Freesurfer December 2022

freesurfer@nmr.mgh.harvard.edu

75 participants
92 discussions

TRACULA cluster statistics visualization
by Makenna B McGill 19 Dec '22

19 Dec '22

External Email - Use Caution Hi Freesurfer Developers, I'm using FS v7.2 to conduct along-tract statistics using trac-all -stat, and I was wondering how to best visualize and interpret the results of the cluster-wise correction in freeview. I referenced this page ( https://secure-web.cisco.com/1rtane6ARuP3X8AuU2py8u1aHHy9K5qYs7DI1jVqCAg3GH…) which describes how to do this for uncorrected statistics, and used dmri_trk2trk to try to embed the *perm.th13.abs.sig.cluster.mgh files produced by mri_glmfit-sim into the template .trk files (--in $FREESURFER_HOME/trctrain/hcp/syn/"$tract".display.trk). I also embedded the *perm.th13.abs.sig.cluster.mgh files into the mean path .trk files (--in $FREESURFER_HOME/trctrain/hcp/syn/"$tract".mean.trk). However, I'm noticing inconsistencies in the location along the tract of significant clusters between the projection of the uncorrected statistics in freeview, projection of the corrected statistics in freeview, and the cluster location as indicated by the cluster summary file (*perm.th13.abs.sig.cluster.summary.txt). I've attached the cluster summary file for FA in the rh.cst tract as an example. My understanding is that for pathways with superior-inferior orientation, points along the tract are ordered from superior to inferior. Given that this significant cluster is at a VoxX of 68 (of 80 total points along the tract), I would have thought that this cluster would be located at a more inferior position along the right cst -- instead, the cluster appears to be located superiorly (trk files for uncorrected and corrected statistics for this pathway are attached). Similar to this FS user ( https://secure-web.cisco.com/1MD72Ga_1F-Q0FFmEMhYJe7s5dOdRHRhGL2ZDfR5AWgoRO…) I'm wondering: (1) Am I missing something regarding this embedding process? (2) Is it appropriate to embed the *perm.th13.abs.sig.cluster.mgh file to visualize the results of the cluster-wise correction? Please let me know if there is any other information or attachments you'd like me to provide. Any thoughts on where I might be going wrong would be greatly appreciated. Thank you! Best, Makenna *Makenna McGill *(she/her) Doctoral Student in Clinical Psychology The University of Texas at Austin

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Re: [Freesurfer] Freeview quit unexpectedly
by fsbuild 19 Dec '22

19 Dec '22

External Email - Use Caution I would downloaded and install the latest Xquartz (X-Windows for MacOS) which is version 2.8.3 from https://secure-web.cisco.com/1opXWtR1b08TpiSxuOjmZYBoO9MYN5pgHsuK…;  This was updated only a week ago and contains universal binaries. After you install Xquartz open a new terminal window and type “glxgears”.  An X-Window should pop up showing the spinning gears. % which glxgears /opt/X11/bin/glxgears % glxgears 303 frames in 5.0 seconds = 60.564 FPS 309 frames in 5.0 seconds = 61.607 FPS …... … close glxgears window to exit ... Then at least your X-Windows graphics will be up to date (which might affect the GUI).  Then try your image again. Do you see any warnings, error, info, etc., listed in the terminal window after the freeview command?   If so, please send that along. Maybe you could send along a screenshot of what “about this mac” displays.  That would tell us if you are using a graphics card or the built-in graphics - and also a screenshot of the freeview window. - R.

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cannot create directory freesurfer
by Nazanin Mirzaei 18 Dec '22

18 Dec '22

External Email - Use Caution Hello when i use recon-all, i get this message: mkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/name': Permission denied I did the solutions that were previously suggested on the site, but it still didn't work. Thank you in advance for your help. Best regards, Nazanin Mirzaei

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bug in pial placement with FLAIR images
by Douglas N. Greve 16 Dec '22

16 Dec '22

I recently found a bug in the pial placement refinement with FLAIR images (recon-all -flair ...) that affects version 7.{0,1,2,3}. This bug caused the pial surfaces to not extend nearly far enough. It has been fixed in the development version of FS and so will be in future versions. If you want to access the fix before then, create a $SUBJECTS_DIR/global-expert-options.txt with this line PlaceMMPialSurf --mm_min_inside 50 --mm_max_inside 200 --mm_min_outside 10 --mm_max_outside 50 sorry for any inconvenience doug

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regress out signal
by Mingyang Xia 16 Dec '22

16 Dec '22

External Email - Use Caution Dear Freesurfer expert: After I used ' fcseed-config' to get wm.dat and csf.dat, how could I get the signal of each voxel that regresses out the nuisance. I do not want to do the analysis. I just want to get the signal after regressing out nuisance. Thank you Mingyang Xia

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Re: [Freesurfer] ERROR: fast_mat2vol
by stdp82＠virgilio.it 16 Dec '22

16 Dec '22

External Email - Use Caution I have resolved by eliminating the option -nowhiten It looks like the anatomical analysis is out of sync with the functional analysis. Is is possible that you ran the functional analysis, then edited the subject, then tried to rerun the analysis? If so, try running preproc-sess with -force to redo all the preprocessing.On 12/1/2022 12:45 PM, std...(a)virgilio.it wrote: > External Email - Use Caution I would extract the rs-fMRI timeseries from Yeo’s Network components. I’m running: preproc-sess -s ${1} -fsd rest -sliceorder up -surface self lhrh -fwhm 0 -per-runfcseed-config -wm -fcname wm.dat -fsd rest -pca -cfg wm.config fcseed-sess -s ${1} -cfg wm.configfcseed-config -vcsf -fcname vcsf.dat -fsd rest -pca -cfg vcsf.configfcseed-sess -s ${1} -cfg vcsf.config mkanalysis-sess -analysis fc.noseed.surf.lh -surface self lh -fwhm 0 -notask -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.67 -per-run -hpf 0.01 -lpf 0.1 -nowhiten mkanalysis-sess -analysis fc.noseed.surf.rh -surface self rh -fwhm 0 -notask -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.67 -per-run -hpf 0.01 -lpf 0.1 -nowhitenThe line below produced this error: selxavg3-sess -s ${1} -a fc.noseed.surf.lh -no-con-ok -svres Saving rho1 ERROR: fast_mat2vol: szvol inconsistent with mat2d nv = 151008, size(mat,2) = 142954 run 2 t= 1.6reading data ... 0.518631Temporally filteringSaving rho1 ERROR: fast_mat2vol: szvol inconsistent with mat2d nv = 151008, size(mat,2) = 142954Found 0 voxels with corrected AR1 > 0.90Not WhiteningFound 8054 zero-valued voxelsComputing contrastsThe res folder in fc.noseed.surf.lh or fc.noseed.surf.rh contains res-001.nii.gz 158KB res-002.nii.gz 158KB that cannot be opended. Stefano > > >

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Use annotation for edgecolor in freeview
by Chris Adamson 16 Dec '22

16 Dec '22

External Email - Use Caution Freesurfer, Is there any way of using an annotation file to set the edge color for a surface so that the annotation labels are visible in the 2D slice view? I'm sure I have seen this working in the past but can't seem to get it working now. Thanks in advance, Chris Adamson. 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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error/cannot create directory freesurfer
by Nazanin Mirzaei 16 Dec '22

16 Dec '22

External Email - Use Caution Hello when i use recon-all i get this message: mkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/a': Permission denied Thank you in advance for your help. Best regards, Nazanin Mirzaei

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Re: [Freesurfer] Freeview quit unexpectedly
by fsbuild 16 Dec '22

16 Dec '22

External Email - Use Caution Please try the following: 1)  Open a new terminal window and run the bash shell as, $ arch -arm64 /bin/bash 2) set FS_LICENSE to point to your license.txt file.  Say it is in your home directory, e.g., $HOME/license.txt.  It can be anywhere but you just have to set FS_LICENSE to its absolute path and test it can be read. $ ls $HOME/license..txt/Users/<your userid>/license.txt$ export FS_LICENSE=$HOME/license.txt$ head -1 $FS_LICENSEyou(a)youremail.something     <— email you used to register with 3) setup the environment $ export FREESURFER_HOME=/Applications/freesurfer/7.3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-darwin-macOS-7.3.2-20220803-878457d -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /Applications/freesurfer/7.3.2 FSFAST_HOME       /Applications/freesurfer/7.3.2/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /Applications/freesurfer/7.3.2/subjects MNI_DIR           /Applications/freesurfer/7.3.2/mni 4) Try running freeview w/o any arguments to see if it opens an empty window. $ freeview 5)  If that worked,  quit freeview and then try running freeview to open one of the provided volumes in the 7.3.2 release, $ freeview $SUBJECTS_DIR/bert/mri/brain.mgz 5) If that worked, then try running freeview on your file again. - R.

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Re: [Freesurfer] Creating and analyzing combined ROIs, combining different FreeSurfer versions
by Trolle, Carl 15 Dec '22

15 Dec '22

Ok, thank you! Would the command to add the label to glmfit then be --label file.label or --label fsaverage/label/file.label? I found different suggestions in the mail_archives, with some explicitly specifying the fsaverage-path and some not. Is it possible to then run permutations as per the FS permutation tutorial with the output from above (after including the --eres-save flag in the mri_glmfit command)? Kind regards, Carl On 12/12/2022 6:14 PM, Trolle, Carl wrote: > Thank you for the reply, > > 1. Once each participant's aparc has been broken and we've created > the desired new label for each participant, should we create this, > the desired label, for fsaverage and follow the remaining steps of > the ROI-tutorial (e.g resample with mris_label2label using > fsaverage as the srcsubject)? Sorry didn't quite understand this part. > Nope, once you have the ROI you want in the native subject space, just use it, no need to go to fsaverage at all. That was only for if you were going to draw your own label. Instead of drawing it on 10s or 100s of subjects you would draw it once on fsaverage then transfer it to all your subjects. But you don't need to do that. > > 1. > > > > ??? 3. We can't seem to get mris_register and mri_ca_label working > with FS711 or 720, it's running fine with 732 and the dev-version > (attaching a simple montage to show the output we're getting; we've > tried to force FreeSurfer to use a manually designated central sulcus > to move the pre and post central gyri "forward"). I think there was a > mention that mris_register wasn't running as intended prior to 732 > <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg73308.html>.? > Thank you for the clarification! Unfortunately, I don't remember what I was referring to. As far as I know mris_register and mri_ca_label were working normally pre 732. > > Kind regards, > > Carl > > > > Message: 7 > Date: Mon, 12 Dec 2022 10:34:15 -0500 > From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>> > Subject: Re: [Freesurfer] Creating and analyzing combined ROIs, > ??????? combining different FreeSurfer versions > To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> > Message-ID: <8e7e390b-bbef-00cd-29c6-bda799bfd81e(a)mgh.harvard.edu<mailto:8e7e390b-bbef-00cd-29c6-bda799bfd81e@mgh.harvard.edu>> > Content-Type: text/plain; charset="utf-8" > On 12/2/2022 12:35 PM, Trolle, Carl wrote: > > Dear FreeSurfer team, > > > >? 1. We're trying to focus our cortical analysis following suggestions > >???? here > > > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23939.html.?… > <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23939.html.?…> > >???? FS ROI tutorial page?mentions that labels should be drawn or > >???? registered on the fsaverage template; could we then break the > >???? fsaverage aparc_annot atlas and combine the fsaverage labels of > >???? interest into our new label or should we break each individual > >???? subjects aparc_annot atlas and then create the combined ROI from > >???? the subject specific labels? I'm assuming that we either way will > >???? have to resample the combined label to each subject using > >???? mri_label2label? > > > You should break each subject aparc and then combine. > > > > 1. > > > > > >? 2. When running the mri_glmfit-sim analysis later on, the thread > >???? above mentions not using the --cache option. Can we use "--mczsim > >???? 3 pos" instead for a one-sided test? > > > Yes > > > >? 3. We've had some success in correcting incorrect parcellations using > >???? the mris_register and mri_ca_label functions. As we had some > >???? issues with mris_register in 7.1.1, we used the developer version > >???? for these steps, but 7.1.1 when re-running recon-all as this is > >???? the version we used for our study. Is it ok to combine versions > >???? like this? > > > probably ok in this case, but what is the problem? > > > > 3. > > > > > > Thank you for your time! > > > > Kind regards, > > > > Carl Trolle > > Research fellow > > Spaulding Neuroimaging Lab > > > > > > Platform:?linux-centos7_x86_64-7.1.1-20200723-8b40551 > > FreeSurfer version: 7.1.1 > > > >

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Freesurfer December 2022