Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

Overlap parcellation
by francesca bottino 23 Nov '16

23 Nov '16

Hello, I’d like to ask couple of questions regarding parcellation: First, we used aparc.DKTatalas40.annot implemented in Freesurfer; 1) we used the command mris_make_face_parcellation to have a first parcellation: mri_annotation2label --subject ${subjid1} --hemi lh --annotation ${SUBJECTS_DIR}/${subjid1}/label/lh.aparc.DKTatalas40.annot --outdir ${SUBJECTS_DIR}/${subjid1}/new_label/lh mri_annotation2label --subject ${subjid1} --hemi rh --annotation ${SUBJECTS_DIR}/${subjid1}/label/rh. aparc.DKTatalas40.annot --outdir ${SUBJECTS_DIR}/${subjid1}/new_label/rh mri_convert ${SUBJECTS_DIR}/${subjid1}/func/splitted_0000.nii.gz ${SUBJECTS_DIR}/${subjid1}/func/splitted_0000.mgz mri_convert $d/1mm_low/aseg.mgz -o $d/aseg.mgz --reslice_like ${SUBJECTS_DIR}/${subjid1}/func/splitted_0000.mgz --resample_type nearest mris_volmask_novtk --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance $subjid1 tkregister2 --mov ${SUBJECTS_DIR}/${subjid1}/mri/T1.mgz --noedit --s ${subjid1} --regheader --reg ${SUBJECTS_DIR}/${subjid1}/mri/register.dat tkregister2 --mov ${SUBJECTS_DIR}/${subjid1}/func/splitted_0000.mgz --noedit --s ${subjid1} --regheader --reg ${SUBJECTS_DIR}/${subjid1}/mri/register_functional1.dat P.S. splitted_0000.mgz is a volume from fMRI data. mri_label2vol --label ${f} --temp ${SUBJECTS_DIR}/${subjid1}/mri/T1.mgz --subject ${subjid1} --hemi ${lh_rh} --surf white --fillthresh 0.5 --proj frac 0 1 0.01 --o ${SUBJECTS_DIR}/${subjid1}/new_mri_vol_highres/${lh_rh}/${filename}.nii.gz $register_command mri_binarize --dilate 1 --erode 1 --i ${SUBJECTS_DIR}/${subjid1}/new_mri_vol_highres/${lh_rh}/${filename}.nii.gz --o ${SUBJECTS_DIR}/${subjid1}/new_mri_vol_highres/${lh_rh}/${filename}.nii.gz --min 1 mris_calc -o ${SUBJECTS_DIR}/${subjid1}/new_mri_vol_highres/${lh_rh}/${filename}_ribb_ref.nii.gz ${SUBJECTS_DIR}/${subjid1}/new_mri_vol_highres/${lh_rh}/${filename}.nii.gz mul ${SUBJECTS_DIR}/${subjid1}/mri/${lh_rh}.ribbon.mgz Is this the correct way to make the parcellation or I would need to do something else? I also saw that most of the mask volumes created are overlapped each other in the low resolution (fMRI data) (fabout 10%) Is there any way to overcome the issue? 2)Then to obtain a finer parc, we have tried another method based on ico (icosahedron) that used as input fsaverage to create file.annot using mri_surf2surf that resampled one CorticalSurface onto another.This is the order of commands we used mris_make_face_parcellation ${SUBJECTS_DIR}/${subjid2ref}/surf/lh.sphere.reg ${FREESURFER_HOME}/lib/bem/${ic}.tri ${SUBJECTS_DIR}/${subjid2ref}/label/lh.${ic}.annot mris_make_face_parcellation ${SUBJECTS_DIR}/${subjid2ref}/surf/rh.sphere.reg ${FREESURFER_HOME}/lib/bem/${ic}.tri ${SUBJECTS_DIR}/${subjid2ref}/label/rh.${ic}.annot mri_surf2surf --srcsubject ${subjid2ref} --trgsubject ${subjid1} --hemi lh --sval-annot ${SUBJECTS_DIR}/${subjid2ref}/label/lh.${ic}.annot --tval ${SUBJECTS_DIR}/${subjid1}/label/lh.${ic}.${subjid2ref}2${subjid1}.annot mri_surf2surf --srcsubject ${subjid2ref} --trgsubject ${subjid1} --hemi rh --sval-annot ${SUBJECTS_DIR}/${subjid2ref}/label/rh.${ic}.annot --tval ${SUBJECTS_DIR}/${subjid1}/label/rh.${ic}.${subjid2ref}2${subjid1}.annot mri_annotation2label --subject ${subjid1} --hemi lh --annotation ${SUBJECTS_DIR}/${subjid1}/label/ rh.${ic}.${subjid2ref}2${subjid1}.annot --outdir ${SUBJECTS_DIR}/${subjid1}/new_label/lh mri_binarize --dilate 1 --erode 1 --i ${SUBJECTS_DIR}/${subjid1}/new_mri_vol_highres/${lh_rh}/${filename}.nii.gz --o ${SUBJECTS_DIR}/${subjid1}/new_mri_vol_highres/${lh_rh}/${filename}.nii.gz --min 1 mris_calc -o ${SUBJECTS_DIR}/${subjid1}/new_mri_vol_highres/${lh_rh}/${filename}_ribb_ref.nii.gz ${SUBJECTS_DIR}/${subjid1}/new_mri_vol_highres/${lh_rh}/${filename}.nii.gz mul ${SUBJECTS_DIR}/${subjid1}/mri/${lh_rh}.ribbon.mgz Is this also a correct way to make the parcellation or I would need to do something else? I also saw that, also in this case, most of the mask volumes created are overlapped each other in the low resolution (fMRI data) (about 10%) Is there any way to overcome the issue? Thank you very much.

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Re: [Freesurfer] v6.0_beta - mris_make_surfaces -T2 refinement -issue with overlapping pial surfaces
by Antonin Skoch 22 Nov '16

22 Nov '16

Dear Bruce, thank you very much for your time. Concerning transformations, that is weird since I adopted my code from HCP pipelines https://github.com/Washington-University/Pipelines/blob/master/FreeSurfer/s… and there I think they use the surfaces precisely this way. They are using the surfaces generated by 1mm3 volumes as input and refine them by using co-registered higher resolution volumes. I use full-hires reconstruction, but for my safety and convenience I left the code with transformations, which (I thought) should do not any harm (there is not any resampling in my case). I also checked the white and white.deformed processed by default HCP pipeline and they do NOT have the same ras2vox. BTW, which transformation in mris_info is relevant for this case? I found several of them in mris_info: talairch.xfm surfaceRAS to talaraiched surfaceRAS talairached surfaceRAS to surfaceRAS Volume Geometry vox2ras Volume Geometry vox2ras-tkr Antonin From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> To: Antonin Skoch <ansk(a)ikem.cz> Sent: 11/23/2016 12:42 AM Subject: Re: [Freesurfer] v6.0_beta - mris_make_surfaces -T2 refinement -issue with overlapping pial surfaces yes, and I tracked it down and fixed it. BTW: don't use the white.deformed surface - use the white one. You can't use one surface that has been transformed (i.e. has a different ras2vox) and other surfaces that have not (you can see this if you run mris_info on the surface files, the ras2vox should match in all of them) cheers Bruce

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quantifyHippocampalSubfields.sh
by Alan Francis 22 Nov '16

22 Nov '16

Hi Eugenio - Hope all is well with you at UCL. I have the run the subfields algorithm on a set of subjects using Freesurfer 6.0. All the brains were processed without much fuss. However, when I ran the following: quantifyHippocampalSubfields.sh DM_125 Cannabis_HSF.txt It yielded nothing. Can you please help me? Thanks, Alan -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *Alan N. Francis PhD* Instructor - Imaging Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf(a)bwh.harvard.edu <ezra_wegbreit(a)brown.edu> afrancis(a)mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

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Fwd: recon-all -s Prueba2 exited with ERRORS
by Gabriela De Pino 22 Nov '16

22 Nov '16

Hello FreeSurfer Developers, I'm attempting to compute autorecon1 and everything goes well until mri_nu_correct.mni, where I get the following error: /usr/local/freesurfer/subjects/Prueba2/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux HULK 4.4.0-47-generic #68-Ubuntu SMP Wed Oct 26 19:39:52 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s Prueba2 exited with ERRORS at lun nov 21 19:27:17 ART 2016 For more details, see the log file /usr/local/freesurfer/subjects/Prueba2/scripts/recon-all.log 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Platform: Ubuntu 16.04.1 LTS (Xenial Xerus) Thank you very much! Bets regards, Gabriela

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mris_make_surfaces - longitudinal stream - questions
by Antonin Skoch 22 Nov '16

22 Nov '16

Dear experts, I am trying to understand what is the specificity of the pial and white surface generation in longitudinal stream, i.e. how the information from processing of base template is used for surface estimation in -long step of recon-all. Specifically: Why the maximal thickness is constrained to 3.5 mm (default in cross-sectional stream is 5 mm)? What is precisely the significance of -long parameter of mris_make_surfaces? In the source code is written, that this directive resets starting position of pial surface to be slightly inside the orig_pial. What is the objective of this step? Regards, Antonin Skoch

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Fwd: [HCP-Users] HCP to FreeSurfer Resampling
by Timothy Hendrickson 22 Nov '16

22 Nov '16

Just following up on the message below. Respectfully, -Tim FreeSurfer experts, I am attempting to resample HCP data into FreeSurfer space with the following how to document: https://wiki.humanconnectome. org/display/PublicData/HCP+Users+FAQ. <https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ> I believe I have resampled the GIFTI file into fs_average space, however I am running to problems visualizing it in freeview or tksurfer. Please see the error message in the forwarded message below? -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) ---------- Forwarded message ---------- From: Timothy Hendrickson <hendr...(a)umn.edu> Date: Tue, Nov 8, 2016 at 8:51 AM Subject: Re: [HCP-Users] HCP to FreeSurfer Resampling To: Timothy Coalson <tsc...(a)mst.edu> Cc: "hcp-us...(a)humanconnectome.org" <hcp-us...(a)humanconnectome.org> Hi Tim, Thank you for taking a look at my script, I really appreciate it. I am now running into another problem. After re-sampling into fs_average space I am attempting to visualize that file as an overlay in tksurfer or freeview (freesurfer visualization tools) however I receive the following error: *mriseadGIFTIfile: mris is NULL! found when parsing file rh.43242.32k_TJH_fsavg.func.gii*. I know that freesurfer can handle GIFTI file so that is not the problem. I wonder if the GIFTI file was created incorrectly... Any advice? -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) ______________________________________ Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay)

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how does the content of the curv files compare to that of smoothwm.H.crv
by Bernardoni, Fabio 22 Nov '16

22 Nov '16

Dear Freesurfer experts, I am having troubles interpreting the output of the recon-all output concerning the curvature, in particular in relation with the one from the command mris_curvature_stats. My aim is to compare the absolute value of both the gaussian/intrinsic and the mean/extrinsic curvatures between a group of patients and a group of controls. In particular I would like to obtain a voxelwise statistical maps for the comparison. Browsing the freesurfer mailing list I understood the following (please correct me if I am wrong): - the file $SUBJECTS_DIR/<subjid>/surf/lh.smoothwm.H.crv, produced by mris_curvature_stats, contains the mean/extrinsic curvature map for the left hemisphere, as computed on the white matter surface, for subject <subjid> - the file $SUBJECTS_DIR/<subjid>/surf/lh.curv, produced by recon-all (or by mris_curvature, right?) contains a smoothed version of smoothwm.H.crv - the files $SUBJECTS_DIR/<subjid>/surf/lh.pial.H.crv and $SUBJECTS_DIR/<subjid>/surf/lh.curv.pial are the analogues of the above, but for the pial surface Also the local gyrification index, contained in the file$SUBJECTS_DIR/<subjid>/surf/lh.pial_lgi, is computed on the pial surface and might be compared (I know it is a different measure) with $SUBJECTS_DIR/<subjid>/surf/lh.pial.H.crv and $SUBJECTS_DIR/<subjid>/surf/lh.curv.pial, not with $SUBJECTS_DIR/<subjid>/surf/lh.curv or $SUBJECTS_DIR/<subjid>/surf/lh.smoothwm.H.crv. If this is true I expect that: 1- the histograms of the above quantities for any subject be approximately symmetric around zero. Actually given that the convention chosen is to give a positive curvature to the suci and a negative to the gyri (also read in one email of this list from long time ago - so please correct me if I am wrong), I expect that the mean value would lie a bit below zero if we want the brain surface to close (with this convention a sphere has mean curvature -1/r). This expectation of mine is only a rough expectation, but it would be precise if one had normalized somehow for the area related to the vertex on which the local curvature is computed. 2- the histograms for smoothwm.H.crv and pial.H.crv would have fatter tails than curv and curv.pial, respectively 3- smoothwm.H.crv and pial.H.crv would follow quite closely curv and curv.pial, respectively, for each subject Now please have a look at the attached plots, where in red always appear unsmoothed quantities, while in blue smoothed ones. NB I have extracted the above plotted values using the functions fs_read_Y from the freesurfer longitudinal package by M. Reuter et al. Now I observe that 1,2,3 are true on the white matter surface (see attached *smoothwm* files). Also, if I average the mean curvature for one subject over all vertices I obtain a negative value. When I look at the analogue plots for the pial surface2,3 are still true, but the mean values for the curvatures are now positive! If I look at the *pial* files, the distribution looks clearly different. Therefore I have the following doubts/questions: a) is the convention for the curvature sign different on the pial and on the wm surface? b) if not, can the normalization issue I mention in point 1 above explain the negative mean of the mean-curvature I observe (the subject I used to produce the plots is a healthy control, plots are similar for other subjects)? c) in any case I expected the survatures to be more similar to each other on the wm and on the pial surface, given that they are approximately parallel. Any comment on this would be highly appreciated. d) or do you think my results are wrong/ I am not plotting the right thing? Thanks in advance for any help. Fabio Dr. Fabio Bernardoni wiss. Mitarbeiter Psychosoziale Medizin und Entwicklungsneurowissenschaften Tel. +49 (0)351 458-5245 Fax +49 (0)351 458-7206 URL http://www.uniklinikum-dresden.de/psm; www.transdenlab.de Universitätsklinikum Carl Gustav Carus & Medizinische Fakultät an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://www.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

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Re: [Freesurfer] ASL processing in Freesurfer? (Douglas Greve)
by Elijah Mak 21 Nov '16

21 Nov '16

Many thanks for the information, Doug! I will give it a go. Actually, I would like to carry out the following analyses: Get regional estimates of perfusion within a region of interest as defined by a significant cluster after mri_glmfit-sim. as well as other cortical regions that are connected to that cluster in terms of WM paths. Is it possible to do that in Freesurfer environment? How can I do PVC for perfusion in ROIs? Will the -pv ppvol flag be crucial during the mri_segstats stage? Thanks again for help. Best Wishes, Elijah

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Training Tracula to add more pathways
by Kristafor Farrant 21 Nov '16

21 Nov '16

Hi there, As a complete newbie to the Tracula tool, I have a questions about using it. Is it possible to train tracula to track additional pathways other than the 18 thats are already included? I was to track several pathways that are not included with Tracula. Best, Kris

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[FreeSurfer] TRACULA Registration transform matrix
by Ostrowski, Lauren 21 Nov '16

21 Nov '16

Hi experts, We're trying to convert an ROI in T1 MRI space to diffusion space in order to collect FA values from the ROI (using TRACULA output files). Is there a t1 to dwi transform matrix to use with TRACULA? Thanks, Lauren

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Freesurfer