Freesurfer April 2019

freesurfer@nmr.mgh.harvard.edu

99 participants
136 discussions

ERROR: nu_correct
by Sevan Harootonian 04 Apr '19

04 Apr '19

External Email - Use Caution Hello Freesurfers, I'm running recond-all and getting ERROR: nu_correct. I see a lot of people online have had this problem but I've failed to found a solution. Any suggestions? I'm running freesurfer on a virtual machine and I've attached my recon-all.log thanks, sev -- Sevan Harootonian research specialist Ekstrom's Lab University of Arizona Psychology Department

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Fwd: REMINDER - OHBM Call for Nominations
by Greve, Douglas N.,Ph.D. 03 Apr '19

03 Apr '19

-------- Forwarded Message -------- Subject: REMINDER - OHBM Call for Nominations Date: Wed, 3 Apr 2019 16:22:25 -0500 From: info(a)humanbrainmapping.org Reply-To: info(a)humanbrainmapping.org To: greve(a)nmr.mgh.harvard.edu External Email - Use Caution Organization for Human Brain Mapping Dear OHBM Member: OHBM’s Call for Nominations deadline for open Council positions is fast approaching! Open positions include Chair-Elect, Secretary-Elect, Treasurer-Elect, Program Chair-Elect and Education Chair-Elect. This is your chance to become involved in the identification and election of your association’s leadership. Please make a nomination by completing the Call for nominations form no later than *Monday, April 8^th at 24.00H-US Central./Please note that self-nominations are encouraged!/* We look forward to your involvement in the identification and election of your Society’s leadership. Please contact the OHBM Executive Office at info(a)humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…> with any questions. Sincerely, JoAnn Taie Executive Director Organization for Human Brain Mapping (OHBM) *Register Now <https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3882> for the 2019 OHBM Annual Meeting* *June 9-13, 2019* <https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3882> /The content of this email is confidential and intended for the recipient specified in message only. It is strictly forbidden to share any part of this message with any third party, without a written consent of the sender. If you received this message by mistake, please reply to this message and follow with its deletion, so that we can ensure such a mistake does not occur in the future./ Phone: 1 952-646-2029 · i <tel:1 952-646-2029>nfo(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org>·humanbrainmapping.org <http://humanbrainmapping.org> To opt out of OHBM emails, contact the OHBM Executive Office at info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org>. © 2017 Organization for Human Brain Mapping. All Rights Reserved.

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Hippocampal subfield version
by Emily Schwartz 03 Apr '19

03 Apr '19

External Email - Use Caution Hello FS experts, I was planning to use the hippocampal subfield segmentation module in FreeSurfer 6.0 on a Linux ubuntu computer. I also would like to use the nuclei of the amygdala segmentation, but realized I need to download the development version in order to do that. Is there any reason why I shouldn't use the development version over the 6.0 release? Thank you in advance. Best, Emily

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Transform functional surface data to volume
by Zhi Li 03 Apr '19

03 Apr '19

External Email - Use Caution Dear Freesurfer experts, I would like to transform the task-based surface data to volume. May I know if it is applicable? I tried "mri_surf2vol --o test.nii.gz --subject sub002 --so fs/sub002/surf/lh.white fMRI/sub002/task/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz", but my system frozen. Any suggestions would be appreciated. Another problem is that in some individuals I found the RAS information of preprocessed surface data of different sessions are not identical, that means the "voxel to ras transform" and "ras to voxel transform" in fmcpr.odd.sm5.fsaverage.lh.nii.gz are different between seesion1 (folder 001) and session2 (folder 002). May I know how this happened and will it influence the final result? Should I keep them the same? Thanks, LIzhi

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mris_curvature questions
by Tim Schäfer 03 Apr '19

03 Apr '19

External Email - Use Caution Dear list, I have two questions on mris_curvature command line options: 1) the '-a' option, help text is: '-a <avgs>: perform <avgs> iterative averages of curvature measure before saving': Afaik, this is a smoothing operation. But what exactly is averaged? 2) the '-nbrs' option, help text is '-nbrs <nbrs>: set neighborhood size to nbrs' For this one I would like to know what the default value is if the option is omitted. And what is the unit, is the neighborhood given in hops in the mesh (all vertices reachable by crossing <nbrs> edges)? Best, Tim

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Convert Yeo's 17-network confidence map into MNI152 volumetric space
by huyang 03 Apr '19

03 Apr '19

External Email - Use Caution Dear FreeSurfer experts and users, I would like to convert Yeo's 17-network confidence map into MNI152 volumetric space and I tried the following commands (but failed): (1) mri_surf2vol --so $SUBJECTS_DIR/fsaverage/surf/lh.white $SUBJECTS_DIR/fsaverage/label/lh.Yeo2011_17NetworksConfidence_N1000.mgz \ --so $SUBJECTS_DIR/fsaverage/surf/rh.white $SUBJECTS_DIR/fsaverage/label/rh.Yeo2011_17NetworksConfidence_N1000.mgz \ --lta $FREESURFER_HOME/average/mni152.register.dat --o Yeo2011_17NetworksConfidence.nii.gz (2) mri_surf2vol --surfval $SUBJECTS_DIR/fsaverage/label/lh.Yeo2011_17NetworksConfidence_N1000.mgz --hemi lh --fillribbon \ --reg $FREESURFER_HOME/average/mni152.register.dat --template ${FSLDIR}/data/standard/MNI152_T1_1mm_brain.nii.gz \ --o lh_Yeo2011_17NetworksConfidence.nii.gz Best, Yang Hu

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mris_preproc not running
by Sims, Sara A (Campus) 02 Apr '19

02 Apr '19

External Email - Use Caution Hello! I have 786 subjects that I am trying to do a paired difference analysis using mri_glm. I am getting stuck at the mris_preproc stage. I have tried running it on a handful of subjects and it works wonderfully. However, when I run it on all the subjects it outputs an empty file. I think part of my problem is that I am having to do 1572 flags to enter all the subjects files (which I made a script to create, I did not hand type them). Is there a better way to do this? Do I just have too many subjects? This is what I have that isn’t working: mris_preproc --target fsaverage --hemi lh --isp $in/${network}/100206.${run1}/lhsurf.mgh --isp $in/${network}/100206.${run2}/lhsurf.mgh --isp $in/${network}/100307.${run1}/lhsurf.mgh --isp $in/${network}/100307.${run2}/lhsurf.mgh ……. --out $out/preproc_${network}_${pair}/lh.paired-diff.${network}_${pair}.mgh --f $sublist --paired-diff --no-cortex-only Thanks for the help! Sara Sims

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dt_recon ERROR: DTIloadBValues
by Daniel Callow 02 Apr '19

02 Apr '19

External Email - Use Caution Hello, I am running dt_Recon with the following specifications and am running into this issue? I wasn't running into this issue previously. Two changes I made are I added the --eres-save flag and I am running the code on the dev version instead of the freesurfer6.0 version. Any idea what could be contributing to this issue? I am running the following mri_convert image000001.dcm /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/dwi.nii.gz dt_recon --sd /Volumes/DANIEL/dti_freesurf/diffusion_recons --i /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/dwi.nii.gz --s ${subj}.${cond} --b dwi.bvals dwi.voxel_space.bvecs --eres-save --o /Volumes/DANIEL/dti_freesurf/dtrecon/${cond}.${subj} and get an error at this point #@#------------------------------- Fitting Tensors Mon Apr 1 15:16:29 EDT 2019 cd /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES114.Rest mri_glmfit --y /Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114/dwi-ec.nii.gz --glmdir /Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114 --nii.gz --dti dwi.bvals dwi.voxel_space.bvecs --eres-save $Id: mri_glmfit.c,v 1.246 2017/02/15 21:04:18 greve Exp $ cwd /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES114.Rest cmdline mri_glmfit --y /Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114/dwi-ec.nii.gz --glmdir /Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114 --nii.gz --dti dwi.bvals dwi.voxel_space.bvecs --eres-save sysname Darwin hostname 255a-280.umd.edu machine x86_64 user amos FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114/dwi-ec.nii.gz logyflag 1 usedti 1 glmdir /Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114 IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114 Loading y from /Volumes/DANIEL/dti_freesurf/dtrecon/Rest.AES114/dwi-ec.nii.gz ... done reading. Using DTI Loading BValues from dwi.bvals ERROR: DTIloadBValues(dwi.bvals): could not scan value(s) Found 65 bvalues ERROR: DTIloadBValues(dwi.bvals): could not scan value(s) Loading BVectors from dwi.voxel_space.bvecs ERROR: DTIloadBValues(dwi.voxel_space.bvecs): could not scan value(s) Found 0 bvectorss ERROR: DTIloadBValues: no bvectors found in dwi.voxel_space.bvecs 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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Colourful Brain
by May, Markus 02 Apr '19

02 Apr '19

Hi, My university has a new FDM 3D printer which is able to print colours. They want to print a brain in colour or maybe in multiple colours. Is there anybody who knows how I could get it? Best, Markus ———————————— With best regards, M.Eng. Markus May Ph.D. Student at Technische Hochschule Mittelhessen - University of Applied Sciences Wiesenstr. 14, 35390 Gießen<x-apple-data-detectors://27/0>, Germany Gebäude D10, Raum 0.16 Telefon: 0049 641 309 2646<tel:0049%20641%20309%202646> Mail: markus.may(a)lse.thm.de<mailto:markus.may@lse.thm.de> Web: www.thm.de/imps<http://www.thm.de/imps><http://www.thm.de/imps>

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(no subject)
by Giuliana Klencklen 02 Apr '19

02 Apr '19

External Email - Use Caution Hi FS experts, I use tksurfer (e.g., tksurfer fsaverage/ lh inflated -gray) to open the overlays (i.e., something.sig.cluster.mgh) I generated with the permutation simulation correction. It goes perfectly well for most of them expect for some, where the overlay does not show at all the significant clusters summarized in the something.sig.cluster.summary. I run the mri_glmfit-sim command again but the problem persists. Does anyone have a clue about what is going wrong? Many thanks, Giuliana Klencklen -- Giuliana Klencklen, Ph.D. Helen Wills Neuroscience Institute University of California, Berkeley 118 Barker Hall Berkeley, CA 94720-3190 510-395-0040 giuliana.klencklen(a)berkeley.edu

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Freesurfer April 2019