Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Single SUVr for PETsurfer
by miracle ozzoude 03 Jul '19

03 Jul '19

External Email - Use Caution Hello Expert, How do i get a single SUVr value for PETsurfer? Similar to Mean_Thickness from Freesurfer, I want to extract a global/Mean SUVr value for each of my subjects. Thank you. Paul

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Qdec Message to Mailing List
by Marie Hill 03 Jul '19

03 Jul '19

External Email - Use Caution Dear Sir/Madam, Could I post the following message to the mailing list: I am running a regression testing for significant difference in cortical volume, thickness etc with 3 factors: diagnosis, genotype and gender, with age as a nuisance factor. I am using qdec but receiving Error: factor 2 must have 2 levels. Is it true that Qdec only supports factors with 2 levels? There is a page for qdec levels stating to create a file diagnosis.levels and state the three levels. I did this however the same error occurs. I was going to use glm_fit instead but I think my study isn't a linear regression so isn't suitable (as I am not interested in the change with age, just between groups). Kind regards, Marie

2 6

Differing T1 Acquisition Comparison In Freesurfer
by Keith, Kathryn 03 Jul '19

03 Jul '19

External Email - Use Caution Hello, I’m curious if anyone has any insights about comparing T1s from different subjects that have different acquisition parameters in Freesurfer. I’m trying to get a feel for how different is too different in regards to comparing differently acquired T1s with Freesurfer. Are there any parameters that must stay consistent in order for Freesurfer to generate comparable outputs between subjects? Any other thoughts? Thank you! Kayti Keith Research Specialist I Medical University of South Carolina Department of Neuroscience Center for Biomedical Imaging 68 President Street, BE220 Charleston, SC 29425

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"MATLAB: Undefined variable" error, FSFAST Tutorial, using Octave
by Zacharie Saint-Georges 02 Jul '19

02 Jul '19

External Email - Use Caution Dear Freesurfer Developers, I am running into a "MATLAB: Undefined variable" error while doing the FSFAST tutorial, using Ubuntu 18.04, Freesurfer v6, and Octave***. I did try a few solutions posted already (please see links below), but I still cannot successfully run the tutorial command line. .basrc additions for Octave environment variables (Ref: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21241.html) export FS_OCTAVE_LIB=/usr/bin/octave export FS_OCTAVE_LIB=/usr/bin/octave additional command line: export FS_USE_OCTAVE=1 Ref: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg60448.html main command line: mkcontrast-sess -analysis my-workmem.sm05.lh -contrast encode-v-base -a 1 (tutorial page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0/FsFastFirstLev… ) error output: INFO: Found 5 Non-Null Conditions INFO: Found 1 Delays Condition Weights: 1.00000000000000000000 0 0 0 0 mkcontrast2 -config my-workmem.sm05.lh/encode-v-base.config -anadir my-workmem.sm05.lh -wcond 1.00000000000000000000 0 0 0 0 -sumconds -o my-workmem.sm05.lh/encode-v-base.mat -wdelay 1 -octave $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $ cmtxfile my-workmem.sm05.lh/encode-v-base.mat nconds 5, wcond 1.00000000000000000000 0 0 0 0 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau cmtxfile my-workmem.sm05.lh/encode-v-base.mat monly 0 NCond 5 WCond 1.00000000000000000000 0 0 0 0 NDelay 1 WDelay 1 TER 0.050000 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/mkcontrast2.18977.m MATLAB: Undefined variable. ERROR running mkcontrast mkcontrast2 -config my-workmem.sm05.lh/encode-v-base.config -anadir my-workmem.sm05.lh -wcond 1.00000000000000000000 0 0 0 0 -sumconds -o my-workmem.sm05.lh/encode-v-base.mat -wdelay 1 -octave Tue May 28 16:51:41 EDT 2019 I also modified the mkcontrast freesurfer file according to this post: Ref: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg58758.html Thank you for your assistance! Regards, Zach Zacharie Saint-Georges Research Assistant Royal Ottawa Institute for Mental Health Research Zacharie.Saint-Georges(a)TheRoyal.ca

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Converting mask.mgh to .nii
by Azeez, Azeezat 02 Jul '19

02 Jul '19

External Email - Use Caution Hello, I wish to convert a .mgh file that can be opened in AFNI I've used mri_convert , yet I am still unable to open the .nii file in AFNI. Any assistance in the matter would be greatly appreciated. Thank You, -- Azeezat Azeez PhD Student Brain Connectivity Lab Department of Biomedical Engineering || New Jersey Institute of Technology Graduate School of Biomedical Sciences || Rutgers University E: aka44(a)njit.edu

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Re: [Freesurfer] Question about OptSeq
by Greve, Douglas N.,Ph.D. 02 Jul '19

02 Jul '19

On 7/2/19 6:58 AM, Davide Nardo wrote: > > External Email - Use Caution > > Dear Prof Greve, > > I hope you don’t mind if I ask you another question. > > I assume that for the same reason (i.e., FIR analysis), null events’ > durations are multiple integers of the TR. > Actually, they are multiples of the dPSD > > But what if one wants to jitter events? > It will just put random amounts of dPSD > > Also, OptSeq does not accept --tnullmin and --tnullmax that are > different from multiple integers of the TR. > Again, the dPSD The problem with setting the dPSD to arbitrarily small values for an FIR analysis is that your statistical power drops by a factor of TR/dPSD > > Best. > > Davide > > *From:*Davide Nardo > *Sent:* 01 July 2019 18:38 > *To:* 'Greve, Douglas N.,Ph.D.' <DGREVE(a)mgh.harvard.edu> > *Subject:* RE: Question about OptSeq > > Dear Prof Greve, > > Thank you very much for your prompt and clear reply. It helps a lot!` > > Best. > > Davide > > *From:*Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu > <mailto:DGREVE@mgh.harvard.edu>> > *Sent:* 01 July 2019 15:07 > *To:* Davide Nardo <Davide.Nardo(a)mrc-cbu.cam.ac.uk > <mailto:Davide.Nardo@mrc-cbu.cam.ac.uk>>; Freesurfer support list > <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > *Subject:* Re: Question about OptSeq > > No, there is not. optseq assumes you will be doing an FIR analysis > (=finite impulse response = not assuming a shape to the hemodynamic > response). In this analysis, this must be the relationship. If you > assume a shape, then this relationship is not necessary. In your case, > you can set the dPSD=1. > > On 7/1/2019 7:19 AM, Davide Nardo wrote: > > * External Email - Use Caution * > > Dear Prof Greve, > > I hope you don’t mind if I ask you a question about OptSeq. > > It looks like a constraint in using OptSeq is that any event > duration must be an integer multiple of the dPSD, which in turn > needs to be an integer multiple of the TR, and seemingly there is > no exception to this rule. > > I am in a situation in which my TR = 2 sec, and my event duration > = 3 sec, therefore I get an error message when running OptSeq. > > However, I am puzzled by this, as in my experience with fMRI an > event duration does not necessarily need to be a multiple of the TR… > > Is there any way I can circumvent this requirement in OptSeq? > > Best. > > Davide Nardo > > -- > > Davide Nardo, PhD > > MRC Cognition and Brain Sciences Unit > > University of Cambridge > > 15 Chaucer Road > > Cambridge, CB2 7EF > > Davide.Nardo(a)mrc-cbu.cam.ac.uk <mailto:Davide.Nardo@mrc-cbu.cam.ac.uk> > > The information in this e-mail is intended only for the person to whom > it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. >

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Freesurfer linear mixed models - viewing results
by Mark Wagshul 02 Jul '19

02 Jul '19

External Email - Use Caution Dear FreeSurfer users/experts, I am working on a mass-univariate linear mixed effects model with cortical thickness data, with multiple time points, a cognitive measure as our primary independent variable and the usual covariates (age, gender, etc). Subject is treated as a random variable (i.e. the first column of all ones is the random variable "Zcols"). We have run through the first few steps to produce the covariance matrices, and note a number of clusters of significance using the "patch" function with the results projected onto lhsphere. We would like to view these results in a more conventional manner, e.g. projected onto the inflated cortex of fsaverage. Is this possible? Thanks for any advice you can provide. Best, Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einstein.yu.edu<mailto:mark.wagshul@einstein.yu.edu> [einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

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Error opening Freeview
by Zeng,Victor (BIDMC - Psychiatry) 01 Jul '19

01 Jul '19

?Hi all, I'm having issues opening Freeview (The most recent version): it loads .mgz and labels correctly, but then after 5 seconds it shuts off, giving off this error: qt_xcb_createCursorXRender: query_pict_formats failed [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si… ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Unknown Name on a linux-gnu named beta by nick Mon Jul 1 16:25:24 2019 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 Segmentation fault ? I was wondering if there's anything I can do to debug, or whether it's just a lack of computer capacity on our end. Best, Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab ph: 617 754 1237 -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

2 1

LME - Monte Carlo
by tom parker 01 Jul '19

01 Jul '19

External Email - Use Caution Dear FreeSurfers, I was reading the wiki documents about how to run LME analyses in FreeSurfer. I found that one of the disadvantages is that, at the moment, it only allows FDR corrections to be applied for multiple comparisons. I have 2 patient groups that show cortical thinning compared to controls at baseline when I correct with Monte Carlo but nothing survives with FDR. Now, I would like to see if these cortical thinning patterns change over time so I thought I should keep things consistent and use Monte Carlo for the longitudinal analysis as well. Is there any way of using Monte Carlo for LME? I read some suggestions in emails that were sent 2 years ago but I was wondering if there are any updates or if there is a guide with recommended steps? Thank you so much!

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Citing the development version for use of hippocampal/amygdala sub-field segmentation
by Daniel Callow 01 Jul '19

01 Jul '19

External Email - Use Caution Hello, I used the longitudinal HippocampalSubfieldsAndNucleiOfAmygdala <https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…> pipeline to create subject-specific hippocampal ROI's for a paper I am preparing for submission. I would like to know what the best way to cite this technique is. This is what I currently have in my methods section. Subjects T1-weighted anatomical images were processed with the FreeSurfer image analysis suite (http://surfer.nmr.mgh.harvard.edu/, version 6.0) and Automated hippocampal subfield segmentation was performed for each subjects T1 weighted image using the Freesurfer longitudinal hippocampal subfield segmentation program(Iglesias et al., 2015, 2016). Do I need to cite my use of the development version? And if so how is the best way to go about doing this? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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