Freesurfer May 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
208 discussions

Re: [Freesurfer] Group Analysis Covariates
by Hua, Jessica 24 May '20

24 May '20

External Email - Use Caution Thanks for your help with the code! --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Saturday, May 23, 2020 11:00 AM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer Digest, Vol 195, Issue 56 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. missing files in he v6 fsaverage on the Martinos Center network (Douglas N. Greve) 2. Re: Group Analysis Covariates (Douglas N. Greve) 3. Re: Freesurfer 7.1 hires error (Douglas N. Greve) 4. Re: LGI problem (Angela Favaro) 5. Are my slice-time corrected files being used in selxavg3-sess? (Mcnorgan, Christopher) 6. freeview is RAM greedy in version 7.1.0 (Anton?n ?koch) 7. Re: freeview is RAM greedy in version 7.1.0 (Ruopeng Wang) 8. Re: freeview is RAM greedy in version 7.1.0 (fsbuild) 9. Re: freeview is RAM greedy in version 7.1.0 (Anton?n ?koch) 10. Command cannot recognise session from sessid file (Marco Ninghetto) 11. Longitudinal processing with freesurfer 7.1.0 (Angela Favaro) 12. Re: freeview is RAM greedy in version 7.1.0 (Ruopeng Wang) ---------------------------------------------------------------------- Message: 1 Date: Fri, 22 May 2020 12:02:56 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: [Freesurfer] missing files in he v6 fsaverage on the Martinos Center network To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <fb258210-bab9-dfe2-2039-4ead9e6a64dc(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8"; format=flowed Sorry, I accidentally deleted some files from the v6 fsaverage located on the Martinos Center network. They have been restored, but it might have caused your recon-all process to fail if you had one running last night. Have a good weekend doug ------------------------------ Message: 2 Date: Fri, 22 May 2020 12:14:06 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Group Analysis Covariates To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <23e96fb1-f2b5-8e23-112a-2d0cb9ec3d88(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" Sorry, I left out a key ingredient. Use pmf below X = load('Xg.dat'); y = load('perm.th30.abs.y.ocn.dat'); beta = inv(X'*X)*X'*y; yhat = X(:,[1 2 3])*beta([1 2 3],:); e = y - yhat; pmf = yhat+e; On 5/22/2020 11:55 AM, Hua, Jessica wrote: > > ????????External Email - Use Caution > > I just tried the revised code, and it gave me the adjusted values for > each cluster by group. Is there a way to get covariate adjusted? > values for each participant? > > --- > > Jessica Hua, M.A. > Cognitive and Emotional Control Lab > Doctoral Candidate?Clinical Psychology > University of Missouri > > ------------------------------------------------------------------------ > *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu > <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of > freesurfer-request(a)nmr.mgh.harvard.edu > <freesurfer-request(a)nmr.mgh.harvard.edu> > *Sent:* Friday, May 22, 2020 10:09 AM > *To:* freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> > *Subject:* Freesurfer Digest, Vol 195, Issue 54 > Send Freesurfer mailing list submissions to > ??????? freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > ??????? freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > ??????? freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > ?? 1. Re: Freesurfer 7.1 hires error (Douglas N. Greve) > ?? 2. Re: question on partial volume correction (Barletta, Valeria) > ?? 3. Re: question on partial volume correction (Douglas N. Greve) > ?? 4. Re: Group Analysis Covariates (Hua, Jessica) > ?? 5. Re: Group Analysis Covariates (Douglas N. Greve) > ?? 6. Re: mris_register intermediate results display (Chris Adamson) > ?? 7. Open Postdoctoral Scholar Position (Neva M Corrigan) > ?? 8. Re: Infant Freesurfer: infant_recon_all error (Hoopes, Andrew) > ?? 9. Re: circular/cyclic color map for polar data in freeview > ????? {Disarmed} (Caspar M. Schwiedrzik) > ? 10. OHBM Brainhack registration is open! (Remi Gau) > ? 11. FW: Motion correction files contain 0 0 0 1 > ????? (Camerino, I.L. (Ileana)) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 21 May 2020 12:11:55 -0400 > From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] Freesurfer 7.1 hires error > To: <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <9eaf8c24-3b80-eb34-7cd0-09080c152b03(a)mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > I don't know what is wrong. Can you upload the hires run? Instructions > below > > ?From the linux command line, > Create the file you want to upload, eg, > cd $SUBJECTS_DIR > tar cvfz subject.tar.gz ./subject > Now log? into our anonymous FTP site: > ftp surfer.nmr.mgh.harvard.edu > It will ask you for a user name: use "anonymous" (no quotes) > It will ask you for a password: use "anonymous" (no quotes) > cd transfer/incoming > binary > put subject.tar.gz > Send an email that the file has been and the name of the file. > > > > On 5/21/2020 9:35 AM, Jones, Richard wrote: > > > > ????????External Email - Use Caution > > > > I ran freesurfer 7.1 with the following options:- > > > > -i ./study/T1_SAG/IM-0001-0001.dcm -FLAIR > > ./study/SAG_3D_FLAIR/IM-0001-0001.dcm -s TEST_050620 -3T ?mprage > > ?FLAIRpial ??hires ?parallel ?all > > > > The job failed, the logfile recon-all_hires.log is attached. I then > > reran the job with the same datasets but exchanged ?hires with > > ?conf2hires and used the subject ID TEST_050620c and the job completed > > successfully (the logfile for this job, recon-all_conf2hires.log, is > > also attached). Any idea what the problem is when using the ?hires > option? > > > > Thanks > > > > *Richard* > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Display Errors in Freeview
by Nils Böer 23 May '20

23 May '20

External Email - Use Caution Hello everyone, I'm new to Freesurfer and just got started. I have to analyze data which is already prepared (recon-all is already done). I can load my subjects data into freeview but when i start working on it, e.g. clicking through the slices my freeview (6.0) just freezes everytime without an error message. I can use the mouse to click or scroll through with the arrows but nothing happens on the screen anymore. Sometimes the display in freeview also starts to get gray and i can't see anything of the mri scan anymore (examples are in appendix). I'm running freesurfer 6.0.0 on a Win10 Computer with the Oracle VirtualBox using Ubuntu 18.04.4 LTS. I hope you can help me, i couldn't find anything related to this problem. Can it be related to problems with the RAM (Virtualbox is allowed to use 10GB of Ram).? Best regards, Nils -- Nils Böer Research Assistant with Bachelor Degree (WHB) *Psychology and Movement* University of Paderborn Department of Sports and Health Warburger Str. 100 33098 Paderborn Room: Sp 1.401 Email: nils.tobias94(a)gmail.com / nboeer(a)mail.uni-paderborn.de <nils.tobias94(a)gmail.com> Web: https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/ https://sug.uni-paderborn.de/department/it/ <https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/> <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virenfrei. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Re: [Freesurfer] freeview is RAM greedy in version 7.1.0
by fsbuild 23 May '20

23 May '20

External Email - Use Caution Please also let us know the version of the OS you are comparing running both the 6.0.0 and 7.1.0 release on. - R. On May 22, 2020, at 14:49, Ruopeng Wang <rpwang(a)nmr.mgh.harvard.edu> wrote:Hi Antonin,Thanks for the report. We’ll look into this.Best,RuopengOn May 22, 2020, at 2:42 PM, Antonín Škoch <ansk(a)ikem.cz> wrote:        External Email - Use Caution        Dear experts,I want to use freeview for viewing Gordon surface labels on inflated surface with custom coloring. I am using commandline likefreeview -viewport 3d -f $SUBJECTS_DIR/fsaverage/lh.inflated:label=L_Auditory_10.label:label_color=255,191,0:label=L_Auditory_11.label:label_color=255,140,0....etc (the commandline contains 161 labels)I observe that freeview in version 7.1.0 consumes much more RAM than in version 6.0, using identical command line. The difference is enormous: While in version 6.0 freeview consumes 1.5 GB RAM to successfully display all labels, freeview in version 7.1.0 consumes all memory available on the server (32 GB RAM) while only about 30 labels are actually loaded (then server start to swap and I am forced to kill freeview process).Are you aware of such behaviour?Regards,Antonin Skoch_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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freeview is RAM greedy in version 7.1.0
by Antonín Škoch 22 May '20

22 May '20

External Email - Use Caution Dear experts, I want to use freeview for viewing Gordon surface labels on inflated surface with custom coloring. I am using commandline like freeview -viewport 3d -f $SUBJECTS_DIR/fsaverage/lh.inflated:label=L_Auditory_10.label:label_color=255,191,0:label=L_Auditory_11.label:label_color=255,140,0....etc (the commandline contains 161 labels) I observe that freeview in version 7.1.0 consumes much more RAM than in version 6.0, using identical command line. The difference is enormous: While in version 6.0 freeview consumes 1.5 GB RAM to successfully display all labels, freeview in version 7.1.0 consumes all memory available on the server (32 GB RAM) while only about 30 labels are actually loaded (then server start to swap and I am forced to kill freeview process). Are you aware of such behaviour? Regards, Antonin Skoch

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Freesurfer 7.1 hires error
by Jones, Richard 22 May '20

22 May '20

External Email - Use Caution I ran freesurfer 7.1 with the following options:- -i ./study/T1_SAG/IM-0001-0001.dcm -FLAIR ./study/SAG_3D_FLAIR/IM-0001-0001.dcm -s TEST_050620 -3T -mprage -FLAIRpial -hires -parallel -all The job failed, the logfile recon-all_hires.log is attached. I then reran the job with the same datasets but exchanged -hires with -conf2hires and used the subject ID TEST_050620c and the job completed successfully (the logfile for this job, recon-all_conf2hires.log, is also attached). Any idea what the problem is when using the -hires option? Thanks Richard

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Re: [Freesurfer] Group Analysis Covariates
by Hua, Jessica 22 May '20

22 May '20

External Email - Use Caution I just tried the revised code, and it gave me the adjusted values for each cluster by group. Is there a way to get covariate adjusted values for each participant? --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Friday, May 22, 2020 10:09 AM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer Digest, Vol 195, Issue 54 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Freesurfer 7.1 hires error (Douglas N. Greve) 2. Re: question on partial volume correction (Barletta, Valeria) 3. Re: question on partial volume correction (Douglas N. Greve) 4. Re: Group Analysis Covariates (Hua, Jessica) 5. Re: Group Analysis Covariates (Douglas N. Greve) 6. Re: mris_register intermediate results display (Chris Adamson) 7. Open Postdoctoral Scholar Position (Neva M Corrigan) 8. Re: Infant Freesurfer: infant_recon_all error (Hoopes, Andrew) 9. Re: circular/cyclic color map for polar data in freeview {Disarmed} (Caspar M. Schwiedrzik) 10. OHBM Brainhack registration is open! (Remi Gau) 11. FW: Motion correction files contain 0 0 0 1 (Camerino, I.L. (Ileana)) ---------------------------------------------------------------------- Message: 1 Date: Thu, 21 May 2020 12:11:55 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Freesurfer 7.1 hires error To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <9eaf8c24-3b80-eb34-7cd0-09080c152b03(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" I don't know what is wrong. Can you upload the hires run? Instructions below From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log? into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file. On 5/21/2020 9:35 AM, Jones, Richard wrote: > > ????????External Email - Use Caution > > I ran freesurfer 7.1 with the following options:- > > -i ./study/T1_SAG/IM-0001-0001.dcm -FLAIR > ./study/SAG_3D_FLAIR/IM-0001-0001.dcm -s TEST_050620 -3T ?mprage > ?FLAIRpial ??hires ?parallel ?all > > The job failed, the logfile recon-all_hires.log is attached. I then > reran the job with the same datasets but exchanged ?hires with > ?conf2hires and used the subject ID TEST_050620c and the job completed > successfully (the logfile for this job, recon-all_conf2hires.log, is > also attached). Any idea what the problem is when using the ?hires option? > > Thanks > > *Richard* > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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missing files in he v6 fsaverage on the Martinos Center network
by Douglas N. Greve 22 May '20

22 May '20

Sorry, I accidentally deleted some files from the v6 fsaverage located on the Martinos Center network. They have been restored, but it might have caused your recon-all process to fail if you had one running last night. Have a good weekend doug

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qcache error
by Wang, Lily 22 May '20

22 May '20

Hi FreeSurfer team, I am trying to run qcache but it is exiting with errors because it is not able to find files in the fsaverage/surf directory. I looked in $FREESURFER_HOME/subjects/fsaverage and there is indeed not a surf folder. Should I use one of the other directories like fsaverage3? Thanks, Lily

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Permutation Simulation Question
by Purcell, Juliann 22 May '20

22 May '20

External Email - Use Caution Hello FreeSurfer Experts, When we specify the number of spaces in running permutation simulation (i.e., 2spaces or 3spaces), does the program use a Bonferroni adjustment to correct? I’ve seen a couple references to Bonferroni correction in the wiki pages related to simulation, but I wasn’t sure how that fit in with the simulation. Thank you for clarifying! Best, Juliann Purcell, MSc Doctoral Candidate Medical/Clinical Psychology Doctoral Program University of Alabama at Birmingham Department of Psychology juliannp(a)uab.edu<mailto:juliannp@uab.edu>

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FW: Motion correction files contain 0 0 0 1
by Camerino, I.L. (Ileana) 22 May '20

22 May '20

External Email - Use Caution From: "Camerino, I.L. (Ileana)" <I.Camerino(a)psych.ru.nl> Date: Friday, 22 May 2020 at 14:27 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: Motion correction files contain 0 0 0 1 Dear Freesurfer developpers, I performed tractography analyses by using tracula implemented in freesurfer version 6.0. I am performing the quality check as suggested in: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaOutputs. The problem is that all my motion files (for all subjects) contain the same values: 0 0 0 1. I checked the archive but I could not find an answer to a similar question in there. Please could you suggest me what went wrong? is it possible to recalculate only the motion estimation without having to run again recon all? Thank you in advance Ileana Camerino PhD candidate Donders Institute for Brain, Cognition and Behaviour Centre for Cognition

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Freesurfer May 2020