Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Re: [Freesurfer] Problem with registration (PetSurfer)
by Marina Fernández 14 Feb '20

14 Feb '20

External Email - Use Caution The error was shown after running tkregisterfv. Marina.

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Question re: hippocampal/amygdala subfields
by Tegan Hargreaves 14 Feb '20

14 Feb '20

External Email - Use Caution Hi all, I am fairly new to FreeSurfer and am implanting the hippocampal/amygdala subfields script in our participants. As there are two versions of the hippocampal script (i.e., version 10 that is only hippocampus and version 21 which is both), I wanted to confirm that I should be using FS v6.0 (stable) for recon-all, and then running only the hippocampal/amygdala (v21) script through the dev version of FS. I don't believe that I should be running the exclusively hippocampal script anymore, as the guide states it is now obsolete, but I just wanted to confirm. Thank you so much! Best, Tegan Tegan Hargreaves, MSc Research Assistant Peter Boris Centre for Addictions Research | St. Joseph's Healthcare Hamilton 100 West 5th Street, Hamilton, ON L8P 3P2 P: 905-522-1155 ext. 36368 | E: thargrea(a)stjoes.ca<mailto:thargrea@stjoes.ca> ________________________________ Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and/or privileged information. Any unauthorized review, use, copying, saving, disclosure, re-transmission or distribution is strictly prohibited. If you are not the intended recipient or this information has been inappropriately forwarded to you, please contact the sender by reply e-mail or the Privacy Office via privacy(a)stjoes.ca. Thank you. ________________________________

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Thickness group normalization
by Vyacheslav Yarkin 14 Feb '20

14 Feb '20

External Email - Use Caution Hello Freesurfer Team, Would you be so kind to provide freesurfer steps to implement warping fsaverage mean thickness data on individual subject inflated brains ? I am using expert opts to disable cortical thickness restriction, and set mris_thickness -max 20 as I want to find fcd to cortical surfaces. The reason i need normalization is that there is zones like sulci orbitales have bigger thickness accross subjects group ( control ) and have red LUTs on inflated thickness map. So i would like to normalize thickness over control group, to use it on patients to exclude "normal" thickness excedings to include only increased FCD zones. The main issue I faced is how to warp fsaverage mean thickness data on individual subject's inflated brain as they have vertices number missmatch. Steps I tried: 1) make_average_subject 2) mri_concat --mean to create mean thicknesses over group? Thank you

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recon-all -make all
by Benjamin Ineichen 14 Feb '20

14 Feb '20

External Email - Use Caution Dear Freesurfer experts, I ran recon-all on 100 subjects. Around 20 of them needed manual corrections of the pial surface on the brainmask.mgz. 1.) Can I run the command: "recon-all -make all- s <subject>" on all 100 subjects and it will only recon-all the manually edited ones or do I need to run it individually for the 20 subjects? 2.) Do I need to add the flags which I used for the original recon-all command to the "recon-all -make all- s <subject>, e.g. -qcache -T3 -hippocampal subfields etc? Many thanks! /Ben -- ____________________________________ Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen(a)protonmail.ch +41 76 391 04 01 Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen(a)protonmail.ch +41 76 391 04 01

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Three qdec analyses, different results
by Wang, Lily 14 Feb '20

14 Feb '20

Hi Freesurfer Team, I made a qdec table with columns fsid, disease status (control and diseased), age, df, db, dtotal (which are three continuous psychological test scores). I performed one analysis in qdec with disease status as the discrete factor and each of the three test scores as the continuous factor with no nuisance factor chosen, for a total of three analyses. All three analyses ran successfully but when I choose "Does the average thickness differ between Control and Diseased?", which should ignore the test scores (right?), and applied an FDR = 0.05, I get wildly different results among the three analyses even though I believe I should get the same results since it is the same pool of subjects in all three analyses. Did I do something wrong? Thank you, Lily

2 1

Conversion between lta file type
by Christian O'Reilly, Dr 14 Feb '20

14 Feb '20

External Email - Use Caution Hi, How can I convert a LTA file type 0 (LINEAR_VOX_TO_VOX) to a type 1 (LINEAR_RAS_TO_RAS)? Also, given a volume x.nii.gz and a file y.lta, how do I obtaijn z.nii.gz as the original volume x.nii.gz transformed according to y.lta? I tried with mri_vol2vol but somehow I could not figure a way to make it work properly. Also, given a volume containing a full head and a second volume containing a stripped skull, what is the best approach with FreeSurfer to transform the brain so that it is properly registered with the full head (using an affine transform)? I tried many different ways to get it done with mri_robust_register and also with bbregister, but somehow I could not get a satisfactory result (i.e., I could always get a much better fit by hand using freeview).... Thank you! Christian

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Re: [Freesurfer] PetSurfer questions
by Soo-Jong Kim 14 Feb '20

14 Feb '20

External Email - Use Caution Thank you, Dr. Greve I checked all about your comment. I have questions more. 1. I found that volumes or counts in gtm.stats.dat are for native PET space. If co-registered PET onto corresponding MRI(i.e. MRI space) is available using rbv.nii.gz from mri_gtmpvc, Or if you recommend it by gtm.stats.dat, I can use gtm.stats.dat --rescale (reference regions) for SUVR in PET space. What do you prefer or recommend? 2. I used mri_vol2vol --mov rbv.nii.gz --targ original_PET.nii --o test.nii --regheader because rbv.nii.gz is in different space. but when overlaid with them, registration is not correct. (WHY) rbv.nii.gz is in different space, even not in T1.mgz space. (DKT space) I just wanted to use the pv-corrected image for image processing. and you also said, smoothing is required after PVC. (Surface or volume based smoothing (resonable). Best regards, Soo

2 1

mri_glmfit-sim error
by Kim, Gwang-Won 14 Feb '20

14 Feb '20

Hi there, I ran “mri_glmfit-sim -glmdir g2v3.wls -2spaces -perm 1000 1.3 abs”. But, there was error message as follow: “design matrix is not orthogonal, cannot be used with permutation. If this something you really want to do, run with -perm-force” Please let me know how to process mri_glmfit-sim. Thank you, Gwang-Won

2 1

Cluster-wise correction for multiple comparisons
by Kim, Gwang-Won 14 Feb '20

14 Feb '20

Hi there, First, I ran "mri_glmfit" using mask including 4 ROIs(file name: 4_ROI.label) as follows: mri_glmfit --glmdir g2v3.wls --y ces.nii.gz --wis cesvar.nii.gz --fsgd 2group.fsgd --C group.diff.mtx --lable 4_ROI.label --surface fsaverage lh - --fwhm 5 -eres-save. Second, I'm going to process "mri_glmfit-sim" to perform a cluster-wise correction for multiple comparisons. Please let me know how to process "mri_glmfit-sim" using masks (file name: 4_ROI.label) . Is it right? “mri_glmfit-sim --glmdir g2v3.wls --perm 1000 3 abs --2spaces --bg 1” Thank you, Gwang-Won

2 1

New release plans?
by Dan Fitch 14 Feb '20

14 Feb '20

External Email - Use Caution Hi folks! I checked the wiki and github, but couldn't find anything about milestones or plans for the next major release of Freesurfer. Are there any loose dates or targets? (We're near the start of a 5-year imaging study, and trying to plan for training and pipeline changes...) Thanks for any hints you can drop! Dan Fitch Research Software Engineer University of Wisconsin-Madison Center for Healthy Minds

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