Freesurfer June 2021

freesurfer@nmr.mgh.harvard.edu

97 participants
140 discussions

Visualization of specific regions
by Jennifer James 23 Jun '21

23 Jun '21

External Email - Use Caution Hi FreeSurfer experts, We have used FreeSurfer version 6.0 to extract thickness values from MRI data of our subjects and then used SPSS for statistical modeling. We found significant results in the thickness of the following two regions: *lh_G&S_cingul-Mid-Ant_thickness* *lh_S_front_middle_thickness* We want to make a simple figure showing these two areas of the brain just for visualization purposes (similar to the attached figure from another paper). Could you tell us how we can make such an image in Freeview? We tried to use mri_extract_label but the figures we got are not really what we are looking for. Any help is highly appreciated! Best, Jennifer

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Calculating group-wise Dice Similarity Coefficient and corresponding surface map
by Hye Min Shin 23 Jun '21

23 Jun '21

External Email - Use Caution Hello experts, I apologize if this has been asked before- but I couldn't find a question that was similar to what I wanted to know about so I decided to ask this question(s). I am trying to calculate dice similarity coefficient (DSC) for a group of subjects and I was wondering if it is possible to calculate this on FreeSurfer. I understand that FreeSurfer has mri_compute_overlap that can compute dice coefficient but I wasn't sure if this can be done on group-level. Do I have to first calculate dice for each subject and then calculate the average dice for the subjects? Also I was wondering if there is a way to visualize group-level dice coefficient map on inflated lh/rh surface. Best, Julia Shin

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InfantFS witg segfile exiting with errors
by Fernanda Hansen P. de Moraes 22 Jun '21

22 Jun '21

External Email - Use Caution Dear FreeSurfer experts, I am trying to process some newborn subjects including the segfile. In both situations, including the mask file and using the --forceskullstrip flag I get the following error (log file attached): *lta_convert successful./home/fernanda/Documentos/dHCP/freesurfer1 ERROR: Option --noverbose unknown* This is the exact command I am running: *infant_recon_all --s sub-CC00060XX03 --age 0 --segfile sub-CC00060XX03/sub-CC00060XX03_ses-12501_desc-drawem87_space-T2w_dseg.nii.gz --forceskulltrip --force* How can I overcome this? Thank you very much. Fernanda Hansen P. de Moraes fernandahmoraes(a)gmail.com Doutoranda em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino

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Re: [Freesurfer] bias field correction and intensity normalization
by Marina Fernández 22 Jun '21

22 Jun '21

External Email - Use Caution Hi Matt, We always really appreciate your help and advice. Thank you very much for your answer, now we understand much better why it is correct not to apply this correction. Best, Marina

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Using control points for intensity normalization
by Kadwani, Manorama 22 Jun '21

22 Jun '21

Hi, I am trying to correct the white matter segmentation in the second image shown below. It doesn't include chunks of the temporal lobe with low intensity on both hemispheres. [cid:977433f0-d665-4dd2-b8a9-463c131c6d5f][cid:63b66545-8090-443e-a26d-be2b5e4c98f9] I placed many control points on every slice in the brainmask.mgz file. Then I re-ran recon-all using -autorecon2-cp argument. But the white matter volume did not grow into those regions with control points. The process completed without any errors. [cid:17cf9ce4-170e-46c3-9b8b-0fb1d5ed83e3] Any idea on how I can include those regions in white matter? I also tried to use 'mri_segment' for lowering the white matter low limit to 60. That did include some parts of the missing lobes, but also included grey matter from frontal and parietal lobes. So, that approach was not ideal. Thank you, Manorama

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External 3D View Issue
by Harriet Cornwell 22 Jun '21

22 Jun '21

External Email - Use Caution Hi Bruce, Thank you for your helpful suggestion - re-running it seems to have fixed the issue. Harriet Cornwell -----Original Message----- 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 Sent: 19 June 2021 17:00 To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 208, Issue 38 CAUTION: This email came from outside of the University. To keep your account safe, only click on links and open attachments if you know the person who sent the email, or you expected to receive this communication. Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://secure-web.cisco.com/1ESEFRVPJOXvrqrCraDs60Nf6XUlaSbTCL_Oh3P-TEbPTv… 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: External 3D View Issue (Fischl, Bruce) 2. Yeo atlas for children! (Martin Juneja) 3. Running Freesurfer in the Desktop (Rosalia Dacosta Aguayo) ---------------------------------------------------------------------- Message: 1 Date: Fri, 18 Jun 2021 17:25:18 +0000 From: "Fischl, Bruce" <BFISCHL(a)mgh.harvard.edu> Subject: Re: [Freesurfer] External 3D View Issue To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <BL0PR04MB660946EB4496CCA774BCC1F4EF0D9(a)BL0PR04MB6609.namprd04.prod.outlook.com> Content-Type: text/plain; charset="utf-8" Hi Harriet Is that a parcellation overlaid on the brain? Usually this means something was not regenerated when you reran (like the parcellation). Try just recreating it an see if it fixes your problems. Should just take a couple of min to run just the parcellation stage Cheers Bruce From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Harriet Cornwell Sent: Friday, June 18, 2021 9:54 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] External 3D View Issue External Email - Use Caution External Email - Use Caution Hello, We thought we had finished manually editing a T1 scan and so opened it in the external 3D view to perform final checks and it looks incredibly messy (see attached screenshot). Are you able to advise whether this is an issue? If so, is it possible to fix it and, if it can be fixed, how we should go about doing so? Also, do you have any idea what might have caused this to happen? Thank you in advance! Harriet Cornwell

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Alveus voxels in the hippocampus
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 22 Jun '21

22 Jun '21

?Hi, Sometimes I see empty space inside the CA1 in the FS7 hippo parcellations. These are voxels of bright intensities. Is this where the alveus is supposed to be labelled and are these brain scans that we should still be using for hippo? 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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Open PhD position - University of Oslo / Norway
by sf 22 Jun '21

22 Jun '21

External Email - Use Caution Applications are invited for a 3-4 year PhD fellowship available at the Department of Psychology, University of Oslo, Norway. All details about the position and a link to the application form can be found here: https://secure-web.cisco.com/1M7SwYGwD7yvTe-flXA8JZhkQanRTNHyQIRAney7-l-8i7… The position is open for candidates with a Master’s degree or equivalent in Psychology, Cognitive Neuroscience, Biology, or other relevant areas. The successful applicant will join the lab of Prof. Sascha Frühholz, which is part of the Section for Cognitive and Clinical Neuroscience. Our lab studies the neural foundations of emotional processing from various social and environmental signals using a variety of neuroscientific methods (fMRI, EEG, intracranial recordings, psycho-acoustic experiments, etc.). For further information about the lab, please visit https://secure-web.cisco.com/1XIcu-FoU5rESyFVtBeAsoTdcpzpBKJlUFlPo_hdYkzhSp… The appointment is a full time position available for a period of 3-4 years. Fellows who are appointed for a period of four years are expected to contribute to teaching and administration with about 25% of their working time. Teaching and administrative duties would contribute to activities of the Department of Psychology. The project aims to study the neural processes that underlie the perception and classification of emotional signals from natural and digital voices.The project mainly focuses on the use of functional magnetic resonance imaging (fMRI) to study the neural network that allows healthy humans to detect emotions in various voice signals.The project especially tries to investigate the neural interactions between the limbic and the auditory system that support the classification of emotions perceived from digital and computer-generated voices. The applicant will have the opportunity to contribute to the shaping of the research agenda. For informal inquiries and questions about the position, please get in contact: sascha.fruhholz(a)psykologi.uio.no <https://secure-web.cisco.com/1TWx0cYtCAcMV6x0X8M3IGwEWi2UMwb80IPpq9zTl5Twvm…>

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bias field correction and intensity normalization
by Marina Fernández 22 Jun '21

22 Jun '21

External Email - Use Caution Dear experts, I would like to create myelin maps calculating the T1w/T2w ratio. Should I apply bias field correction and intensity normalization (i.e., "nu correction" in the Freesurfer pipeline) to T1w and T2w images separately before calculating the T1w/T2 ratio? I applied nu correction to T1w images and worked fine but results were weird when nu correction was applied applied to T2w images. I am not sure if nu correction must only be applied to T1w images for this purpose, or if I have to modify some parameters to apply nu correction to T2w images. Thank you in advance for your help. Best, Marina

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Hippocampal Subfields/ASEG
by Panayiota Ventura 21 Jun '21

21 Jun '21

External Email - Use Caution Hello, I have a couple of questions concerning the hippocampal subfield extractions as well as the hippocampus extraction included in ASEG. I have looked around and tried to find as much information as possible about the two but I can't seem to find a clear answer. I'm hoping someone can help me out with this. 1. In the hippocampal subfields extraction, one of the labels is called "whole hippocampus". I would like to know what exactly is meant by that? In other words, what hippocampal regions are included in this "whole hippocampus" label? 2. The ASEG atlas also includes a hippocampus extraction. However this value is different from that of the hippocampal subfield extraction. What hippocampal regions are being included in this hippocampal extraction. 3. Which of the two would be a better estimate of hippocampal volume? Thank you for your time and help! Kind regards, Yiota Ventura

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Freesurfer June 2021