Freesurfer December 2018

freesurfer@nmr.mgh.harvard.edu

109 participants
175 discussions

Increasing the Number of a non-FreeSurfer Parcellation
by Maedeh Khalilian 10 Dec '18

10 Dec '18

External Email - Use Caution Dear experts, I have a question, if I have a parcellation which is not the output of FreeSurfer, can i increase the number of its parcels in FreeSurfer? Maybe if I can change my file into an annotation file.... is it possible? I would be grateful if u could help me. Cheers, Maedeh.

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Extracting ROI from atlases
by Song, Da-Yea 10 Dec '18

10 Dec '18

External Email - Use Caution Hello, Is there a command to extract ROIs from atlases (ex. desikan) in nifti file formats? Thank you so much in advance for your time. Best, Da-Yea ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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fdr correction problem
by 1013364183 10 Dec '18

10 Dec '18

External Email - Use Caution Dear Bruce， I have fdr correction for sig.mgh obtained by mri_glmfit, but the corrected graphs are all 0. Why is this, the instructions and the running results are as follows: mri_fdr --fdr .05 --i lh2.gender_age.glmdir/group2/sig.mgh lh2.gender_age.glmdir/mask.mgh 2.mgh $Id: mri_fdr.c,v 1.2 2016/01/07 22:23:57 greve Exp $ cwd /usr/local/freesurfer/subjects cmdline mri_fdr --fdr .05 --i lh2.gender_age.glmdir/group2/sig.mgh lh2.gender_age.glmdir/mask.mgh 2.mgh sysname Linux hostname xiaorn machine x86_64 user xiaorn fdr 0.050000 ninputs 1 MRIfdr2vwth: np = 149953, nv = 163842 MRIfdr2vwth: vwth = 0.000003, log10(vwhth) = 5.583609 voxel-wise-threshold 5.5836093010 Writing to 2.mgh mri_fdr done yours yujunjie

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Re: [Freesurfer] Fwd: Overall maxima is high and still no significant cluster
by Antonin Skoch 09 Dec '18

09 Dec '18

External Email - Use Caution Dear Martin, actually, when your primary problem is very high local maxima on p-map, but no significant cluster-wise p after thresholding, I guess, that you should try the opposite, i.e. increase cluster forming threshold. This will increase sensitivity to clusters with smaller extent but comprising larger p-values before thresholding. Antonin Skoch did you do this? First, install a new version of mri_glmfit-sim from ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/mri_glmfit… (copy it to $FREESURFER_HOME/bin and make it executable with chmod a+rx mri_glmfit-sim).On 12/06/2018 01:28 PM, Martin Juneja wrote: > > External Email - Use Caution > > Thanks Dough for your suggestions. I tried to use permutation method, > but its giving me following error: > > ERROR: design matrix is not orthogonal, cannot be used with permutation. > > If this something you really want to do, run with --perm-force > > > Can you please tell me how can I fix this issue or if I can run with > --perm-force? > > > Thanks for the help. > > > On Thu, Dec 6, 2018 at 9:37 AM Greve, Douglas N.,Ph.D. > <dgr...(a)mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: > > For it to show up in the output file, the cluster-wise pvalue must > be < > .05 (CWT). To see all the clusters regardless of significance, run it > with a CWT of 1. If you want to run with a more liberal cluster > forming > threshold (CFT), you can try using permutation. See > http://freesurfer.net/fswiki/FsTutorial/MultipleComparisonsV6.0Perm > > On 12/05/2018 11:44 PM, Martin Juneja wrote: > > > > External Email - Use Caution > > > > > > Dear experts, > > > > Could you please help me in resolving following issue? > > > > Thanks. > > ---------- Forwarded message --------- > > From: *Martin Juneja* <mj70...(a)gmail.com > <mailto:mj70...@gmail.com> <mailto:mj70...@gmail.com > <mailto:mj70...@gmail.com>>> > > Date: Wed, Nov 28, 2018 at 2:23 PM > > Subject: Overall maxima is high and still no significant cluster > > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > > > > Hi FS experts, > > > > I am estimating the group-behavioral thickness interaction using > > contrast 2 FSGD file: > > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V at CFT < > 0.01 and > > CWT < 0.05 at FWHM of 12 mm. > > > > I do not find any significant clusters and my output summary > text file > > looks like the following. This file shows that overall maxima is > > 4.58212 (which corresponds to p < 0.0001 because -log (0.0001) = > 4, so > > I am just wondering despite the fact that maxima is > 4, why I > do not > > see this cluster in the summary/output *.mgh file? > > > > I would really appreciate any clarification and tips to modify my > > input thresholds so that I do not miss any significant findings > here. > > > > Thanks. > > ----------------------------- > > > > # SearchSpace_mm2 76467.1 > > # SearchSpace_vtx 149953 > > # Bonferroni 2 > > # Minimum Threshold 2 > > # Maximum Threshold infinity > > # Threshold Sign abs > > # AdjustThreshWhenOneTail 1 > > # CW PValue Threshold: 0.05 > > # Area Threshold 0 mm^2 > > # CSD thresh 2.000000 > > # CSD nreps 10000 > > # CSD simtype null-z > > # CSD contrast NA > > # CSD confint 90.000000 > > # Overall max 4.58212 at vertex 10608 > > # Overall min -2.84277 at vertex 75476 > > # NClusters 0 > > # FixMNI = 0 > > # > > # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP > > CWPLow CWPHi NVtxs WghtVtx Annot > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@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] 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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Freesurfer December 2018