Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

Make BEM with corrected brainmask
by Kadwani, Manorama 21 Sep '20

21 Sep '20

Hi, Why does the "mri_watershed" function create a new brainmask? Is there a way to create BEM surfaces from an existing or already corrected brainmask? I had manually edited the brainmask during recon-all process. After the recon-all process completed, the pial surfaces looked good. But when I ran 'make_watershed_bem', the BEM surfaces came out incorrect. The function 'mri_watershed' re-created a brainmask with the same errors that I had corrected earlier. I saw there was a question on this topic already, but couldn't find answers: https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subj… Thanks, Manorama

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Functional connectivity preprocessing and seed analysis
by Wenzhen Zhao 21 Sep '20

21 Sep '20

External Email - Use Caution > Dear freesurfer developers, > > I’m attempting to analyze my resting -state fMRI data, and I followed > procedures on your functional connectivity page. When I tried to run > preprocessing with my data, but it turns out that default mri_coreg did not > register my fMRI template volume onto anatomical scan well. So, I went on > to register fMRI to anatomical space on my own using bbregister with > (init-rr method - rigid transformation). I re-ran preprocessing without > registration (-noreg) to correct motion and slice-timing. My commands > looked like below: > #bbregister —mov fMRI_template_volume —bold —s subject —init-rr —lta > functional2anatomical.lta > #preproc-sess -s sess01 -fsd rest -stc siemens -noreg -surface fsaverage > lhrh -surf-fwhm 5 -mni305-2mm -vol-fwhm 0 -per-run -force > > Then, I configured seeds (ex. Hippocampus), and ran following commands: > #fcseed-config -segid 17 -fcname left_hippocampus.dat -fsd rest -mean > -cfg left_hippocampus.config > #fcseed-sess -s sess01 -cfg left_hippocampus.config > > It did run smoothly, but what I noticed from fcseed-sess script was it was > transforming anatomical aseg mask into functional space. I am confused on > this part, because during processing step, we only make registration file > for transformation from functional space to anatomical space, but > fcseed-sess command needs registration file that moves anatomical scan to > functional scan. > > # Convert segmentation to native functional space (##from fcseed-sess script##) > > set cmd = (mri_label2vol --seg $seganat \ > > --reg $reg --temp $template --fillthresh $FillThresh \ > > --o $seg --pvf $pvf); > > echo $cmd | tee -a $LLF > > > Then, Later, during mkanalysis-sess step, the command seems to use functional 2 anatomical transformation. Could you please clarify which registration file it uses to process each step that I talked about above? Do I also need to make anatomical to functional transformation registration? > > > I deeply appreciate your help. > > > Sincerely, > > Wenzhen > >

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Problem running infant FreeSurfer - failure to create symbolic link
by Fleur Warton 21 Sep '20

21 Sep '20

External Email - Use Caution Hi FreeSurfer team, I'm trying to run the infant freesurfer (version: freesurfer-infant-20200205 ) and get the following error: ln: failed to create symbolic link 'brain.nii.gz': Operation not supported The command I used was: infant_recon_all --s 002B --age 0 I think this may have to do with the fact that my subjects_dir is located on a server (not the computer I'm running FreeSurfer on), since when I ran the command with the subjects_dir located on my local computer it ran fine and completed without errors. Unfortunately for space reasons it isn't possible for me to do that for my entire dataset. Thanks, Fleur -- Fleur Warton

2 1

error message using mri_robust_template
by Marisa Nordt 21 Sep '20

21 Sep '20

External Email - Use Caution Hello, I am using mri_robust_template with the ‘--affine’ option to create individual templates (using freesurfer version freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c). For each timepoint I use that timepoint's T1.mgz as the input. For some subjects this works well. However, for others I am receiving an error message (* WARNING: TP 3 to 1 did not converge !! MatrixLog Error: Result too imaginary to ignore). I am attaching the full command and the error message below. Do you have thoughts on how to trouble-shoot this issue? I have looked at the input files and these seem to be ok. Thank you! Best, Marisa ---------------------------------------------------- mri_robust_template --template template.nii.gz --affine --satit \ --mov Tp1T1.mgz Tp2T1.mgz Tp3T1.mgz \ --lta Tp1totemplate.lta Tp2totemplate.lta Tp3totemplate.lta \ --mapmov Tp1totemplate.nii.gz Tp2totemplate.nii.gz Tp3totemplate.nii.gz ---------------------------------------------------- - running loop to estimate saturation parameter: * WARNING: TP 3 to 1 did not converge !! MatrixLog Error: Result too imaginary to ignore! ( 6.23199e-16 ) A = 1.006576323240725 0.003084002656233406 -0.03645397216347104 -0.006991580325416484 1.011866325424678 -0.05229335553407307 0.03777040431253831 0.04392492645068569 1.002740736902102 T = (1.00563233346774,0.0606675705194677) (0.001071185761943805,0.00660486005552916) (0.006657281419514499,0.004121077514717164) (0,0) (1.009918718632024,-3.183217578417441e-16) (-0.001219644877272269,-0.006241389920134279) (0,0) (0,0) (1.00563233346774,-0.06066757051946813) U = (0.06522427283350557,-0.4086418628970923) (-0.4512115300813958,-0.6429736578063935) (0.4435972821778756,0.1223605486029275) (0.1324402433691656,-0.5811769288411271) (0.396861124383305,0.4645450375452963) (0.5209342533284942,0.004429342327522456) (-0.6671781011025059,-0.1682972455202441) (-0.001010631409214958,0.09844371568609764) (-0.1111959193687357,0.7102764951350742) fro( real(U * T * U^*) - A) = 1.736855929375805e-15 log(A) = (0.007247004124560403,-2.550043509685906e-16) (0.003840124735798771,3.469446951953614e-17) (-0.03616149457717018,1.07552855510562e-16) (-0.00594730233232413,1.249000902703301e-16) (0.0129351237191556,-2.289834988289385e-16) (-0.05197693653405921,5.334274688628682e-17) (0.03770072871406291,-2.432949675057472e-16) (0.0434964642601452,7.199102425303749e-17) (0.004553620359034822,-2.775557561562891e-16) fro( exp(real(log(A))) - A) = 1.311226128713136e-15

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Re: [Freesurfer] Prescan normalize and freesurfer
by Glasser, Matthew 21 Sep '20

21 Sep '20

External Email - Use Caution What head coil did you use? Do you have a highres T2w or FLAIR? Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Mikolas, Pavol" <Pavol.Mikolas(a)uniklinikum-dresden.de> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, September 17, 2020 at 7:12 AM To: "'freesurfer(a)nmr.mgh.harvard.edu'" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Prescan normalize and freesurfer External Email - Use Caution Dear Freesurfer Developers, I am analyzing the T1 Data of a multicentric study (N=309, 6 Centers) using Freesurfer. I found out, that most of the scans were performed with the ‘prescan normalize’ option. However, by approx.. 12 % of participants, this option is missing. I also have complete data of all participants WITHOUT prescan normalize. In this analysis, we are interested in the correlation of GM volume in specific ROIs with clinical symptoms. Now we have two options: 1. Use the ‘prescan normalize’ dataset and account for the 12% without this option as a covariate 2. Use the complete dataset without ‘prescan normalize’ It would be very helpful, if you could share your arguments / experience with this, so that we proceed in the best manner. Thank you, best regards Pavol ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Re: [Freesurfer] recon-all 7.1.1
by fsbuild 20 Sep '20

20 Sep '20

External Email - Use Caution Hello James, Maybe you could do a quick check to see if sudo permission is working for you. This should always work to create and remove a file…. $ cd /tmp$ touch foo$ rm foo … but sudo has to work for your account to do the same under /Applications $ cd /tmp$ sudo touch /Applications/foo$ sudo rm /Applications/foo If sudo does not work for you, then you will need to find someone with an account that has sudo privileges. Assuming sudo works for you in the above example, then you could also try using the bash shell instead of zsh.  Just type “bash" at the terminal to get a bash shell and try the sudo mv command again.  (Zsh is not going to read your .bashrc file if you set it up for Freesurfer, umask, etc.) $ bash On Sep 19, 2020, at 10:17, James Hartzell <james.hartzell(a)gmail.com> wrote:        External Email - Use Caution        Hi AndrewThanks for the suggestions. I removed freesurfer and reinstalled just 7.1.1.When I try to run the original patch you suggested I still get permissions problems, even with sudo.(base) jameshartzell@Jamess-MacBook-Pro ~ % which freesurfer/Applications/freesurfer/7.1.1/bin/freesurfer(base) jameshartzell@Jamess-MacBook-Pro freesurfer % cd $FREESURFER_HOME/bin(base) jameshartzell@Jamess-MacBook-Pro bin % sudo mv recon-all recon-all.backupPassword:(base) jameshartzell@Jamess-MacBook-Pro bin % sudo curl https://raw.githubusercontent.com/freesurfer/freesurfer/fs-7.1/sc… recon-allzsh: permission denied: recon-allHere's hoping you can send another fix!CheersJames-- James Hartzell, PhD (2x) Donostia-San Sebatián, SpainCenter for Mind/Brain Sciences (CIMeC), The University of Trento, ItalyCenter for Buddhist Studies, Columbia University, USA_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mkcontrast-sess error
by Bianca Sieveritz 18 Sep '20

18 Sep '20

External Email - Use Caution Dear FreeSurfer Developers, I have preprocessed my functional data using the FsFast function preproc-sess and am now attempting to set up contrasts for first level analyses. I have been able to run mkanalysis-sess, but am receiving an error when I try to run mkcontrast-sess. I am receiving the following output, when attempting to run mkcontrast-sess: Command: mkcontrast-sess -analysis task-ARC_events.mni305 -contrast low-baseline-response -a 6 Output: INFO: Found 15 Non-Null Conditions INFO: Found 1 Delays Condition Weights: 0 0 0 0 0 1.00000000000000000000 0 0 0 0 0 0 0 0 0 mkcontrast2 -config task-ARC_events.mni305/low-baseline-response.config -anadir task-ARC_events.mni305 -wcond 0 0 0 0 0 1.00000000000000000000 0 0 0 0 0 0 0 0 0 -sumconds -o task-ARC_events.mni305/low-baseline-response.mat -prestim 0 -wdelay 1 -no-octave mkcontrast2 7.1.1 cmtxfile task-ARC_events.mni305/low-baseline-response.mat nconds 15, wcond 0 0 0 0 0 1.00000000000000000000 0 0 0 0 0 0 0 0 0 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 1.75 rdelta rtau cmtxfile task-ARC_events.mni305/low-baseline-response.mat monly 0 NCond 15 WCond 0 0 0 0 0 1.00000000000000000000 0 0 0 0 0 0 0 0 0 NDelay 1 WDelay 1 TER 1.75 sumconds 1 sumdelays 0 nircorr 0 TPreStim 0 RmPreStim 0 rdelta 0 0 rtau 0 0 ndelays 1 CNorm 1 setwdelay 0 setwcond 0 Matlab file is /tmp/mkcontrast2.21185.m ------- matlab output -------------------- MATLAB: Undefined variable. ERROR running mkcontrast mkcontrast2 -config task-ARC_events.mni305/low-baseline-response.config -anadir task-ARC_events.mni305 -wcond 0 0 0 0 0 1.00000000000000000000 0 0 0 0 0 0 0 0 0 -sumconds -o task-ARC_events.mni305/low-baseline-response.mat -prestim 0 -wdelay 1 -no-octave I have searched the web but was unable to find a solution. Do you have any ideas, what may be causing the error? 1) freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 2) Platform: I am running the script on our university's cluster. The cluster is Linux based but I am unable to provide details regarding the specific Linux version. Thank you for your help! Best regards, Bianca Sieveritz

2 2

Re: [Freesurfer] Account password on Virtualbox VDI
by fsbuild 18 Sep '20

18 Sep '20

External Email - Use Caution Hello Chris, Sending the password to your account shortly. - R. On Sep 18, 2020, at 13:10, Mcnorgan, Christopher <cpmcnorg(a)buffalo.edu> wrote:        External Email - Use Caution        Hi,I have a couple students who are windows users who I am training remotely. They’ll be using the VDI found at:https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67I’ve never tried this and can give no guidance, as I have no Windows computers at my disposal. A student tried this and said it had a default ‘developer’ user, and asked what the password was for this account. A google search revealed this question has been posted in the past, with a reply that the password would be sent via email./*********************************************** Chris McNorgan* Assistant Professor* Department of Psychology* University at Buffalo, * The State University of New York* http://ccnlab.buffalo.edu/* Office: 716.645.0236* Lab: 716.645.0222**********************************************/_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Cohen's D calculation and interpretation
by Alejandro Meruelo 18 Sep '20

18 Sep '20

External Email - Use Caution Hi everyone, I reviewed some of the other answers on the mailing list to compute a Cohen's d value following the sequence of commands below for a Qdec Freesurfer analysis: 1) cd glmdir/contrast fscalc gamma.mgh div ../rstd.mgh -o cohensd.mgh 2) mri_segstats --i cohensd.mgh --seg cluster.sig.ocn.mgh --exclude 0 --sum test.output However, my test.output file looks like: # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 1 2398 2398.0 Seg0001 4.9611 0.8313 3.6525 7.3172 3.6647 2 2 5893 5893.0 Seg0002 5.1281 1.1535 3.6520 8.8040 5.1520 Why are the mean Cohen's d values (4.9611, 5.1281) so large? Am I interpreting these incorrectly? Many thanks in advance for your help, Josh

3 3

--inittp 0 in mri_robust_template
by Marisa Johanna Nordt 18 Sep '20

18 Sep '20

External Email - Use Caution Hi, I have a question regarding the flag -- inittp 0 (no init ) in mri_robust_template. What does ‘no init’ mean in this context and which consequences arise from using this flag? Thank you! Best, Marisa

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