Freesurfer September 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
165 discussions

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

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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

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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

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--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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Account password on Virtualbox VDI
by Mcnorgan, Christopher 18 Sep '20

18 Sep '20

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_67 I’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 **********************************************/

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voxel to ras transform written by mri_convert -c
by Billah, Tashrif 18 Sep '20

18 Sep '20

Hi there, How is the rightmost column in `mri_convert -c` calculated? I have the following fslhd (relevant fields shown only) in a NIFTI image: ``` dim1 208 dim2 300 dim3 320 qto_xyz:1 0.799690 0.022176 0.001352 -86.687996 qto_xyz:2 -0.021442 0.783122 -0.162051 -62.728546 qto_xyz:3 -0.005816 0.161952 0.783414 -174.620270 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 ``` After `mri_convert -c`, mri_convert reports the following (relevant fields shown only) in the MGZ image: ``` voxel to ras transform: -1.0000 -0.0000 0.0000 128.0225 -0.0000 0.0000 1.0000 -101.4184 0.0000 -1.0000 -0.0000 102.4140 0.0000 0.0000 0.0000 1.0000 ``` Shouldn't the right-most column be: 128.5 -128.5 128.5 1 The numbers are (256+1)/2=128.5 Best, Tashrif

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Autorecon after control points error
by Eleni Nikalexi 18 Sep '20

18 Sep '20

External Email - Use Caution Dear Freesurfer developers, After we run recon-all in a subject we noticed some mistakes, so we added manually some control points in a point set we named control.dat. Then we tried to run autorecon, with the command: recon-all -autorecon2-cp -autorecon3 -subjid Sub42 but we stumbled upon the following error message: using control points from file /project/data/scans/subject/Sub42/tmp/control.dat... assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... Reading 133 control points... only using 133 control points from file, mean 69.1, scaling by 1.59... building Voronoi diagram... performing soap bubble smoothing, sigma = 8... processing with aseg removing outliers in the aseg WM... 580 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction HISTOalloc(-2147483648): could not allocate histogram building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 Cannot allocate memory Linux hpc137 2.6.32-696.16.1.el6.x86_64 #1 SMP Wed Nov 15 16:51:15 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s Sub42 exited with ERRORS What do you think is the problem? Thank you in advance! Best regards, Eleni

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Freesurfer September 2020