Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30093 discussions

Regarding: mris_label2annot
by Dr Sampada Sinha 06 Feb '17

06 Feb '17

Dear freesurfer experts, I am trying to create medial temporal lobe and for that I ran the command mri_annotation2label to create ?h.entorhinal.label, ?h.temporalpole.label and ?h.parahippocampal.label from fsaverage and stored these labels in labels.?h directory. After this I ran mris_label2annot, taking cue from page https://surfer.nmr.mgh.harvard.edu/fswiki/mris_label2annot. My command line is the following (fsaverage has been linked to my subject directory: rmbp:AD Sampada$ mris_label2annot --s fsaverage --h lh --ctab /Applications/freesurfer/subjects/bert/label/aparc.annot.ctab --a myaparc --l ./labels_lh/lh.temporalpole.label --l ./labels_lh/lh.parahippocampal.label --l ./labels_lh/lh.entorhinal.label --nhits nhits.mgh However, it comes with following error *Writing annot to /Users/Sampada/Desktop/AD/fsaverage/label/lh.myaparc.annot* *could not write annot file /Users/Sampada/Desktop/AD/fsaverage/label/lh.myaparc.annot* *Permission denied* Will you please let me know how to fix this problem . I can see its a permission error but don't know how to overcome it. Thanks for your help Kind regards, Sampada -- Sampada Research medical scientist (B) Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 , Uttar Pradesh India

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T2 and control points
by miracooloz＠gmail.com 06 Feb '17

06 Feb '17

2 1

Problem with using tksurfer to take snap shot with .tcl
by Hao wen 06 Feb '17

06 Feb '17

Hello: FS experts: I am now integrating to use tksurfer to take snapshot from command line automatically, and my command is like this: ``` cmd = "tksurfer %s %s inflated -tcl %s" % (subject, hemi, os.path.join(os.path.dirname(sys.argv[0]), "snap_tksurfer.tcl")) ``` so i use -tcl to define the behavior of tksurfer, but I go t a bug inside the tickle script, ##curv puts "shitaaaaa" puts stdout [pwd] puts stdout $env(SUBJECT_NAME) puts [trace vinfo lablpth] read_binary_curv puts "shittttttttt!!!, has bug here" I debug it and found that it can not really run this command: read_binary_curv, before, it can take some snapshots and save it to be rgb format, and i will also give you the output from the terminal: Successfully parsed tksurfer.tcl shitaaaaa /Users/junhao.wen/Hao/Dataset/test-data/recon-alled-result-1sub/analysis-series-default/subjects/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional sub-PREVDEMALS0010001BE_ses-M0 subject is sub-PREVDEMALS0010001BE_ses-M0 hemi is lh surface is inflated surfer: current subjects dir: /Users/junhao.wen/Hao/Dataset/test-data/recon-alled-result-1sub/analysis-series-default/subjects/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/junhao.wen/Hao/Dataset/test-data/recon-alled-result-1sub/analysis-series-default/subjects/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional checking for nofix files in 'inflated' Reading image info (/Users/junhao.wen/Hao/Dataset/test-data/recon-alled-result-1sub/analysis-series-default/subjects/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/sub-PREVDEMALS0010001BE_ses-M0) Reading /Users/junhao.wen/Hao/Dataset/test-data/recon-alled-result-1sub/analysis-series-default/subjects/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/sub-PREVDEMALS0010001BE_ses-M0/mri/orig.mgz surfer: Reading header info from /Users/junhao.wen/Hao/Dataset/test-data/recon-alled-result-1sub/analysis-series-default/subjects/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/sub-PREVDEMALS0010001BE_ses-M0/mri/orig.mgz surfer: vertices=98465, faces=196926 surfer: single buffered window surfer: tkoInitWindow(sub-PREVDEMALS0010001BE_ses-M0) setting percentile thresholds (-1.00, 0.00, 0.00) surfer: using interface /Applications/freesurfer/tktools/tksurfer.tcl tksurfer: run tcl script: /Users/junhao.wen/Hao/Project/clinica_realted/CAPS_qa_clinica/snap_tksurfer.tcl Reading /Applications/freesurfer/tktools/tkm_common.tcl Reading /Applications/freesurfer/tktools/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/tktools/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... I will also attach you the tcl file, any suggestion will be appreciated:) PS: I know that FS right now recommand us to use freeview, do you have the similar behavior like using tcl file to define the behavior of freeview to take the snapshots??? Good day Hao

3 3

freeview problem with w-file overlay
by Björn Herrmann 06 Feb '17

06 Feb '17

Dear list, I would like to use freeview to display my activations patterns. I source-localized MEG data in matlab using the freesurfer standard brain as a source space. I saved the source localization as a w-file, that is, as an overlay. I used to display the overlay in tksurfer, but I cannot adjust the colorbar thresholds using my keyboard in tksurfer (probably due to new linux and freesurfer versions). I read in an older post about that problem and it was suggested that freeview might be a better option. Unfortunately, I cannot load my w-files in freeview (similar problems as in the post below). Since I only work in matlab up to the point when I would like to save my data for plotting with freesurfer (e.g., freeview), I do not know how else (if not as a w-file) I could save my activations to display them as an overlay. I do not have volume data, I only have a vector of activation values corresponding to the vertices. Is there a different way to save my data in matlab so that I can display them as an overlay onto a surface in freeview? I would be thankful for any input. Best, Bjorn Older post below: Re: [Freesurfer] Loading .w surface overlay in Freeview can you use vol2surf to generate a .mgz/.mgh file instead? We have deprecated the use of .w files On Thu, 13 Aug 2015, Ivan Alvarez wrote: > Dear all, > > I am wondering if there is a facility for loading .w overlay files in > Freeview? In the surface section of the GUI, the overlay tab is for > volumetric files (.mgz, .nii, etc.). In the command line, the overlay > option fails - for example: > > freeview -f /path/to/lh.inflated:overlay=/path/to/overlay.w > > returns this error message in the GUI: > > "Failed to load surface overlay. mri_read()" > > and this one in the command line: > > : couldn't determine type of file /path/to/overlay.w" > > The .w file in question was produced with mri_vol2surf. Any suggestions? > > ---------- Björn Herrmann Brain and Mind Institute The University of Western Ontario London, Ontario N6A 5B7 Canada email: herrmann.b(a)gmail.com web: www.bjoernherrmann.com

3 2

infant brain segmentation
by Alena Piovar 06 Feb '17

06 Feb '17

Dear Freesurfer experts, I was curious whether there is any update regarding infant brain segmentation? Are the atlases going to be released anytime soon? Looking forward to your response. Best Alena

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R: Re: R: Re: Hipposubfields in FreeSuerferColorLUT.txt
by stdp82＠virgilio.it 06 Feb '17

06 Feb '17

Thank you very much.Could you provide me any suggestion to extract CA1 left or CA1 right?And how can I use them in FAST? By codes?Regards,Stefano ----Messaggio originale---- Da: "Iglesias Gonzalez, Eugenio" <e.iglesias(a)ucl.ac.uk> Data: 6-feb-2017 17.42 A: "stdp82(a)virgilio.it"<stdp82(a)virgilio.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: Hipposubfields in FreeSuerferColorLUT.txt You would extract CA1 left from lh.hippoSfLabels-T1.v10.mgz and CA1 right from rh.hippoSfLabels-T1.v10.mgz (assuming you’ve used T1s to segment the subfields). Cheers, /E Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 6 Feb 2017, at 16:17, stdp82(a)virgilio.it wrote: Thanks Eugenio for your response. My apologies but this matter is unclear to me. If I would use results for FS-FAST how I can identify for example CA1 right from CA1 left? Additionally, for enthorinal which is the correct code in FAST? Stefano ----Messaggio originale---- Da: "Iglesias Gonzalez, Eugenio" <e.iglesias(a)ucl.ac.uk> Data: 6-feb-2017 15.54 A: "stdp82(a)virgilio.it"<stdp82(a)virgilio.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] Hipposubfields in FreeSuerferColorLUT.txt Ciao Stefano, The results for the left and right hippocampi are in different files, so there’s no ambiguity despite the fact that they indeed share the same label codes. Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 6 Feb 2017, at 13:18, stdp82(a)virgilio.it wrote: Hi list, within FreeSuerferColorLUT.txt, do the numbers between 200-226 descrived the hippo-subfield outputs? Additionally, how can I obtain separate right and left masks? Thanks Stefano _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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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R: R: Re: FS-FAST 6.0
by stdp82＠virgilio.it 06 Feb '17

06 Feb '17

Thanks I wonder whether the followed link is still timely. http://surfer.nmr.mgh.harvard. edu/fswiki/FsFastFunctionalConnectivityWalkthrough Regards Stefano >----Messaggio originale---- >Da: stdp82(a)virgilio.it >Data: 6-feb-2017 22.24 >A: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> >Ogg: [Freesurfer] R: Re: FS-FAST 6.0 > >Thanks I wonder r whether this link is still timely. >Regards >Stefano > > >>----Messaggio originale---- >>Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>Data: 6-feb-2017 18.52 >>A: <freesurfer(a)nmr.mgh.harvard.edu> >>Ogg: Re: [Freesurfer] FS-FAST 6.0 >> >>Not much has changed outwardly. It uses the FS-generated brainmask >>instead of running a skull stripping program on the functionals, and it >>supports CVS (combined-volume-surface) registration for subcortical >>analysis. Note sure what you mean by the second question. >> >> >>On 02/06/2017 07:54 AM, stdp82(a)virgilio.it wrote: >>> Hi list, >>> I wonder which are the main changes in FS-FAST 6.0? >>> The links used in previous version are still useful? >>> >>> Thanks >>> Stefano >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>-- >>Douglas N. Greve, Ph.D. >>MGH-NMR Center >>greve(a)nmr.mgh.harvard.edu >>Phone Number: 617-724-2358 >>Fax: 617-726-7422 >> >>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >>_______________________________________________ >>Freesurfer mailing list >>Freesurfer(a)nmr.mgh.harvard.edu >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >>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. >> >> > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

2 1

R: Re: FS-FAST 6.0
by stdp82＠virgilio.it 06 Feb '17

06 Feb '17

Thanks I wonder r whether this link is still timely. Regards Stefano >----Messaggio originale---- >Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >Data: 6-feb-2017 18.52 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] FS-FAST 6.0 > >Not much has changed outwardly. It uses the FS-generated brainmask >instead of running a skull stripping program on the functionals, and it >supports CVS (combined-volume-surface) registration for subcortical >analysis. Note sure what you mean by the second question. > > >On 02/06/2017 07:54 AM, stdp82(a)virgilio.it wrote: >> Hi list, >> I wonder which are the main changes in FS-FAST 6.0? >> The links used in previous version are still useful? >> >> Thanks >> Stefano >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >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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R: Re: Perirhinal 6.0 error
by stdp82＠virgilio.it 06 Feb '17

06 Feb '17

I have resolved my error in running old script Thanks Stefano >----Messaggio originale---- >Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >Data: 6-feb-2017 19.12 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] Perirhinal 6.0 error > >please send more info > > >On 02/03/2017 04:09 PM, stdp82(a)virgilio.it wrote: >> Hi, >> >> by running the mri_label2label to calculate perirhinal morphometry the >> following error occurs with FS6.0 >> >> ERROR reading sub_DIR/label/rh.perirhinal.label >> >> >> Thanks >> >> >> Stefano >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >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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Using the "Smooth Surface" tool in Freeview
by Huang, Caleb (NIH/NINDS) [F] 06 Feb '17

06 Feb '17

Hi, I'm new to Freesurfer and am still figuring out the ins and outs of cortical reconstructions. One option I've been looking into is the "Smooth Surface" tool in Freeview. It seems to make it easier to identify handles and other errors especially in subjects with significant atrophy, but I'm not sure what's the best way to use it. I did a few trial runs with various smoothing parameters, and it looks like running autorecon2-wm and autorecon2-pial with autorecon3 both eliminate the effects of the smoothing (parcellation stats don't change), while running autorecon3 alone changes all the stats other than the number of vertices and thickness averages. In particular, the surface area and gray matter volume decrease by 5-10% depending on the parameters I choose (taubin vs. standard, number of iterations, lambda/frequency cutoff), which isn't unexpected. Would you recommend using smoothing to help fix small errors and if so, what parameters would you recommend? Thanks, -Caleb

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Freesurfer