Freesurfer November 2021

freesurfer@nmr.mgh.harvard.edu

77 participants
118 discussions

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.

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

15 Nov '21

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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.

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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

2 1

lh.thickness can not found
by a Chinese reader 11 Nov '21

11 Nov '21

External Email - Use Caution Hello FreeSurfer Developers,I'm attempting to compute the thickness of the grey matter ,but for some of my subjects I get the following error when I run the recon-all -s <> -all command:Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue.I've searched the list and no similar errors have been reported. Did this warning have any effect for my outcome?And why my lh.thickness cannot generated? Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. Best regards, Zhang Xia

2 1

T1 aparc.stats vs T1 with T2 aparc.stats
by Castro Leal, Gonzalo 11 Nov '21

11 Nov '21

External Email - Use Caution Hello, I wanted to compare the results of the aparc.stats on the same subjects when only the T1 is used and when T2 is used for pial refinement along with the same T1. To my surprise the tickness increased (on average across regions), the gm volume decreased and the surface didnt change. My questions is how is that the thickness increased and the volume decresed if the surface did not change? (I used freesrufer 7.1.1) Many thanks, Gonzalo.

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question regarding FSGD file for coding discrete regressors
by Zeng, Qi 11 Nov '21

11 Nov '21

External Email - Use Caution Hi Freesurfer experts, Here, I want to design a simple group comparison (two levels: Case vs. Control) and also count for 4 covariates (two continuous and two categoricals). However, the GLM model cannot recognize my discrete variables. What do you suggest to change? >> FSDG file: GroupDescriptorFile 1 Title MyStudy Class Control Class Case Variables age gender race eTIV Input sub001_base Control 85 Female White 1350519 Contrast: >> Design matrix for Case-Control and regress out the effect of age, gender, race, and eTIV. -1 1 0 0 0 0 0 0 0 0 Best, Zeng

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Freesurfer November 2021