Freesurfer January 2022

freesurfer@nmr.mgh.harvard.edu

69 participants
112 discussions

VM password
by REEM ABU BAKR BAHATHIQ 23 Jan '22

23 Jan '22

External Email - Use Caution ---------- Forwarded message --------- From: REEM ABU BAKR BAHATHIQ <rbahathiq0001(a)stu.kau.edu.sa> Date: Wed, Jan 19, 2022, 3:11 PM Subject: VM password To: <freesurfer(a)nmr.mgh.harvard.edu> Dear Freesurfer mailing list, I have just downloaded the virtual machine + ubuntu package, as outlined on the website when running a VM in windows. However, ubuntu is asking for a developer password to open within the VM. I see on the help page (on the website) that the log in ID could be in the README doc, but I can't actually get the VM open to get there. Does anyone know the password so I can set up the VM and get started with freesurfer? Thanks so much in advance!

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Re: [Freesurfer] VM password
by fsbuild 21 Jan '22

21 Jan '22

External Email - Use Caution Sending the password to your email shortly …. On Jan 21, 2022, at 15:35, REEM ABU BAKR BAHATHIQ <rbahathiq0001(a)stu.kau.edu.sa> wrote:        External Email - Use Caution        Dear Freesurfer mailing list,I have just downloaded the virtual machine + ubuntu package, as outlined on the website when running a VM in windows. However, ubuntu is asking for a developer password to open within the VM. I see on the help page (on the website) that the log in ID could be in the README doc, but I can't actually get the VM open to get there.Does anyone know the password so I can set up the VM and get started with freesurfer? Thanks so much in advance!_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Fwd: VM password
by REEM ABU BAKR BAHATHIQ 21 Jan '22

21 Jan '22

External Email - Use Caution Dear Freesurfer mailing list, I have just downloaded the virtual machine + ubuntu package, as outlined on the website when running a VM in windows. However, ubuntu is asking for a developer password to open within the VM. I see on the help page (on the website) that the log in ID could be in the README doc, but I can't actually get the VM open to get there. Does anyone know the password so I can set up the VM and get started with freesurfer? Thanks so much in advance!

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-hires recon-all error w MP2RAGE
by Fred Dick 21 Jan '22

21 Jan '22

External Email - Use Caution Hi all I'm following up on a previous report from May of 2021 that seemed to have the same issue. When running an MP2RAGE (7T, 0.65mm isotropic, pTx), I got the following error using recon-all -all -hires that seemed line one that Corinna did: ##### 3d normalization pass 1 of 2 error: MRInormFindControlPoints: could not find enough control points error: MRInormFindControlPoints failed Darwin Unknown-a0:78:17:6c:fe:8f 20.6.0 Darwin Kernel Version 20.6.0: Wed Nov 10 22:23:05 PST 2021; root:xnu-7195.141.14~1/RELEASE_ARM64_T8101 arm64 ###### [Note this is on an M1 chip mac] The same volume works when it's conformed to 1mm. Happy to supply said volume if helpful, and also try on different architecture. cheers Fred

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mri_glmfit-sim error: Flag --1d unrecognized
by Tarumi Takashi 20 Jan '22

20 Jan '22

External Email - Use Caution Dear FreeSurfer Developers: I am attempting to perform cluster-wise correction for the along-tract measures, as described on the Tract statistics tutorial ( https://secure-web.cisco.com/1k_UHTgDkMyztiBV5VO6PazEUkIHIp4tFCos8o1vMfT5Xa… But, when I run the command below, the flag --1d is not recognized. Command: mri_glmfit-sim --glmdir cc.bodyp.FA_Avg.glmdir --1d --cwp .05 --perm 1000 1.3 pos Error: Flag --1d unrecognized. I could not find similar errors reported. Does anyone have any thoughts on how to trouble-shoot this? The FreeSurfer version I'm using is 7.2.0 on an M1 Mac machine with macOS 12.1. Thank you so much for your help. Sincerely, Taka

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In the Desikan-Killiani parcellatino scheme, which parcellations contain the extrastriate cortex?
by Knut J Bjuland 20 Jan '22

20 Jan '22

External Email - Use Caution Dear freesurfer experts In the Desikan-Killiani parcellatino scheme, which parcellations contain the extrastriate cortex? Knut Jørgen Bjuland

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opposite result between SPSS and QDEC
by baobao 20 Jan '22

20 Jan '22

External Email - Use Caution Hello, Freesurfer experts: I have performed group analysis using QDEC in Freesurfer 6.0 to examine difference between MDD and HC group in surface area with age, sex, and eTIV as covariates and identified one significant region (MDD > HC, warm color, shown in Figure.1). Figure.1 Statistically significant regions where averaged surface area is differed between MDD and HC. The significance value is positive, which mean the surface area in MDD is bigger than that in HC. Then I drew this ROI as a label (defined as lh.daccarea.label), mapped the label to all subjects, and extracted the average surface area of this ROI from every subject. The following is the command: >>mri_label2label --srclabel lh.daccarea --srcsubject fsaverage –trgsubject M001 --trglabel lh.daccarea --regmethod surface --hemi lh >>mris_anatomical_stats -l M001/label/lh.daccarea.label -f M001/stats/lh.untitled.stats M001 lh >>aparcstats2table --hemi lh --subjects 001 002 003 004 --parc lh.daccarea --meas area --tablefile lh.daccarea.stats.txt However, when I conducted a GLM model analysis in SPSS with age, sex, and eTIV as covariates, the result (MDD<HC) is opposite to the QDEC result. And the results of SPSS can be seen in Figure2. I am writing to see if you could kindly provide me with information regarding this question. Is my analysis set up correctly in QDEC for what I’m trying to do? Figure.2. The results of SPSS, as shown in picture, the surface area of MDD is smaller than health group. Following is some information of QDEC analysis: 1.Fsgd: GroupDescriptorFile 1 Title lh_area MeasurementName area Class groupMDD-genderMALE Class groupHC-genderMALE Class groupMDD-genderFEMALE Class groupHC-genderFEMALE Variables age TIV Input M001 groupMDD-genderFEMALE 16.000000 1455607.658680 And so on... 2.contrast matrix DODS Thank you for your kindness, and your prompt attention to this letter will be highly appreciated. Sincerely， Weijie Bao Tel: 86-13594527190 Email: 13594527190(a)163.com

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Trac-all -prep -c error
by Salar Dini, Elaheh 19 Jan '22

19 Jan '22

External Email - Use Caution Dear Freesurfer developers and Anastasia, Happy new year. I am trying to run trac-all -pep -c dmriEla. dmriEla is my config file which is also attached to this message. I am also attaching the trac-all.log file to this email. I am getting the following error: Segmentation fault (core dumped) When I check the /home1/es2263/freesurfer_7.2.0/trctrain/hcp/mgh_1024/mni folder, there is a file named acomm.bbr.prep.trk, but no file with the name acomm.flt.prep.trk. I uninstall and reinstalled freesurfer 7.2.0, considering there might be a problem in installation and some files might be missed, but I still face the same error. I'm running freesurfer on Linux Centos7, the version of freesurfer is 7.2.0 and the installed package is freesurfer-linux-centos7_x86_64-7.2.0.tar.gz. The installed fsl version is 6.0.5.1 . Thank you for your help and best wishes in 2022, Ela

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Question about fsaverage
by Dongyue Zhou 17 Jan '22

17 Jan '22

External Email - Use Caution Dear FreeSurfer experts: I have known the distance between two vertices different. And are vertices detemined by triangles? Points where all triangles meet are vertices. But how triangles are dividied on surface? Bests， dongyue

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Web Developer Position
by Billah, Tashrif 15 Jan '22

15 Jan '22

We are hiring a data engineer at Massachusetts General Hospital to visualize various human subject data through web applications. You need to be fluent in web application building. * Immediate start date * Master's degree preferred * Visa sponsorship available See details and apply directly through the portal below: https://partners.taleo.net/careersection/jobdetail.ftl?job=3178611&lang=en#… You can use the following for referral: Tashrif (tbillah(a)bwh.harvard.edu)

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Freesurfer January 2022