Freesurfer

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17 participants
30086 discussions

the -label flag in mri_cnr
by Pradyumna Bharadwaj 27 May '20

27 May '20

External Email - Use Caution Hello! I had a couple of questions about how mri_cnr computes the contrast to noise ratio. From previous posts, a command such as mri_cnr $FREESURFER_HOME/subjects/bert/surf $FREESURFER_HOME/subjects/bert/mri/norm.mgz gives the lh cnr, rh cnr, and total cnr for bert. 1) What exactly is happening when you reference the /surf directory here? 2) Are the CNR values for the norm.mgz volume being computed by using the lh white + lh pial; and rh white + rh pial surfaces? 3) Are the subcortical gm structures somehow involved in this calculation as well? I'm asking question 3 because when you add a -label $FREESURFER_HOME/subjects/bert /label/lh.cortex.label $FREESURFER_HOME/subjects/bert/label/rh.cortex.label the lh cnr, rh cnr, and total cnr values that you get are now different. The outputs for bert for each case is as follows (FreeSurfer v6 bert was used here): 1) *With /surf alone* white = 96.6+-6.0, gray = 75.7+-13.5, csf = 55.3+-16.6 gray/white CNR = 1.983, gray/csf CNR = 0.907 *lh CNR = 1.445* white = 96.4+-6.0, gray = 76.0+-13.3, csf = 55.6+-16.2 gray/white CNR = 1.952, gray/csf CNR = 0.943 *rh CNR = 1.448* *total CNR = 1.446* *2) With /surf and -label * white = 96.6+-6.0, gray = 73.1+-18.9, csf = 50.8+-20.5 gray/white CNR = 1.389, gray/csf CNR = 0.644 *lh CNR = 1.016* white = 96.4+-6.0, gray = 73.4+-18.8, csf = 51.0+-20.3 gray/white CNR = 1.353, gray/csf CNR = 0.652 *rh CNR = 1.002* *total CNR = 1.009* Any inputs or thoughts on this matter are greatly appreciated! Thanks, Prad

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Thalamic Segmentation of Post Contrast MRI
by barış genç 26 May '20

26 May '20

External Email - Use Caution Dear FreeSurfer Experts, I have a data set (control and patients) that has 3DT1 , acquired on 3 T Philips Achieva scanner after post contract (Gadolinium). Can I use his data set to measure the thalamic nuclei segmentation or amygdala segmentation? Is gadolinium can interferes results? Any suggestions will be great.

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BIDS Derivatives final request for comments
by Franklin Feingold 25 May '20

25 May '20

External Email - Use Caution The BIDS community is preparing to merge the Common Derivatives extension. The updated draft is available for review at https://bids-specification.readthedocs.io/en/common-derivatives/, and comments and suggestions may be submitted on GitHub at https://github.com/bids-standard/bids-specification/pull/265. The scope of this extension is establishing a set of common principles for organizing derivative datasets, dataset-level metadata, and naming conventions for minimally preprocessed files. Additionally, some common imaging derivatives (e.g., brain masks) have been specified. More detailed modality-specific derivatives are scheduled for inclusion in the next few months. The final review process entails a minimum of one week for public comment, with a possibility of extension for unresolved discussion. Once public comments are concluded, there will be a one week freeze, during which only critical issues will be considered. (For more details on the release protocol, see https://github.com/bids-standard/bids-specification/blob/master/Release_Pro….) We look forward to hearing your feedback! Franklin

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Re: [Freesurfer] Display Errors in Freeview
by fsbuild 25 May '20

25 May '20

External Email - Use Caution Hello Nils, The first thing to check would be the video memory - I would try to give it the maximum. Another thing to check if that does not help is the CPU's.  You could try increasing it from say 1 to 2 CPU's if you have a 4 core machine. Take a look at the instructions we post for setting up a VM (and we also have an Ubuntu VM to download with FS 6 and 7 on it) - see,https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67 -R. On May 23, 2020, at 14:16, Nils Böer <nils.tobias94(a)gmail.com> wrote:        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 BöerResearch Assistant with Bachelor Degree (WHB) Psychology and MovementUniversity of PaderbornDepartment of Sports and HealthWarburger Str. 10033098 PaderbornRoom: Sp 1.401Email: nils.tobias94@gmail.com / nboeer@mail.uni-paderborn.deWeb: https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/         https://sug.uni-paderborn.de/department/it/Virenfrei. www.avast.com<Freeview display error and frozen.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] circular/cyclic color map for polar data in freeview
by Devavrat Vartak 24 May '20

24 May '20

External Email - Use Caution Hi, Yes, it remains linear i.e it does not warp around. I am trying to display my theta (polar) values, and a circular map will help. Additionally, I am trying to determine why my distribution of data (in freeview) seems different compared to when I just plot my theta(polar) as a histogram. Thank you! (Apologies, if this reply doesn't reach the intended thread) Cheers, DV On Tue, May 19, 2020 at 7:27 PM <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > 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. Freeview on debian (Gian Marco Duma) > 2. Uploading fs7.1 to hms o2 cluster > (Zeng, Victor (BIDMC - Keshavan - Psychiatry)) > 3. Re: Volume timeseries to native and fsaverage (?zen? ta?k?n) > 4. Re: FREESURFER-7.1: recon-all exited with error "ERROR: > cannot find or read transforms/talairach.m3z" (Safi Ullah .) > 5. circular/cyclic color map for polar data in freeview > (Devavrat Vartak PhD) > 6. Re: Freeview on debian (fsbuild) > 7. Re: Freesurfer Digest, Vol 195, Issue 47 (Douglas N. Greve) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 19 May 2020 18:14:38 +0200 > From: Gian Marco Duma <gianmarco.duma(a)phd.unipd.it> > Subject: [Freesurfer] Freeview on debian > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CABaZGscZTrMVq2AVhahXuXgwiHKgwTfrPe= > ywxLiqitz_3+qhg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hi everyone, I have a problem with freeview. My university created for me a > virtual machine in a small analysis cluster. Unfortunately, they installed > Debian 4.19.98. I read that freeview has some problems with Debian, and in > fact I am not able to open it. Unfortunately I need to visualize the data > because we are conducting an anatomical study with patients with lesions. > All the processes I ran until now, like automatic segmentation and surface > generation like recon all, worked perfectly, but I need to visualize the > data. Do you have suggestions to solve this problem? > Thanks >

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FSFAST retinotopy output interpretation: questions {Disarmed}
by Kasia Siuda-Krzywicka 24 May '20

24 May '20

External Email - Use Caution Dear FreeSurfer community, I am running retinotopy analysis with FSFAST using: - FreeSurfer version: FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c - on Linux 4.15.0-55-generic I have only the polar angle condition, in two runs, one with positive and second with negative direction. To process the data, I followed the steps listed here: https://kylemathewson.com/retinotopy-in-freesurfercnl-protocol/#FUNC For the analysis to run, I created "dummy" eccentricity folders, as advised here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48640.html The pipeline seem to have worked (no error messages, no warnings, I enclose the analysis.info <http://mkanalysis.info/> and the selxavg.log files). I am now trying to visualize the data to check the results. In the tutorial I followed, it is recommended to view the real.nii.gz and imag.nii.gz files. You will find the screen shots of those files visualized in freeview attached. To my eyes, none of those images look like polar angle retinotopy maps. I then visualized the angle.masked file (if I understand correctly, it is the angle map masked with p=0.01 significance), you can find the screen shot attached. It also doesn't look right, more importantly - it doesn't seem to be masked by significance. I have then followed the visualization instructions from the official FreeSurfer wiki, i.e: tksurfer-sess -a rtopy.self.?h -s sessid -map angle.masked I attach the screen shot (tk_surfer_file.png). Frankly, I'm not sure what I'm looking at there :) Looking for documentation that would describe retinotopy output files, I found the selfreq.pdf file, a documentation explaining *programs for computing the amplitude and phase of the hemodynamic response at a certain frequency.* In this file I found a c shell script to visualize the processed data: #!/bin/csh -f set name = subject # put the subject’s name here set hemi = lh setenv eccendir eccen setenv polardir polar 4 #setenv patch occip.patch.flat setenv revpolarflag 1 setenv rgbname eccenthinmot setenv fthresh 0.4 setenv fslope 1.3 setenv fmid 0.8 setenv angle_offset 0.77 setenv noexit tksurfer -$name $hemi I adjusted this script to my environment and run it on my machine. It doesn't work because it's missing the following input files: sigf-lh.w sig2-lh.w sig3-lh.w Indeed, those files do not exist in my folders. Does it mean that I made a mistake somewhere in the pipeline? Should those files be in my folders? To sum up, these are my questions: 1) Do the enclosed maps seem alright to you? 2) If not, do you have any idea at which processing stage there was an error? Or is it just a visualisation issue? 3) If this is a visualization error, how should I visualize the angle maps in freeview? Specifically, what output files should I use for this visualization? More specifically, what commands should I use to visualize these output files? For your information, these are my output files in the retino.lh/polar folder: angle.masked.nii.gz cesvar.nii.gz fsig.nii.gz mc.sig.dat angle.nii.gz cesvarpct.nii.gz imag.nii.gz minsig.nii.gz cesmag.nii.gz cwmap-imag.nii.gz iminsig.nii.gz real.nii.gz cesmagpct.nii.gz cwmap-real.nii.gz mag.nii.gz sig.nii.gz ces.nii.gz efficiency.dat mc.ces.dat z.nii.gz cespct.nii.gz F.nii.gz mc.minsig.dat 4) what do the imag.nii and real.nii maps correspond to? I believe they represent the real and imaginary component of the Fourier transform, but how do I interpret it in terms of retinotopy results? I would be very grateful for any help. Take care, Kasia -- Kasia Siuda-Krzywicka, PhD Physiological Investigation of Clinically Normal and Impaired Cognition Lab Institut du Cerveau et de la Moelle Épinière 47 bd. de l’Hôpital 75013 Paris office: +33 (0)1 57 27 41 53 mobile: +33 (0)6 52 69 46 49

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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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