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30080 discussions

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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Recon-all for multiple cases
by Loong, Spencer 21 Jun '21

21 Jun '21

External Email - Use Caution Hello FreeSurfer specialists, I am new to FreeSurfer and I am trying to learn how to run the basic recon-all command for multiple subjects at once. Could someone help me with what the command would look like to run a folder full of .nii files (e.g., 01.nii, 02.nii, 03.nii, etc). If I only have 8 cores, am I limited to running 8 cases per command, or can I include all of the cases (40) in the command? I’ve run the command for single cases successfully, now I would like set it and forget it. Your help is greatly appreciated, thank you! Spencer Loong Doctoral Student | Clinical Psychology Department of Psychology Loma Linda University SLoong(a)llu.edu CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential and privileged information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please notify me immediately by replying to this message and destroy all copies of this communication and any attachments. Thank you.

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Problem to run recon-all in one subject
by Rosalia Dacosta Aguayo 21 Jun '21

21 Jun '21

External Email - Use Caution Dear Freesurfer's experts I am trying to run recon-all -all in a subject and it seems there is a problem I do not know how to solve. rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ recon-all -s sub-001_ses-BSL -i /home/rosalia/Desktop/ARTICO/sub-001_ses-BSL_T1w -T2 /home/rosalia/Desktop/ARTICO/sub-001_ses-BSL_T1w -T2pial -all *ERROR: cannot find /home/rosalia/Desktop/ARTICO/sub-001_ses-BSL_T1w* Linux rosalia-Lenovo-Y520-15IKBN 4.10.0-40-generic #44~16.04.1-Ubuntu SMP Thu Nov 9 15:37:44 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-001_ses-BSL exited with ERRORS at Mon 21 Jun 16:45:13 CEST 2021 For more details, see the log file *(there is no log file created)* To report a problem, see http://secure-web.cisco.com/1fl8R1eHZCuzU6FCHJEl-s4FAaPFJk5v8HULKxGhhH_IJIs… rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ cd ARTICO *rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/ARTICO $ ls* fsaverage sub-001_ses-BSL_T2w.nii sub-003_ses-BSL_T1w.nii sub-001_ses-BSL_T1w.nii sub-003_ses-BSL sub-003_ses-BSL_T2w.nii rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/ARTICO $ Any idea would be very appreciated. Kind regards, Rosie

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Issues with recon-all hanging
by Michael Datko 21 Jun '21

21 Jun '21

External Email - Use Caution Hello, I have been collecting data on a 7T scanner, with functional EPI data collected with 1.5mm voxels, and I have been having an issue with some of our data where recon-all just hangs after producing only a small amount of outputs. For instance, it might get to a point where it has generated 5-10 of the “lh” left hemisphere outputs in the surf folder, and then appears as if it continues to run for hours or days but no other outputs get produced and eventually the process times out and quits. I estimate that this happens for about 5-10% of the participants we have collected so far. If it doesn’t work for a particular participant, it will do the same thing again if I delete their temporary working folder and any outputs and try to run again from scratch. This is not happening with data from the same participants collected from a 3T scanner with 3mm EPI voxels, with recon-all run at 2mm. The only difference is the resolution of the data and therefore the resolution at which we are running recon-all. Our 7T functional EPI data is collected at 1.5mm resolution, so for those scans we run recon-all at 1mm resolution. Do you have any advice for how to get these participant’s data to finish with recon-all at 1mm? Thank you, Mike Datko

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Research Assistant Position in ECoG Lab (New York)
by Mishra, Akash 21 Jun '21

21 Jun '21

External Email - Use Caution Dear all, The human intracranial EEG (iEEG/ECoG) Laboratory for Human Brain Mapping at the Feinstein Institutes for Medical Research – Hofstra Northwell School of Medicine is looking for one research assistant with earliest start date in July 2021. The successful candidate will help with the lab’s research into (1) improving the identification of functional and pathological brain regions in individuals suffering from epilepsy, (2) the neural mechanisms of cognition, and (3) characterization of macroscale human brain networks. The lab works exclusively with patients being evaluated for epilepsy surgery using methods such as invasive stereo EEG and electrocorticography recordings (iEEG, ECoG), anatomical MRI, fMRI, DTI, and direct electrical brain stimulation. The responsibilities will include assisting with the collection and analysis of the aforementioned data, project management, assistance with preparing progress reports and grant applications, and helping to present lab findings at conferences and in journals. In addition, if there is interest, the RA will have her/his own scientific project with dedicated time to work on it. Past research assistants in the lab have presented their work at clinical and basic research conferences, co-authored lab publications, and are working on first author publications. They have gone on to medical schools or PhD programs after spending 1-3 years in the lab. This unique position will expose the successful applicant to basic and clinical neuroscience as well as neurosurgery, neurology, and neuropsychology. The location of the institute allows living either in the suburban neighborhoods of Long Island, or in vibrant Brooklyn or Queens. Some employees also commute from Manhattan. It is a great opportunity for recent post-bacs interested in medical school or graduate school in neuroscience/biomedical engineering. ------------- Qualifications ------------- Minimum: -B.A./B.S./B.E. in an appropriate discipline (e.g., neuroscience, psychology, biomedical engineering, computer science, physics) -1 year commitment Desirable: -Prior experience working with neuroimaging, EEG/MEG, or brain stimulation data -Previous experience working with patients -Previous work in a research laboratory that shows evidence of independent scholarship, problem solving, and motivation -Experience with at least one programming language (MATLAB, R, or Python) and statistical analyses -2-year commitment preferred For more information about the position please send your CV along with your questions to Drs. Stephan Bickel (sbickel(a)northwell.edu<mailto:sbickel@northwell.edu>) and Ashesh Mehta (amehta.northwell.edu<http://secure-web.cisco.com/1EUBMRvU22CDa5zzZqplYWfCju5FtyqFJQdEYK6ame8M6ox…>). We are looking forward to hearing from you! The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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