Freesurfer June 2019

freesurfer@nmr.mgh.harvard.edu

82 participants
138 discussions

Advantage of having skull for longitudinal processing?
by Adam Martersteck 22 Jun '19

22 Jun '19

External Email - Use Caution Hi Freesurfer team, I'm thinking of pre-skullstrip'ing my brains prior to being input into FreeSurfer. My fear was this information in the skull might be useful during mri_robust_register or mri_robust_template for longitudinal analyses: Martin discusses this in his Freesurfer workshop talk at 9 minutes in (youtube: http://www.youtube.com/watch?v=vxJODPBLd3M&t=9m21s) where the heatmap covers parts of the skull and the Freesurfer wiki which mentions that the Tukey biweight will deweight regions of noise like tongue/eye/neck differences. But it appears the longitudinal stream registers everything on each cross-sectional's norm.mgz to create the fused norm -- which is skullstripped and missing neck/tongue/eyes/skull already. Am I missing something? Is it alright if my T1.mgz, rawavg.mgz, orig.mgz, etc. do not have a skull for longitudinal processing? Thanks, Adam

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translations and rotations from an affine transform matrix
by Pfannmoeller, Joerg Peter 21 Jun '19

21 Jun '19

Hello, is there a tool to extract the translations and rotations from an affine transform matrix (register.dof6.dat)? Best Joerg

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examining between group differences using DODS
by Avi Gharehgazlou 21 Jun '19

21 Jun '19

External Email - Use Caution Hi experts, I want to examine between-group differences in LGI controlling for age, sex and surface area (all except sex demeaned). To do so, I ran the DODS model on QDEC selecting: - “diagnosis” and “sex” as discrete (fixed factors) - “age” and “surface area” as nuisance factors - And selected this question à “Does the average pial_lgi, accounting for sex, differ between TD and NDD? Nuissance factors: Age Surface area” 1) I wanted to ask you what the significant results from the above analysis means? I was under the impression that the significant clusters represent clusters where there are significant group differences in LGI while controlling for age, surface area and sex. But I am confused because I know from previous threads that you recommend to run DODS to check for interactions first, and if there is no interaction to then run DOSS to see differences between groups. So: 2) Do my significant results mean that I have an interaction between diagnosis and sex OR diagnosis and age OR diagnosis and surface area? 3) Considering that I have an interaction, how do I now examine between-group differences in LGI? Is what I have done (through the DODS model) correct? I'd really appreciate your help, Thanks so much, Avi

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Confirmation regarding running GLM on command line stream
by Avi Gharehgazlou 21 Jun '19

21 Jun '19

External Email - Use Caution Hi experts, Will you please confirm below command lines I run to examine between group differences in LGI? I have 3 questions listed. I can’t run the below line, it gives an error: mris_preproc --fsgd TDvsNDDageSAsex.fsgd --cache-in lh.pial_lgi.fwhm0.fsaverage --target fsaverage --hemi lh --meas pial_lgi --out lh.pial_lgi.0.mgh mris_preproc --fsgd TDvsNDDageSAsex.fsgd --cache-in rh.pial_lgi.fwhm0.fsaverage --target fsaverage --hemi rh --meas pial_lgi --out rh.pial_lgi.0.mgh Therefore, I run the below line instead - although I know it’s for uncached data and I have already ran qcache for my subjects (using: recon-all -s 101031_01 -qcache -measure pial_lgi) mris_preproc --fsgd ASDvsADHD.txt --target fsaverage --hemi lh --meas pial_lgi --out lh.pial_lgi.mgh mri_surf2surf --hemi lh --s fsaverage --sval lh.pial_lgi.mgh --fwhm 0 --cortex --tval lh.pial_lgi.0.mgh # I run above line separately for right hemisphere 1. Do I have to write “cortex” in above command line or not? 2. Is it okay to run this command line considering that qcache has already been run on all my subjects? 3. I’ve ran qcache (and above command line) multiple times on each subject in my data. Is this ok? Or does this mess up anything? To test for main effect of group, I ran below line: mri_glmfit --y lh.pial_lgi.0.mgh --fsgd ASDvsADHD.txt dods --C betweengroupdifferencecontrollingforageSAsex.mtx --C agebydiagnosisinteraction.mtx --surf fsaverage lh --cortex --glmdir lh.ASDvsADHD.glmdir mri_glmfit --y rh.pial_lgi.0.mgh --fsgd ASDvsADHD.txt dods --C betweengroupdifferencecontrollingforageSAsex.mtx --C agebydiagnosisinteraction.mtx --surf fsaverage rh --cortex --glmdir rh.ASDvsADHD.glmdir To correct for multiple comparisons using monte carlo: mri_glmfit-sim --glmdir lh.ASDvsADHD.glmdir --cache 1.3 abs --cwp 0.05 --2spaces mri_glmfit-sim --glmdir rh.ASDvsADHD.glmdir --cache 1.3 abs --cwp 0.05 --2spaces I'd really appreciate your soon reply, Thanks so much for all your support, Avi

2 1

4dfp data format
by Francesca Pentimalli 21 Jun '19

21 Jun '19

External Email - Use Caution Dear freesurfer experts, I am trying to use the 4dfp data format, but I am not able to find the 4dfp suite of tools developed by Dr. Avi Snyder. Can someone please point me in the right direction? Regards, Francesca -- *Francesca Pentimalli Biscaretti di Ruffia * Via S. Eufemia 3, 35121 Padova (Italy) Mobile: +39 3483862788 francesca.pentimallibiscarettidiruffia(a)studenti.unipd.it fpentimallibdr(a)gmail.com fpenti(a)mit.edu fpbdr(a)bu.edu

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Tksurfer and qdec: error sourcing and floating exception
by Wafaa Sweidan 21 Jun '19

21 Jun '19

External Email - Use Caution Hello all, I have been using freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c on macos high sierra, then I updated to mojave 10.14. freeusrfer was working all good for a while. BUT, for unknown reasons, I am no longer able to overlay the significance maps using tksurfer and cant open qdec, like below: command: tksurfer fsaverage lh inflated output error: subject is fsaverage hemi is lh surface is inflated surfer: current subjects dir: /Users/wsweidan/Desktop/GLM_trial surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/wsweidan/Desktop/GLM_trial checking for nofix files in 'inflated' Reading image info (/Users/wsweidan/Desktop/GLM_trial/fsaverage) Reading /Users/wsweidan/Desktop/GLM_trial/fsaverage/mri/orig.mgz surfer: Reading header info from /Users/wsweidan/Desktop/GLM_trial/fsaverage/mri/orig.mgz surfer: vertices=163842, faces=327680 surfer: single buffered window surfer: tkoInitWindow(fsaverage) setting percentile thresholds (-1.00, 0.00, 0.00) surfer: using interface /Applications/freesurfer/tktools/tksurfer.tcl Reading /Applications/freesurfer/tktools/tkm_common.tcl Reading /Applications/freesurfer/tktools/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/tktools/tkUtils.tcl Error sourcing /Applications/freesurfer/tktools/tksurfer.tcl: bad distance "0.125i": can't be negative reading white matter vertex locations... % Floating exception command: qdec output error: Floating exception I reinstalled freesurfer again and I still get the same errors. Freeview works just fine. Any input of how to solve this issue? Thanks in advance, Wafaa

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Re: [Freesurfer] hippocampal subfield as CONN seeds
by Greve, Douglas N.,Ph.D. 21 Jun '19

21 Jun '19

There are several things that will need to be done, and they can be quite tricky. Since you already have a registration between the fMRI and the MNI, you will have to create a rigid registration from the FS anatomical to the fMRI, then concatenate the registrations into a single registration. You can then apply the registration to the FS segementation with mri_label2vol using the --seg option. It will not be easy to extract all these matrices, sorry, I don't know enough about SPM to help you out much more. On 6/13/2019 5:37 PM, Nelson, Eric A wrote: External Email - Use Caution Thanks for your response, I believe CONN should be using SPM linear? Best, Eric From: Greve, Douglas N.,Ph.D. [mailto:DGREVE@mgh.harvard.edu] Sent: Wednesday, June 12, 2019 8:27 AM To: Nelson, Eric A <eanelson(a)uab.edu><mailto:eanelson@uab.edu> Subject: Re: [Freesurfer] hippocampal subfield as CONN seeds I meant how does CONN do the registration? SPM linear? FSL non-linear? That command definitely will not work. You have to do it in exactly the same way as CONN or else the segmentations won't align. On 6/12/2019 2:39 PM, Nelson, Eric A wrote: External Email - Use Caution Hi, Not sure I sent this correctly the last time. Im not sure I understand the question because I have not successfully registered the hippoSfLabels file to mni space. I can load the hippoSfLabels.mgz file into CONN at the subject level, but I have two problems. 1st it is not in MNI space. 2nd it is the whole hippocampus and I want to be able to use masks of the individual subfields. To try and convert the hippoSfLabels file to MNI space though I used the following. mri_vol2vol --mov lh.hippoSfLabels-T1-T2.v10.mgz \ --targ $FREESURFER_HOME/average/mni305.cor.mgz \ --xfm transforms/talairach.xfm \ --o test.mgz Eric 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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registration with bbr and determination of motion regressors with mcdat2mcextreg
by Pfannmoeller, Joerg Peter 21 Jun '19

21 Jun '19

Hello, I have used bbr to register all EPI volumes in my time series to the brains of my participants. The fMRI time series at each vertex was determined based on this registration. I would like to use motion regressors in the GLM analysis. Is it appropriate to extract the motion parameters from the bbr registration matrices to use them as input to mcdat2mcextreg? Are there any conventions I need to take into account? Best Joerg

2 1

freesurfer picture
by Abby tang 21 Jun '19

21 Jun '19

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to get some pictures about my results , so QDEC was used. However I can't adjust those pictures which QDEC produced, such as picture1. When I read other's paper, they provided different pictures just like picture2. If there any other methods to produce statistic pictures of brain? Can you give me some advices? Thank you for your help. Best regards Abby

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bbregister- switched coronal and axial views error
by Wenzhen Zhao 21 Jun '19

21 Jun '19

External Email - Use Caution Dear list, After running preproc-sess on fmri data, bbr-sum was 0.94. After looking through images of template.nii.gz with register.dof6.lta file, I found that coronal and axial views of template(w/ registration applied) are switched. $preproc-sess -s sess01 -fsd rest -surface fsaverage lhrh -mni305 -fwhm 5 -per-run Is there any possible error that I might have made? or is there any way to fix it? I appreciate your help! Thanks, Wenzhen

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Freesurfer June 2019