Freesurfer

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30132 discussions

Compiling freesurfer 6.0 on centos 8.1
by Aaron Tanenbaum 01 Jun '20

01 Jun '20

External Email - Use Caution Hello All, I was wondering have any of you compiled FreeSurfer 6.0 on centos 8.1. And if so, have you had problem with it. Our lab got a new server, we are contemplating which operating system we should install. So I am going through the software to see what works and what does not on different versions of centos. Aaron Tanenbaum

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Re: [Freesurfer] Running amygdala segmentation on a warped brain (fsaverage-to-MNI152)
by Iglesias Gonzalez, Juan E. 01 Jun '20

01 Jun '20

Hi Elizabeth, segment_T1.sh uses a bunch of files in native space for initialization that you’d also have to deform, if you wanted to run it in MNI space. I think the easiest would be to run it in native space, and then warp the segmentation to MNI, using e.g., the registration given by CVS. 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> on behalf of Elizabeth Haris <e.haris(a)unsw.edu.au> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, May 27, 2020 at 23:11 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Running amygdala segmentation on a warped brain (fsaverage-to-MNI152) External Email - Use Caution Hi guys, I’m wanting to run segmentHA_T1.sh on an MNI152 registered brain. On my subject, I have run recon-all, then run mri_cvs_register to obtain a brain image registered in MNI152 space. My questions are: 1. In recon-all, is there a way to specify registration to MNI152 space, or is it necessary to first run recon-all and then to run mri_cvs_register? 2. Is it possible to run the segmentHA script on the brain registered in MNI152 space? I’m unable to find where I would specify the use the cvs/norm.mgz (instead of the mri/norm.mgz file). And from what I can see in the script, the parameters set in lines 179/180/181 (below) point to fsaverage brain files, which don’t appear to be the correct targets for the new MNI152 brain; however, there are no corresponding output files in the cvs folder, so I am unsure how to define these parameters. 3. Is there anything I have missed and would also need to do to run the segmentHA script on an MNI152 brain? (I have previously run the script on the average brain and all went well.) 179 set ATLASMESH="$FREESURFER_HOME/average/HippoSF/atlas/AtlasMesh.gz"; 180 set ATLASDUMP="$FREESURFER_HOME/average/HippoSF/atlas/AtlasDump.mgz"; 181 set LUT="$FREESURFER_HOME/average/HippoSF/atlas/compressionLookupTable.txt"; Thanks in advance, Elizabeth

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mri_vol2surf
by Nasr, Shahin,Ph.D. 01 Jun '20

01 Jun '20

Hi Surfers, Is there anyway to pass the full address of a surface to mri_vol2surf? To clarify, we are using surfaces that are saved outside <SBJ>/surf/ and we prefer not to relocate them every time that we want to use mri_vol2surf. Thanks

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Freesurfer 7 long -> cross surfaces
by Chris Adamson 01 Jun '20

01 Jun '20

External Email - Use Caution I had a script that transformed volumes and surfaces from long (base) space back to cross space for comparison. It doesn't work in Freesurfer 7 and I haven't been able to figure out why. Volumes work with the same code but surfaces are misaligned in cross space. The code is below, any thoughts on how to fix it? Cheers. SURFS="white pial inflated" HEMIS="lh rh" cd $SUBJECTS_DIR/$LONG/surf lta_convert --inlta $SUBJECTS_DIR/$BASE/mri/transforms/${CROSS}_to_${BASE}.lta --outreg register.native.dat --src $SUBJECTS_DIR/$CROSS/mri/rawavg.mgz for CURHEMI in $HEMIS do for CURSURF in $SURFS do mri_surf2surf --sval-xyz $CURSURF --reg-inv register.native.dat --tval $SUBJECTS_DIR/$OUTDIR/surf/$CURHEMI.$CURSURF --tval-xyz $SUBJECTS_DIR/$CROSS/mri/rawavg.mgz --hemi $CURHEMI --s $LONG done done Dr Chris Adamson Senior Research Officer, Developmental Imaging, Clinical Sciences (0.3 EFT) Software Engineer, Cardiovascular Research (0.7 EFT) Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adamson(a)mcri.edu.au<mailto:chris.adamson@mcri.edu.au> www.mcri.edu.au<http://www.mcri.edu.au/> Disclaimer This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Children’s Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.

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Issues with bbregister
by Mason Wells 01 Jun '20

01 Jun '20

External Email - Use Caution Hi Experts, I am using bbregister to align functional data to anatomical space. I have been using the bbregister command with a combination of different flags. However, there appears to be varying levels of poor registration. The first command I used included flags for a whole brain reg image and the --init-header flag. As you can see in the attached image titled tkreg 1, there is a misalignment. bbregister --s PPT_1x --feat /Data/PMA_retinoScans/PPT_1x/run1_pre_processed_functional.feat/ --int Data/PMA_retinoScans/PPT_1x/WholeEPI.nii.gz --init-header I then removed the –int (whole brain reg image) flag. Again the registration is massively misaligned (image titles reg1) bbregister --s PPT_1x --feat /Data/PMA_retinoScans/PPT_1x/run1_pre_processed_functional.feat --init-header I then removed the –init-header flag. Again poor registration (image titled reg 2) Then I removed both flags. This was the best registration (see attached image titled reg 3), but even this still looks a little bit off to me. You can see that around the occipital lobe, there white matter isn't aligned very well. bbregister --s PPT_1x --feat /Data/PPT_1x/run1_pre_processed_functional.feat/ Can anyone give me any advice on this? I really am unsure as to which why these flags failed to aid registration. I have 3 other participants from a different dataset for which the bbregister pointing to the feat directory and the –init-header flag worked perfectly. Any advice would be great. Thanks in advance, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628

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Re: [Freesurfer] Convert mgz to nii
by Hua, Jessica 31 May '20

31 May '20

External Email - Use Caution Hi FreeSurfer experts, Also in case the code is different, how would I convert my T1.mgz file to a .nii file to be used in DTI analyses? Thanks! Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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Convert mgz to nii
by Hua, Jessica 31 May '20

31 May '20

External Email - Use Caution Hi FreeSurfer experts, I would like to convert my .mgz parcellation file to a .nii file to be used in DTI analyses. How would I convert my participant's aparc+aseg.mgz file to a .nii file? Best, Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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Longitudinal study dimension mismatch
by KennethSPrice 30 May '20

30 May '20

External Email - Use Caution Hello Freesurfers! I am running a recon-all -long study and one of my subjects is giving me trouble. The brain segmentation volume for tp2 is greater than tp1. The scans were taken from the same machine with the same parameters, but the dimensions are mismatched: Volumes differ in dimension v1dim 512 512 32 1 v2dim 560 560 30 1 I am worried that dimension mismatch is causing an error in brain volume estimation. I have tried reslicing v1 to v2 dimensions but freesurfer did not like it. Would a dimension mismatch lead to significant volume differences, and is there any work around? \ Thanks, Ken Sent with [ProtonMail](https://protonmail.com) Secure Email.

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Cannot execute Binary file
by Graduate Imaging 30 May '20

30 May '20

External Email - Use Caution Hi, I recently downloaded fspalm, mri_surfcluster and mri_volcluster for freesurfer v6.0 from ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/PALM/ and added them to the freesurfer/bin folder (had to replace the previous versions of mri_surcluster and mri_volcluster) and ran chmod a+x on all three to make them unix executable files. When I ran fspalm the permutation part of the command worked however when it reached the mri_surfcluster command it produced the following error in terminal "-bash:/Applications/freesurfer/bin/mri_surfcluster: cannot execute binary file" I'm running freesurfer on a MacOS system, are these the correct versions of the files I should be using? Thanks

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Re: [Freesurfer] Cannot execute Binary file {Disarmed}
by fsbuild 30 May '20

30 May '20

External Email - Use Caution Hello, The files mri_surcluster and mri_volcluster that you downloaded are patched versions for the linux distribution, so they won’t run on MacOS. But you should need to download them as they should already exist in the MacOS freesurfer distribution.  Or you should already have them under ./freesurfer/bin ($FREESURFER_HOME/bin in the freesurfer shell/environment) - under wherever your MacOS installation of freesurfer lives.   If you need to, you can download the freesurfer 6 MacOS distribution from https://surfer.nmr.mgh.harvard.edu/fswiki/rel6downloads, install it on your own Mac and get those files. - R. On May 29, 2020, at 23:20, Graduate Imaging <graduate.imaging(a)gmail.com> wrote:Hi, I recently downloaded fspalm, mri_surfcluster and mri_volcluster for freesurfer v6.0 from ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6..0.0-patch… added them to the freesurfer/bin folder (had to replace the previous versions of mri_surcluster and mri_volcluster) and ran chmod a+x on all three to make them unix executable files. When I ran fspalm the permutation part of the command worked however when it reached the mri_surfcluster command it produced the following error in terminal "-bash:/Applications/freesurfer/bin/mri_surfcluster: cannot execute binary file" I'm running freesurfer on a MacOS system, are these the correct versions of the files I should be using? Thanks

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