Freesurfer February 2017

freesurfer@nmr.mgh.harvard.edu

162 participants
277 discussions

mri_glmfit-sim
by Shane Schofield 21 Feb '17

21 Feb '17

Hi, I have 3 beginner questions about the use of mri_glmfit-sim 1. Under what type of circumstances should I run mri_glmfit-sim with permutation simulations? 2. The voxel threshold of 0.01 (cache 2) is used a lot. Is this too lenient in cortical thickness comparisons? 3. About the sign of the test (abs, neg, pos): is a one-tailed sign justified if I have an hypothesis? If the uncorrected (mri_glmfit) test shows a significant difference in one direction but not the other, am I justified to use pos/neg (instead of abs) in the mri_glmfit-sim stage and explicitly state that in the manuscript? Thanks. Hope to learn more. Have a good week. Cheers, Shane

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Re: [Freesurfer] Convolving external regressors with HRF
by Reza Rajimehr 21 Feb '17

21 Feb '17

Hi Doug, Since our external regressors are stimulus-related (e.g. mean luminance of stimuli), we need to convolve them with a hemodynamic response function. In mkanalysis-sess, we have used -spmhrf 0 to model conditions. Is there a code or Matlab script for HRF convolution, so that we apply exactly the same spmhrf function for modeling the external regressors? Thanks, Reza No, they are not On 02/17/2017 05:09 PM, Reza Rajimehr wrote: >* During the functional analysis in FS-FAST, are the external regressors *>* convolved with the hemodynamic response function? *>>* Thanks, *>* Reza *>>>* _______________________________________________ *>* Freesurfer mailing list *>* Freesurfer at nmr.mgh.harvard.edu <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> *>* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> * -- Douglas N. Greve, Ph.D. MGH-NMR Centergreve at nmr.mgh.harvard.edu <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harvard.edu/facility/… Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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cluster as ROI
by Clara Kühn 21 Feb '17

21 Feb '17

Dear FreeSurfer Experts, I compared 2 groups in QDEC in spc (from pre to post) and found a cluster that survives Monte Carlo correction. Now I would like to extract the data for each participant and each time point from that cluster so that I can plot the change. How could I do this? I tried this so far: aparcstats2table --qdec-long $SUBJECTS DIR/qdec/2016.12.06-40kids-long.qdec.table2-1.dat --hemi rh - -tablefile $SUBJECTS DIR/qdec/2016.12.08-40kids-2stagemodel/rharea-cluster-extracted.txt --parc $SUBJECTS DIR/qdec/2016.12.08-40kids-2stagemodel/rh-area again/rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh But I get this error: ERROR: The stats file /nobackup/etsch2/kids/prepost-61kids/AL3K_1.long.AL3K.base/stats/rh./nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again/rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files Do I have to define my cluster as a ROI and then warp it onto the single time points? How would I do that? Any help is much appreciated! Thank you Clara -- Clara Kühn, Phd Student Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

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Convolving external regressors with HRF
by Reza Rajimehr 21 Feb '17

21 Feb '17

During the functional analysis in FS-FAST, are the external regressors convolved with the hemodynamic response function? Thanks, Reza

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“ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!"
by Uquillas, Federico D'Oleire 21 Feb '17

21 Feb '17

Dear FreeSurfer experts, I ran mri-glmfit-sim using mc-z, for both hemispheres, and the right hemi finished with the message “mri_glmfit-sim done”. However, for the left hemi, I got the following: “ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!” I believe this is signifying that there were no clusters that survived the correction, but would like to verify with you guys. Thank you so much. Best, Fred

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Freeview X Error: BadValue
by Lebois, Lauren Ann Mcdonough 21 Feb '17

21 Feb '17

Hi FS gurus, I am remote logging in to nmr nexlin machines from my work iMAC and I am trying to view some freesurfer results with Freeview, but I am getting the following error: llebois@nexlin9:/eris/ressler/DD_FS_160222/150305_NTD015_FS/mri/assembly$ freeview -v nu.mgz left_discreteLabels.mgz X Error: BadValue (integer parameter out of range for operation) 2 Extension: 149 (Uknown extension) Minor opcode: 3 (Unknown request) Resource id: 0x0 Abort (core dumped) I have searched the archives and as far as I can tell, didn't find anything related to this error. Any ideas on how to troubleshoot this one? Thank you for your help and time. Sincerely, Lauren

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-no-isrunning flag question
by Joe Necus (PGR) 21 Feb '17

21 Feb '17

Hello, As I understand, adding the -no-isrunning flag will cause recon-all to ignore the 'isrunning.pial' file. I previously interrupted recon-all (while it was in the middle of a process) and I have now begun to re-run my subjects using this flag. I just wanted to check that any data which has previously been generated by freesurfer will now be overwritten. I.e. that there are no disadvantages to using this flag? Thanks , Joe

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mri_normalize 5.4 vs v6
by Arman Eshaghi 21 Feb '17

21 Feb '17

Dear All, When I run mri_normalize on the same image using two freesurfer versions I get distorted results only on the V6. Can someone let me know how I can get the same results with V6? command: mri_normalize <input> <output> V5 output: voxel value range: 0 - 182 [image: Inline image 1] v6 output: voxel value range: 0-255 [image: Inline image 2] Thanks

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Comparability of FreeSurfer segmentations across different MRI acquisition specs
by Darko Sarovic 21 Feb '17

21 Feb '17

Hi, I’m doing volumetric analyses on MR structural data. The problem is that the scanning has been done on different MR machines, as well as with different sequences in some cases. This leads to different absolute values between subjects for volumes and thicknesses when being run through the FreeSurfer segmentation. My questions regarding this are: - Is there any way to standardize the results so that the segmentations with different acquisition specs (different MR sequences, MR machine developers) can be comparable? - I have used v5.3.0 for my segmentations; Is any part of v6.0.0 improved in this regard so that using that version would give more comparable results? Regards, Darko Sarovic Gothenburg University, Sahlgrenska Academy

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mri_cvs_register error : PETSC Error
by Bhavana Ganesh 21 Feb '17

21 Feb '17

Hi Developers, I'm receiving this error while I try to run mri_cvs_register. The same error was received when I reran the same even after increasing the memory allocated to my VB. Can anybody help me with the issue I am facing. Below are the details of my system and software configurations. PFA error log files. FreeSurfer version: freesurfer-Linux-centos6_x86_ 64-stable-pub-v6.0.0-2beb96c Platform: CentOS7 on VirtualBox Command Run: mri_cvs_register --mov bert2 0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Out of memory. This could be due to allocating [0]PETSC ERROR: too large an object or bleeding by not properly [0]PETSC ERROR: destroying unneeded objects. [0]PETSC ERROR: Memory allocated 0 Memory used by process -2147483648 <%28214%29%20748-3648> [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. [0]PETSC ERROR: Memory requested 576224344! [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: surf2vol on a linux-gnu named localhost.localdomain by root Thu Feb 16 09:57:44 2017 [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: PetscMallocAlign() line 61 in src/sys/memory/mal.c [0]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 2818 in src/mat/impls/aij/seq/aij.c [0]PETSC ERROR: MatTranspose_SeqAIJ() line 1460 in src/mat/impls/aij/seq/aij.c [0]PETSC ERROR: MatTranspose() line 3500 in src/mat/interface/matrix.c [0]PETSC ERROR: TSolver::setup_load_sym() line 1130 in unknowndirectory/solver.h after setup_load_mfc Linear solve converged due to CONVERGED_ITS iterations 1 Thank You *Regards,* *Bhavana* <https://www.linkedin.com/in/bhavanaganesh> <https://www.linkedin.com/in/bhavanaganesh> <https://www.linkedin.com/in/bhavanaganesh> <http://bhavanaganesh.weebly.com/>

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Freesurfer February 2017