Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

pass code virtual machine Free Surfer
by Luisa Klahn 22 Sep '22

22 Sep '22

External Email - Use Caution Hi, I am installing the virtual machine to run Free Surfer on my windows computer and I need the pass code to open the 7zip files archive. Can someone please send that to me? Thank you very much! Best, Luisa Klahn

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Voxel to mm coordinates
by Fotiadis, Panagiotis 21 Sep '22

21 Sep '22

External Email - Use Caution Hello, I was wondering what the best way would be to extract the coordinates of each voxel in my nifti volume in mm. I have used MRIread to load the nifti volume into Matlab (=mri) and wanted to essentially create a new variable that takes each (voxel) entry in mri.vol and exports its three coordinates in mm. Would I just need to multiply the mri.vox2ras 4x4 matrix to each voxel’s [X Y Z 1]’ (where X,Y,Z are the voxel’s coordinates in mri.vol) or are there different steps involved? Thank you in advance for your time and help! Best, Panos

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unziping problems
by TAIB Simon 21 Sep '22

21 Sep '22

External Email - Use Caution Good afternoon, I am having trouble unzipping the freesurfer folder downloaded from your website as a password is required and I could not find it. I have done my registration and got the licence.txt file, but I don't know if the password is in it. Is there something I am missing ? If so, please enlight me. Have a good day Dr Simon TAIB Centre Régional Psychotraumatisme Occitanie - CHU de Purpan INSERM U1214 ToNIC - Université Toulouse 3 ________________________________ Ce message et les éventuelles pièces jointes sont confidentiels et peuvent être protégés par la loi. Ils s'adressent uniquement aux personnes destinataires. Si vous n'êtes pas dans la liste des destinataires, veuillez en informer immédiatement l'expéditeur et ne pas utiliser, divulguer, stocker ou copier sur un quelconque support l'information qu'il contient. Il appartient au destinataire de vérifier que les messages et pièces jointes ne contiennent pas de virus. This message and any attachments are confidential and may be protected by law. They are intended only for the individual(s) or entity named above. If you are not the intended recipient, any disclosure, copying, or distribution is strictly prohibited. Please notify the sender that you have received this email by error. It belongs to each recipient to check that e-mails and attachments are free from viruses.

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Unable to run trac-all -prep : cannot file bvals bvecs file
by Ashwati Vipin (Dr) 20 Sep '22

20 Sep '22

External Email - Use Caution Dear Freesurfer developers, I am running the trac-all -prep for my DWI data on Freesurfer version 7.2.0. The configuration file seems to be alright but when I start running the -prep step it gives me the error: writing to /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/dmri/dwi_orig.1.nii.gz... /Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula//Volumes/DRCS_MAIN_SERVER/DRCS/BIOCIS/Neuroimaging/Stats/Freesurfer/diffusion_tracula/BIOC_0001_v01_FS/bvecs.txt: No such file or directory. Darwin DRCSs-iMac.local 21.5.0 Darwin Kernel Version 21.5.0: Tue Apr 26 21:08:22 PDT 2022; root:xnu-8020.121.3~4/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Mon Aug 15 11:32:11 +08 2022 I have attached the log file, error file, bvals and bvecs and the configuration file and as the screenshot below shows: the directory does have the bvals.txt and bvecs.txt files, so I’m not sure why it’s giving me this error? I thought the error was because the bvals and bvecs were given in rows, so I transposed them so they are now in columns but it still doesn’t work. [cid:image001.png@01D8B09D.94718010] I have run tracula before with no issues so I’m really lost here. Could you please help? Thank you so much! Best, Ashwati ________________________________ CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its contents. Towards a sustainable earth: Print only when necessary. Thank you.

3 11

Vanderbilt University HBCD postdoc opportunity
by Harriott, Emily M 20 Sep '22

20 Sep '22

External Email - Use Caution Dear FreeSurfer subscribers, The HBCD site at Vanderbilt University (Nashville, TN) is taking applications for a postdoctoral fellow in developmental neuroscience. Please see the below posting. Feel free to forward to anyone you know who might be interested. Thank you, Emily Applications are invited for a postdoctoral fellowship in developmental neuroscience at Vanderbilt University’s Peabody College of Education. Individuals will be mentored by Laurie Cutting and an interdisciplinary mentorship team formed from Vanderbilt investigators studying the neuroscience of child development (the Healthy Brain and Cognitive Development (HBCD) study, a national study recruiting women during pregnancy and following their infants through the first five years of their lives. https://secure-web.cisco.com/1frP8amkag6ZDNAEQpQAaB7mFxlhssq5t7iEFI6-gfjtx6…) Composition of the mentor team will be tailored to the individual’s interests; possible members include Kate Humphreys, Autumn Kujawa, Sarah Osmundson, Sasha Key, Seth Smith, and Bennett Landman. Individuals will have the opportunity to work on several large NIH-funded projects, including the HBCD study, as well as other longitudinal neuroimaging studies focused on academic, cognitive, behavioral outcomes in early childhood development (starting at perinatal period) through elementary school. Research opportunities will include analysis and writing manuscripts using already collected multimodal MRI datasets, travel and conference presentations, and support for writing mentored grant proposals. Ideal candidates should be highly motivated to publish first-author papers and present at conferences, and should possess a background in advanced statistics, strong experimental and scientific writing skills, ability to work in a team environment, and be self-motivated. Experience working with children in a research setting is also desired. Additional desired strengths include competence in MRI and/or EEG data acquisition/analysis and/or assessment training, including programming skills (e.g., Matlab, R, and/or Python) and experience with multimodal neuroimaging (DWI, fMRI, and/or EEG) analysis. If you are interested in the position, please email Laurie Cutting (Laurie.Cutting(a)Vanderbilt.Edu<mailto:Laurie.Cutting@Vanderbilt.Edu>) a recent CV, a brief statement of research interests (1 page), and the contact information for 2 references. Applications will be considered on a rolling basis until position(s) are filled. Salary is highly competitive and reimbursement for moving expenses will be considered.

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Re: [Freesurfer] White matter normalization
by James Brown 20 Sep '22

20 Sep '22

External Email - Use Caution Thank you very much for the follow up. I have attached the recon-all.log once again for your kind review Hello James, I apologize that your message containing the log file got rejected. Can you please re-send it? I will manually approve it so your conversation with Doug can continue. Liam Sennott On Fri, Sep 16, 2022 at 10:25 AM James Brown <jb1979000(a)gmail.com> wrote: > Hi Dr Greeve, > I greatly apologize if I missed in the log file (attached) how freesurfer > normalizes flair. but I couldn't figure it out. Thanks for guidance > > James > > > > can you send your recon-all.log file? >  > > > > On Thu, Sep 15, 2022 at 4:04 PM James Brown <jb1979000(a)gmail.com> wrote: > >> Hi Dr Greeve, >> I ran recon-all using the flag -flair. I couldn't find any command in >> recon-all.log that normalizes the flair images. It seems just normalization >> to the T1. >> I would like to inquire about the flag sigma in the command >> "mri_normalize" the default is 8. when it is recommended to increase this >> value? and how much can weincrease it? >> >> I'm not sure of the order. You can run recon-all passing in the flair >> with -flair flair.mgz. At some point in the process it will apply a >> normalization to the flair (it will not necessarily be the same >> normalization that is applied to the t1) >>  >> >> >> >> On Mon, Sep 12, 2022 at 4:01 PM James Brown <jb1979000(a)gmail.com> wrote: >> >>> Dear Freesurfer experts, >>> In order to normalize white matter intensity of T1 images and correct >>> for bias field. I do the following steps: >>> mri_convert T1.nii.gz T1.mgz >>> mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2 >>> mri_normalize -g 1 T1_N3.mgzT1_norm.mgz >>> mri_convert T1_norm.mgz T1_norm.nii.gz >>> >>> I would like to apply bias field correction on FLAIR images then >>> normalize white matter intensity. >>> I tried N4biasfieldcorrection from ANTS but it didn't work as expected. >>> Reviewing documents about N4biasfieldcorrection I realize that the >>> algorithm has been developed to correct bias field correction in T1. >>> >>> Are the steps above valid for FLAIR images or it can only be applied on >>> T1 images. We appreciate any feedback about the proper way to correct FLAIR >>> images for bias field and normalize white matter intensity. >>> >>> Thank you >>> JamesB >>> >>>

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NIH/NIDA-Funded Postdoc in Developmental Neuroscience (Penn State)
by emma jane 20 Sep '22

20 Sep '22

External Email - Use Caution We are seeking a qualified Postdoctoral Scholar with expertise in human magnetic resonance imaging (MRI) with developmental cohorts to work on a study of the impacts of food insecurity on reward neurobiology in children (8 – 10 years old). This position is supported by a research award from the National Institute on Drug Abuse (1R21DA050164-01) and will be based in the Child Study Center in the Department of Psychology, at the Pennsylvania State University, University Park campus in State College, PA. The primary responsibility of this position will be to provide neuroimaging research support. The successful candidate will be expected to contribute to experimental design, project coordination, oversight of junior research associates and/or trainees, and data analyses. Candidates must demonstrate expertise in functional and structural MRI analysis methods using standard processing packages (e.g., SPM, AFNI, FSL, Freesurfer etc.) and experience with advanced data analysis methods (e.g., structural equation modeling) would be advantageous. The Postdoctoral Scholar will also be expected to contribute to manuscript preparation and presentation of study-related outcomes at key scientific meetings. Extensive mentorship will be provided to the successful candidate in order to facilitate transition to an independent research career. This position will also provide an opportunity to interact with several vibrant research communities at Penn State, including the Social Sciences Research Institute (http://secure-web.cisco.com/1XorkVil5MVPrdwXEupIRqiuusTzbXVJDXz5aDRjCfFNcij…) and the Social, Life and Engineering Science Imaging Center (http://secure-web.cisco.com/1AarimGjPrU-Cc4Cvwd8oKbumIZf7_U5_0ou7l0ev3HpymT…) among others. In addition, successful candidates must either have demonstrated a commitment to building an inclusive, equitable, and diverse campus community, or describe one or more ways they would envision doing so, given the opportunity. The initial appointment will be for one year, with the possibility of renewal in subsequent years. Salary and benefits are based on NIH guidelines, commensurate with experience and qualifications. Interested candidates should upload a CV, cover letter, statement of research interests, and 2-3 relevant publications at https://secure-web.cisco.com/1nkotB-vek0CbiLW5z4qJCX_eoxqRKjrnuO4_so2iQCKPp… In addition, applicants should arrange for 3 professional references to be submitted separately to Dr. Emma Jane Rose (PI & Director ROAR (Research On Adversity and Risk) Lab) at emmajanerose(a)psu.edu. Review of applications will begin immediately and will continue until the position is filled. Applications received by November 1, 2022, will be given full consideration, although the position will remain open until filled. For further information about this appointment, please contact Dr. Emma Jane Rose at emmajanerose(a)psu.edu or 814-865-0114. The Pennsylvania State University is committed to and accountable for advancing diversity, equity, inclusion, and sustainability in all of its forms. We embrace individual uniqueness, foster a culture of inclusion that supports both broad and specific diversity initiatives, leverage the educational and institutional benefits of diversity in society and nature, and engage all individuals to help them thrive. We value inclusion as a core strength and an essential element of our public service mission. This position requires the following clearances: · PA State Police Criminal Background Check · PA Child Abuse History Clearance Form · Federal (FBI) Fingerprint Criminal Background Check To review the Annual Security Report which contains information about crime statistics and other safety and security matters and policies, please go to https://secure-web.cisco.com/1joFRvRo8-jTlBa2LpM8TrL4XwSfnJfZuS1AJ9al1q54Hp…, which will also explain how to request a paper copy of the Annual Security Report. Penn State is an equal opportunity, affirmative action employer, and is committed to providing employment opportunities to all qualified applicants without regard to race, color, religion, age, sex, sexual orientation, gender identity, national origin, disability or protected veteran. *Emma Jane Rose Ph.D.* *Department of Psychology, **Pennsylvania State University (PSU)* *Director/Principal Investigator* *ROAR (Research On Adversity & Risk) Lab* *Child Study Center (PSU)* *Office: (814)865-0114 <callto:(814)865-0114>*

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Re: [Freesurfer] White matter normalization
by James Brown 20 Sep '22

20 Sep '22

External Email - Use Caution Thank you very much for the follow up. I have attached it again Hello James, I apologize that your message containing the log file got rejected. Can you please re-send it? I will manually approve it so your conversation with Doug can continue. Liam Sennott On Fri, Sep 16, 2022 at 10:25 AM James Brown <jb1979000(a)gmail.com> wrote: > Hi Dr Greeve, > I greatly apologize if I missed in the log file (attached) how freesurfer > normalizes flair. but I couldn't figure it out. Thanks for guidance > > James > > > > can you send your recon-all.log file? >  > > > > On Thu, Sep 15, 2022 at 4:04 PM James Brown <jb1979000(a)gmail.com> wrote: > >> Hi Dr Greeve, >> I ran recon-all using the flag -flair. I couldn't find any command in >> recon-all.log that normalizes the flair images. It seems just normalization >> to the T1. >> I would like to inquire about the flag sigma in the command >> "mri_normalize" the default is 8. when it is recommended to increase this >> value? and how much can weincrease it? >> >> I'm not sure of the order. You can run recon-all passing in the flair >> with -flair flair.mgz. At some point in the process it will apply a >> normalization to the flair (it will not necessarily be the same >> normalization that is applied to the t1) >>  >> >> >> >> On Mon, Sep 12, 2022 at 4:01 PM James Brown <jb1979000(a)gmail.com> wrote: >> >>> Dear Freesurfer experts, >>> In order to normalize white matter intensity of T1 images and correct >>> for bias field. I do the following steps: >>> mri_convert T1.nii.gz T1.mgz >>> mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2 >>> mri_normalize -g 1 T1_N3.mgzT1_norm.mgz >>> mri_convert T1_norm.mgz T1_norm.nii.gz >>> >>> I would like to apply bias field correction on FLAIR images then >>> normalize white matter intensity. >>> I tried N4biasfieldcorrection from ANTS but it didn't work as expected. >>> Reviewing documents about N4biasfieldcorrection I realize that the >>> algorithm has been developed to correct bias field correction in T1. >>> >>> Are the steps above valid for FLAIR images or it can only be applied on >>> T1 images. We appreciate any feedback about the proper way to correct FLAIR >>> images for bias field and normalize white matter intensity. >>> >>> Thank you >>> JamesB >>> >>>

1 0

forcing use of ants-n3 with FS 7.2
by Alexopoulos, Dimitrios 20 Sep '22

20 Sep '22

External Email - Use Caution Just want to confirm the following change is good to use to force use of ants-n3 with FS 7.2. It appears as though FS 7.2 with ants-n3 gives us better results than the default n4. We changed /etc/recon-config.yaml to the following, and it appears to work and the recon-all log file appears to indicate N3 Nu intensity correction being used (see below). Is this change acceptable. [cid:image001.png@01D8C9C1.E2130CC0] #-------------------------------------------- #@# Nu Intensity Correction Thu Sep 15 14:56:09 CDT 2022 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --cm --n 2 --ants-n3 /usr/bin/bc /data/shimony/shimony2/neonatal/freesurfer7_elabe_3yo/elabe_3yo_gdc_rdc_dn/MOD2532_Y3_a_fs7p2/mri /usr/local/pkg/freesurfer7.2/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --cm --n 2 --ants-n3 nIters 2 mri_nu_correct.mni 7.2.0 Linux holowach 5.3.0-53-generic #47~18.04.1-Ubuntu SMP Thu May 7 13:10:50 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux Thu Sep 15 14:56:10 CDT 2022 tmpdir is ./tmp.mri_nu_correct.mni.43277 cd /data/shimony/shimony2/neonatal/freesurfer7_elabe_3yo/elabe_3yo_gdc_rdc_dn/MOD2532_Y3_a_fs7p2/mri /opt/ANTs/bin/N3BiasFieldCorrection 3 orig.mgz ./tmp.mri_nu_correct.mni.43277/nu0.mgz mri_binarize --i ./tmp.mri_nu_correct.mni.43277/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.43277/ones.mgz 7.2.0 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

2 2

Re: [Freesurfer] White matter normalization
by James Brown 20 Sep '22

20 Sep '22

External Email - Use Caution I received the email below. any idea how I can send the recon-all log file to Dr Greeve? Thank you our mail to 'Freesurfer' with the subject Re: White matter normalization Is being held until the list moderator can review it for approval. The reason it is being held: Message body is too big: 1086006 bytes with a limit of 1000 KB Either the message will get posted to the list, or you will receive notification of the moderator's decision. If you would like to cancel this posting, please visit the following URL: https://secure-web.cisco.com/1a6oqvHB07_iY6H_SQ1OjB5CDduMv9shLwG6PDU5knaobT… On Fri, Sep 16, 2022 at 10:25 AM James Brown <jb1979000(a)gmail.com> wrote: > Hi Dr Greeve, > I greatly apologize if I missed in the log file (attached) how freesurfer > normalizes flair. but I couldn't figure it out. Thanks for guidance > > James > > > > can you send your recon-all.log file? >  > > > > On Thu, Sep 15, 2022 at 4:04 PM James Brown <jb1979000(a)gmail.com> wrote: > >> Hi Dr Greeve, >> I ran recon-all using the flag -flair. I couldn't find any command in >> recon-all.log that normalizes the flair images. It seems just normalization >> to the T1. >> I would like to inquire about the flag sigma in the command >> "mri_normalize" the default is 8. when it is recommended to increase this >> value? and how much can weincrease it? >> >> I'm not sure of the order. You can run recon-all passing in the flair >> with -flair flair.mgz. At some point in the process it will apply a >> normalization to the flair (it will not necessarily be the same >> normalization that is applied to the t1) >>  >> >> >> >> On Mon, Sep 12, 2022 at 4:01 PM James Brown <jb1979000(a)gmail.com> wrote: >> >>> Dear Freesurfer experts, >>> In order to normalize white matter intensity of T1 images and correct >>> for bias field. I do the following steps: >>> mri_convert T1.nii.gz T1.mgz >>> mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2 >>> mri_normalize -g 1 T1_N3.mgzT1_norm.mgz >>> mri_convert T1_norm.mgz T1_norm.nii.gz >>> >>> I would like to apply bias field correction on FLAIR images then >>> normalize white matter intensity. >>> I tried N4biasfieldcorrection from ANTS but it didn't work as expected. >>> Reviewing documents about N4biasfieldcorrection I realize that the >>> algorithm has been developed to correct bias field correction in T1. >>> >>> Are the steps above valid for FLAIR images or it can only be applied on >>> T1 images. We appreciate any feedback about the proper way to correct FLAIR >>> images for bias field and normalize white matter intensity. >>> >>> Thank you >>> JamesB >>> >>>

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