Freesurfer December 2018

freesurfer@nmr.mgh.harvard.edu

109 participants
175 discussions

Setting the origin in native space
by Nillo, Ryan Michael R 06 Jan '19

06 Jan '19

External Email - Use Caution Hello FreeSurfer users, I want to use the suit software to segment the cerebellum, however the software requires the origin be set at the anterior composure. I know the Talairach image’s origin is set at the anterior commisure and that there is a Talairach transformation in mri/transforms. Is there a way to use this information to set the origin to the anterior commisure in the native space image? Thanks in advance, Ryan Nillo Staff Research Associate UCSF Department of Radiology and Biomedical Imaging

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FSGD file
by Raffaele Dubbioso 06 Jan '19

06 Jan '19

External Email - Use Caution Dear Freesurfer team, I'm running a group analysis where I'd like to compare myelination between two groups regressing out cortical thickness. Unfortunately I get always the same error message: dimension mismatch between X and contrast group.diff.mtx X has 3 cols, C has 4 cols. Is my group.mtx correct? My command line is: mri_glmfit --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd thickness.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --C group-x-thick --Cg1g2.intercept.mts --C g1g2.thick.mtx --surf fsaverage rh --cortex --glmdir rh_allbrain_t1t2_group_thickness.glmdir My group_diff.mtx: 1 -1 0 0 This is my FSGD FILE: GroupDescriptorFile 1 Title Myelin Class HC Class CMT Input fs_VF HC ........ Thank you very much for your help Best regards, Raffaele

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recalculate mean cortical thickness and/or regional thickness using a SD threshold or exclusion mask
by lindsay hanford 04 Jan '19

04 Jan '19

External Email - Use Caution Hello Freesurfer Community, I am wondering if it is possible to recalculate cortical thickness metrics (perhaps using mri_segstats or aparcstats2table) while including either a SD threshold or an exclusion mask. Using mri_surf2surf to register scans to the same space and then mri_surface_stats to create the std maps I have been comparing the variability of cortical thickness across the cortex for multiple scans across the same subject. From this I can determine a SD threshold point (0.5 say) or create a mask that includes all regions above that threshold. I would like to use this to threshold the regions showing the highest variability out of my calculations for mean hemispheric thickness and also regional thickness. Is there a way to use an SD threshold within mri_segstats or aparcstats2table? Otherwise apply a mask image to exclude specific vertices? Thank you in advance, Lindsay

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-qcache error
by 塩浜直 03 Jan '19

03 Jan '19

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to do group analysis for cortical thickness map using Qdec GUI. We've already have recon-all files that were made by “recon-all –s subjid –i subjid.nii –all” on other Linux OS (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) Firstly, I try to run command “recon-all –s subject –qcache” for each subject floders. However, the program stopped with error 1 minutes after starting. Last line of recon-all.log showed as follows. #@# Qdec Cache preproc lh white.K fsaverage Thu Dec 20 12:03:25 EST 2018 /Users/emitakahashi/freesurfer/subjects/ASD001/surf \n mris_preproc --s ASD001 --hemi lh --meas white.K --target fsaverage --out lh.white.K.fsaverage.mgh \n nsubjects = 1 ERROR: cannot find /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.white.K Darwin emis-mbp.tch.harvard.edu 18.0.0 Darwin Kernel Version 18.0.0: Wed Aug 22 20:13:40 PDT 2018; root:xnu-4903.201.2~1/RELEASE_X86_64 x86_64 I've searched the list but I can find no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: Free Surfer 6.0 2) Platform: macOS Mojave (64b Intel) 3) recon-all.log: see attached Tadashi Shiohama

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Re: [Freesurfer] recon-all error : Too many intersected faces for face 120047
by 허정선 03 Jan '19

03 Jan '19

External Email - Use Caution Thank you for your reply. Is it impossible with 2mm? Unfortunately, the data we collect for the study all have same thickness of voxel. And, there was a problem like the photo below, and only the recon-all.log could be attached to you. Thanks, Jeongson ---------------------------------------------------------------------- Message: 1 Date: Thu, 20 Dec 2018 10:13:16 -0500 (EST) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all error : Too many intersected faces for face 120047 (60827, 60826, 59444) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1812201012130.17732(a)gate.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi Jeongson it certainly looks like something went badly wrong. 2mm may be too thick - we typically recommend <=1.5mm for any voxel direction. Can you send us the recon-all.log? And maybe a snapshot of the volume with the lh.orig.nofix and rh.orig.nofix overlaid? cheers Bruce On Thu, 20 Dec 2018, ??? wrote: > External Email - Use Caution > > Hello Freesurfer developers > I'm starting using FS and I have a problem running recon-all. > #recon-all -s /usr/local/freesurfer/subjects/20180108 -all > I've attached the output to a ERROR image file. > > We're doing on a GE scanner 3T, T1-FSPGR axial slices, 3D with a slice thickness of 2.0mm. > freesurfer version : freesurfer-x86_64-unknown-linux-gnu-stable6-20170118 > > Any help is greatly appreciated. > > Thanks. > > Jeongson ------------------------------

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Which T1 volume to use for coregistration with PET volume
by Matthieu Vanhoutte 03 Jan '19

03 Jan '19

External Email - Use Caution Dear Freesurfer’s experts, I used mri_coreg command to coregister PET image onto T1 volume. Basically, this command coregister PET image onto orig.mgz volume (default target). However, I wonder if T1.mgz wouldn’t be a better target since it has been corrected for inhomogeneities and intensity normalized ? Thanks for helping ! Best, Matt

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voxel cordinates
by Sadia Sheikh 02 Jan '19

02 Jan '19

External Email - Use Caution Dear Freesurfer experts I am using freesurfer version 6.0. I have extracted ROI's from the aseg.mgz file. Now is it possible to get the cordinates of each voxel for a particular ROI? Thanks in advance Regards Research student

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map parcellations into DWI space?
by Yerong Li 31 Dec '18

31 Dec '18

External Email - Use Caution Dear FreeSurfer experts: I am trying to map ./mri/aparc.a2009s+aseg.mgz and ./mri/aparc+aseg.mgz into DTI file. Let's say, we have a DTI file with its b-vectors: ./bvals ./bvecs ./data.nii.gz I am trying to use the command from this webpage: https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat So I used the command : mri_label2vol --seg aparc+aseg.mgz --temp ./data.nii.gz --o dk-in-rawavg.mgz --regheader aparc+aseg.mgz The output file seems not very reasonable. Could you help me with this? Yerong ================================== Can you be more specific about which files you want to map into your DWI space? Eg, if you want to map wmparc.mgz, then use mri_label2vol. You will need a registration file which you can obtain with bbregister On 12/05/2018 02:34 AM, Maedeh Khalilian wrote: [Hide Quoted Text] External Email - Use Caution Dear FreeSurfer experts, I have a parcellation and a whole brain white matter files which are the outputs of FreeSurfer. I want to register them to my DWI. I mean I want my parcellation and white matter to be in the physical space of my DWI. Can FreeSurfer do it for me? If not , can you suggest me a toolbox that can do it fast? I would be grateful if u could help me. Cheers, Maedeh,

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plotting mean T1/T2 values in the different cortical layers
by Anik Dar 31 Dec '18

31 Dec '18

External Email - Use Caution Hi All, I have created cortical surfaces corresponding to 25%, 50%, 75% of the cortex. Now I want to plot the T1/T2 values corresponding to these different layers.I believe I have to use mri_vol2surf. What options in the mri_vol2surf do I need to use to create these T1/T2 maps corresponding to these different layers of the cortex ? Please let me know. Merry christmas and a happy New Year. Thank you, Ani

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Notebook specification
by mustafa amin 30 Dec '18

30 Dec '18

External Email - Use Caution Dear Freesurfer Members, First I would like to introduce myself my name is Mustafa Amin, and I’m planning to do a study to measure the volume of prefrontal cortex, hippocampus, and ventricle of patients with schizophrenia comparing them with control in Medan Indonesia. I read and saw information that freesurfer is capable in doing the measurement, however I am still not sure about what kind of notebook specification that I need to download and install it. For my knowledge, this is the first study that will be done in Indonesia so every explanation and further information about freesurfer and the notebook will make me very grateful. I’m thinking to buy an I5 intel core processor, with 8GB RAM, 1 TB HDD, and full HD Nvidia MX130 2G8 specification notebook. If there is anyone in here that can share the minimum requirements of the notebook, it will help me a lot to choose which one to buy. Thank you in advance. Yours faithfully, Mustafa M. Amin Consultant Psychiatrist in Biological Psychiatry Department of Psychiatry Faculty of Medicine Universitas Sumatera Utara

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Freesurfer December 2018