Freesurfer

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30070 discussions

mris_anatomical_stats and cortical thickness
by Taylor Hilton 15 Jun '17

15 Jun '17

Hi all, I’m trying to extract individual cortical thickness values using the output of the annotation file from mri_glmfit-sim. This worked well for the left hemisphere, we got values that were significantly different between groups we had specified in mri_glmfit, but for the right hemisphere we get all values of 0 for the cortical thickness and mean curvature. I’ll post the commands I’m running below. Essentially I’m attempting to take the annot file from mri_glmfit-sim, convert it to a label, then put that label onto a subject (which may or may not be necessary), and pull out the anatomical stats using that label. Below is the example code for one subject. I did also confirm that the initial annot file, and the final subject label both sit on the right hemisphere when loading them up in freeview. I’ll also attach the summary file from mri_glmfit-sim for the cluster and a sample recon-all log. Any help is appreciated! - Taylor H. Lab Data Coordinator LRDC, University of Pittsburgh mri_annotation2label --subject fsaverage --hemi rh --outdir ./scripts --annotation archive/rh.PYS_Can3_2.glmdir/PYS_Can3_2/cache.th40.neg.sig.ocn.annot --label 1 mri_label2label --srcsubject fsaverage --srclabel scripts/rh.cluster-001.label --trglabel s72064/label/rh.cluster-001.label --trgsubject s72064 --hemi rh --regmethod surface mris_anatomical_stats -l s72064/label/rh.cluster-001.label -b s72064 rh >> s72064/scripts/rh-cluster001.txt Using TH3 vertex volume calc Total face volume 228346 Total vertex volume 224557 (mask=0) 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 86 64 179 0.000 0.000 0.108 0.018 1 0.1 s72064/label/rh.cluster-001.label

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Viewing 3D surfaces
by Michael Davies 15 Jun '17

15 Jun '17

Hello, i am having problems loading the 3D surface for my data. I was wondering if you could provide any advice please? This is the command code i put into the terminal; bash-4.1$ freeview -f/projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ > /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 \ > /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visible=0 \ > /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visible=0 \ > /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial \ > --viewport 3d bash: freeview: command not found bash-4.1$ Kind regards, Michael University of Birmingham

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viewing surfaces in 3D using freeview
by Michael Davies 14 Jun '17

14 Jun '17

Hello i am trying to access the data files in 3D but i am having problems opening the files using the command syntax given on the website. I have set my own pathway using my own data; “/projects/pbic1030/Micahel/subjects/Subj1/fsaverage/surf/” However, one i progress with the code past this point i am unable to load the data and get the error message No file or directory in the terminal even though this is the correct pathway to the data. When i enter the rest as follows this is when the problems begin to occur lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ Could you please advise me how to proceed? Kind regards, Michael University of Birmingham

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aparc.a2009s+aseg.mgz
by Almarshad F. 14 Jun '17

14 Jun '17

Dear FreeSurfer expert is it possible to create "aparc.a2009s+aseg.mgz" from custom parcellation i have.. i used label2annot to create the 2.annot files from my none overlapping labels.. ! i think mri_aparc2aseg<https://surfer.nmr.mgh.harvard.edu/fswiki/mri_aparc2aseg> --s <subjid> --ribbon --annot aparc.a2009s would create the file .. however i could not understand how the command works, in terms of my two (label/lh.aparc.annot and label/rh.aparc.annot).. if you please can clarify what are the steps i need to make to get the aparc.a2009s+aseg.mgz based on my parcellation many thinks fatima

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Subcortical Segmentation
by AKUDJEDU, THEOPHILUS 14 Jun '17

14 Jun '17

Hi FreeSurfers, Are we able to correct the anatomical boundaries of subcortical structures delineated with FreeSurfer? On which output file do we do this if it's possible? Thank you Theo

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Re: [Freesurfer] Freesurfer Digest, Vol 160, Issue 25
by KALEY E ELLIS 14 Jun '17

14 Jun '17

Hi Doug, Our freeview command is: freeview -v ${fs_id}/mri/T1.mgz ${fs_id}/mri/brainmask.mgz:colormap=heat:opacity=0.4 Thank you, Kaley ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Wednesday, June 14, 2017 11:00 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 160, Issue 25 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Freesurfer Info Page - Harvard University<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ... or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: difference in T1 and T2 resolution (Douglas Greve) 2. Re: viewing surfaces in 3D using freeview (Ruopeng Wang) 3. Re: mri_vol2surf: visualising the edges at projfrac 0.1 - 0.5 (Elijah Mak) 4. Re: difference in T1 and T2 resolution (John Anderson) 5. Re: recon-all exits with error at surf/lh.thickness, mghRead looks for .mgh/.mgz filename extension (Bruce Fischl) 6. Re: difference in T1 and T2 resolution (Douglas Greve) 7. Re: Brainmask Shifted (Douglas Greve) 8. Re: separate medial from lateral part in superiorfrontal parcel of Desikan-Killiany atlas (Bruce Fischl) 9. Re: Applying an affine transformation to a surface (Douglas Greve) 10. Re: Surface area of a define volume projection on cortical surface (Douglas Greve) 11. Re: viewing surfaces in 3D using freeview (Michael Davies) 12. Re: Merging outputs of mri_label2vol across hemi (Douglas Greve) 13. Re: Merging outputs of mri_label2vol across hemi (Elijah Mak) 14. Re: Merging outputs of mri_label2vol across hemi (Douglas Greve) 15. Re: Longitudinal Pipeline (Martin Reuter) 16. Re: viewing surfaces in 3D using freeview (Ruopeng Wang) ---------------------------------------------------------------------- Message: 1 Date: Wed, 14 Jun 2017 16:02:10 +0200 From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] difference in T1 and T2 resolution To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <9ddd5b02-e0df-ffbb-1515-e5bf02a622aa(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" This is not due to a difference between T1 and T2 resolution. The problem is that the two T1 volumes (001.mgz and 002.mgz) are difference sizes. It is probably not a good idea to try to combine them, but if you really want to, I can supply you with a solution. On 6/14/17 1:12 PM, John Anderson wrote: > Thank you for your response. The log file is attached > *Sent:* Tuesday, June 13, 2017 at 2:02 AM > *From:* "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> > *To:* freesurfer(a)nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] difference in T1 and T2 resolution > > can you send the log file? > > On 6/11/17 10:08 PM, John Anderson wrote: > > In the log file the error was: > ERROR: MultiRegistration::loadMovables: images have different > voxel sizes. > Currently not supported, maybe first make conform? > Debug info: size(1) = 1, 1, 1 size(0) = 0.7, 0.7, 0.8 > MultiRegistration::loadMovables: voxel size is different > /recons/subj1/mri/orig/002.mgz. > Jon > *Sent:* Sunday, June 11, 2017 at 2:12 PM > *From:* "Matt Glasser" <matt(a)ma-tea.com> > *To:* "Freesurfer support list" <freesurfer(a)nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] difference in T1 and T2 resolution > What was the error message? > Peace, > Matt. > From: <freesurfer-bounces(a)nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of John > Anderson <j.anderson(a)publicist.com <mailto:j.anderson@publicist.com>> > Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Date: Sunday, June 11, 2017 at 9:06 AM > To: <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Subject: [Freesurfer] difference in T1 and T2 resolution > Dear Freesurfer experts, > I have T1 and T2 images were unfortunately acquired with different > resolution (i.e the voxel sizes is not the same) > T1 is 280X280X208 > T2 is 270X270X200 > > I tried to run "recon-all" but it failed to process the data. The > command that I used is : > pbsubmit -c " recon-all -subjid subj1 -T2 PATH_TO_/T2.nii.gz > -qcache -T2pial -all" > How can I analyze these images? Is it a correct procedure to > conform the voxels using "mri_convert". Is this procedure correct? > does it hurt the anatomy of the images? > I highly appreciate your help > John > _______________________________________________ Freesurfer mailing > list Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. > _______________________________________________ Freesurfer mailing > list Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing > list Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Longitudinal stats: target space
by Chris Watson 14 Jun '17

14 Jun '17

Hi Doug, Martin, et al., I am going to use the LME tools for a study in kids 8-15 y.o. (some with brain injury). RE the target space (mris_preproc and mri_surf2surf), the LME wiki page <https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels#Preparin…> says "study_average". I am unclear if this should be a) average of all subjects at TP 1 (or final, or mid) b) average of all subjects and all TP's c) average of all within-subject templates (created from recon-all -base) d) *fsaverage* I suspect (d) is wrong for this study and (c) is right, but want to double-check. In that case, would I then follow the steps on the wiki page for creating a template <https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates#Creatingar…> ? Thanks, Chris

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Extracting cortical PET data from T1: aparc+aseg.mgz vs surface
by Elijah Mak 14 Jun '17

14 Jun '17

Hi Freesurfer team, I am trying to extract ROI PET data from the cortical regions using the Desikan atlas, and I am wondering which is the recommended approach. 1) mri_segstats on resampled aparc+aseg.mgz in PET space or 2) mri_segstats on lh.PetSurface.mgh in native surface (not fsaverage). Option (1) always lead to to substantially lower BPND values in some regions compared to the measures derived on the surface. If I would like to take the cortical measurements from lh.PetSurface.mgh, should I smooth the data first? A second question relates to projfrac. I am working with tau BPND data and there is quite a bit of CSF smearing in the outer layers of the cortex, resulting in negative BPND voxels. However, even without CSF contamination, there is quite a steep drop off in BPND intensity from the WM boundary to the pial surface (projfrac 0.5). The registration is OK too. For my data, sampling nearer to the WM surface (0.1) seems to result in positive BPND voxels compared to projfrac 0.5. As such, is it OK to use projfrac 0.1 for all subjects in my study? Thanks for taking the time to read this! Best Wishes, Elijah

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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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