Re: [Freesurfer] increasing thickness threshold
') if i want to remove the timepoints with high motion. I run fsl_motion_outliers in order to perform scrubbing as suggested by Power et al. (2012, 2013). fsl_motion_outliers -i subject_rest_reorient.nii.gz -o DVARS --dummy=4 --dvars -s dvars_value -p dvarsimg. The DVARS indicated which frames should be ignored in the following analysis. a. So which step should i do the scrubbing if i use the following pipleline do the fcMRI processing: -skip-faln-mc-bpss-resid-fsaverage6_sm6_fsaverage4 (skip: skip 4 dummy frames; faln: slice timing, mc: motion correction; bpss: band pass; resid: regress 18 covariables including 6 motion parameters,global signal,ventral,white matter signal and their derivates ) b. How can i use the confound matrix to remove the effect of frames with high motion, just paste the confound matrix to the 18 covaribles? c. How can i check the effect of high motion frames actually be removed? Thank you for your help! Meiling -- next part -- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150801/db5778ec/attachment.html -- next part -- A non-text attachment was scrubbed... Name: Remove_motion.PNG Type: image/png Size: 113793 bytes Desc: not available Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150801/db5778ec/attachment.png -- Message: 2 Date: Fri, 31 Jul 2015 11:00:24 -0700 From: Jesse Bledsoe bleds...@msu.edu Subject: Re: [Freesurfer] increasing thickness threshold To: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Message-ID: CAL6n2hN87f3jK=sxry_tyxtuj0yqcmhmjwur1vsdfvfuia7...@mail.gmail.com Content-Type: text/plain; charset=utf-8 Hi Bruce, Thanks again. I tried the following from the command line to increase thickness estimates to 10mm but get the same error when using both mris_make_surfaces and mris_thickness: $ recon-all -expert mris_make_surfaces -max 10 Epi003 l lh.thickness ERROR: cannot find mris_make_surfaces Linux ivan 2.6.32-32-generic #62-Ubuntu SMP Wed Apr 20 21:52:38 UTC 2011 x86_64 GNU/Linux recon-all -s exited with ERRORS at Fri Jul 31 10:48:01 PDT 2015 and: $ recon-all -expert mris_thickness -max 10 Epi003 l lh.thickness ERROR: cannot find mris_thickness Linux ivan 2.6.32-32-generic #62-Ubuntu SMP Wed Apr 20 21:52:38 UTC 2011 x86_64 GNU/Linux Thank you for your help, Jesse On Thu, Jul 30, 2015 at 6:33 AM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Send Freesurfer mailing list submissions to freesurfer@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-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@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: recon-all -white does not respect wm edits (Antonin Skoch) 2. Re: wm parcellation freesurfer (Bruce Fischl) 3. randmoness flag and aseg.stats measures (Keith Harenski) 4. Increasing thickness threshold? (Jesse Bledsoe) 5. Re: Increasing thickness threshold? (Bruce Fischl) 6. Pial surface in dural sinus in Longitudinal processing (Justin McKee) 7. Re: cluster_wise correction (Meiling Li) 8. Re: dev version of mri_ca_label memory leak? (Chris Adamson) 9. FreeSurfer Courses 2015 (Charalambous, Thalis) 10. Re: FreeSurfer Courses 2015 (Christophe Destrieux) 11. Re: Repost: problem with mri_label2label - large amount of holes (Caspar M. Schwiedrzik) 12. Re: dev version of mri_ca_label memory leak? (Bruce Fischl) -- Message: 1 Date: Wed, 29 Jul 2015 18:08:34 +0200 From: Antonin Skoch a...@medicon.cz Subject: Re: [Freesurfer] recon-all -white does not respect wm edits To: freesurfer@nmr.mgh.harvard.edu Cc: a...@medicon.cz Message-ID: 20150729160834.7ad5a...@posta.medicon.cz Content-Type: text/plain; charset=us-ascii Dear Bruce, no, both ?h.orig.nofix and ?h.orig are ok (respecting my wm.mgz edits), but only ?h.white (result of mris_make_surfaces
Re: [Freesurfer] increasing thickness threshold
parcellation freesurfer To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.11.1507291223320.24...@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Hi Owais do you mean the wmparc.mgz or the aparc+aseg.mgz? You can use mris_divide_parcellation or mris_make_face_parcellation to subdivide or make an isotropic finer scale one if you want. I believe that you can then create a new aparc+aseg from one of those and then the wmparc from that to get a finer one cheers Bruce On Tue, 28 Jul 2015, Owais Syed wrote: Hi, Is it possible to increase the number of parcellations when making the aparc+aseg file? I have a high resolution MRI, and one parcellation will match every three slides, but I want a better match overall. Thanks, Owais -- Message: 3 Date: Wed, 29 Jul 2015 11:48:43 -0600 From: Keith Harenski kharen...@mrn.org Subject: [Freesurfer] randmoness flag and aseg.stats measures To: freesurfer@nmr.mgh.harvard.edu Message-ID: cagdev2u02pa+zbovgvquehm3i7k06vviafq8vg8_gavftn0...@mail.gmail.com Content-Type: text/plain; charset=utf-8 Hello, Similar to the thread below we ran several subjects through the freesurfer (v5.3.0) using the -randomess flag and noticed no differences in the volumes in aseg.stats across the runs. Is this by design? This thread ended here. Pernille, Can you send me the recon-all.log file of one of the subjects? Nick On Fri, 2009-08-21 at 15:19 +0200, Pernille Iversen wrote: * Dear Nick, ** I have now used version 4.5.0 and the -randomness flag no longer gives ** errors, however, after 10 parallel runs of a subject with the ** -randomness flag set, I observe that the stats are completely ** identical. In the logs I can see that the line setting seed for ** random number generator to 1234 is no longer there. In the earlier ** versions where the random initialisation was default I observed ** differences in the stats when I made the 10 parallel runs on the same ** subject as I have used this time - so it would seem that the random ** initialisation is not turned on when I use the flag. Can you please ** comment on this :) * * Thanks, ** Pernille* I also came across this thread separately which seems to indicate that the -randomness flag only changes the cortical measures (which were different across runs for the subjects): Hi Andreia, Then I would guess that your error comes from the fact that you didn't rerun the autorecon3 at that stage for these 2 subjects. *As the randomness flag changes the number of vertices when recreating the surfaces*, that explains the error. I'd appreciate any clarification. Thanks, Keith -- Keith Harenski Mobile MRI Manager Mobile MRI Core and Clinical Cognitive Neuroscience Laboratory The Mind Research Network 1101 Yale Blvd NE Albuquerque, NM 87106-4188 Office: 505.504.1338 | Fax: 505.272.8002 kharen...@mrn.org | www.mrn.org | www.lrri.org -- next part -- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150729/c989432e/attachment.html -- Message: 4 Date: Wed, 29 Jul 2015 12:32:29 -0700 From: Jesse Bledsoe bleds...@msu.edu Subject: [Freesurfer] Increasing thickness threshold? To: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Message-ID: CAL6n2hM0y77-povyGkSv= wo1h16nycioyp352-maxe_y3xk...@mail.gmail.com Content-Type: text/plain; charset=utf-8 Hi FreeSurfer community, I would like to see if FreeSurfer could be used to improve clinical detection of cortical dysplasia. Given that dysplasias can be several mm thicker than typical cortex, are there ways to increase the thickness thresholds to improve detection of cortex that may be up to 10mm thick? Is it possible to increase the thickness measurements beyond 5mm? freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Thank you, Jesse -- next part -- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150729/9ba33e30/attachment.html -- Message: 5 Date: Wed, 29 Jul 2015 15:35:05 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Increasing thickness threshold? To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.11.1507291534370.24...@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed yes, specify -max something biggger than 5 on the command line to mris_thickness and mris_make_surfaces (you can do this in recon-all with expert options) cheers Bruce On Wed, 29 Jul 2015, Jesse Bledsoe wrote: Hi FreeSurfer community, I would like to see if FreeSurfer could be used to improve clinical detection of cortical
Re: [Freesurfer] increasing thickness threshold
in coronal view, two quite large areas in both hemispheres at the convexity - slices 88-95 in coronal view, quite large areas at righ hemispheres at the convexity and other areas in following slices, there are quite large amount of them in this subject. Could you please look at the data to find where could be the problem? Thank you very much for all your help. Best regards, Antonin Skoch -- next part -- An HTML attachment was scrubbed... URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150729/0 a8d4c9b/attachment.html -- Message: 2 Date: Wed, 29 Jul 2015 12:25:02 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] wm parcellation freesurfer To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.11.1507291223320.24...@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Hi Owais do you mean the wmparc.mgz or the aparc+aseg.mgz? You can use mris_divide_parcellation or mris_make_face_parcellation to subdivide or make an isotropic finer scale one if you want. I believe that you can then create a new aparc+aseg from one of those and then the wmparc from that to get a finer one cheers Bruce On Tue, 28 Jul 2015, Owais Syed wrote: Hi, Is it possible to increase the number of parcellations when making the aparc+aseg file? I have a high resolution MRI, and one parcellation will match every three slides, but I want a better match overall. Thanks, Owais -- Message: 3 Date: Wed, 29 Jul 2015 11:48:43 -0600 From: Keith Harenski kharen...@mrn.org Subject: [Freesurfer] randmoness flag and aseg.stats measures To: freesurfer@nmr.mgh.harvard.edu Message-ID: cagdev2u02pa+zbovgvquehm3i7k06vviafq8vg8_gavftn0...@mail.gmail.com Content-Type: text/plain; charset=utf-8 Hello, Similar to the thread below we ran several subjects through the freesurfer (v5.3.0) using the -randomess flag and noticed no differences in the volumes in aseg.stats across the runs. Is this by design? This thread ended here. Pernille, Can you send me the recon-all.log file of one of the subjects? Nick On Fri, 2009-08-21 at 15:19 +0200, Pernille Iversen wrote: * Dear Nick, ** I have now used version 4.5.0 and the -randomness flag no longer gives ** errors, however, after 10 parallel runs of a subject with the ** -randomness flag set, I observe that the stats are completely ** identical. In the logs I can see that the line setting seed for ** random number generator to 1234 is no longer there. In the earlier ** versions where the random initialisation was default I observed ** differences in the stats when I made the 10 parallel runs on the same ** subject as I have used this time - so it would seem that the random ** initialisation is not turned on when I use the flag. Can you please ** comment on this :) * * Thanks, ** Pernille* I also came across this thread separately which seems to indicate that the -randomness flag only changes the cortical measures (which were different across runs for the subjects): Hi Andreia, Then I would guess that your error comes from the fact that you didn't rerun the autorecon3 at that stage for these 2 subjects. *As the randomness flag changes the number of vertices when recreating the surfaces*, that explains the error. I'd appreciate any clarification. Thanks, Keith -- Keith Harenski Mobile MRI Manager Mobile MRI Core and Clinical Cognitive Neuroscience Laboratory The Mind Research Network 1101 Yale Blvd NE Albuquerque, NM 87106-4188 Office: 505.504.1338 | Fax: 505.272.8002 kharen...@mrn.org | www.mrn.org | www.lrri.org -- next part -- An HTML attachment was scrubbed... URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150729/c 989432e/attachment.html -- Message: 4 Date: Wed, 29 Jul 2015 12:32:29 -0700 From: Jesse Bledsoe bleds...@msu.edu Subject: [Freesurfer] Increasing thickness threshold? To: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Message-ID
[Freesurfer] Increasing thickness threshold?
Hi FreeSurfer community, I would like to see if FreeSurfer could be used to improve clinical detection of cortical dysplasia. Given that dysplasias can be several mm thicker than typical cortex, are there ways to increase the thickness thresholds to improve detection of cortex that may be up to 10mm thick? Is it possible to increase the thickness measurements beyond 5mm? freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Thank you, Jesse ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Increasing thickness threshold?
yes, specify -max something biggger than 5 on the command line to mris_thickness and mris_make_surfaces (you can do this in recon-all with expert options) cheers Bruce On Wed, 29 Jul 2015, Jesse Bledsoe wrote: Hi FreeSurfer community, I would like to see if FreeSurfer could be used to improve clinical detection of cortical dysplasia. Given that dysplasias can be several mm thicker than typical cortex, are there ways to increase the thickness thresholds to improve detection of cortex that may be up to 10mm thick? Is it possible to increase the thickness measurements beyond 5mm? freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Thank you, Jesse ___ Freesurfer mailing list Freesurfer@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.
