_preproc.70069/MRI_sMRI_fs_reconall_fs_reconall_gcv6s.1.mgh >> --sval >> /Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.pial_lgi >> --sfmt curv --noreshape --cortex >> >> srcsubject = MRI_sMRI_fs_reconall_fs_reconall_gcv6s >> srcval =/Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.pial_lgi >> srctype = curv >> trgsubject = fsaverage6 >> trgval = >> ./tmp.mris_preproc.70069/MRI_sMRI_fs_reconall_fs_reconall_gcv6s.1.mgh >> trgtype = >> srcsurfreg = fsaverage6.sphere.reg >> trgsurfreg = sphere.reg >> srchemi = lh >> trghemi = lh >> frame = 0 >> fwhm-in = 0 >> fwhm-out = 0 >> label-src = lh.cortex.label >> label-trg = lh.cortex.label >> OKToRevFaceOrder = 1 >> UseDualHemi = 0 >> Reading source surface reg >> /Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.fsaverage6.sphere.reg >> No such file or directory >> >> I guess it's because the naming of the sphere file is now different >> compared to v.5.3 (it was sufficient to run recon-all with the >> additional -qcache -target fsaverage6 flag), so it can't be found by >> mri_surf2surf. I tried to run mris_preproc instead of recon-all but I >> still get the same error. Could you please help me with the right command? >> >> Thank you very much in advance! >> >> Best >> Rachele >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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Re: [Freesurfer] fsaverage6 FS6
by Sanfelici, Rachele 07 Dec '18

07 Dec '18

External Email - Use Caution Many thanks Doug, that worked! Now that I resampled my data I'm having the next issue: smoothing. I'm using mri_surf2surf specifying the same source and target subject (resampled to fsaverage6), but apparently to skip the registration I need to also specify the ?h.sphere.reg. I get this error: Reading source surface reg /Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.sphere.reg Loading source data ERROR: dimension inconsistency in source data Number of surface vertices = 151901 Number of value vertices = 40962 Which I guess it's because the sphere is not "registered" to fsaverage6, right? My solution would be to copy and rename fsaverage6 ?h.sphere.reg to the subject directory to bypass this problem. Can you please confirm that this approach is valid? Or otherwise would you have a better solution? Thanks a lot in advance! Rachele ________________________________________ Von: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> im Auftrag von Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu> Gesendet: Donnerstag, 6. Dezember 2018 18:33 An: freesurfer(a)nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] fsaverage6 FS6 Try using mris_apply_reg. The command line is simpler (but otherwise gives the same result). On 12/06/2018 11:44 AM, Sanfelici, Rachele wrote: > > External Email - Use Caution > > Dear FreeSurfer experts, > > > I am encountering a problem when trying to downsample to fsaverage6 > with FreeSurfer v.6.(see below): > > > mri_surf2surf --srcsubject MRI_sMRI_fs_reconall_fs_reconall_gcv6s > --srchemi lh --srcsurfreg fsaverage6.sphere.reg --trgsubject > fsaverage6 --trghemi lh --trgsurfreg sphere.reg --tval > ./tmp.mris_preproc.70069/MRI_sMRI_fs_reconall_fs_reconall_gcv6s.1.mgh > --sval > /Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.pial_lgi > --sfmt curv --noreshape --cortex > > srcsubject = MRI_sMRI_fs_reconall_fs_reconall_gcv6s > srcval =/Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.pial_lgi > srctype = curv > trgsubject = fsaverage6 > trgval = > ./tmp.mris_preproc.70069/MRI_sMRI_fs_reconall_fs_reconall_gcv6s.1.mgh > trgtype = > srcsurfreg = fsaverage6.sphere.reg > trgsurfreg = sphere.reg > srchemi = lh > trghemi = lh > frame = 0 > fwhm-in = 0 > fwhm-out = 0 > label-src = lh.cortex.label > label-trg = lh.cortex.label > OKToRevFaceOrder = 1 > UseDualHemi = 0 > Reading source surface reg > /Data/48/MRI_sMRI_fs_reconall_fs_reconall_gcv6s/surf/lh.fsaverage6.sphere.reg > No such file or directory > > I guess it's because the naming of the sphere file is now different > compared to v.5.3 (it was sufficient to run recon-all with the > additional -qcache -target fsaverage6 flag), so it can't be found by > mri_surf2surf. I tried to run mris_preproc instead of recon-all but I > still get the same error. Could you please help me with the right command? > > Thank you very much in advance! > > Best > Rachele > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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gray intensity
by 1013364183 07 Dec '18

07 Dec '18

External Email - Use Caution Dear Bruce, I want to get the percent gray-white contrast((white-gray)/(white + gray).100%) and gray intensity sampled at 30% cortical depth. What should I do? yours yujunjie

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