Freesurfer January 2020

freesurfer@nmr.mgh.harvard.edu

97 participants
156 discussions

Anterior parts of Temporal Lobe missing
by Meike Hettwer 10 Jan '20

10 Jan '20

External Email - Use Caution Hi everyone, I am currently working on cortical thickness analyses using freesurfer v. 6.0.1. (on Debian /Linux 7). All of my data sets show a segmentation error in the anterior protions of the temporal lobe (mostly STG and almost always bilateral). I tried adding control points as well as editing wm.mgz manually. It does not seem to help much, though. After running "recon-all -autorecon2-cp -autorecon3 subjid .." without errors, the images look just the same (just with the green control points lighting up). I saw that other users encountered similar problems but did not find a solution in the archives. Does anyone have an idea how to fix this? The intensity values are around 73 for white matter and 46 for grey matter. Thanks a lot in advance, Meike Hettwer

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Fixing wm/gm in brain with a cyst
by Laurel Quinlan 09 Jan '20

09 Jan '20

External Email - Use Caution Hi FS Support, I am working on manual edits to a brain with a suspected cyst. Attached is an axial view of the original recon. As you can see, there appears to be wm missing from the segmentation right next to the cyst. I am wondering how I should go about fixing the segmentation with this brain. Should I fill in the missing white matter next to the ventricular hole, and avoid adding anything to the hole itself? Or is there another step I should take? Thanks! Laurel Quinlan Research Specialist Center for Healthy Minds University of Wisconsin-Madison

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Re: [Freesurfer] Error
by fsbuild 09 Jan '20

09 Jan '20

External Email - Use Caution Hello Kirill, Is the shared folder where the “ln -s” command is running to create a soft link on a disk that is formatted to have a Windows file system, e.g., NTFS?   My understanding is that Linux/Unix style soft linking via the “ln” command does not work on such a windows file system.  Freesurfer scripts assume the file system supports standard Unix/Linux soft links via the ln command, e.g., where the disk partition or volume it runs on is formatted as ext3 or ext4. You can install software in Windows to *read* a linux file system.  The link below talks about 2 software applications for windows -  one can read linux file systems, and the other can read both linux and Mac file systems. https://www.howtogeek.com/112888/3-ways-to-access-your-linux-partitions-fro… - R. A Windows NTFS file system does not support Unix soft links On Jan 9, 2020, at 08:58, Kirill Elin <ekirling(a)gmail.com> wrote:       External Email - Use Caution        Dear FreeSurfer Developers,I am trying to run the script and the recon-all command and gettingExited with errors output.1. FreeSurfer Version freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c2. Platform, VM Ware Workstation 15, host OS: Windows 10, Guest:Ubuntu ubuntu-18.04.3-LTS, 64 Bit, 2 GB RAM3. See the log file and the screenshot.In the script I have not found any other errors so I am not even sure,what I should be looking for.If it plays a role, my MRI folder, where original T1s are as well asthe output folder are in the shared folder (shared between the hostwindows OS and the virtual machine).I would be grateful if you could help me out with this.Thank you in advance.Sincerely yours,Kirill<Finish_Errors.PNG><recon-all.log>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Projection on fsaverage5
by Marina Fernández 09 Jan '20

09 Jan '20

External Email - Use Caution Hi Doug, Thank you for your advice. I checked the results using ico 5 and fsaverage5 and it seems to have exactly the same values, but we are going to use --trgsubject fsaverage5, as you told me. On the other hand if we use EPI that it is coregistered to the T1 of Freesurfer there is no problem with the projection on fsaverage5. Thank you very much! Cheers, Marina

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RB_all_2020-01-02.gca and RB_all_withskull_2020_01_02.gca public permissions
by Kostakis Gkiatis 08 Jan '20

08 Jan '20

External Email - Use Caution Dear Freesurfer experts, I am trying to compile freesurfer from source. It is nicely performed expect the "git annex get ." command which fails in these two files, RB_all_2020-01-02.gca and RB_all_withskull_2020_01_02.gca. I searched github's annex branch but no sign of the files. Do I have, as public, the right permissions to download them? Can I find these two files somewhere else? Thank you in advance. Yours sincerely, Kostakis -- Electrical and Computer Engineer Phd Candidate in Brain Imaging Medical Image Processing, Algorithms and Applications National Technical University of Athens 9,Iroon Polytechneiou str., 157 73 Zografou Campus, Athens, GREECE phone:+30 210 772 3577

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Projection on fsaverage5
by Marina Fernández 08 Jan '20

08 Jan '20

External Email - Use Caution Hi Bruce, Thanks for the quick response. I found that the problem was the input. If I use the EPI that it is coregistered to the T1 of Freesurfer instead of the EPI that it is also normalized to the MNI space, it works and I can project the surface (that I created with the command that I sent you) on fsaverage 5. Could you confirm that the command has no errors? mri_vol2surf --mov EPI.nii --reg register.dat --hemi [l/r]h --projfrac 0.5 --interp trilinear --trgsubject ico --icoorder 5 --o EPI_surface.mgh Best wishes, Marina

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FsFast Question
by Swetara Joshi 08 Jan '20

08 Jan '20

External Email - Use Caution Hello, I am new to fmri processing/FsFast and I had a question on creating nuisance variables. Is it possible to set a block-design task fMRI paradigm file as a nuisance variable, so that it can be inputted at a .dat file for the mkanalysis-sess command? Thank you! Best, Sweta Sweta Joshi Research Assistant Department of Neurology ------------------------------------- GW Medical Faculty Associates George Washington University Hospital 2150 Pennsylvania Ave, NW, 9th Floor, Washington, DC 20037 Office: 202.655.5888 Email: sjoshi(a)mfa.gwu.edu Confidentiality Note: This e-mail is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential or otherwise protected from disclosure. Dissemination, distribution or copying of this e-mail or the information herein by anyone other than the intended recipient, or an employee or agent responsible for delivering the message to the intended recipient, is prohibited. If you have received this e-mail in error, please call (202) 741-3636 and destroy the original message and all copies.

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Projection on fsaverage5
by Marina Fernández 08 Jan '20

08 Jan '20

External Email - Use Caution Dear Freesurfer experts, I would like to convert the individual preprocessed EPI volume (that it is normalized to MNI152 space and without smoothing) to surface and project it on fsaverage5. I used the following command: mri_vol2surf --mov EPI.nii --reg register.dat --hemi [l/r]h --projfrac 0.5 --interp trilinear --trgsubject ico --icoorder 5 --o EPI_surface.mgh Is it correct? Then, I tried to project the surface in fsaverage5 and it seems to be rotated (it doesn't match). What should I do to project it correctly? Thank you in advance. Best regards, Marina.

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Re: [Freesurfer] Amygdala Segmentation T1.v20 Command
by Deng, Yushan Wisteria 08 Jan '20

08 Jan '20

Hi Eugenio, Thank you so much for your response! I did use the development version to run the command. Would you have any other ideas what the possible cause might be? Best, Wisteria Date: Tue, 7 Jan 2020 09:05:32 +0000 From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu<mailto:JIGLESIASGONZALEZ@mgh.harvard.edu>> Subject: Re: [Freesurfer] Amygdala Segmentation T1.v20 Command To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <8970525B-ED9A-4F56-901A-50F5787C925D(a)mgh.harvard.edu<mailto:8970525B-ED9A-4F56-901A-50F5787C925D@mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" Dear Wisteria, Did you run the command segmentHA_T1.sh on those subjects using the development version? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Deng, Yushan Wisteria" <YWDENG(a)mgh.harvard.edu<mailto:YWDENG@mgh.harvard.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Friday, 3 January 2020 at 20:31 To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Amygdala Segmentation T1.v20 Command Dear Freesurfer experts, Happy new year! I encountered an issue with the quantifyHAsubregions.sh command as I tried to extract amygdala subnuclei values from a previously segmented dataset. I tried both commands below, specifying the version (v20) and not: quantifyHAsubregions.sh amygNuc T1 All_Amyg [subjects_dir] quantifyHAsubregions.sh amygNuc T1.v20 All_Amyg [subjects_dir] The command did not run. No error message was given. It just skipped to a new command line. Please see attached for a screenshot. The recon was done in Freesurfer 5.3 and the sample size is very big (~1400). I wonder if that or anything else could be causing the problem. Any guidance is immensely appreciated! Thank you! Wisteria Wisteria Deng Clinical Research Coordinator Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Rm 2611 Charlestown, MA 02129 Phone: 617-643-4441

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PALM - MATLAB error
by Martin Juneja 07 Jan '20

07 Jan '20

External Email - Use Caution Hi, I am trying to run PALM in MATLAB. After I run the following command, I get following error: palm -i SPSX/lh.SPS_vol.10.mgh -s fsaverage/surf/lh.white.avg.area.mgh -d SPSX/lh.SPS_vol.glmdir/X.mat -t Corr-SPS-cor.csv -m SPSX/lh.SPS_vol.glmdir/mask.mgh -o SPSX/PT -C 1 -twotail -n 1000 -nouncorrected Running PALM alpha116 using MATLAB 9.6.0.1072779 (R2019a) with the following options: -i SPSX/lh.SPS_vol.10.mgh -s fsaverage/surf/lh.white.avg.area.mgh -d SPSX/lh.SPS_vol.glmdir/X.mat -t Corr-SPS-cor.csv -m SPSX/lh.SPS_vol.glmdir/mask.mgh -o SPSX/PT -C 1 -twotail -n 1000 -nouncorrected -noniiclass Loading surface 1/1: fsaverage/surf/lh.white.avg.area.mgh Reading input 1/1: SPSX/lh.SPS_vol.10.mgh Dot indexing is not supported for variables of this type. Error in palm_takeargs (line 1679) if any(size(plm.srf{s}.data.vtx,1) == ... Error in palm_core (line 33) [opts,plm] = palm_takeargs(varargin{:}); Error in palm (line 81) palm_core(varargin{:}); Any help in resolving this issue would be really appreciated. Thanks.

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Freesurfer January 2020