Freesurfer June 2017

freesurfer@nmr.mgh.harvard.edu

116 participants
186 discussions

Re: [Freesurfer] Applying an affine transformation to a surface
by Daniel Gallichan 14 Jun '17

14 Jun '17

That appears to work perfectly, thanks! I’m confused, though, as to me the direction of the operations appears to be reversed (the reg.dat file was obtained by moving the hires MRI to match the low-res surface). How do I know which one to use? On 14 Jun 2017, at 17:00, freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote: Date: Wed, 14 Jun 2017 16:56:17 +0200 From: Douglas Greve <greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Applying an affine transformation to a surface To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <ba337251-ab46-8ef2-a1f3-25dbbd353776(a)nmr.mgh.harvard.edu<mailto:ba337251-ab46-8ef2-a1f3-25dbbd353776@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset="windows-1252" Can you try it with --reg instead of --reg-inv ? On 6/13/17 8:55 PM, Daniel Gallichan wrote: Hello In a very similar situation to a post I found in the Freesurfer archive, I have low-resolution (3T) and high-resolution scans (7T) of the same subject - and would like to put the surfaces from the low-resolution scan into the space of the hi-res data. The instructions from the previous thread say to check example 4 when running ?mri_surf2surf --help? - which I tried, but I cannot get the result to overlap in freeview. I have a registration file which looks very good from running bbregister on the high-res data into the low-res space - but I cannot perform the registration the other way around as I?m still having trouble getting the hi-res data to process properly through recon-all (it?s acquired at 350um, and I?m currently running it downsampled to 500um, but that?s still a work-in-progress?). So this is the command-line that I tried to apply the transformation from the registration to a surface: mri_surf2surf --reg-inv hires_to_lowres.dat ${SUBJECTS_DIR}/subj_hires/mri/T1.mgz --hemi lh --sval-xyz white --tval-xyz ${SUBJECTS_DIR}/subj_hires/mri/T1.mgz --tval lh.white.hires --s subj_lowres If I then try to view the result: freeview -v ${SUBJECTS_DIR}/subj_hires/mri/T1.mgz -f ${SUBJECTS_DIR}/subj_lowres/surf/lh.white.hires it is clear that the two are far from being aligned? I?m afraid I may be misunderstanding how to control the coordinate systems in the mri_surf2surf command - especially as the source and targets are different ?subjects? (the same actual subject, though?). I can?t used the ?--trgsubject? option because recon-all has not completed properly on the hires data, and there is no sphere.reg file (although I have to confess, I haven?t understood why it would need it if I am specifying my own registration file?) . Any suggestions very gratefully received. Thanks Daniel *Dr Daniel Gallichan* *Lecturer* CUBRIC School of Engineering Cardiff University Maindy Road Cardiff CF24 4HQ Wales, United Kingdom Tel: +44 (0) 29 208 70045 Email: gallichand(a)cardiff.ac.uk<mailto:gallichand@cardiff.ac.uk> <mailto:gallichand@cardiff.ac.uk> *Dr Daniel Gallichan* *Ddarlithydd* CUBRIC Ysgol Beirianneg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ Cymru, y Deyrnas Unedig Ff?n: +44 (0) 29 208 70045 E-bost: gallichand(a)caerdydd.ac.uk<mailto:gallichand@caerdydd.ac.uk> <mailto:gallichand@caerdydd.ac.uk> Personal website: http://www.cardiff.ac.uk/people/view/507850-gallichan-daniel CUBRIC - *C*ardiff *U*niversity *B*rain *R*esearch *I*maging *C*entre - http://sites.cardiff.ac.uk/cubric/ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170614/b…

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Re: [Freesurfer] LME correction in longitudinal analysis
by Livia Liu 14 Jun '17

14 Jun '17

Dear Martin, Thank you very much again for your reply. I did better with your help, but I am really sorry that I still have some questions. 1. I found there are positive and negative regions in the result “sig.mgh” map. I wonder “lme_mass_F” is a kind of F analysis or T analysis in fact. How to get the F value or T value? I can only get P value. 2. And I tried to use the cmd “mri_surfcluster” to generate the set of detected clusters and their anatomical coordinates like the file "...sig.cluster.summary" in GLM analysis. Unfortunately,I failed to get the correct command. Could you tell me right way? 3. I load sig.mgh file and save ROIs’ label file in qdec tool, then I use the cmd "mri_label2label" and "mris_anatomical_stats" to get the value of thickness. For area and volume, can I get in the same way? In the stats:# ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd lh.1.label 25 19 51 3.044 0.237 0.105 0.068 0 0 I think that the “SurfArea” is the value of area, “GrayVol” is the value of volume.In my other GLM analysis, I found that cortical surface area or volume is not an integer in the file “…y.ocn.dat”.Is it right way to get the ROI value? 4.If there are any way to convert the file “lh.thickness”"lh.area" or "lh.volume" in every subject to the format “nii” which can be used in SPM. I want to do a same analysis in SPM to compare my result. I use the cmd: mri_surf2vol --surfval $SUBJECTS_DIR/sub01/surf/lh.thickness --hemi lh --fillribbon --subject fsaverage --template $SUBJECTS_DIR/fsaverage/mri/orig --o lh.thickness01.nii then I use the cmd: tkregister2 --mov $SUBJECTS_DIR/fsaverage/mri/orig.mgz --noedit --s fsaverage --regheader --reg $SUBJECTS_DIR/register.dat But in the terminal output: A volume registration file must be supplied. I don’t know how to get the volume registration file. I failed to get the correct cmd by searching in mail-list. Please give me some help. I am sorry again to bring you a lot of questions. Thank you very much, and looking forward to reply. Kind regards, Livia

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Longitudinal Pipeline
by AKUDJEDU, THEOPHILUS 14 Jun '17

14 Jun '17

Hi All, Is it standard practice to conduct reliability when corrections are made in freesurfer for subcortical structure volumes? Also, are you able to analyse data acquired (1.5T - time point one) with time-point two (3T) in the longitudinal pipeline? Thanks Theo

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Merging outputs of mri_label2vol across hemi
by Elijah Mak 14 Jun '17

14 Jun '17

Hi Freesurfer Team, I am trying to resample the aparc annotation into functional space using mri_label2vol. It works fine and the script produced the segmentation for each hemisphere. Is there a way to merge both the left and right volumes together? Thanks for your help. Best Wishes, Elijah

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Surface area of a define volume projection on cortical surface
by Matthieu Vanhoutte 14 Jun '17

14 Jun '17

Dear Freesurfer's experts, Given the well known size of a voxel I would like to know the equivalent surface area once projected on the white fsaverage cortical surface. Could anyone give me a proper way of computing this ? Best regards, Matthieu

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Applying an affine transformation to a surface
by Daniel Gallichan 14 Jun '17

14 Jun '17

Hello In a very similar situation to a post I found in the Freesurfer archive, I have low-resolution (3T) and high-resolution scans (7T) of the same subject - and would like to put the surfaces from the low-resolution scan into the space of the hi-res data. The instructions from the previous thread say to check example 4 when running ‘mri_surf2surf --help’ - which I tried, but I cannot get the result to overlap in freeview. I have a registration file which looks very good from running bbregister on the high-res data into the low-res space - but I cannot perform the registration the other way around as I’m still having trouble getting the hi-res data to process properly through recon-all (it’s acquired at 350um, and I’m currently running it downsampled to 500um, but that’s still a work-in-progress…). So this is the command-line that I tried to apply the transformation from the registration to a surface: mri_surf2surf --reg-inv hires_to_lowres.dat ${SUBJECTS_DIR}/subj_hires/mri/T1.mgz --hemi lh --sval-xyz white --tval-xyz ${SUBJECTS_DIR}/subj_hires/mri/T1.mgz --tval lh.white.hires --s subj_lowres If I then try to view the result: freeview -v ${SUBJECTS_DIR}/subj_hires/mri/T1.mgz -f ${SUBJECTS_DIR}/subj_lowres/surf/lh.white.hires it is clear that the two are far from being aligned… I’m afraid I may be misunderstanding how to control the coordinate systems in the mri_surf2surf command - especially as the source and targets are different ’subjects’ (the same actual subject, though…). I can’t used the ‘--trgsubject’ option because recon-all has not completed properly on the hires data, and there is no sphere.reg file (although I have to confess, I haven’t understood why it would need it if I am specifying my own registration file…) . Any suggestions very gratefully received. Thanks Daniel Dr Daniel Gallichan Lecturer CUBRIC School of Engineering Cardiff University Maindy Road Cardiff CF24 4HQ Wales, United Kingdom Tel: +44 (0) 29 208 70045 Email: gallichand(a)cardiff.ac.uk<mailto:gallichand@cardiff.ac.uk><mailto:espezi@cardiff.ac.uk> Dr Daniel Gallichan Ddarlithydd CUBRIC Ysgol Beirianneg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ Cymru, y Deyrnas Unedig Ffôn: +44 (0) 29 208 70045 E-bost: gallichand(a)caerdydd.ac.uk<mailto:gallichand@caerdydd.ac.uk> Personal website: http://www.cardiff.ac.uk/people/view/507850-gallichan-daniel CUBRIC - Cardiff University Brain Research Imaging Centre - http://sites.cardiff.ac.uk/cubric/

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separate medial from lateral part in superiorfrontal parcel of Desikan-Killiany atlas
by Caspar M. Schwiedrzik 14 Jun '17

14 Jun '17

Hi! Is there by any chance a known demarcation line in in the XYZ coordinates of the Desikan-Killiany atlas that could be used to separate the superiorfrontal parcel into a medial and a lateral part? Thanks! Caspar

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Brainmask Shifted
by KALEY E ELLIS 14 Jun '17

14 Jun '17

Dear FreeSurfer Developers, We are using FreeSurfer v6.0 and our operating system is OS X El Capitan version 10.11.6. We are going through the manual editing process and are checking the brainmask by following these instructions: http://freesurfer.net/fswiki/FsTutorial/SkullStripFixV6.0 We have two subjects who appear to have brainmasks that are shifted up considerably (see attached image). The recon-all.log file indicates that it finished without errors: reading volume /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/mri/wm.mgz... reading input surface /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.white... reading input pial surface /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.pial... reading input white surface /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.white... INFO: assuming MGZ format for volumes. table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 277 173 970 3.493 0.659 0.107 0.039 3 0.4 ./rh.entorhinal_exvivo.label #------------------------------------------ Started at Thu Jun 8 10:50:24 CDT 2017 Ended at Fri Jun 9 00:06:58 CDT 2017 #@#%# recon-all-run-time-hours 13.276 recon-all -s 2083_base finished without error at Fri Jun 9 00:06:58 CDT 2017 Could you please advise me on how to correct this issue? We have run all of these subjects the same way, but only two have had this problem. Thank you! Kaley Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison

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difference in T1 and T2 resolution
by John Anderson 14 Jun '17

14 Jun '17

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recon-all exits with error at surf/lh.thickness, mghRead looks for .mgh/.mgz filename extension
by Anup Bidesi 14 Jun '17

14 Jun '17

Hello FreeSurfer Users, New to Freesurfer, I'm attempting to recon-all using : recon-all -all -i T1.nii -s op.nii.mgz (Attached recon-all log) The automated process begins normally and seems to run Autorecon Prrocessing Stages 1-25, but at step 26 (I think) and then exits with Error, per log as seen below: ------------------------------------------------------------- mghRead(/home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/surf/lh.thickness, -1): could not open file. Filename extension must be .mgh, .mgh.gz or .mgz ------------------------------------------------------------- Within the subject .mgz folder in Surf there was a tmp.pctsurfcon.14807 folder with a file named lh.wm.mgh (size 569 kb). I ran this process a couple of times and the autorecon process would exit at same step.I tried looking up the Archive for any similar previous error messages but did not find any. Please advise. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Platform: Ubuntu 14.04 3) uname -a: Linux brainmindengineer-Precision-Tower-7910 3.13.0-117-generic #164-Ubuntu SMP Fri Apr 7 11:05:26 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thanks for your help, Anup

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Freesurfer June 2017