Freesurfer November 2018

freesurfer@nmr.mgh.harvard.edu

121 participants
189 discussions

[PETSurfer] MGX and RBV Correction
by Matthieu Vanhoutte 28 Nov '18

28 Nov '18

External Email - Use Caution Dear Freesurfer's experts, I tried to use PETSurfer to correct partial volume effect on my FDG PET images, testing both Muller-Gartner and RBV corrections. I ran the commands specified in PETSurfer website and used the two following commands for both MGX and RBV corrections respectively: mri_gtmpvc --i PET.nii.gz --reg register.dof6.lta --psf-col 5.51 --psf-row 5.51 --psf-slice 5.9 --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o ./gtmpvc.output mri_gtmpvc --i PET.nii.gz --reg register.dof6.lta --psf-col 5.51 --psf-row 5.51 --psf-slice 5.9 --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o rbv.output.orig 1) However, I found that cortical output mgx.ctxgm.nii.gz of MGX correction encompass more than just GM and values at the boundaries of mgx.ctxgm.nii.gz seem to me very high or aberrant. 2) Concerning RBV correction, output rbv.nii.gz seems to me following more precisely the GM ribbon. However contrary to what is said in PETSurfer website, rbv.nii.gz seems to be in the anatomical space (not in native PET) at the resolution of gtmseg.mgz. How then map rbv.nii.gz to the anatomical space when mapping the volume to the surface ? 3) What are the advantages/inconveniences of RBV vs GMX ? 4) Would it be beneficial to upsample native PET to the anatomical resolution before launching gtmpvc in order to preserve the high resolution of the anatomical tissues during partial volume correction ? Thank you. Best, Matthieu

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Freesurfer tutorial datasets v5.1/5.3
by Amy Barzgari 28 Nov '18

28 Nov '18

External Email - Use Caution Hello FreeSurfer Experts, I'm following the longitudinal FreeSurfer tutorial using v5.1 to become acquainted with stream prior to analyzing our own data. I was able to follow the QDEC tutorial using this version on the Buckner data, however, I kept getting error messages in the QDEC when using the longitudinal data. I created the cross-sectional .dat file using: long_qdec_table --qdec ./qdec/long.qdec.table.dat --cross --out ./qdec/cross.qdec.table.dat The longitudinal measures (i.e. long.thickness-avg) did not appear in the QDEC, and I've tried to look at thickness alone, and got an error message after hitting 'Analyze'. I assumed these issues were arising due to the fact I downloaded the tutorial dataset for v6, when FreeSurfer v5.1 was installed. I then tried to download the datasets for versions 5.1/5.3, but the files seem to be missing. Can these links be updated? (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data#FreeSurferTutoria…) Thank you, Amy

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average of surfaces
by john Anderson 28 Nov '18

28 Nov '18

External Email - Use Caution Dear Freesurfer experts, I have multiple PET volumetric images in MNI standard space. I can average (or get the Tmean) of these images using fslmerge then fslmaths. I would like to do something similar on surfaces images. I registered the images from native space to Freesurfer space using spmregister as follows: spmregister ---s $subject -mov PET.nii.gz --reg reg.dat --o PET_T1.mgh Then I used mris_preproc with the flag --mean to register the volumetric images to fsaverage, then concatenate the surfaces and average it as follows: mris_preproc --target fsaverage --hemi lh --projfrac 0.5 --iv PET_T1_subj1 reg_subj1.dat --iv PET_T1_subj2 reg_subj2.dat . ...... .--iv PET_T1_subjN reg_subjN.dat --mean --o lh.mgh the final output "lh.mgh" is an empty image. I am not sure what I am doing wrong here. Any guidance to average the surfaces images in fsaverage would be highly appreciated. john

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GM and WM intensity thresholds (Manual Edits)
by David S Lee 27 Nov '18

27 Nov '18

External Email - Use Caution Hello FreeSurfer Experts! I currently supply inhomogeneity-corrected (via N4 biascorrection) 3T T1w scans through recon-all pipeline. The correction has solved many segmentation errors which reduced the time spent on manual editing. I have several questions related to this: 1. I am aware of the "3T" flag that can be supplied to recon-all command. It seems redundant to use this flag for already-bias-corrected 3T scans (testing from my end also confirms this), but do you recommend any other bias-correction steps? 2. What are the minimum and maximum intensity thresholds set for GM and WM during recon-all? In the official control point tutorial <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPointsV6.0>, it suggests that WM should be "close" to intensity of 110, but I wanted to know the exact thresholds to perform more accurate manual editing. 3. If these GM and WM intensity parameters can be changed from default, do you recommend doing so? If there is a documentation I can refer to find answers (I've failed to find one so far), please let me know. Thank you for your time as always, -- David S. Lee Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115

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re-run fsaverage only
by Ryan Wales 27 Nov '18

27 Nov '18

External Email - Use Caution Hello, I accidentally renamed my fsaverage directory when I was renaming my subjects' directories. Since I was still in the process of running subjects, a new fsaverage directory was automatically created. Now I have two fsaverage directories that each have a different subset of my participants, but I'd like there to be one directory that has all my participants. Is there any command that I could run that would generate a new fsaverage from subjects in the same output directory? Thanks, Ryan Wales -- Ryan Wales Graduate Student Cognition and Motor Control Neuroscience Laboratory Integrative Neuroscience Psychology Department Stony Brook University E-mail: ryan.wales(a)stonybrook.edu <ryanwales(a)stonybrook.edu>

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Running selxavg with many (~5000) different conditions
by Anna Mynick 27 Nov '18

27 Nov '18

External Email - Use Caution Hi, I'm currently running an analysis that requires defining each of 5000 stimuli as a condition during processing, and for each subject, I have about 140 runs. As a result, selxavg is taking a very long time and huge amounts of memory to run. For instance, it has gotten about 5 runs into "GLS Beta Pass" after 60 hours of running with 200G. Is there a way to (a) predict based on runs and conditions how long and how much compute power selxavg will need to run? (b) speed up running selxavg (maybe there is a lighter-weight version of selxavg that requires less compute power? Thanks very much for any input, Anna

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segmentHA_T2.sh: amygdala recon-all command stoped.
by qimo601 27 Nov '18

27 Nov '18

External Email - Use Caution hi,FreeSurfer experts. I am trying to use segmentHA_T2.sh command to segment the T2 FLAIR Sequence MRI Data. Also I am now only having T2 Data. But there was a mistake in the first step. Sincerely ask for help. (1)First I use recon-all command to generate the subject file from my nii file.But it stop in Correct Defect step. I have run three times after 48 hours. It also stop there. I dont't know why. Can you help me? my command: recon-all -all -i nii-004/ADNI_004_3D_FLAIR.nii.gz -s Subj004 -itkthreads 4 The output of the terminal is as follows： CORRECTING DEFECT 45 (vertices=24, convex hull=53, v0=135114) After retessellation of defect 45 (v0=135114), euler #=96 (83072,238273,155297) : difference with theory (-19) = -115 CORRECTING DEFECT 46 (vertices=97, convex hull=30, v0=136402) After retessellation of defect 46 (v0=136402), euler #=97 (83078,238301,155320) : difference with theory (-18) = -115 CORRECTING DEFECT 47 (vertices=74, convex hull=24, v0=138982) After retessellation of defect 47 (v0=138982), euler #=98 (83088,238338,155348) : difference with theory (-17) = -115 CORRECTING DEFECT 48 (vertices=83, convex hull=55, v0=139717) After retessellation of defect 48 (v0=139717), euler #=99 (83098,238391,155392) : difference with theory (-16) = -115 CORRECTING DEFECT 49 (vertices=141431, convex hull=17606, v0=149662) (2)Because of the above mistakes, I haven't tried the next step yet. segmentHA_T2.sh subject004 ADNI_004_3D_FLAIR.nii.gz T2 0 (3)Attached is the log(recon-all.log). (4)My envientment as follows: Ubuntu 16.04 amd_x64 freesurfer-linux-centos6_x86_64-dev.tar.gz(21-Nov-2018) My data type: 3D-FLAIR (Pixel Spacing X=1.0 mm; Pixel Spacing Y=1.0 mm; Pulse Sequence=SE/IR; Slice Thickness=1.2000000476837158 mm; TE=441.0 ms; TI=1650.0 ms; TR=4800.0 ms; Weighting=T2;) Thanks, Qimo

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Combining voxel-wise and vertex-wise data
by Carola Mayer 26 Nov '18

26 Nov '18

External Email - Use Caution Hello Freesurfer Developers, I have a general question about how to analyse a certain combination of data. I have an independent variable that contains voxel-wise data and I have a dependent variable that contains vertex-wise cortical thickness values. I would like to do a between-subjects analysis correlating the voxel-wise and vertex-wise data. What is a valid approach to do this? Should I first register the voxel-wise data onto the vertex-wise data and then register them into an average space to do group analysis? Or is a different method more valid? Thanks in advance for your time and help, Carola

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Gray Matter Manual Edit Reverting
by David S Lee 26 Nov '18

26 Nov '18

External Email - Use Caution Hello Experts, I am currently using FreeSurfer version 6.0 to make manual edits to T1w images. In an earlier version 5.3, when GM has been erroneously removed, I used the "clone tool" to bring back voxels based on the original T1w. However, this tool seems to be not working in 6.0. Would you be able to help me troubleshoot this? If there is a better alternative to revert GM removal, please let me know! Thank you for your help. -- David S. Lee Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115

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Re: [Freesurfer] [EXTERNAL] Re: extracting FA from FA_skeletonised with freesurfer parcellation
by Yendiki, Anastasia 26 Nov '18

26 Nov '18

In that case, it seems that the low values are introduced when transforming the skeleton from template space to individual space. If this is so, it has nothing to do with using the freesurfer segmentation per se. I would ask on the FSL list. On Nov 26, 2018 3:41 PM, "Winkelbeiner, Stephanie A" <Swinkelbei(a)northwell.edu> wrote: External Email - Use Caution So, I initially did that with the all_FA_skeletonised and got values around 0.6 for the Cc as expected. Interestingly enough though, when I do the same with the individual FA_skeletons that I obtained with the tbss_deproject command the values are around 0.1… Could you think of a reason why that is? From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Monday, November 26, 2018 1:58 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [EXTERNAL] Re: extracting FA from FA_skeletonised with freesurfer parcellation External Email. Use Caution. You don't want to be averaging zero voxels, so masking makes sense. When you click on the voxels inside one of those segmentation regions (e.g. one of the CC regions) in freeview, are the FA values that you see high? On Nov 25, 2018 8:42 AM, "Winkelbeiner, Stephanie A" <Swinkelbei(a)northwell.edu<mailto:Swinkelbei@northwell.edu>> wrote: External Email - Use Caution Hi Anastasia, I have checked and they do align. However the freesurfer parcels naturally cover more of the brain than the FA skeletons. I was wondering if this was the problem? Therefore I added a binary mask of the FA skeletons. I also tried subtracting the parcels from the FA skeletons with fslmaths to make sure that only the area of the skeleton is read out. But that doesn't give convincing results either. Anyone having other suggestions? Thanks, Steph Sent from my Samsung Galaxy smartphone. -------- Original message -------- From: "Yendiki, Anastasia" <AYENDIKI(a)mgh.harvard.edu<mailto:AYENDIKI@mgh.harvard.edu>> Date: 23/11/18 17:50 (GMT-05:00) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [EXTERNAL] Re: [Freesurfer] extracting FA from FA_skeletonised with freesurfer parcellation Have you checked if the registered segmentation and the FA map align correctly in freeview? On Nov 23, 2018 1:27 PM, "Winkelbeiner, Stephanie A" <Swinkelbei(a)northwell.edu<mailto:Swinkelbei@northwell.edu>> wrote: Hi, I try to extract FA values from the FSL FA skeleton using the freesurfer aparc.a2009s+aseg+2mm parcellations. I did the following: 1. Recon-all to obtain à aparc.a2009s+aseg+2mm 2. TBSS in FSL to obtain à all_FA_skeletonised 3. Tbss_deproject to split up all_FA_skeletonised into individual skeletons (native space) (*_FA_FA_all_FA_skeletonised.nii.gz) 4. Non-linear transformation of aparc.a2009s+aseg+2mm to subjects’ native space (parc2dwi.nii.gz) 5. Creating binary mask for each subjects FA skeleton to exclude 0 voxels (*_FA_skeleton_mask.nii.gz) 6. Extracting FA values using mri_segstats with the following command: cd subj1/ mri_segstats \ --seg mri/parc2dwi.nii.gz \ --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \ --i skeletons/SPN01_CMH_0001_01_FA_FA_all_FA_skeletonised.nii.gz \ --mask skeletons/SPN01_CMH_0001_01_FA_skeleton_mask.nii.gz \ --excludeid 0 \ --sum skeletons_FA.stats The FA values I obtain are around 0.1 which is highly unlikely, especially for regions such as the corpus callosum. Is there some obvious error in my approach? Or can someone recommend a different approach? I would be very grateful for some help! Thanks, Steph Stephanie Winkelbeiner, MSc Research Coordinator Psychiatry Research Zucker Hillside Hospital 75-59 263 Street Glen Oaks, NY 11004 Tel: (718) 470-4588 Email: swinkelbei(a)northwell.edu<mailto:swinkelbei@northwell.edu> Northwell Health Visit us at Northwell.edu<http://northwell.edu/> The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege. The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege. The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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Freesurfer November 2018