Freesurfer

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30083 discussions

FSGD and Contrast file for scanner and sex correction
by Thalhammer, Melissa 17 Nov '21

17 Nov '21

External Email - Use Caution Dear Freesurfers, I am struggling with the group analysis (FT vs. PT) to investigate cortical thickness while correcting for scanner (4 sites) and sex. I have posted a question already regarding the handling of discrete variables and I got to know that all discrete variables should be treated as classes rather than variables in the FSGD file. However, I have difficulties implementing the correct Contrast file right now. My classes are the following: PTMaleScanner1 FTMaleScanner1 PTMaleScanner2 FTMaleScanner2 PTMaleScanner3 FTMaleScanner3 PTMaleScanner4 FTMaleScanner4 PTFemaleScanner1 FTFemaleScanner1 PTFemaleScanner2 FTFemaleScanner2 PTFemaleScanner3 FTFemaleScanner3 PTFemaleScanner4 FTFemaleScanner4 where the two groups FT vs. PT should be compared while regressing out scanner and sex. As far as I understood, we need "1 -1" for the group difference as well as "1 -1" for the gender difference. But how should the complete contrast matrix look like? Thank you in advance! Best, Melissa

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Full-time post-doctoral position at Barcelonabeta Brain Research Center
by Juan Domingo Gispert López 17 Nov '21

17 Nov '21

External Email - Use Caution The Barcelonabeta Brain Research Center (BBRC) invites applications for a full-time post-doctoral position within the context of the ALFA Study, as part of the Neuroimaging Research Group from the Alzheimer’s Prevention Program. *Responsibilities* - Lead and/or collaborate with other researchers neuroimaging analyses of the ALFA+ and related studies - Prepare publications, presentations and internal project reports - Contribute to BBRC’s scientific work in the field of imaging - Required qualifications, competences and technical skills The ideal candidate will have a PhD in a related field with extensive knowledge in the analysis and interpretation of results obtained though human brain imaging (MRI, PET) and with a thorough understanding of Alzheimer’s pathophysiological processes, particularly at preclinical stages. Excellent communication and writing skills in English are necessary as well as the ability to think independently and work collaboratively. *Selection Process* - Pre-selection: The pre-selection process will be based on qualifications, expertise and motivation reflected on the candidate cover letter and CV. It will be merit-based. - Interview: Preselected candidates will be interviewed by an internal scientific committee. - Offer Letter: Once the successful candidate is identified the Human Resources department will send a Job Offer, specifying the start day, salary, working conditions, among other important details. *Benefits* We offer a unique research opportunity in a highly innovative project in a multidisciplinary institution. - Starting date: ASAP - The position is scheduled initially for 3 years - Salary will depend on experience and will be in accordance to BBRC’s salary scales. - We offer and promote a diverse and inclusive environment and welcomes applicants regardless of age, disability, gender, nationality, ethnicity, religion, sexual orientation or gender identity. *Application process* To apply, please submit a single PDF file containing the following: - Cover letter addressed to Dr Juan Domingo Gispert describing research interests and relevant background - CV - The names of up to three individuals who could provide reference letters. All files or inquiries should be submitted electronically to: rh(a)barcelonabeta.org Subject: Post-Doctoral position in the Neuroimaging Research Group Deadline: December 30th 2021 Click here <https://secure-web.cisco.com/13cwhRjdcRHPPe-8xDp2j2y8N9AFYRuVUoin8qYoM_J4tj…> for additional info. -- *Juan Domingo Gispert*Group Leader - Neuroimaging *BarcelonaBeta* * Brain Research Center (BBRC) *jdgispert(a)barcelonabeta.org T. (+34) 93 326 31 67 C/ Wellington, 30 <https://secure-web.cisco.com/1zP4b-68JcaLTeuY7cv5dEnYFEXTatDJltZ18aK8PV3H4D…> 08005 Barcelona <https://secure-web.cisco.com/1zP4b-68JcaLTeuY7cv5dEnYFEXTatDJltZ18aK8PV3H4D…> http://secure-web.cisco.com/15a2Ixd8m4Qhdy_9LDhNwmw6ChXiqFErJn3z25MWJLZyb4p… http://secure-web.cisco.com/1sBhbeGpbzUZ0csHOvR17uMKvE4MHbWTAGCbmwi0Y49SCvi… ------------------------------ Confidencialitat correu electrònic BBRC <https://secure-web.cisco.com/153Q9mbmJOHl6fAJ-x4o5vN8ZuG3r4-nGX20X54CZjW0D5…>. Confidencialidad correo electrónico BBRC <https://secure-web.cisco.com/1Et8vH3ow2yrmwIfvJzHkVQgyzEsKoEA_NPq8joFXk5FOa…>. E-mail confidentiality BBRC <https://secure-web.cisco.com/1tqmgN9YeJMg9QrjBSUGkT6v3QfftbgXk1-69Uvcz8_Pn4…>. Gràcies per estalviar paper. *Gracias por ahorrar papel. *Thanks for saving paper.

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recon-all
by a Chinese reader 17 Nov '21

17 Nov '21

External Email - Use Caution Dear Freesurfer experts,When I run the command "recon-all -s <> -qcache" , ERROR: cannot find /home/siying/sharefolder/piantoutong/freesurfer_1/NC1/surf/lh.thickness Could you help me solve this problem? Thanks in advance.

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Re: [Freesurfer] freeview error after installation: Segmentation fault(core dumped) / free( ): invalid pointer, Aborted(core dumped)
by fsbuild 17 Nov '21

17 Nov '21

External Email - Use Caution Hello Xuxiao, In a terminal window in Ubuntu running under WSL, please try just running a simple X windows program like xeyes to test that your X-server is running on Windows,  $ xeyes (see attachment for what it should look like) Keep an eye out for a flashing X server icon at the bottom of your Windows desktop.  You may have to click on that flashing icon for the xeyes X window to open.  But if you can’t display something simple like xeyes with the X server on Windows 10, then freeview is not going to work. If you installed the Xming X-server on Windows, then you should see an X icon on your desktop that you can click on to start the X-server.  And you can check you see the X icon in the “hidden” area at the bottom of the screen which shows the X server is running on Windows.  See the bottom of this page for how to see Xming is running and then scroll up to see the X windows desktop icon, https://secure-web.cisco.com/1OO6_69UmGU84poSsYr7cookfWG3oW-9wCm… If xeyes works, then check your freesurfer license file can be found.  One way to do that is to set the environment variable FS_LICENSE to the absolute path to your license file.  So you could for example call your license file “license.txt” and copy it into your home directory (denoted by the environment variable $HOME).  You can also set FS_LICENSE in your shell init file. $ cd $HOME$ pwd<output deleted> $ ls license.txtlicense.txt$ export FS_LICENSE=$HOME/license.txt … check it can be read … $ cat $FS_LICENSE<output deleted> Now set FREESURFER_HOME, source the setup environment script as you did in the screenshot you sent below, and try running freeview with no arguments to see if a blank window opens. $ freeview Another thing to consider is to try and install the latest version of freesurfer (7.2.0) using the Ubuntu .deb package installer from https://secure-web.cisco.com/1WCN8dpJeL5ctI2hET4QOYyxIu9gxAiTFJ_bFQH-ZV0hRC… and install it with, $ sudo apt-get install ./freesurfer_7.2.0_amd64.deb Then you should see 7.2.0 installed as something like /usr/local/freesurfer/7.2.0 which you would use for FREESURFER_HOME - R. On Nov 16, 2021, at 07:26, 许霄 <xuxiao(a)xii.ac.cn> wrote:        External Email - Use Caution        Hello FreeSurfer Developers,I can't access the website of archives, so I have to ask questions in this way. I installed freesurfer7-dev in Ubuntu18 in wsl according to the tutorials  FS7_wsl - Free Surfer Wiki (harvard.edu) and FS7_wsl_ubuntu - Free Surfer Wiki (harvard.edu) After adding the license, when I tried to run the 'freeview' command to test if everything works well, an error popped out: Segmentation fault(core dumped). more information about my freesurfer environment is shown as attached. Could anyone help me figure it out? Thanks in advance.<freeview-Segmentation fault.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Segmentation of thalamic nuclei
by Katherine Andrade 16 Nov '21

16 Nov '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run thalamic segmentation using the following command: segmentThalamicNuclei.sh SUBJID. I've been able to run segmentation in the past. However, this time when I execute the command, I receive the following error: /home/bdl/freesurfer/subjects/SD027/scripts/IsRunningHPsubT1.lh+rh: No such file or directory. I opened the scripts folder and did not find the "IsRunningHPsubT1.lh+rh." I've looked through the other subjects I've run segmentation of the thalamic nucleus for and they also didn't have this script. Yet for some reason I was able to run the segmentation. Is this a new feature? Do I need to rerun segmentation again? Please advise. Best, Katie -- Katherine D. Andrade Pronouns: she/her/hers Ph.D Student SDSU/UCSD Joint Doctoral Program in Language and Communicative Disorders

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freeview error after installation: Segmentation fault(core dumped) / free( ): invalid pointer, Aborted(core dumped)
by 许霄 16 Nov '21

16 Nov '21

External Email - Use Caution Hello FreeSurfer Developers, I can't access the website of archives, so I have to ask questions in this way. I installed freesurfer7-dev in Ubuntu18 in wsl according to the tutorials FS7_wsl - Free Surfer Wiki (harvard.edu) and FS7_wsl_ubuntu - Free Surfer Wiki (harvard.edu) After adding the license, when I tried to run the 'freeview' command to test if everything works well, an error popped out: Segmentation fault(core dumped). more information about my freesurfer environment is shown as attached. Could anyone help me figure it out? Thanks in advance.

1 0

SUBJECT_DIR using bbregister
by m-maiworm＠web.de 15 Nov '21

15 Nov '21

3 3

Freesurfer: Re-run recon-all in older versions
by Steve Petersen 12 Nov '21

12 Nov '21

External Email - Use Caution Dear all, We conducted the recon-all and applied a quality control protocol in several subjects using the FSurfer 6 version. Now, we would like to run the recon-all again on an older version of FSurfer (5.3 v) but considering the edits we made on those previous recon-all. Is this possible?, and if so, what would be the command? Thank you very much in advance. Best regards, Steve.

3 4

Transform matrix
by Alberto Del Cerro Leon 12 Nov '21

12 Nov '21

External Email - Use Caution Hello Freesurfer team, I did a white matter atlas from surface annot with mri_aparc2aseg. However, when I use this atlas in comparison with the original T1 I have observed that both images don't share the transformation matrix. Do you know how I could I fix this issue?

3 2

FsFastFunctionalConnectivityWalkthrough
by Alice Giubergia 12 Nov '21

12 Nov '21

External Email - Use Caution Thanks for your replies Doug! I copied the previous messages below, since I did not menage to retrieve the original email. 1) Thanks. 2) Regarding question number 2, yes that was what I meant. 3) I ran the task analysis and extracted time series from unwhitened residuals by mri_segstats, upon a specific segmentation. I was thinking now of a correlation matrix by Pearson's coeff. Any further suggestions? Also, I've got a pheraps silly question: - When running a task analysis, I could specify -taskreg and -nuisreg separetly. My assumption is that only -nuisreg are regressed out from the data and that the residuals saved got task-related bold signal. Is it correct? - If so, could I use task regressors as -nuisreg to get a "pseudo" resting state? Hoping all question are clear, Thanks for your patience, Alice Dear FreeSurfer experts, I'm interested in performing a functional analysis on task-based data. I was taking as an example the "FsFastFunctionalConnectivityWalkthrough" tutorial but, if I got it correctly, is specific for resting state data. So I've got some doubts and questions: 1) Given the steps described in the above mentioned tutorial, the file "pcc.mgz" generated in the session folder gives me the correlation strength between the time series of each voxel and the seed (L_Posteriorcingulate in the tutorial)? Yes, correct 2) If I want to make a functional analysis on task data, similar to the one described in that tutorial, could I just add the -event-related option instead of -notask option? (mkanalysis-sess -analysis fc.lpccseed.surf.lh -surface fsaverage lh -fwhm 5* -notask* -taskreg L_Posteriorcingulate.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR <TR>) Do you mean you want to do a simultaneous analysis of the task and the connectivity? I just tried what you suggested and it looked like it worked. 3) Otherwise, does it make sense to you If I run a simple task analysis to regress nuisances out (without seed region), extract time series and get the pair-wise correlation with Pearson coefficient? This is possible, and makes sense. It is a little difficult to do, but not terrible. If you want to go this route, you would need to first analyze your task data as task without FC, specifying -svres-unwhitened to save the residuals. Let me know when you get to that point and I can push you further. Hoping my questions are clear, Thanks a lot for your patience and help, Alice

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