Freesurfer February 2021

freesurfer@nmr.mgh.harvard.edu

98 participants
118 discussions

-hires vs -conf2hires in 7.1.1.
by Alexopoulos, Dimitrios 21 Mar '21

21 Mar '21

External Email - Use Caution Does the hires flag still generate segs at the native hi resolution and place surfaces on the 1mm volumes, whereas conf2hires generates volumes at 1mm but places surfaces on the hires images? Which option is recommended and why? Jim Get Outlook for Android<https://aka.ms/ghei36> ________________________________ 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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Samseg longitudinal processing
by Jayachandra Raghava 18 Mar '21

18 Mar '21

External Email - Use Caution Hello Freesurfer Experts, I am using Freesurfer version 7.1.1 to perform longitudinal Samseg processing (using run_samseg_long) on my T1 longitudinal data. 1) First, I run the mri_robust_template to generate the mean.mgz using T1.mgz from the cross sectional recon-all pipeline. Would it be better to use T1.mgz from the longitudinally processed data? 2) There are few subjects who do not have followup data. How do I process these subjects to avoid the bias introduced by the longitudinal Samseg pipeline? 3) For the same subject, I see that the subcortical volumes from longitudinal recon-all pipeline from aseg.stats (e.g Left-Hippocampus volume is 3321.5mm3) are different to the subcortical volumes from longitudinal samseg pipeline from samseg.stats (e.g Left-Hippocampus volume is 3899.628686mm3). Which of these measures would be recommended? Thank you very much for your support! Best wishes Jay

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Matlab version 2012b installation problem
by Georgia Kapizioni 11 Mar '21

11 Mar '21

External Email - Use Caution Dear Freesurfer experts, I am trying to install Matlab version 2012b but a message appears: command not found. Firstly, I ran: sudo cd $FREESURFER_HOME/bin && curl https://secure-web.cisco.com/1aj9gsBgtgn7YY-Cjp-4RTDQ9ZZ-zSt6U2uLhCNs0DAt-2… -o fs_install_mcr && chmod +x Then I typed: fs_install_mcr R2012b and I receive: command not found. My FS version is 6 and I have already install Matlab2016_b on my Mac. Could you please help me resolve this issue? Thank you in advance, Georgia

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Hippocampus subfield segmentation error on Ubuntu 20.04.1 LTS
by Ishi Tandon AIB, Jaipur 05 Mar '21

05 Mar '21

External Email - Use Caution Hello experts, In response to the previous email about matlab installation error while attempting to use hippocampal subfields. I tried the following command as suggested by you :- sudo apt-get install libcurses5-dev But I get the following error :- Reading package lists... Done Building dependency tree Reading state information... Done E: Unable to locate package libcurses5-dev Also, I am using fs version 7.1.1. I installed freesurfer-linux-centos7_x86_64-7.1.1.tar.gz file. *Regards,* *Ishi Tandon* *B.Tech + M.Tech - Cognitive Neuroscience* *Amity University, Rajasthan* *Contact- +918239259846* *Email - ishi.tandon99(a)gmail.com <ishi.tandon99(a)gmail.com>*

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Re: [Freesurfer] longitudinal group analysis displaying results
by Agurne Sampedro Calvete 03 Mar '21

03 Mar '21

External Email - Use Caution Dear Freesurfer experts, In relation to the previous question, could I obtain a Z value of the significant cluster obtained by opening in freeview the z.mgh and place the cursor on the point with the highest value? Is there another way to obtain a Z value or alternatively, a t-value? Thank you very much in advance, Best regards, Agurne El mar, 23 feb 2021 a las 13:25, Agurne Sampedro Calvete (< a.sampedro(a)deusto.es>) escribió: > Dear Freesurfer experts, > > I am doing a longitudinal repeated measures analysis and after correcting > for multiple comparisons with Z Monte Carlo simulation (with the "mri_glmfit-sim > ... --cache 3 ..." command), I obtained a significant cluster for my > experimental group (pre-post). > > In order to obtain the information for displaying the results in the > paper, I am looking at the cluster summary table. I have seen that some > papers include the t value in addition to the p value, cluster size and > coordinates, but how can I obtain the t value? Does it appear in the > cluster summary table or elsewhere? > > Thank you very much in advance, > > Kind regards, > > Agurne > > > > >

2 4

Recon-all exiting with Errors during surface inflation
by Koch, Erin M. 01 Mar '21

01 Mar '21

External Email - Use Caution Hi all, The lab I work in recently upgrade to freesurfer-linux-centos7x_86_64-7.1.1 from freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I am trying to use a series of shell scripts (that call freesurfer) which we successfully used to run to create flatmaps for non-human primate sessions. I am stuck when using recon-all to inflate the surface. Specifically, I am running the command: "recon-all -autorecon2-wm \ -subjid ${tmp_subj} ${corpcal_coord_string} ${pons_coord_string}\ -noaseg \ -mprage \ -xopts-use\ -debug\" This step runs for quite some time, seemingly making progress and then "Exits with errors" . In the terminal the error message that I can see is: "ERROR: need seg for ripping". This is followed by: "recon-all - s SUBJECTNAME exited with ERRORS." (Screen shot of this error is attached). I will also attach the recon-all.log. This issue does not seem to be a problem of quality of skull stripping or white matter segmentation, as the session can be completed with the older version of freesurfer, adn I get the same error with different sessions and subjects. Can you please shed some light on this? The machine I am using is running Linux 3.10.0-1127.18.2.e17.x86_64 . As an aside - Do you have any references or outline for flat map creation (specifically for non-human primates) with the newer versions of Free surfer? It is possible adapting our old pipeline is not ideal / there are more efficient or "better" ways to do this now. Thank you for your help. Best, Erin

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mri_vol2surf resolution warning
by Russo, Andrew William 01 Mar '21

01 Mar '21

Hello, I am moving a 6mm volume from MNI152 to fsaverage for group analysis and I get the following warning: mri_vol2surf --src MNI_6mm.nii.gz --out surf_sm4_lh.mgh --mni152reg --hemi lh --interp nearest --surf-fwhm 4 WARNING: the voxel resolution in the source volume (6,6,6) differs from that listed in the registration file (1,1,1) Do you know if this needs to be corrected or if there is a better method? Thanks for the help, Andrew Andrew Russo Clinical Research Coordinator Multiple Sclerosis Imaging Lab Massachusetts General Hospital 149 13th Street | Boston, MA 02129 617-726-7531

2 1

Talairach to RAS conversion
by Nasiriavanaki, Zahra 01 Mar '21

01 Mar '21

Hi Freesurferers I have some talairach coordinates on the cortical surface (extracted from a paper) and I need to see their location on my fmri maps. I used "tksurfer> go to saved point “ to see the location of that coordinate on my map. However, that coordinate is in talairach. Should I convert it to RAS and then save it as a point in tmp folder? If so, could you please let me know how I should convert them from talairach to RAS? Thanks MOna Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry Massachusetts General Hospital 149 13th Street, 149-2615 Boston, MA, USA, 02129

2 4

Hippocampal segmentation
by Alberto Del Cerro Leon 01 Mar '21

01 Mar '21

External Email - Use Caution Hello Freesurfers, I am doing an AAL atlas on freesurfer using mri_vol2surf and editing the labels manually. However when I was editing the labels in tksurfer the hippocampal field is quite bad. I tried to look the segmentation used by you in labels but I didn't find it. How could I segment the Hippocampus????

2 3

Installing freesurfer 6 in a preexisting conda environment
by Bruno Mansur 01 Mar '21

01 Mar '21

External Email - Use Caution Dear community members, I created a conda environment for installing MNE. Now I want to install freesurfer in this same environment to use freesurfer in combination with MNE. Does anyone have already installed and configured freesurfer in an environment and could give me some support with it? The mailing list has no entries related to 'conda environment' and the freesurfer installation guide webpage has no instructions related to this. I would appreciate any help, Best regards -- *Bruno*

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Freesurfer February 2021