Freesurfer

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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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Amygdala Segmentation T1.v20 Command
by Deng, Yushan Wisteria 07 Jan '20

07 Jan '20

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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Re: [Freesurfer] When rerunning recon-all from a later stage, are only edited participants' reconstructions recalculated?
by Mohammad Rashid 06 Jan '20

06 Jan '20

External Email - Use Caution Ah okay, I understand now, thank you very much for the help! In hindsight this was a stupid question. What you said makes things perfectly clear. Thanks again! ________________________________ From: Mohammad Rashid <17mrr6(a)queensu.ca> Sent: Monday, January 6, 2020 12:04 PM To: Tim Schäfer <ts+ml(a)rcmd.org> Subject: Re: [Freesurfer] When rerunning recon-all from a later stage, are only edited participants' reconstructions recalculated? Ah okay, I understand now, thank you very much for the help! In hindsight this was a stupid question. What you said makes things perfectly clear. Thanks again! ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Tim Schäfer <ts+ml(a)rcmd.org> Sent: Monday, January 6, 2020 3:29 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] When rerunning recon-all from a later stage, are only edited participants' reconstructions recalculated? External Email - Use Caution In your command line: `recon-all -autorecon2-noaseg -autorecon3 -subjid subj507` you run the command only for that single subject, 'subj507'. That is exactly what will happen, no command will be run for the other subjects, so their data remains unchanged. It has nothing to do with editing or not. If you want to run again for other subjects, you would have to run the recon-all command with their subject IDs (one command per subject). I hope I did not misunderstand your question? Tim > On January 4, 2020 at 6:09 PM Mohammad Rashid <17mrr6(a)queensu.ca> wrote: > > > External Email - Use Caution > > I recently ran this command: > `recon-all -autorecon2-noaseg -autorecon3 -subjid subj507` after having edited aseg.mgz (there was too much matter labelled as right hippocampus, so my edit was simply overwriting Right-Hippocampus voxels with Right-Cerebral-White-Matter ones). > > After the command's error-free completion, I checked the hippocampal volume measurements of all of the participants again using asegstats2table and found that they were all unchanged, except slight changes to subject subj507's measurements. > > So when instructed, does freesurfer only redo the reconstruction and recalculate stats only for those subjects that you've edited? If so, is there a way to have it recalculate every subject, not just those I've edited? > > Thank you in advance. > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.… -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.…

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Re: [Freesurfer] Run Recon-all Parallel on Linux
by Frank Chau 06 Jan '20

06 Jan '20

External Email - Use Caution Dear Bruce, No, I want to run recon-all on 4-8 subjects at the same time. I could find detail tutorial on the Mac platform (Run: "ls *.nii | parallel --jobs 4 recon-all -s {.} -i {} -all -qcache", after installing Xcode and Homebrew.) But I couldn't find any similar information on the Linux platform. Regards Frank On Jan 3, 2020 11:15 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: Hi Frank do you mean completing a single recon faster? The easiest way to do that is to use the -openmp <N> flag, and set <N> to the number of threads/cores you want to use. Alternatively if you have enough RAM you can just run multiple recon-alls at the same time (which will give you a bigger effective speed increase) cheers Bruce On Fri, 3 Jan 2020, Frank Chau wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > > > May I know how to run Recon-all in parallel on Linux? I have read some > source said that can use "gnu parallel" to complete it. But they do not > describe it in detail how to perform it. > > > Regards > > > Frank > > --------------------------- > > FRANK C Y CHAU > > > Research assistant > > Division of Neurology > > Department of Medicine > > > Tel: +852 6340 2553 > > Fax: 2872 5828 > > > E-mail : cyfrank(a)hku.hk > > > > Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, > Hong Kong > > >

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Question regarding T1 map from spoiled 3D GRE
by joe vanderlo 06 Jan '20

06 Jan '20

External Email - Use Caution Dear Freesurfer community, I computed T1 maps from Siemens VIBE (a spoiled 3D GRE variant; instead of Siemens FLASH (RF-Spoiled GRE)). I utilized mri_ms_fitparms to compute the T1 map (which looks ok) and compared the result to a T1 map (inline) from MP2RAGE. However, T1 values based on Siemens VIBE (FA: 4, 8, 13, 21, 34) are much lower than from MP2RAGE: (results from the same subject, same day/position/setup scan, same ROIs) WM/Corpus callosum: 652 ms (VIBE) vs 859 ms (MP2RAGE) Cerebellaer WM: 583 ms vs 834 ms --- GM/Cortex: 845 ms vs 1184 ms Deep/Inner GM: 780 ms vs 920 ms --- Liquor: 2222 or 3121 vs 2758 or 3652 ms Eye-Bulb: 112 vs 588 The literature suggests (mouse brain, 3T): Corpus callosum 1108±9 Internal capsule 913±16 Hippocampus 1310±15 Cortex 1246±28 (DOI: 10.1118/1.2968092) The literature suggests (rat brain, 3T): WM: 1084 or 1110 ms GM: 1820 or 1470 ms (DOI: 10.1002/mrm.20605) However, it appears that T1 values can be quite different (Fig. 3 from 10.1002/mrm.21313) #-----------# Therefore, I would like to ask: (1) Is it to be expected that T1 values differ dependent on the method used at same field strength and same scanner/setup? (2) Considering that mri_ms_fitparms has not option for B1 correction, can I "optimize" the maps in a different manner? Would it make sense to run N4B on the respective VIBE scans (before map computation) or maybe directly on the T1 map? (3) I would assume that the application of the VIBE sequence should be acceptable. Are there reasons not to believe so? Thanks in advance

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