Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30081 discussions

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

2 1

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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recon-all: error in creating rh.white.H
by Peled, Noam 14 Jan '22

14 Jan '22

Dear group A colleague of mine was trying to run recon-all on one of her patients and received an error message. After looking at the attached log, I'm not sure what is the source of the problem. The T1 looks quite good. She is using freesurfer-linux-centos8_x86_64-7.2.0-20210720-aa8f76b Thanks! Noam From: Gumenyuk, Valentina <vgumenyuk(a)unmc.edu> Sent: Friday, January 14, 2022 10:48 AM To: Peled, Noam <NPELED(a)mgh.harvard.edu> Subject: UNMC error External Email - Use Caution freesurfer-linux-centos8_x86_64-7.2.0-20210720-aa8f76b Thanks! -Valia The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

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Fwd: INS Meeting
by Rosalia Dacosta Aguayo 14 Jan '22

14 Jan '22

External Email - Use Caution FYI!!

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Question about fsaverage
by zhoudongyue＠mail.dlut.edu.cn 14 Jan '22

14 Jan '22

External Email - Use Caution Dear FreeSurfer experts: I am confused how vertex position is determined. Is the vertex's position on surface is determined? And is the distance between each two vertex the same？ Bests， dongyue External Email - Use Caution

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Re: [Freesurfer] Request for the Developer password
by fsbuild 14 Jan '22

14 Jan '22

External Email - Use Caution Sending to your email shortly. - R. On Jan 13, 2022, at 02:31, krystaly <krystaly(a)hku.hk> wrote:        External Email - Use Caution        Dear to Whom It may Concern, I am writing the email of request for a Developer password. As I downloaded Freesurfer by following this link, there was a sign-in page that required the password as shown below:<3F84E90C1E1A49C6BDBEE1CBCDE247FF.png>Would you please kindly send it to me? Thanks.  Best regards, Krystal _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Inconsistent contrasts on longitudinal Samseg
by peder lillebostad 13 Jan '22

13 Jan '22

External Email - Use Caution Dear Freesurfer experts, I want to run a multi-contrast longitudinal Samseg (ms lesions), but not all timepoints are consistent with regards to which contrasts are available (some have only T1s, some have both T1 and T2). As stated in the wiki, `run_samseg_long` does not accept such inconsistent input, but is there a natural workaround for it? So far I lean towards running only those timepoints that contain the full set of contrasts, and subsequently running the cross sectional stream on those timepoints that don't. Does that make sense? Thank you very much! - Peder

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Request for the Developer password
by krystaly 13 Jan '22

13 Jan '22

External Email - Use Caution Dear to Whom It may Concern, I am writing the email of request for a Developer password. As I downloaded Freesurfer by following this link<https://secure-web.cisco.com/1fxAaxGHQxN25yymFu6CFok7OB1Y211kRGwYTn6wh4aXkx…>, there was a sign-in page that required the password as shown below: [cid:image003.png@01D80892.7BA70360] Would you please kindly send it to me? Thanks. Best regards, Krystal

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