Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

question regarding FSGD file for coding discrete regressors
by Zeng, Qi 11 Nov '21

11 Nov '21

External Email - Use Caution Hi Freesurfer experts, Here, I want to design a simple group comparison (two levels: Case vs. Control) and also count for 4 covariates (two continuous and two categoricals). However, the GLM model cannot recognize my discrete variables. What do you suggest to change? >> FSDG file: GroupDescriptorFile 1 Title MyStudy Class Control Class Case Variables age gender race eTIV Input sub001_base Control 85 Female White 1350519 Contrast: >> Design matrix for Case-Control and regress out the effect of age, gender, race, and eTIV. -1 1 0 0 0 0 0 0 0 0 Best, Zeng

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turning a surface label into 3d object
by Trisanna Sprung-Much 11 Nov '21

11 Nov '21

External Email - Use Caution Hi there I realize this may be a bit of a stretch, but I wonder if there is any way to turn a surface label into its own 3D object that can then be examined on its own (to observe morphology) in Freeview? Similar to, for example, the sulcal skeletons that can be extracted in BrainVisa? Many thanks~ Trisanna -- Trisanna Sprung-Much, PhD Research Associate McGill University Montreal Neurological Institute

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[Re]:FsFastFunctionalConnectivityWalkthrough
by Alice Giubergia 11 Nov '21

11 Nov '21

External Email - Use Caution Thanks for your replies Doug! 1) Thanks. 2) Regarding question number 2, yes that was what I meant. 3) I ran the task analysis and extracted time series from unwhitened residuals by mri_segstats, upon a specific segmentation. I was thinking now of a correlation matrix by Pearson's coeff. Any further suggestions? Also, I've got a pheraps silly question: - When running a task analysis, I could specify -taskreg and -nuisreg separetly. My assumption is that only -nuisreg are regressed out from the data and that the residuals saved got task-related bold signal. Is it correct? - If so, could I use task regressors as -nuisreg to get a "pseudo" resting state? Hoping all question are clear, Thanks for your patience, Alice

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"No such file or directory" in wm
by Devarajan, Alex 11 Nov '21

11 Nov '21

External Email - Use Caution Hello, I'm running a fairly large database of MRIs through freesurfer for a project and have come into a number of errors - though I'm learning how to fix many of them, there are a few major categories of errors which are still difficult to parse out. This was a sagittal T1 FLAIR sequence that I ran which produced the error "no such file or directory" when trying to access wm. I know that sometimes processing errors can lead to segmentation dumps, etc., but I'm unsure of where to proceed in fixing this and any help would be appreciated immensely. I've attached a recon-all log as an example of this error for reference. Thank you!

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permutation simulation error
by Brown, Alexander 10 Nov '21

10 Nov '21

External Email - Use Caution Hello, I am attempting to run a permutation simulation to correct for multiple comparisons and am getting the following error: < mri_glmfit-sim --glmdir /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled --perm 1000 1.3 neg --perm-resid ERROR: cannot find residual /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled/eres needed with --perm-resid when running mri_glmfit, make sure to include --eres-save > Attached is the mri glmfit log. I ran the command with the --eres-save flag, and the eres.mgh file is generated in the glm directory. I have downloaded the patch and have run this style of analysis multiple times without issue until today. I appreciate any help! Please let me know if you need any additional information. Thanks, Alex Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779

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smoothing images using mri_surf2surf command line
by Yangwen Xu 10 Nov '21

10 Nov '21

External Email - Use Caution Hello FreeSurfer Developers, I am trying to smooth images using mri_surf2surf. Here is the command line: 'mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval ',InputImagePath,' --fwhm 6 --tval ', OutputImagePath The Input Image is 10242 (number of vertices) * 475 (number of time points) in the func.gii format. The output image is supposed to be in the same dimensions. However, it only smoothed the image of the first time point, i.e., the dimension of the output Image is 10242 * 1. I have implemented this before but never met this problem. The only difference seems that I am now using freesurfer-darwin-macOS-7.2.0. Does anyone have any thoughts on how to solve this problem? Thanks for the help, Yangwen

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FsFastFunctionalConnectivityWalkthrough
by Alice Giubergia 10 Nov '21

10 Nov '21

External Email - Use Caution Dear FreeSurfer experts, I'm interested in performing a functional analysis on task-based data. I was taking as an example the "FsFastFunctionalConnectivityWalkthrough" tutorial but, if I got it correctly, is specific for resting state data. So I've got some doubts and questions: 1) Given the steps described in the above mentioned tutorial, the file "pcc.mgz" generated in the session folder gives me the correlation strength between the time series of each voxel and the seed (L_Posteriorcingulate in the tutorial)? 2) If I want to make a functional analysis on task data, similar to the one described in that tutorial, could I just add the -event-related option instead of -notask option? (mkanalysis-sess -analysis fc.lpccseed.surf.lh -surface fsaverage lh -fwhm 5* -notask* -taskreg L_Posteriorcingulate.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR <TR>) 3) Otherwise, does it make sense to you If I run a simple task analysis to regress nuisances out (without seed region), extract time series and get the pair-wise correlation with Pearson coefficient? Hoping my questions are clear, Thanks a lot for your patience and help, Alice

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Re: [Freesurfer] Aseg and wm edits? + white/pial overlap near subcortical structures
by Kang, Jee Won 09 Nov '21

09 Nov '21

External Email - Use Caution Hi, Thank you for your clarification on these points. I had a few follow-up questions regarding the responses: The response to 2) What is the proper command to use for re-running with aseg edits? was: If you are editing the aseg to help fix the surfaces, then use -autorecon2-noaseg -autorecon3 Should a different command be used if we are editing the aseg to fix segmentation? I mentioned that for some subjects we have the lateral ventricles being mislabeled as white matter, but the surfaces are fine. For such cases, should the same command be used? Thank you, Jee Won ________________________________________ On 10/29/2021 10:46 AM, Kang, Jee Won wrote: > > ????????External Email - Use Caution > > Hello all, > > > There are two topics I would appreciate your expert advice on: > > > Topic 1: Aseg and wm edits > > > I was going through the wiki and the archive of past inquiries and was > unable to find a clear answer to whether you can make aseg edits and > wm edits, and then re-run in Freesurfer at the same time. Furthermore, > I was just a little unclear as to how exactly to perform aseg edits. > > > According to this post: > > *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/16PK1H0u9E6mE1WX3TwIYQluoFkIv776Yq8LGwEmvCd-zF… , > <https://secure-web.cisco.com/1nGb7btrh06X-vkKS8yIIYEfPF2uhxx3qc5NIMOfcvI_qc… >?you > are supposed to edit aseg.manedit.mgz, and only make edits to wm.mgz > if segmentation is still incorrect after re-running. The command > suggested to be used is recon-all -s subject -autorecon2 -nogcareg > -nocanorm -nocareg -autorecon3. > > > However, according to this post: > > *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1AH6E_VONenrYL1903pMClalcawzSAuIFulfW2e3NQqiAp… > <https://secure-web.cisco.com/142s7iELeKJ3UC-QhbfhnDCUV9xSabwPrU6R5jHZ6L8cBS… >?and > the wiki page it references here: > > *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1SgCX2gfkJmu1SDxDsAhR2feVME1Me_6R71jeMv7Zm5TmN… , > <https://secure-web.cisco.com/1bYdoYwl6jacI08RwuMH7zHVUMEjgziQUSo2bLQDldJesG… > > you are supposed to edit aseg.presurf.mgz, and doesn't mention whether > aseg edits are compatible with wm.mgz edits. The command these posts > say you should run is recon-all -autorecon2-noaseg -autorecon3 -s > subject, and this is also listed in the "OtherUsefulFlags" table. > > > My questions are: > > 1) Does it matter which volume, aseg.presurf.mgz or aseg.manedit.mgz > that you edit? > manedit does not exist in version 7, so that is where the confusion comes from > > 2) What is the proper command to use for re-running with aseg edits? > If you are editing the aseg to help fix the surfaces, then use -autorecon2-noaseg -autorecon3 > > 3) Can you make edits to wm.mgz and aseg edits and re-run with both > edits being taken into account? > Yes, both will be taken into account > > > For some background into why I've been looking into editing aseg > segmentations, we have a sizeable portion of our data for whom the > lateral ventricles are being mislabeled as wm (for some this is quite > mild, for others it is pretty extensive). I know the -big-ventricles > flag is an option, but we are not looking to re-run all of our subject > with it at this time, as we have 100+ subjects. > > > Topic 2: White/pial overlap near subcortical structures > > Sometimes, the pial surface near the subcortical structures will "pull > back" too much, I've attached an example image. This "pull back" > sometimes appears after I've re-run the subject after making wm edits, > when it was not present in before re-running. In the attached example > image, the original pial surface before re-running is in blue, the new > pial surface is in red. The original white surface is in green, the > new white surface is in yellow. I have the aparc+aseg.mgz and wm.mgz > visible. As shown in the image, this "pull back" will?often end up > exclude a chunk of voxels from the aseg?and aparc+aseg, even if there > are wm.mgz voxels filled in that area. > > > How important is it to fix errors in this area in general, and would > aseg edits be appropriate since wm edits don't seem to address the > problem? > It is hard to tell what is going on there from the pictures that you have sent. That spot may just be part of the medial wall, in which case it can be ignored > > > Thank you for your insight into these topics! > > > Sincerely, > > Jee Won > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://secure-web.cisco.com/1zlsHCIa2xCi_msGM-6zWUzwZkONzU65MwX-b1r1hg32ns…

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temporal filtering and nuisance regression
by Turnbull, Adam 09 Nov '21

09 Nov '21

External Email - Use Caution ??Hello, I just wanted to confirm whether Freesurfer performs temporal filtering simultaneously with nuisance regression, or whether it performs these steps subsequently in either order (temporal filtering then nuisance regression or vice versa). I have read about some issues reintroducing artifacts (https://secure-web.cisco.com/1A5LZX65RHFsaEwnh06Bs0tVJd4h-tKWpquKqpSZzVe1Ov…) when these steps are not performed simultaneously. Thank you for your help! I am posting the analysis below just to confirm both approaches are being performed. mkanalysis-sess -analysis fc.surface.lh \ -surface fsaverage lh \ -per-run \ -fwhm 5 \ -notask \ -nuisreg vcsf.dat 1 \ -nuisreg wm.dat 1 \ -nuisreg global.waveform.dat 1 \ -mcextreg \ -polyfit 1 \ -fsd bold \ -TR 2.5 \ -stc siemens \ -hpf 0.009 \ -lpf 0.08 \ -inorm \ -force? Best, Adam

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Re: [Freesurfer] crash (on MacOS)
by fsbuild 08 Nov '21

08 Nov '21

External Email - Use Caution Hello Nikolai, You could let us know what version of MacOS you are running, e.g., $ sw_versProductName: Mac OS X ProductVersion: 10.15.7 BuildVersion: 19H1419 I would try setting the environment variable FS_LICENSE to the absolute path of your license.txt file, e.g, copy it to your home directory (making up this example path /Users/nikolai/license.txt), and then (in sh or zsh), $ export FS_LICENSE=/Users/nikolai/license.txt … check you can read the file ...$ cat  $FS_LICENSE<output deleted> If you used the Mac 7.2.0 .pkg file to install freesurfer (https://secure-web.cisco.com/1BjdSMX3DYaaOUbJpXNlOtIpG2b3NTtqLXZsH01ATERZNw…) then it should be installed under /Applications/freesurfer/7.2.0. If your version of MacOS is too old, I believe the installer will tell you and refuse to install freesurfer.  If it did install it then you should see the following,  … set FREESURFER_HOME ...$ export FREESURFER_HOME=/Applications/freesurfer/7.2.0 … source setup file ...$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /Applications/freesurfer/7.2.0 FSFAST_HOME       /Applications/freesurfer/7.2.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /Applications/freesurfer/7.2.0/subjects MNI_DIR           /Applications/freesurfer/7.2.0/mni $ which freeview/Applications/freesurfer/7.2.0/bin/freeview … try running freeview w/o any arguments to see if an empty window will open …$ freeview If you get an error notification, then try to capture the error report (core dump). You can send it to me directly if you like as it’s kind of long to post to the list. - R. On Nov 8, 2021, at 14:02, Nikolai Chapochnikov <nchapochnikov(a)gmail.com> wrote:        External Email - Use Caution        Hello,Thank you for your help!I have an old intel mac (not M1). I allowed Freeview to access all my disk. I also put the license file and run the export commands (but not sure if it useful to run freeview.app?). But still it crashes when I try to open a volume file... Any other suggestions?Thank you very much!Best wishes,NikolaiOn Sat, Nov 6, 2021 at 10:56 PM fsbuild <fsbuild(a)contbay.com> wrote:Hello Nikolai,A posting from September lists some things you can try,MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/10a0eVDt9auSme4IenYkBDjOIN6hJeUWiUlu2q… would try getting a new license file first..  I will send the text to your email as well.- R.On Nov 6, 2021, at 16:30, Nikolai Chapochnikov <nchapochnikov(a)gmail.com> wrote:        External Email - Use Caution        Hello,I just installed freesurfer 7.2.0 on mac os 11.6 using the pkg. Freeview opens, but as soon as I select a nii file to load, it crashes.Here is the report I get:MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1-Vjdg5pZ9iowlHgUQ_UOjr1a62L81ZJWIQfbT… someone please help with this?Thank you very much!Nikolai_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr..mgh.harvard.edu/mailman/listinfo/freesurfer____________… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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