Freesurfer September 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
165 discussions

mri_segstats quetsion
by Nasiriavanaki, Zahra 04 Sep '20

04 Sep '20

Dear Freesurferers Hi I am trying to extract the BOLD signal values from a functional subcortical area. I did the below steps to make the functional thalamus ROI and then used the mri_segstats to extract the BOLD signal from it. I would like to know 1-if my approach is correct? 2- should I use “lhthal3” as a mask? if so, what should I use as an input? 3-I see that the “mri_segstats” outputs one value for each voxel inside my ROI, is there a way to get one value across the whole ROI (lhthal3.nii.gz)? fslmaths 'aseg.nii.gz' -thr 10 -uthr 10 'lhthal.nii.gz' fslmaths 'lhthal.nii.gz' -mul 'sig.nii.gz' 'lhthal2.nii.gz' fslmaths 'lhthal2.nii.gz' -bin 'lhthal3.nii.gz' mri_segstats --seg aseg.nii.gz --i lhthal3.nii.gz --sfavg this.txt Thanks a lot M0na Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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Error loading custom labels
by Catherine Tallman 04 Sep '20

04 Sep '20

External Email - Use Caution Hello, After running mri_vol2label I created a custom label named lh.parahippocampal.label. When I try to load the label onto lh.pial, I receive the following error: "Could not load label from <path>". The file is saved within the path folder itself. I was wondering if there is a workaround for this issue? mri_vol2label --c mri/aparc+aseg.mgz --id 1016 --l label/lh.parahippocampal.label Thank you, Catherine -- ------------------------------------------------ Catherine Tallman, M.A. Graduate Student CNS Laboratory of Memory and Brain University of California, San Diego

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autorecon2, error MRISreadCurvature:
by James Hartzell 03 Sep '20

03 Sep '20

External Email - Use Caution Hi When running recon-all autorecon2, on a single subject with (Macbook Pro 10.15.6 (19G2021), freesurfer-darwin-macOS-7.1.0-20200511-813297b) it handles the rh.curv without a problem, but for the lh kicks out this error: /Users...$subj.../surf \n mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm $subj lh curv sulc \n Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ $subj./lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture...error: No such file or directory error: MRISreadCurvature: could not open /Users/$subj./surf/lh.curv ***WARNING!*** Some error has occurred while reading 'lh.curv'. This might be due a vertex incompatibility between the surface 'lh.smoothwm' and curv 'lh.curv'. You might be able to correct this by re-running 'mris_make_surfaces' on this dataset. Skipping this (and any remaining) curvature files. Any measurements / calcuations that depend on the curvature file will be skipped. ************* Note /Users/$subj./surf/lh.curv does exist in the subject's surf folder. I ran it twice just to be sure. I don't find an answer for the problem in the freesurfer list. Any guidance will be much appreciated! Cheers James Hartzell, PhD (2x) Donostia-San Sebatián, Spain

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how to calculate Euler number
by C.P.E. Rollins 03 Sep '20

03 Sep '20

External Email - Use Caution Dear Freesurfer Developers, It is not clear to me how to calculate the Euler number. Using mri_segstats reports something like: Computing euler number orig.nofix lheno = -18, rheno = -20 orig.nofix lhholes = 10, rhholes = 11 However, I had understood from previous comments that the Euler number should be around 2. I'm wondering which of the above numbers I could report. Thanks, Colleen

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Re: [Freesurfer] G_subcallosal region is missing
by Marina Fernández 03 Sep '20

03 Sep '20

External Email - Use Caution Hi Doug, I sent you the images attached to the email and also through FTP File Exchange. Thank you for your attention. Best regards, Marina > ____________________________________________ > Douglas N. Greve > I'm still not understanding what is happening. Can you send three pics of > the inflated surface of same location, one with cortex.label, one with > aparc.annot, and one with aparc.a2009s.annot? Also, please remember to > include previous emails so that I have context, thanks > > On 9/3/2020 9:55 AM, Marina Fernández wrote: External Email - Use Caution Sorry for the misunderstanding Doug . I have checked the lh.aparc.annot on the surface and there is no G_subcallosal label in these subjects. In that region are the G_and_S_cingul-Ant label / S_pericallosal labels. On the other hand, the surface appears normal. What do you recommend us to do? Thank you in advance. Marina. Douglas N. Greve <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Wed, 02 Sep 2020 10:31:13 -0700 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> Sorry, I meant to look on the surface and see if the label is there and what the lh.aparc.annot looks like there On 9/2/2020 11:05 AM, Marina Fernández wrote: External Email - Use Caution Hi Doug, When I load the volume aparc.a2009s+aseg.mgz in a subject without the G_subcallosal region in the lh.aparc.a2009s.stats file, I can see that in the other hemisphere (right in this case) there is G_subcallosal while in the left hemisphere this contralateral region is filled by the lh_S_suborbital region. So, it's covered by another label. What should we do? Best wishes, Marina ---------------------------------------------------------------------------------------------------------------------------- Douglas N. Greve < https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from… > Wed, 02 Sep 2020 07:23:58 -0700 < https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date… > Does the cortex label cover it? What does the aparc look like in that area? On 9/2/2020 6:09 AM, Marina Fernández wrote: External Email - Use Caution Dear experts, I have noticed that some subjects don't show the G_subcallosal region in the *h.aparc.a2009s.stats file. Do you know why is this happening? Is there a way to fix it? Thank you in advance. Best regards, Marina _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.edu https://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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Re: [Freesurfer] G_subcallosal region is missing
by Marina Fernández 03 Sep '20

03 Sep '20

External Email - Use Caution Doug, I sent you the pictures. Thank you for your attention. ____________________________________________ > > I'm still not understanding what is happening. Can you send three pics of > the inflated surface of same location, one with cortex.label, one with > aparc.annot, and one with aparc.a2009s.annot? Also, please remember to > include previous emails so that I have context, thanks > > On 9/3/2020 9:55 AM, Marina Fernández wrote: External Email - Use Caution Sorry for the misunderstanding Doug . I have checked the lh.aparc.annot on the surface and there is no G_subcallosal label in these subjects. In that region are the G_and_S_cingul-Ant label / S_pericallosal labels. On the other hand, the surface appears normal. What do you recommend us to do? Thank you in advance. Marina. Douglas N. Greve <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Wed, 02 Sep 2020 10:31:13 -0700 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> Sorry, I meant to look on the surface and see if the label is there and what the lh.aparc.annot looks like there On 9/2/2020 11:05 AM, Marina Fernández wrote: External Email - Use Caution Hi Doug, When I load the volume aparc.a2009s+aseg.mgz in a subject without the G_subcallosal region in the lh.aparc.a2009s.stats file, I can see that in the other hemisphere (right in this case) there is G_subcallosal while in the left hemisphere this contralateral region is filled by the lh_S_suborbital region. So, it's covered by another label. What should we do? Best wishes, Marina ---------------------------------------------------------------------------------------------------------------------------- Douglas N. Greve < https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from… > Wed, 02 Sep 2020 07:23:58 -0700 < https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date… > Does the cortex label cover it? What does the aparc look like in that area? On 9/2/2020 6:09 AM, Marina Fernández wrote: External Email - Use Caution Dear experts, I have noticed that some subjects don't show the G_subcallosal region in the *h.aparc.a2009s.stats file. Do you know why is this happening? Is there a way to fix it? Thank you in advance. Best regards, Marina _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.edu https://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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Re: [Freesurfer] G_subcallosal region is missing
by Marina Fernández 03 Sep '20

03 Sep '20

External Email - Use Caution Sorry for the misunderstanding Doug . I have checked the lh.aparc.annot on the surface and there is no G_subcallosal label in these subjects. In that region are the G_and_S_cingul-Ant label / S_pericallosal labels. On the other hand, the surface appears normal. What do you recommend us to do? Thank you in advance. Marina.

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tkregister2 deprecated for FS7.1?
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 02 Sep '20

02 Sep '20

Hi FS devs, I am following https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview? as a tutorial to fix the bad talaiarch file I have. I know that tkmedit is deprecated, but I was wondering if tkregister2 is too. If so, I was wondering what software I would use (or commands, I assume using freeview) since that page still refers to tkregister2. Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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midline to cut the brain stem into Left and Right
by 刘梦醒 02 Sep '20

02 Sep '20

External Email - Use Caution Hi Freesurfer group, For some reason, I have to use the left and right brain stem separately. I wonder if there is one way to have a midline, to cut the brain stem into Left and Right? Many thanks, Mengxing

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Re: [Freesurfer] G_subcallosal region is missing
by Marina Fernández 02 Sep '20

02 Sep '20

External Email - Use Caution Hi Doug, When I load the volume aparc.a2009s+aseg.mgz in a subject without the G_subcallosal region in the lh.aparc.a2009s.stats file, I can see that in the other hemisphere (right in this case) there is G_subcallosal while in the left hemisphere this contralateral region is filled by the lh_S_suborbital region. So, it's covered by another label. What should we do? Best wishes, Marina ---------------------------------------------------------------------------------------------------------------------------- Douglas N. Greve <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Wed, 02 Sep 2020 07:23:58 -0700 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> Does the cortex label cover it? What does the aparc look like in that area? On 9/2/2020 6:09 AM, Marina Fernández wrote: External Email - Use Caution Dear experts, I have noticed that some subjects don't show the G_subcallosal region in the *h.aparc.a2009s.stats file. Do you know why is this happening? Is there a way to fix it? Thank you in advance. Best regards, Marina _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer September 2020