Freesurfer May 2021

freesurfer@nmr.mgh.harvard.edu

97 participants
125 discussions

Recon-all error
by g.toniol＠libero.it 25 May '21

25 May '21

External Email - Use Caution Hello FreeSurfer Developers, Thank you for your work ! I am new to Freesurfer and I apologize if my question is naive but I cannot find a solution in any of the online resources. I successfully set up Freesurfer and I am now attempting to run recon-all on a .nii file ("s44891-153636-00001-00192-1.nii") on a MacOs Big Sur. To do so, I run the command below, where "S001" is the subject name and "/Users/giorgio/Documents/MATLAB/spm12/Group 0/S001/scans/struct/s44891-153636-00001-00192-1.nii " is the path to the .nii image file: ..$ recon-all -s S001 -i /Users/giorgio/Documents/MATLAB/spm12/Group 0/S001/scans/struct/s44891-153636-00001-00192-1.nii -all However, I get the following error: "ERROR: You cannot give recon-all a folder as input. It must be an image file. If you have multiple files, you need multiple -i flags. Darwin macbook-pro.home 20.4.0 Darwin Kernel Version 20.4.0: Thu Apr 22 21:46:47 PDT 2021; root:xnu-7195.101.2~1/RELEASE_X86_64 x86_64 recon-all -s S001 exited with ERRORS at Mon May 24 15:50:32 CEST 2021" My input volume is a .nii, an image file, and I copied its pathway automatically so I do not think there are mistakes in the pathway to the image: do you see why is it considered as a folder? Can you help me troubleshoot? Thank you! Best, Giorgio PS I have already tried to restart the program, to change directory on terminal, to convert manually the files to .mgz, or to move the .nii file in the freesurfer home (which gives the following error: ERROR: You are trying to re-run an existing subject with (possibly) new input data (-i). If this is truly new input data, you should delete the subject folder and re-run, or specify a different subject name. If you are just continuing an analysis of an existing subject, then omit all -i flags.)

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Re: [Freesurfer] Processing MRI help
by Selvarajah, Arunan 25 May '21

25 May '21

External Email - Use Caution After subscribing to the mail list, I am re-trying this again. Best, Arunan From: "Selvarajah, Arunan" <Arunan.Selvarajah(a)uhnresearch.ca> Date: Monday, May 24, 2021 at 8:38 PM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Cc: Hanna Vasilevskaya <hanna.vasileuskaya(a)mail.utoronto.ca> Subject: Processing MRI help Hi, I am currently using this program to process and eventually analyze MRIs. I was able to process most of our patients, except one. It gets to the “Correcting defect” command and does not proceed any further. I waited about 24 hours before re-running the program. It still stops in the exact same spot. Below is the image of where it stops: [cidimage001.png(a)01D750DB.A767B310] What should I do? Thanks, Arunan This e-mail may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this e-mail may not be that of the organization. If you feel you have received an email from UHN of a commercial nature and would like to be removed from the sender's mailing list please do one of the following: (1) Follow any unsubscribe process the sender has included in their email (2) Where no unsubscribe process has been included, reply to the sender and type "unsubscribe" in the subject line. If you require additional information please go to our UHN Newsletters and Mailing Lists page. Please note that we are unable to automatically unsubscribe individuals from all UHN mailing lists. Patient Consent for Email: UHN patients may provide their consent to communicate with UHN about their care using email. All electronic communication carries some risk. Please visit our website here<https://secure-web.cisco.com/1-qRtOqEpyj1C59blW0xVmKSl5xzdr2h9bzCdySuGi7dgW…> to learn about the risks of electronic communication and how to protect your privacy. You may withdraw your consent to receive emails from UHN at any time. Please contact your care provider, if you do not wish to receive emails from UHN.

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FreeSurfer (v 6.0) skull stripping problems
by BDiB10 25 May '21

25 May '21

External Email - Use Caution Hi everyone, I am processing the NIFD dataset (visit 1) and the FS (v 6.0) segmentation consistently includes dura mater in the pial boundary in most subjects (I could not attach example snapshots to this email, but they are available if required). I have tried -gcut and the watershed algorithms for FS and they do not seem to be making a difference. Considering that the default preflooding height in FS is 25, I chose 20 and 1 for additional processing. While PFH=1 (and -gcut) does not remove the skull left behind (just shaves off some boundary pixels), using PFH=20 (oddly) seems to actually add more pixels. These observations are based on the brainmask.mgz output after running “ recon-all -skullstrip -wsthresh <pf height> -clean-bm -subjid <subid>” and “recon-all -skullstrip -clean-bm -gcut -subjid <subjid>” (and without fully reprocessing the data). - I would be very grateful for any insights about additional methods to try to remediate this problem, short of manual editing. This is a widely occurring issue in the dataset, so we cannot just exclude the problem cases. - Would it be advisable to use different software for the skull stripping (such as BET) and use that output in the FS pipeline? - Could I be missing something (this is the first time I am using FS)? Thank you very much for your time! Best regards, Divya

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Fwd: confirm 8038f95159942b876b5e8f8110930301c8222d61
by Andrew Raines 24 May '21

24 May '21

External Email - Use Caution Hi there, I really need some help…I have experienced a mild/moderate head injury in 1997 which caused me to go into seizures (no family history of epilepsy) I have had MRI recently done as my cognitive function and memory have declined rapidly over the years, after the accident I apparently changed from very happy and a large group of friends to being grumpy and short with people and making inappropriate comments... i also lost all my friends at the time as my mood changed and i have struggled to retain friendships (even new ones) since the accident. I have tried to follow your instructions of how to install free surfer but despite once being proficient on c basic programming I have been unable to follow instruction on how to install run and process my MRI data. I was hoping that you may have an angel that would be able to uplift my MRI data from dropbox, process and send it back to me, in lou of being able to use my MRI for any research, the neurologist only look at the MRI data with the naked eye and say i look normal…im hoping that freesurfer will show evidence otherwise so that the government based accident coverage can get me sent to australia for analysis as there is no way the hundreds of falls and head injury i have had can leave me “normal” yet barely functional thank you for any help you may be able to give Kind Regards Andrew Raines > Begin forwarded message: > > From: Andrew Raines <andrewraines(a)me.com> > Subject: Re: confirm 8038f95159942b876b5e8f8110930301c8222d61 > Date: 25 May 2021 at 11:04:46 AM NZST > To: freesurfer-request(a)nmr.mgh.harvard.edu > > > >> On 25/05/2021, at 11:03 AM, freesurfer-request(a)nmr.mgh.harvard.edu <mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote: >> >> confirm 8038f95159942b876b5e8f8110930301c8222d61 >

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Thalamus/hippocampus subfield question
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 24 May '21

24 May '21

?Hi, I am visually quality checking the hippocampal and the thalamic subnuclei parcellations that Iglesias designed. I see that the hippocampal tail and the PuM (pulvinar) overlay with each other. What should I make of that? Is that a brain worth removing from analysis? 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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Job opportunity (ResearchAssistant/Lab Manager) at Boys Town National Research Hospital
by Sahil Bajaj 21 May '21

21 May '21

External Email - Use Caution *Business:* Boys Town National Research Hospital *Job Summary:* As a Research Assistant/Lab Manager of the Center for Neurobehavioral Research (CNR), you join us in our work understanding the neurobiological bases of adolescent externalizing and internalizing conditions. In this role, you will be an integral member of the scientific team and will have rich opportunities to participate in and learn from the Neurobehavioral Development Study and multiple other neurodevelopmental studies from across the CNR. The CNR and Boys Town National Research Hospital provide an ideal training environment for research assistants with extensive opportunities to learn about clinical practice and fMRI. Review of applications will begin as soon as they are received and will continue until the position is filled. Anticipated start date is July to August 2021. *Schedule*: Full-Time, 40 hours a week *Responsibilities:* - Ensures that all laboratory materials, supplies, and equipment are ordered and available. - Performs or assists in the recruitment of research participants, including patients. Collaborates with laboratory PI to understand their recruiting needs. - Performs or assists in testing of research subjects. - Maintains detailed records of test conditions and results. - Manages purchasing of equipment and financial details (e.g. subject payment, petty cash, and mileage reimbursements). - Regularly enters data into lab databases and ensures scoring and data accuracy. *Required Qualifications:* - Requires a BSc/BA degree directly related to the work involved in the research program (i.e., Psychology or Neuroscience). - Experience in Mental Health or other forms of psychological research, preferred - Job requires interpersonal skills, close attention to detail, and flexibility in duties performed. About us: The Center for Neurobehavioral Research was established in 2016 to help improve the care of children through a better understanding of the neurobiology of mental health. With a new, dedicated and state-of-the-art 3 Tesla scanner as well as fNIRS capability, the CNR assesses approximately 300 adolescents and a comparable number of young children annually on a large neuroimaging battery, including tasks indexing emotion processing, decision-making and response control, to determine dysfunction in specific neuro-cognitive systems that underpin different forms of impaired mental health. In addition to in-home family services and residential treatment centers, Boys Town provides the Family Home ProgramSM, a treatment foster-case program serving over 400 youth annually on the Boys Town campus in Omaha, Nebraska. Youth participating in the Family Home ProgramSM are scanned before and after treatment completion to determine treatment response. The CNR is also involved in the assessments of other interventions – both pharmacological and psychosocial. The CNR therefore offers a unique opportunity to study mechanisms underlying mental health issues in large samples, with a translational focus. The CNR provides a vigorous and highly collaborative research environment in which post-doctoral fellows participate in team-based projects. *For any questions/queries, please contact:* *Sahil Bajaj, PhD* Director Multimodal Clinical Neuroimaging Laboratory (MCNL) E-mail: sahil.bajaj(a)boystown.org *&* *James Blair, PhD* Director, Center for Neurobehavioral Research E-mail: james.blair(a)boystown.org *About Boys Town:* Boys Town has been changing the way America cares for children and families since 1917. With over a century of service, our employees have helped us grow from a small boarding house in downtown Omaha, Nebraska, into one of the largest national child and family care organizations in the country. With the addition of Boys Town National Research Hospital in 1977, our services branched out into the health care and research fields, offering even more career opportunities to those looking to make a real difference. Our employees are our #1 supporters when it comes to achieving Boys Town's mission, which is why we are proud of their commitment to making the world a better place for children, families, patients, and communities. Unique perks to Boys Town employees and their families include free visits to Boys Town physicians and free prescriptions under the Boys Town Medical Plan, tuition assistance, parenting resources from our experts and professional development opportunities within the organization, just to name a few. Working at Boys Town is more than just a job, it is a way of life. *Boys Town National Research Hospital is a tobacco free campus. * *This advertisement describes the general nature of work to be performed and does not include an exhaustive list of all duties, skills, or abilities required. Boys Town is an equal employment opportunity employer and participates in the E-Verify program. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, age, disability or veteran status. To request a disability-related accommodation in the application process, contact us at 1-877-639-6003.* -- ------------------------------------- *Sahil** Bajaj, Ph.D.* Director, Multimodal Clinical Neuroimaging Laboratory (MCNL) Center for Neurobehavioral Research sahil.neurores(a)gmail.com <sahil.neuro(a)gmail.com> | *p:* 531.355.1053 | *f:* 531.355.1213 Boys Town National *ResearchHospital* Boys Town, NE 68010 Twitter <https://secure-web.cisco.com/1GhmQmh4D8P6bUJ0iA6LJTAMyO9fslBVipNwyODy2iO0hz…> | LinkedIn <https://secure-web.cisco.com/1MbBJOYkdkPSNlqZd9IFIr7yku1XwF8sFCDJsw_2p3tjAb…>

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Long_stats_slopes
by AJ 21 May '21

21 May '21

External Email - Use Caution Hi, Is there any way to run long_stats_slopes on the aseg.stats file on the total thalamic structure instead of separately as right and left. Many thanks. AJ

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Re: [Freesurfer] blurring average label files
by Kristi Drudik 20 May '21

20 May '21

External Email - Use Caution Hi Bruce, Thank you very much! Apologies for my simple questions but just to clarify: In Freeview, where do I select to show the p-vals instead of the binary level? Also, how would the entire command be listed with the required flags? Would it be something along the lines of mris_spherical_average -prior <iterations> -o fsaverage <which> <fname> <hemi> <spherical surf> <subjects…> outputname Best, Kristi From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Fischl, Bruce" <BFISCHL(a)mgh.harvard.edu<mailto:BFISCHL@mgh.harvard.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Thursday, May 20, 2021 at 1:35 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] blurring average label files Hi Kristi You can change the display in freeview to show the p-vals instead of just the binary label. Actually you can blur and write the output in mris_spherical_average (undocumented) with: mris_spherical_average -prior <# of iterative averages> <file name to write blurred pattern to> cheers Bruce From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> On Behalf Of Kristi Drudik Sent: Thursday, May 20, 2021 1:29 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Cc: Kristi Drudik <kristina.drudik(a)mail.mcgill.ca<mailto:kristina.drudik@mail.mcgill.ca>> Subject: Re: [Freesurfer] blurring average label files External Email - Use Caution External Email - Use Caution Hi Bruce, In that case, how would I tell the command “mris_spherical_average” to blur the output? Also, how can I display the probability values in a colour scale? Thank you very much! Best, Kristi From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Fischl, Bruce" <BFISCHL(a)mgh.harvard.edu<mailto:BFISCHL@mgh.harvard.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Thursday, May 20, 2021 at 12:57 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] blurring average label files Hi Kristi I don’t think it does any blurring unless you tell it to. The output should reflect the actual alignment of those labels Cheers Bruce From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> On Behalf Of Kristi Drudik Sent: Thursday, May 20, 2021 12:48 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] blurring average label files External Email - Use Caution External Email - Use Caution Hi again! On second thought, we are wondering if this averaged .label file was already blurred during the mris_spherical_average command. If this is the case, do you know what smoothing has been done and by how much? We are interested in seeing the probability of each vertex after the average of the labels. Thank you as always for all of your help!! Best, Kristi From: Kristi Drudik Sent: May 19, 2021 6:42 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: blurring average label files Hello Freesurfer group, I am using the command ‘mris_spherical_average’ to map and average a series of label files onto fsaverage (I have created the label files manually by drawing directly on subject surfaces in FreeView). This has allowed me to create a surface probability map, where each vertex on the FreeSurfer fsaverage surface is represented from 0% to 100% as belonging to my sulcus of interest (see screenshot ‘.label’). I would like to blur the data and load this blurred average as an overlay onto the fsaverage pial. However, when I run ‘mri_label2vol’ followed by ‘mris_fwhm’, I lose the probability map and the average label is turned into one large label (see screenshot ‘overlay’, where most of the map has 99% overlap). Would there be a way to blur this averaged label (obtained from mris_spherical_average) with a similar command to ‘mris_fwhm’ but for label files? Let me know if you have any questions regarding the procedure. Very much looking forward to your response and thank you for all your time! Best, Kristi Kristi Drudik Montreal Neurological Institute McGill University Montreal, Canada

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Issue Pertinent To Freesurfer Usage
by Noyan Jawed 20 May '21

20 May '21

External Email - Use Caution Dear Freesurfer, I have downloaded the application but I am unable to run it. Can you please help me in resolving this issue? Regards, Noyan Jawed

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Re: [Freesurfer] blurring average label files
by Kristi Drudik 20 May '21

20 May '21

External Email - Use Caution Hi Bruce, In that case, how would I tell the command “mris_spherical_average” to blur the output? Also, how can I display the probability values in a colour scale? Thank you very much! Best, Kristi From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Fischl, Bruce" <BFISCHL(a)mgh.harvard.edu<mailto:BFISCHL@mgh.harvard.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Thursday, May 20, 2021 at 12:57 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] blurring average label files Hi Kristi I don’t think it does any blurring unless you tell it to. The output should reflect the actual alignment of those labels Cheers Bruce From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> On Behalf Of Kristi Drudik Sent: Thursday, May 20, 2021 12:48 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] blurring average label files External Email - Use Caution External Email - Use Caution Hi again! On second thought, we are wondering if this averaged .label file was already blurred during the mris_spherical_average command. If this is the case, do you know what smoothing has been done and by how much? We are interested in seeing the probability of each vertex after the average of the labels. Thank you as always for all of your help!! Best, Kristi From: Kristi Drudik Sent: May 19, 2021 6:42 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: blurring average label files Hello Freesurfer group, I am using the command ‘mris_spherical_average’ to map and average a series of label files onto fsaverage (I have created the label files manually by drawing directly on subject surfaces in FreeView). This has allowed me to create a surface probability map, where each vertex on the FreeSurfer fsaverage surface is represented from 0% to 100% as belonging to my sulcus of interest (see screenshot ‘.label’). I would like to blur the data and load this blurred average as an overlay onto the fsaverage pial. However, when I run ‘mri_label2vol’ followed by ‘mris_fwhm’, I lose the probability map and the average label is turned into one large label (see screenshot ‘overlay’, where most of the map has 99% overlap). Would there be a way to blur this averaged label (obtained from mris_spherical_average) with a similar command to ‘mris_fwhm’ but for label files? Let me know if you have any questions regarding the procedure. Very much looking forward to your response and thank you for all your time! Best, Kristi Kristi Drudik Montreal Neurological Institute McGill University Montreal, Canada

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Freesurfer May 2021