Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

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 >>> >>>

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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.

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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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Specifying contrasts for an unbalanced design
by Trolle, Carl 20 Sep '22

20 Sep '22

Dear FreeSurfer team, We are investigating if there is a difference in cortical thicknesses between persons with a condition and controls, regressing out the effect of site, sex, age, but have some concerns on how to specify our contrasts. We don’t think that the age-slopes will be different between the patients and the controls but would like to check that formally using DODS before trying DOSS. Currently, we have only one female control from two of the sites and are left with 10 instead of 12 classes. Would be very grateful if you have time to check that we’ve got this right. Also, when we want to check for interactions between class and age to see if we can use DOSS instead, is the attached “interactionmatrix” correct? I’ve looked at the tutorials and this example<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg49602.html>, but tried to adapt it to our situation. If we do find an interaction, would that cluster then show up on the cluster summary in the glmdir-folder? Thank you and sorry for all the questions, just wanting to make sure we are doing this correctly. Kind regards, Carl Trolle Research Fellow Spaulding Neuroimaging Lab FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 Platform: CentOS Stream 8

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password
by Nail Bulakbasi 20 Sep '22

20 Sep '22

External Email - Use Caution Dear administrator I downloaded the FS_7_2_0_Ubuntu_18_04_06.ova.7z file to run with Oracle virtual box but I need the password to open the file. I will be grateful if you send me the password. Thanks in advance ADDRESS: Nail BULAKBASI, M.D. Professor of Radiology & Neuroradiology (EDINR, EDiPNR) Director, Dr.Suat Günsel University of Kyrenia Hospital Chairman, Department of Radiology Turkish Republic of Northern Cyprus nail.bulakbasi(a)neu.edu.tr nail.bulakbasi(a)kyrenia.edu.tr nbulakbasi(a)yahoo.comADDRESS: P Please consider the environment before printing this email.

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Help - segmentHA_T1_long.sh "list of time points not found"
by Raikkonen Kimi 19 Sep '22

19 Sep '22

External Email - Use Caution Dear FreeSurfer, Hi, I was trying to run longitudinal analysis of the hippocampus and amygdala segmentation pipeline after running the main FreeSurfer longitudinal pipeline. I ran segmentHA_T1_long.sh 101_MRI1.long.101_template segmentHA_T1_long.sh 101_MRI2.long.101_template segmentHA_T1_long.sh 101_MRI3.long.101_template etc. but I got the following error message: List of time points: /study/101_MRI1.long.101_template/base-tps does not exist I think I’ve headed the wrong direction, I was wondering how to do the list of time points for a subject. Thanks so much for your help in advance. Best regards, Alex

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Zip folder passcode
by Chi-Wen Jao 19 Sep '22

19 Sep '22

External Email - Use Caution Dear freesurf developer I was trying to install FreeSurfer on a virtual machine and was asked for the password to open the archive in the zip folder FS_7_2_0_Ubuntu_18_04_06.ova.7z – I just wanted to ask for that password. Thank you for your help! Kind regards, Chi-Wen

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Zip folder passcode
by Enya Weidner 19 Sep '22

19 Sep '22

External Email - Use Caution Hi everyone, I was trying to install FreeSurfer on a virtual machine and was asked for the password to open the archive in the zip folder FS_7_2_0_Ubuntu_18_04_06.ova.7z – I just wanted to ask for that password. Thank you for your help! Kind regards, Enya ---------------------- M.Sc. Enya Weidner Universität Bielefeld Fakultät für Psychologie und Sportwissenschaft AE02 Affektive Neuropsychologie Raum: T5-220 Telefon: 0521-106 4533 Email: enya.weidner(a)uni-bielefeld.de

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